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Microbiomics
Dimensions, Applications, and
Translational Implications of
Human and Environmental
Microbiome Research
Translational and Applied Genomics Series
Microbiomics
Dimensions, Applications, and
Translational Implications of
Human and Environmental
Microbiome Research
Edited by
Manousos E. Kambouris
The Golden Helix Foundation, London, United Kingdom
Aristea Velegraki
Mycology Research Laboratory and UOA/HCPF culture collection,
Department of Microbiology, School of Medicine, National and Kapodistrian
University of Athens, Athens, Greece
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Contents
List of Contributors ............................................................................................................................ xiii
CHAPTER 1 Introduction: The Microbiome as a Concept: Vogue

or Necessity? ........................................................................................ 1
Manousos E. Kambouris and Aristea Velegraki
References................................................................................................................... 4
PART I CLASSES AND KINDS OF MICROBIOMES ..................................... 5

CHAPTER 2 Bacteriome and Archaeome: The Core Family Under the
Microbiomic Roof.................................................................................. 7
George P. Patrinos, Loukia Zerva, Michael Arabatzis, Ioannis Giavasis
and Manousos E. Kambouris
Introduction................................................................................................................. 7
DNA Exchange........................................................................................................... 9
The Pioneers, Their Vision and Their Means.......................................................... 10
Diversity.................................................................................................................... 12
Habitats, Settings, and Formats................................................................................ 14
Environmental Adaptability, Monitoring, and Engineering .................................... 16
The (Near-Term) Way Ahead .................................................................................. 20
References................................................................................................................. 22
CHAPTER 3 Myc(et)obiome: The Big Uncle in the Family .................................... 29

Manousos E. Kambouris and Aristea Velegraki
Introduction............................................................................................................... 29
Emergence and Establishment ................................................................................. 29
Definition and Identity ............................................................................................. 30
Mycobiome: Status, Categories, and Essence.......................................................... 33
Mycobiome: Structure and Composition ................................................................. 36
Studying the Mycobiome ......................................................................................... 39
Microscopy .......................................................................................................... 42
Culture and Culturomics ..................................................................................... 42
Immunoassays...................................................................................................... 43
Metagenomics...................................................................................................... 43
Select Mycobiomic Research: Some Working Examples ....................................... 45
Human Mycobiomes............................................................................................ 45
v
vi Contents
Remote Effects, Communication, and Control Functions of Mycobiomes ............ 47

Gut Brain Axis and the Mycobiome Factor...................................................... 48
Mycorrhizal Databuses ........................................................................................ 48
References................................................................................................................. 49
CHAPTER 4 Virome: The Prodigious Little Cousin of the Family.......................... 53

Yiannis N. Manoussopoulos and Cleo G. Anastassopoulou
Introduction............................................................................................................... 53
The Viral Components of the Microbiome.............................................................. 54
The Environmental Virome................................................................................. 55
The Plant Virome ................................................................................................ 55
The Human Virome............................................................................................. 56
Methodological Challenges Associated With Virome Studies........................... 56
The Host Virus Interactome ................................................................................... 58
Network Analysis: A Roadmap to Explore Host Virus Interactions ............... 58
Prospecting the Continuum of Interactions Within the Virosphere ................... 59
The Double-Stranded DNA Virus Host Interactome........................................ 61
Humans, Apes, and Monkeys.............................................................................. 63
Dolphins............................................................................................................... 65
Bats ...................................................................................................................... 66
Birds..................................................................................................................... 66
Amoebas .............................................................................................................. 67
Fishes ................................................................................................................... 67
Bacteria ................................................................................................................ 67
Future Perspectives, Aspects, and Prospects ........................................................... 68
References................................................................................................................. 68
PART II THE STUDY OF MICROBIOTA AND MICROBIOMES.................... 75

CHAPTER 5 Identifying Microbiota: Genomic, Mass-Spectrometric, and
Serodiagnostic Approaches................................................................ 77
Aristea Velegraki and Loukia Zerva
Introduction—The Romantic Past............................................................................ 77
The Modern Pedigree ............................................................................................... 78
Metamodernism: The Changing Environment......................................................... 79
Metamodernism: The Methods ................................................................................ 82
Mass Spectrometry .............................................................................................. 85
Immunoassays...................................................................................................... 85
Genomics ............................................................................................................. 86
Microscopy .......................................................................................................... 88
Contents vii
Conclusion: A Peek of the Future............................................................................ 90

References................................................................................................................. 90
CHAPTER 6 Panmicrobial Microarrays .................................................................. 95

Aristea Velegraki
Introduction............................................................................................................... 95
Invention, Definition, and Rationale of Microarrays............................................... 96
Pedigree and Categories of Microarrays.................................................................. 96
Comparison to the State of the Art ........................................................................ 101
Trade-Offs and Prospects ....................................................................................... 102
Methodology ........................................................................................................... 104
Development and Optimization ........................................................................ 104
Types of Labeling Signal .................................................................................. 105
Amplification ..................................................................................................... 106
The Microbiomic Aspect of Microarray Concepts ................................................ 108
The Genomic Aspect ......................................................................................... 108
Phenotypic Microarrays..................................................................................... 111
Live Cell Microarrays ....................................................................................... 111
Conclusion .............................................................................................................. 113
References............................................................................................................... 116
CHAPTER 7 Metagenomics in Microbiomic Studies ........................................... 121

Martin Laurence
Introduction............................................................................................................. 121
Commensals and Infectious Agents ....................................................................... 122
Five Key Metrics .................................................................................................... 124
Sensitivity .......................................................................................................... 124
Efficiency........................................................................................................... 125
Bias/Universality ............................................................................................... 125
Taxonomic Classification of Novel Microbes .................................................. 125
Contamination.................................................................................................... 126
Total DNA or RNA Sequencing Using Illumina................................................... 126
Specimen Collection and Storage ..................................................................... 127
DNA/RNA Extraction ....................................................................................... 127
Isolation of Relevant DNA/RNA ...................................................................... 129
Library Preparation............................................................................................ 129
Sequencing......................................................................................................... 129
Alignment .......................................................................................................... 133
Tabulation .......................................................................................................... 133
viii Contents
Ribosomal RNA Genes rrs and rrl ........................................................................ 133

Conserved Sequences ........................................................................................ 135
Divergent Sequences ......................................................................................... 136
Modified Bases .................................................................................................. 138
Introns ................................................................................................................ 139
Sensitivity (Metagenomics).................................................................................... 139
Sensitivity (Aliquoting and Consensus PCR) ........................................................ 141
Nearly Universal Consensus PCR.......................................................................... 142
Nearly Universal Consensus PCR With Blocking Primers ................................... 143
Nearly Universal Consensus RT-PCR With Blocking Primers............................. 144
Custom Illumina Library Preparation .................................................................... 148
Bioinformatics ........................................................................................................ 149
Multiple Alignment Passes................................................................................ 149
Gapped Alignment............................................................................................. 150
Word Length...................................................................................................... 150
Host Versus Non-Host....................................................................................... 150
Databases ........................................................................................................... 152
Aligning Ribosomal RNA Against SILVA ...................................................... 152
Conclusion .............................................................................................................. 152
Disclosures.............................................................................................................. 153
References............................................................................................................... 153
CHAPTER 8 Culturomics: The Alternative From the Past .................................... 155

Introduction............................................................................................................. 155
Culturomics: Inventing or Recasting?.................................................................... 156
Phylogenesis of Culturomics.................................................................................. 158
The Technical Dimension: Instrumentation and Devices...................................... 161
Simulating Infectivity: Legacy and Innovative Applications................................ 164
Affiliations, Opportunities, and Impact ................................................................. 167
References............................................................................................................... 168
CHAPTER 9 Next-Generation Sequencing: The Enabler and the Way Ahead..... 175
Sonja Pavlovic, Kristel Klaassen, Biljana Stankovic, Maja Stojiljkovic and
Branka Zukic
Introduction............................................................................................................. 175
Next-Generation Sequencing: A General Overview.............................................. 176
Next-Generation Sequencing: General Technical Aspects.................................... 177
Next-Generation Sequencing Platforms Used for Metagenomics......................... 178
Contents ix
Roche 454 Pyrosequencing ............................................................................... 178

Illumina Sequencing .......................................................................................... 179
Ion Torrent Sequencing ..................................................................................... 179
Sequencing by Oligonucleotide Ligation and Detection .................................. 180
Third-Generation Sequencing................................................................................. 181
Single-Molecule Real-Time Sequencing .......................................................... 181
Nanosequencing................................................................................................. 183
Helicos Sequencing ........................................................................................... 184
GnuBIO Sequencing.......................................................................................... 184
DNA Nanoball Sequencing ............................................................................... 185
Big Data in Genomics ............................................................................................ 187
Bioinformatic Methods for Analyzing Metagenomic Data ................................... 187
Preprocessing of Sequence Data ....................................................................... 188
16S rRNA Analysis ........................................................................................... 189
Whole-Genome Shotgun Analysis .................................................................... 190
Conclusion .............................................................................................................. 193
Acknowledgment .................................................................................................... 194
References............................................................................................................... 194
PART III NOVEL AND LEGACY FIELDS OF MICROBIAL

APPLICATIONS........................................................................................ 201
CHAPTER 10 Cancer Microbiomatics?................................................................... 203
Georgios Gaitanis and Martin Laurence
Introduction............................................................................................................. 203
Important Holdouts................................................................................................. 203
Microbiomics and Cancer ...................................................................................... 204
Koch’s Blind Spots................................................................................................. 205
Breakthroughs in Establishing Microbiomic Causality in Cancer ........................ 206
Becoming Wiser ..................................................................................................... 207
Malassezia as an Inducer........................................................................................ 208
Skin Microbiome and Carcinogenesis ................................................................... 208
Malassezia in Internal Organs and Cancer ............................................................ 213
Conclusion .............................................................................................................. 216
Disclosures.............................................................................................................. 216
References............................................................................................................... 216
x Contents
CHAPTER 11 A Prerequisite for Health: Probiotics............................................... 225

Rodnei Dennis Rossoni, Felipe de Camargo Ribeiro, Patrı´cia Pimentel de
Barros, Eleftherios Mylonakis and Juliana Campos Junqueira
Introduction: Definitions and Terminology ........................................................... 225
Mechanisms of Action of Probiotics Against Pathogens ...................................... 227
Competitive Exclusion of Pathogens by Blocking Binding Sites .................... 227
Production of Bioactive Compounds ................................................................ 228
Modulation of Immune System......................................................................... 231
Bioengineering for Enhancing the Functional Properties of Probiotics Strains ... 232
Clinical Applications .............................................................................................. 233
Bacterial Infections of the Gastrointestinal Tract............................................. 233
Oral Infections ................................................................................................... 234
Vulvovaginal Candidiasis.................................................................................. 236
Conclusion .............................................................................................................. 237
Acknowledgment .................................................................................................... 237
References............................................................................................................... 237
CHAPTER 12 Microbiomic Prospects in Fermented Food and Beverage

Technology ........................................................................................ 245
Paraskevi Bouki, Chrysanthi Mitsagga, Manousos E. Kambouris and
Ioannis Giavasis
Introduction............................................................................................................. 245
The Microbiome of Naturally Fermented Dairy Products .................................... 247
Resolving the Composition of the Microbiomes .............................................. 250
Wild Lactococci................................................................................................. 252
Mesophilic Lactobacilli ..................................................................................... 252
Thermophilic Lactic Acid Bacteria................................................................... 253
The Microbiome of Naturally Fermented Meat Products ..................................... 255
The Microbiome of Naturally Fermented Olives and Pickles............................... 259
Table Olives....................................................................................................... 259
Pickles ................................................................................................................ 261
The Microbiome of Naturally Fermented Wine and Beer .................................... 262
Wine................................................................................................................... 262
Beer .................................................................................................................... 265
References............................................................................................................... 267
Contents xi
CHAPTER 13 Legacy and Innovative Treatment: Projected Modalities for

Antimicrobial Intervention ................................................................ 279
Mohammad Al Sorkhy and Rose Ghemrawi
Introduction............................................................................................................. 279
A Brief History of the Antimicrobial Struggle...................................................... 279
The History of Chemotherapy Originated With Paul Ehrlich.......................... 279
Fleming’s Observation of the Penicillin Effect Ushered in the Era of
Antibiotics.......................................................................................................... 280
The Current Antibacterial Arsenal ......................................................................... 280
Metabolic Antagonists ....................................................................................... 280
Nucleic Acids Inhibitors.................................................................................... 281
Cell Wall Synthesis Inhibitors .......................................................................... 282
Protein Synthesis Inhibitors............................................................................... 284
Nonbacterial Microbes ........................................................................................... 286
Antiviral Drugs .................................................................................................. 286
Antifungal Agents.............................................................................................. 287
Antiprotist Agents.............................................................................................. 288
Antihelminthic Drugs ........................................................................................ 289
Antibiotic Resistance.............................................................................................. 289
Offensive Resistance Strategies ........................................................................ 290
Defensive Resistance Strategies........................................................................ 291
New Approaches of Antimicrobial Discovery....................................................... 292
The Two-Component System............................................................................ 293
Beta-Lactamase Inhibitors................................................................................. 294
Efflux Pump Inhibitors ...................................................................................... 294
Outer Membrane Permeabilizers....................................................................... 295
Conclusion Remarks............................................................................................... 295
References............................................................................................................... 296
CHAPTER 14 Electromagnetism and the Microbiome(s)....................................... 299

Stavroula Siamoglou, Ilias Boltsis, Constantinos A. Chassomeris and
Introduction............................................................................................................. 299
History and Lore................................................................................................ 299
Electrons and Microbes: The Formal Meeting ................................................. 300
Formats, Conditions, and Effects ........................................................................... 301
Magnetic Fields ................................................................................................. 303
Electric Fields .................................................................................................... 307
Electromagnetic Fields ...................................................................................... 311
Currents.............................................................................................................. 312
xii Contents
The New Generation of Electrostimulation: WMCS-NCCT............................ 315

Electroresistance and Electrostimulation Interaction With Antibiotics ........... 319
References............................................................................................................... 323
CHAPTER 15 Microbiomics: A Focal Point in GCBR and Biosecurity................... 333

Manousos E. Kambouris, Konstantinos Grivas, Basilis Papathanasiou,
Dimitris Glistras and Maria Kantzanou
Introduction............................................................................................................. 333
Emergence of New, Aggressive, and Better Adapted Pathogens ......................... 334
Into the Future: Projecting a Responsive Strategy and Defining Operational
Procedures............................................................................................................... 336
Surveillance Vigilance..................................................................................... 338
Intervention Containment Management ........................................................ 343
Fresh From the Past: Adapting Our Cognitive Dimension to an Evolving
Universe .................................................................................................................. 345
Traits of the Threats/Compilation of a Threat Library..................................... 346
“Measured, Weighed and Found. . . Threatening”. Assessing the Threat Factor
of an Agent ........................................................................................................ 349
Conclusion—Is It a Dream or a Nightmare? ......................................................... 351
References............................................................................................................... 353
CHAPTER 16 Epilogue............................................................................................. 361

References............................................................................................................... 364
Index .................................................................................................................................................. 367

List of Contributors
Cleo G. Anastassopoulou
Department of Biology, University of Patras, University Campus Rio, Patras, Greece; Metabolic
Biology Laboratory, Center for Translational Medicine, Department of Pharmacology, Lewis Katz
School of Medicine, Temple University, Philadelphia, PA, United States
Michael Arabatzis
First Department of Dermatology-Venereology, Medical School, Aristotle University of
Thessaloniki, Thessaloniki, Greece
Ilias Boltsis
Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
Paraskevi Bouki
Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Nutrition,
University of Thessaly, Karditsa, Greece
Constantinos A. Chassomeris
Department of Pharmacy, University of Patras, Patras, Greece
Patrı́cia Pimentel de Barros
Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo
State University (UNESP), São José dos Campos, São Paulo, Brazil
Georgios Gaitanis
Department of Skin and Venereal Diseases, Faculty of Medical Sciences, School of Medicine,
University of Ioannina, Ioannina, Greece
Rose Ghemrawi
College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
Ioannis Giavasis
University of Thessaly, Karditsa, Greece; General Department, University of Thessaly, Karditsa,
Greece
Dimitris Glistras
Department of History and Archaeology, National and Kapodistrian University of Athens,
Athens, Greece
Konstantinos Grivas
Hellenic Military Academy, Kitsi, Greece
Juliana Campos Junqueira
The Golden Helix Foundation, London, United Kingdom
xiii
xiv List of Contributors
Maria Kantzanou
Department of Hygiene, Epidemiology & Medical Statistics, National Retrovirus Reference
Center, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
Kristel Klaassen
Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade,
Serbia
Martin Laurence
Shipshaw Labs, Montreal, QC, Canada
Yiannis N. Manoussopoulos
Laboratory of Virology, Plant Protection Division of Patras, ELGO-Demeter, NEO & Amerikis,
Patras, Greece
Chrysanthi Mitsagga
University of Thessaly, Karditsa, Greece
Eleftherios Mylonakis
Infectious Diseases Division, Alpert Medical School & Brown University, Providence, RI, United
States
Basilis Papathanasiou
Department of Turkish and Contemporary Asian Studies, National and Kapodistrian University
of Athens, Athens, Greece
George P. Patrinos
Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece;
Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates
University, Al-Ain, Abu Dhabi, United Arabic Emirates; Faculty of Medicine and Health
Sciences, Department of Pathology, Bioinformatics Unit, Erasmus University Medical Center,
Rotterdam, The Netherlands
Sonja Pavlovic
Serbia
Felipe de Camargo Ribeiro
Rodnei Dennis Rossoni
Stavroula Siamoglou
Department of Pharmacy, University of Patras, Patras, Greece
Mohammad Al Sorkhy
College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
List of Contributors xv
Biljana Stankovic
Serbia
Maja Stojiljkovic
Serbia
Aristea Velegraki
Mycology Research Laboratory and UOA/HCPF culture collection, Department of Microbiology,
School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
Loukia Zerva
Department of Pathophysiology, School of Medicine, National and Kapodistrian University of
Athens, Athens, Greece
Branka Zukic
Serbia
CHAPTER
INTRODUCTION: THE
MICROBIOME AS A CONCEPT:
VOGUE OR NECESSITY? 1
Manousos E. Kambouris1 and Aristea Velegraki2
1
The Golden Helix Foundation, London, United Kingdom 2Mycology Research Laboratory, Department of
Microbiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
The notion of “microbiome” has no negative or threatening sound on principle. Both its standard
and its projected forms (with a multitude of new microbiota) are applicable and important in bioin-
dustry, bioremediation, biotechnology, in environmental applications, and perhaps even in energy.
But the aspect of pathogenicity is undeniably the most important, and the one able to threaten our
species with extinction. Thus this aspect is always preferentially studied in terms of resources of
any kind.
The universe of OMICS is now a tridimensional one; the first, original dimension, coined before
the turn of the millennium, referred to collectivities within a cell: genomics, proteomics, transcrip-
tomics, metabolomics, interactomics, and their special subsets such as pharmaco/toxico/immunoge-
nomics. The second dimension emerged in the late 2000s, and referred to collectivities or
interactions of multiple cells or organisms. It was the time of infectiomics, microbiomics, and the
different levels and categories of the latter. A third iteration appeared in the 2010s, centered on the
methods of study and not the organisms or their constituents: metagenomics, radiomics, and
culturomics.
The -ome/-omic sciences are really, at least in part, something of a vogue. The use of the suf-
fixes has grown out of all proportion and necessity, to retouch sectors, make studies more relevant
and projects more promising, even in cases that are accurately and correctly described by previous,
pre-Omics terminology. But in Microbiology, the Microbiomic Culture is a true necessity, as it
encompasses the multidimensional and holistic view of an integrative picture, where biotic (micro-
biota and macrobiota) and abiotic elements interact in multiple levels, which are digested in much
deeper zoom than previously done by ecological studies through the concept of niches, cycles, and
networks.
The concept of Microbiome is not entirely novel: the term contains the word “microbe” almost
intact, with the suffix “-ome,” a latinicized version of the Greek suffix “-ωμα” denoting entirety,
sum, or collectivity. Thus the Microbiome is the sum of all microbes sharing a common denomina-
tor, usually a common location/environment within a defined timeframe, as initially proposed in a
largely forgotten stroke of foresight by Whipps et al. (1988), pg. 176: “A convenient ecological
framework in which to examine biocontrol systems is that of the microbiome. This may be defined
as a characteristic microbial community occupying a reasonably well defined habitat which has
Microbiomics. DOI: https://doi.org/10.1016/B978-0-12-816664-2.00001-3
© 2020 Elsevier Inc. All rights reserved. 1
2 CHAPTER 1 INTRODUCTION: THE MICROBIOME AS A CONCEPT
distinct physio-chemical properties. The term thus not only refers to the microorganisms involved
but also encompasses their theatre of activity.”
There has been a tendency to use the term Microbiome to denote the sum of microbial genomes,
as proposed by Hooper and Gordon (2001): “The Nobel laureate Joshua Lederberg has suggested
using the term ‘microbiome’ to describe the collective genome of our indigenous microbes (micro-
flora), the idea being that a comprehensive genetic view of Homo sapiens as a life-form should
include the genes in our microbiome. . ..” This context, apart from being hopelessly restrictive as it
focuses solely in colonizing microbiota and, even worse, colonizers exclusively of Homo sapiens,
and unimaginatively unidisciplinary, since it includes only a genetic/genomic aspect, is also both
unclear, in its qualitative dimension, and inaccurate. Inaccurate, because there is not any letter in
the word “microbiome” to attest to the genetic constituent of “genome,” as the suffix “-ome” is
about collectivity and entirety. And unclear, as it does not unequivocally describe, even qualita-
tively, the entirety of microbial genomes, as it does not define the genomic unit within a taxon
horizon: genomes of different subgenera and, even more prominently, of different subspecies is
unclear whether they are scored as one or as multiple entities.
In its organism-centered use the term Microbiome supplants a very well-established concept,
the microbial flora (Tancrede, 1992). The latter term denoted possible heterogeneity and a
dynamic, multi-level structure expressed by multiple and different interactions, mainly with the
“environment” but also among the different species and niches; the concept of “micro-
biome” though, infers to much higher, more diverse and more impactful interactions. In addition, it
remedies the conceptual pitfall of flora, which by definition denotes kingdom Plantae, or, in a func-
tional, food-chain aspect, photosynthetic organisms that can be expanded to include autotrophs/pro-
ducers in general. On the contrary, many if not most members of microbial floras are heterotrophs
(consumers and decomposers).
Another similar term has been the Microbial Community, denoting microbes coexisting in space
and time (Escobar-Zepeda et al., 2015). The term and concept were quite handy, lacking only the
pertaining notion of collectivity and conceptual unity needed to describe the constituting microbiota
as one entity, differentiated from and possibly opposed to other entities participating actively in the
definition of their environment or coexisting in the same spatiotemporal window. Furthermore, the
unity or common denominator which defines a certain Microbiome does not have to be a 3D loca-
tion, possibly augmented by a temporal dimension, although it usually is. But the microbiome
might be a functional or other sum of microbial populations.
Moreover, “microbiome” pertains to two aspects previously underappreciated and not appropri-
ately covered by the notion of “microbial flora.” The first such aspect is the motion of microbiota.
Microbial flora echoes of motionlessness in spatial terms, while many microbiota are endowed with
active motion/motility. Actually the concept of microbiome unifies both microbial flora and any
functional concept of microbial fauna. Even in the lower microbiomatic levels, that is bacteriomes
and viromes, the existence of actual predators or consumers, as are the predatory bacteria (Sockett,
2009) and the virophages (Bekliz et al., 2016; Katzourakis and Aswad, 2014), is analogous rather
to faunal than to floral attributes and reminiscent of the more evolved, eukaryotic hyperparasites
(Parratt and Laine, 2016).
The second aspect is that the microbial flora as a term and concept projects no notion whatso-
ever of the intense genetic processes inherent among microbiotes. The Plantae, which constitute the
regular flora (or macroflora), are restricted to mispollination in this respect, with misfertilized
INTRODUCTION: THE MICROBIOME AS A CONCEPT 3
plants producing sterile or dysfunctional fruit or ploidal variations. In stark contrast, microbiota,
and especially Prokarya, present vigorous genetic mobility and exchange, a fact so prominent that
the term “microbiome” is often erroneously used to denote the sum of genomes of the microbes,
and not the microbiota proper, of a certain environment (Hooper and Gordon, 2001).
The concept of Microbiome is suitable for current and future needs to analyze and describe the
explosive changes expected in microbiology due to biotechnology endeavors. It is the correct
approach to investigate and comprehend intermingled and interacting microbial populations, as it
does not imply the stable, dynamic but balanced condition of the microflora, where disturbances
and changes are a diversion from the normality. The Microbiome may be understood as an instanta-
neous OR continuous entity, which incorporates the phenomena of nonlinear genetic exchange. It
allows conceptual flexibility and room to accommodate (1) novel, engineered, or fully artificial
microbiota (Hutchison et al., 2016; Smith et al., 2003; Malyshev et al., 2014), tentatively called
“metapathogens” and “neopathogens” in their pathogenic capacities and depending on the degree
of engineering (Kambouris et al., 2018); (2) the microbiota as appendages or symbiotic exo-organs
of macroorganisms (Hooper and Goron, 2001), thus constituting (sub)microbiomes and individual
microbiomes; (3) our expanded concept of microbiota, with the viruses being counted as proper
lifeforms of acellular nature (Pearson, 2008) and an open door to extend such status to viroids; and
(4) the genomic interactions implicating any nucleic acid form, from the single, possibly decaying
DNA strands used in transformation to the elaborate mechanisms of transposition and transduction,
which should be included, when in extracellular phase, in the “exogenome” (Kambouris et al.,
2018).
The latter should be viewed as a collective, prospective pool of genetic information, which is
potentially translatable depending on the receiver. The mind goes to prokaryotes, which incorporate
any naked DNA by transformation, without any concern over its origin or sequence/meaning. Such
randomly incorporated DNAs might introduce completely new protein threads, which may prime
equal revolutionary events rather than evolutionary ones, by accumulating amino acid changes
(individual or “en block”) in existing proteins or adding/eliminating protein families by transferable
elements.
When considering eukaryotes, naked DNAs are used for catabolism and lateral transfer intercel-
lularly is of questionable applicability. But transduction by viruses is another issue altogether. Gene
disruption and specialized transduction are well-attested events, but insertion in an exomic
sequence, especially if the viral function is inert (pseudovirus) or becomes so (either randomly or
by cellular defense mechanisms), equally produces a totally novel protein. The event introduces
within an open reading frame a sequence possibly read in a different one and definitely having dif-
ferent length and embedded regulation, and this holds true for both eukaryotic and prokaryotic host
genomes.
The alleged “democratization” in different scientific and technological areas provides prospects
but also hides dangers. The “self-crisping” (Ireland, 2017) of interested individuals toward therapy
or deranged concepts of superpowers is an upsetting and even worrisome fact, mostly in social
terms, but not alarming or unnerving. On the contrary, self-acclaimed microbiologists and biotech-
nologists may have tremendous biological, not social-only, impact. In future, in each block or
neighborhood, a genomics-capable microbiological workshop, mostly illegitimate, may be run to
produce amenities which today are covered by very different products (from drugs to food and
weapons or powerful chemicals); it also may not. But the problem is that it DOES may happen.
4 CHAPTER 1 INTRODUCTION: THE MICROBIOME AS A CONCEPT
The inherent problems in research conduct, the current difficulty in performing second-generation
sequencing, in terms of platform availability but also due to the exceptional needs in computational
power (Escobar-Zepeda et al., 2015), might have been a safety feature, which will be removed by
the oncoming third generation. Thus the methodological and cognitive tools to respond to a reality
where the emergence of a new microbe happens many times a day in multiple, dispersed localities
must be in place, even if this bleak prospect is considered improbable or unlikely. After all, the vir-
tual humanity and the Internet of Things were considered scienceless fiction during the lifetime of
today’s mainstay scientists.
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Hutchison, C.A., Chuang, R.Y., Noskov, V.N., Assad-Garcia, N., Deerinck, T.J., Ellisman, M.H., et al., 2016.
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(Ed.), Fungi in Biological Control Systems. Manchester University Press, pp. 161 178.
CHAPTER
BACTERIOME AND ARCHAEOME:

THE CORE FAMILY UNDER THE
MICROBIOMIC ROOF 2
George P. Patrinos1,2,3, Loukia Zerva4, Michael Arabatzis5, Ioannis Giavasis6
and Manousos E. Kambouris7
1
Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece 2Department of
Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi,
United Arabic Emirates 3Faculty of Medicine and Health Sciences, Department of Pathology, Bioinformatics Unit,
Erasmus University Medical Center, Rotterdam, The Netherlands 4Department of Pathophysiology, School of
Medicine, National and Kapodistrian University of Athens, Athens, Greece 5First Department of Dermatology-
Venereology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece 6General Department,
University of Thessaly, Karditsa, Greece 7The Golden Helix Foundation, London, United Kingdom
INTRODUCTION
The notion of bacteriome is focal in current studies of microbiome at both cognitive and research levels.
Still, the use of the term is not proportional to the scientific weight of the relevant studies and the knowl-
edge gathered, while there are frictions regarding the specific content of this particular biome. A brief
historic account may assist in deconvoluting current misapprehension on the nature and use of the term.
Although PubMed paper returns are not an uncontested source of information, especially when
literature search is limited to inclusion of keywords in titles, they may be considered as an indica-
tive metric for significance and are thus preferred in this chapter to more meticulous approaches,
including, but not restricted to, content browsing for terminology. There is the added advantage
that the use of specific keywords usually implies a declaration or a mature cognitive environment
for reviewers to accept and not edit the title. The first returns of PubMed featuring “bacteriome” in
titles appear relatively early (Wang and Cheung, 1998) but are quite sparse. One may compare with
the first uses of “microbiome” in PubMed titles, introducing the ecocellular notion of this term
(Ordovas and Mooser, 2006; Friedrich, 2008), which described the collectivity of microbes in a
spatiotemporal entity (microbe 1 -ome, a Greek suffix implying a collective entity, as in genome,
etc.). This was much to the dismay of microbial geneticists who revived the term by giving it a
clearly genomic spin: microbe 1 genomics 5 microbiomics (Gill et al., 2006). The comparison of
microbiome entries shows that PubMed title returns lag behind browsing other, more expansive
resources (see Chapter 1, for works coining the two uses of the term “microbiome”). It also shows
that, by 2006, the term was used in both its genomic-centered and its environmental/cellular
contexts (Gill et al., 2006; Ordovas and Mooser, 2006).
Microbiomics. DOI: https://doi.org/10.1016/B978-0-12-816664-2.00002-5

© 2020 Elsevier Inc. All rights reserved. 7
8 CHAPTER 2 BACTERIOME AND ARCHAEOME: THE CORE FAMILY
Still, numbers and metrics do sometimes lie: the notion of bacteriome appearing in late 1990s in
PubMed had nothing to do with the early notion of microbiome—much less with the late, genome-
centric context of the latter. It was used, as a term, to describe a chimeric organ where bacterial
symbionts were residing within adapted host tissues, the adaptation and the resulting functionality
defining the interface as an organ (Chen et al., 1999; Wang and Cheung, 1998). The term kept
appearing in this context until 2013, when a study used it to describe the sum of bacteria in a spa-
tiotemporal entity (Diaz et al., 2013), soon to be followed by a relevant definition (Oever and
Netea, 2014; Probst et al., 2014). As mentioned in Chapter 1, the whole concept of microbiome
had been structured on bacteria and was a spawn of the Human Genome Project (HGP). The mas-
sive investment to accomplish HGP became in essence a quest for “new problems to solve,” or
rather the case of a series of solutions seeking the right problem(s). There were two distinct possi-
bilities: sequencing additional organisms, which raised issues of choice and processing of respective
samples, which may require different handling principles than human ones, or elaborating on the
human subject at large. The latter had some interesting prospects: apart from easier funding, it
organized both genomics and the Omic sciences into an integrated system of study, which was to
revolutionize the core of thinking in bioscience. Human physiologists and geneticists agreed that
the genomic content of the human cell could not account for all metabolites encountered in the
human organism (Turnbaugh et al., 2007; Mammen and Sethi, 2016; de Oliveira et al., 2017) and,
most probably, could not support human life as we know it—in environmentally sustainable condi-
tions, and not in laboratory-like, fully controlled environments. To have a spherical, all-aspect pic-
ture of human physiology, the genes controlling and encoding these metabolites had to be detected,
sequenced, and, most importantly, annotated to their native genomes. The task of elucidating the
genomic dimension of the human microbiome was really grandiose, as some figures were quite
impressive: the number of microbial cells and the number of carried genes were astounding, the lat-
ter more or less equaling the ones of the human genome (Gill et al., 2006; Sender et al., 2016).
Given that many microbes were considered fastidious, a genomic approach was in order, without
intervention of the culturing phase that changes population representativeness both qualitatively
and quantitatively (Lagier et al., 2012). Thus metagenomics were born, first introduced in PubMed
titles in 2003 (Schloss and Handelsman, 2003), although the epithet “metagenomic” had appeared a
year earlier (Gillespie et al., 2002). This was squarely to the point; a molecular biology—or rather
genomic—approach to map the diversity of microbial genes encountered in the human body. But
this procedure meant practically that the output of such analysis was to be metagenomes; there
were no clearly defined and purified cells (cultured or not, irrelevant), the actual genome(s) of
which were going to be explored. It would be a genomic soup, starting and ending with nucleic
acids, initially DNA. It is obvious that the entity thus emerging, the microbiome, was indeed a
genomic one. It did not really have to be defined as such. Whatever the definition of microbiome,
the microbiome emerging by the said process was to be compiled from genomic elements, the
sequences of which were recorded, aggregated, and annotated to create in silico microbial (meta)
genomes attributable to supposed microbiota. To this point, a very thorny issue arose: the number
of projected microbial genes, impressive at the very least as mentioned earlier (Gill et al., 2006;
Sender et al., 2016), was not referring to actual genes, but to gene types. If there was a 1000-cell
population of a certain microbe (or microorganism), its unique genes were counted in the estimates
one time each, not 1000 times each.
This approach creates some issues with gene variants but is straightforward as a scheme. Still,
there are a number of genes (and bacterial genes do not contain introns), which are expected to be
DNA EXCHANGE 9
identical, or at least very similar across many bacterial genera. Many enzymes participating in
DNA processes were expected to be very common and highly conserved. Similarly, within the
Gram groups, many genes coding for cell wall ingredients and enzymes for their synthesis were
expected to be highly conserved among different taxa, but this conservation would be reversely
proportional to the order of the compared taxa. Thus the gene population was estimated very differ-
ently in cases where different taxonomic levels—usually genera or species—were taken as the basis
for declaring two bacteria as different within the microbiome. And that without even starting to
take into consideration viruses and fungi, the latter making the definition of “difference” an impos-
sible task, due to anamorphism and teleomorphism considerations in taxonomy, and hence in
identification.
DNA EXCHANGE
The concept of a single prokaryotic biome, or rather a biome based on the concept of the two
empires (Gupta, 1998), was founded securely, among other factors, on the practice of horizontal
gene transfer (HGT; also known as lateral gene transfer - LGT), which allows an incorporation of
novel genetic blueprints without procreation—and thus an adaptation of the recipient cells/organ-
isms themselves and not of their spawn. Gene transfer actively changes the genomic content, thus
perplexing phylogeny and identification in prokaryotic organisms and is in stark contrast to the
main eukaryotic evolutionary principle of reshuffling existing genes and gene variants into allelic
combinations through recombination. The change of genetic environment, which is brought about
by moving genes and gene clusters within a chromosome, between different chromosomes and also
by the chromosomes proper in different genomes usually—although by no means always—affects
progeny and operates by altering the regulatory environment and the downstream combination of
products or /and feedback signaling. Thus the division of a putative prokaryotic biome where
Archaea and Bacteria coexist and interact (Egert et al., 2017) to two defined ones, bacteriome and
archaeome, practically corresponds to the three-domain system (Woese et al., 1990) but takes into
account this most archetypical genomic process of prokaryota, the HGT (Fig. 2.1). Although
autonomous (nonviral-mediated) HGT occurs within and even across the two prokaryote biomes
(Nelson et al., 1999; Fuchsman et al., 2017), the Archaea enact a number of proprietary such pro-
cesses that are particular to them, such as DNA exchange through vesicles and through cell fusion
FIGURE 2.1
Common grounds across domains. Archaea and bacteria share three major similarities; Archaea and Eukarya one
and two are found in all three domains.
(Wagner et al., 2017). Viral transduction is common in both biomes and although viruses usually
infect either Bacteria or Archaea, there are some that do infect strains of both (Fuchsman et al.,
2017), thus allowing for interdomain transduction. This fact, incidentally, argues in favor of using
the term “archaeophage” rather than terms containing the “virus” theme, as heatedly proposed
(Abedon and Murray, 2013) and despite the fact of virally mediated HGT (transduction) across
domains (Boto, 2010).
THE PIONEERS, THEIR VISION AND THEIR MEANS

The objectives of the Human Microbiome Project (HMP), of the Metagenomics of the Human
Intestinal Tract (MetaHIT) and the abovementioned realities regarding microbial genomic content
and its peculiarities actually triggered a heated discussion on the relative merits of two very differ-
ent approaches: the shotgun approach (literally “metagenomic whole genome shotgun sequencing”)
and the consensus gene metagenomics (Jovel et al., 2016). For certain, metagenomic approaches
had been sought to tackle the issue of fastidious microbiota. The consensus gene—or, rather,
sequences—approach offered some advantages: although the shotgun approach was the only way to
efficiently catalogue and analyze the genomic content of human or any other microbiome, translat-
ing such data to microbiota present, meant that metagenomes had to be compiled. This sounds like
a difficult puzzle to begin with, but it gets even worse in practice, as common sequences, both cod-
ing and regulatory ones—not to mention supposed “junk” sequences—are rather difficult to segre-
gate from the genomic pool in order to determine to how many species/taxa they correspond, not to
mention the endeavor to identify said taxa/species, a number of which are expected to be novel as
they escaped isolation and characterization due to their inherent fastidiousness.
On the other hand, consensus sequences may not reveal genes or any genomic information, but
they do provide a qualitative list of concerned biota, a fact making the compilation of sequences to
metagenomes and their annotation to actual species feasible at a later stage. They represent a far
more robust and informative approach to delineate mixed samples as output sequences variability
permits not only identification of unknown contacts most probably corresponding to unique taxa,
but also phylogenetic categorization of novel taxa. By producing far less sequence noise, the
approach is clearly at its best when striving to determine the content and possibly the abundance of
species/taxa in a sample, and not the genomic content of each member of the community or of the
community as a whole, neither in qualitative nor in quantitative terms. The most suitable approach
in this case was, inescapably, the combination of the two methods (Turnbaugh et al., 2007).
Thus both HMP and MetaHIT may have been initiated explicitly to discover the genes (Human
Microbiome Project Consortium, 2012) and, if possible, the (meta)genomes implicated in human
physiology and responsible for the synthesis of many metabolites, but the explosive microbiomic
research was oriented toward cataloging microbial presence in various habitats, and thus pushed for
the optimization of the consensus gene metagenomic—and metatranscriptomic—approach
(Chapter 7).
Consensus metagenomics, as occasionally referred to for brevity, had a very important draw-
back: such use and approaches were conditional on the very consensus sequences. If these did not
exist, or were not universal, the respective genomes were not analyzed; they were actually passed
THE PIONEERS, THEIR VISION AND THEIR MEANS 11
over, as nonexistent. This uneasy detail led to successive segregation of various biomes from the
microbiome, although it was a known fact that actually when speaking of microbiome, it had been
the bacteria or, in some cases, the prokaryotes as a whole, that were actually discussed or studied
(Ghannoum et al., 2010). Thus viruses were the first to be detached from the microbiome, as the
virome (Anderson et al., 2003), since they possessed no consensus sequences. In addition, the mas-
sive percentage of RNA viruses allowed a reverse-transcriptase-primed procedure, which was more
akin to metatranscriptomics. Thus at least such viruses, amounting to four out of seven Baltimore
classes, were treated in a standardized fashion across all sample types, which was different to that
of entities containing DNA genomes (see Chapter 4). After all the above taken into consideration,
it remains unexplained why a 7-year time lapse was required for the first appearance of the word
“virome” in a title in PubMed (Coetzee et al., 2010).
Fungi followed suit with the term “mycobiome” appearing to describe the “fungal microbiome”
(Ghannoum et al., 2010); the timing and the alternative descriptive term insinuate that the already
mentioned paper introducing it might have been influenced in terms of terminology by the almost
concurrent emergence of Virome in titles (Coetzee et al., 2010). Possessing consensus sequences in
the vicinity of 18S rDNA, patently different than those of the Prokarya (in the environs of 16S
rDNA), fungi were easy to discriminate and analyze with consensus metagenomics. Originally dis-
regarded in terms of significance and research resources allocated to their study, they are now con-
sidered highly important, and not only due to their interaction with bacteria (see Chapter 3). They
were underrepresented in any given environment: their cell number is a fraction of that of Prokarya
(Lai et al., 2019; Wisecaver et al., 2014)—a very small fraction, to the tune of 0.1% (Qin et al.,
2010; Seed, 2015)—and their genomic content is lower than that of the prokarya, albeit not propor-
tionately to their cell number. Eukarya have a much higher genomic content due to their size and
the existence of a defined and organized nucleus with sequentially modular genomes (chromo-
somes) and intriguing gene sets encoding smart approaches in order to adapt to different environ-
ments in a spatiotemporal context (Wisecaver et al., 2014).
The emergence of the term “bacteriome” in the sense of a biome was belated, appearing for the
first time in a paper title during 2014 (Probst et al., 2014), while the other two biomes (i.e., virome
and mycobiome) had already been described by 2010. The respective paper not only introduces
bacteriome but goes a step further and introduces archaeome as well, clearly distinguishing the two
prokaryotic biomes. The domain theory of the phylogenetic tree of life was published a quarter-
century earlier (Woese et al., 1990) and became very popular, as the term “archaeon” appears in
the title of 2080 Pubmed-registered papers ever since. As a result, it remains odd that the concept
of domains needed such a long time to be “officially” acknowledged in the context of biomes.
Moreover, archaeome still shows an absolute minimum of popularity: there exist only two PubMed
returns for paper titles containing this term, from 2014 to early summer of 2019.
Notably, the number of papers with the term “bacteriome” in their title remains extremely low
as well. There are only 44 returns for the biomic sense of the bacteriome, while the field of micro-
biomics flourishes and bacterial populations remain the main focus of microbiomic research (Seed,
2015; Lai et al., 2019; Cui et al., 2013). Microbiologists, and not only the ones involved in the clin-
ical setting, clearly feel that the term “microbe” and any of its spinoffs suit bacteria better than any-
thing else.
The most striking issue, in this widespread reluctance to recognize or refer to bacteriome and
archaeome as such, is that the concept of domains is a purely genomic one. It came around by
FIGURE 2.2
The virtual mechanics of the kingdom/domain/empire system for understanding and viewing the tree of life.
taking the Archaebacteria out of the Kingdom of Monera, to assign them to a status higher than
any other taxon, equal to the rest of Prokarya (which were recast as Bacteria) and Eukarya (which
aggregate all kingdoms of eukaryotes), and finally by changing their name from Archaebacteria to
Archaea (Woese et al., 1990). This massive repositioning and reshuffling (Fig. 2.2) was the result
of stringent comparisons of rDNA sequences, which showed a disproportional difference to respec-
tive sequences of other Prokarya, as well as the result of sanctioning of DNA differences as the
yardstick for phylogenetic relations.
DIVERSITY
Initially the human microbiome was supposed to differ among individuals due to illness and also
due to a number of factors, such as geographical locale, diet, lifestyle, age, and climate (Wilantho
et al., 2017; Lloyd-Price et al., 2016; Christensen and Brüggemann, 2014; O’Toole and Jeffery,
2018; Prohic et al., 2016); but later on, many other issues were implicated as well. Body sites (bio-
compartments) of the same individual may be colonized by wildly dissimilar microbiota per bio-
compartment as a baseline setup of diversity in health (Ma et al., 2018; Perez Perez et al., 2016;
Rogers et al., 2016; Ding and Schloss, 2014). As mentioned earlier, aging is another factor contrib-
uting to this diversity. Turning points of human life such as birth, puberty, adulthood, and old age
represent temporal highlights (Desai and Landay, 2018; Chu et al., 2017) characterized by intense
biochemical and microenvironmental changes within the host, which affect standard microbial sym-
bionts (Wilantho et al., 2017). Notably, microbiomic diversity by biocompartments and differential
DIVERSITY 13
responses/effects of their respective microbiomes to various challenges are also illustrated in plants
(Liu et al., 2017).
Although the distinction between Archaea and Bacteria, and thus between respective biomes, is
very popular and widely accepted, it has to be underlined that it is not unchallenged. Their differen-
tiation is based on nucleic acid sequences and relevant mechanisms (Woese et al., 1990). Still, this
distinction remains a genomic approach, or at the very best a genomic/post-genomic one. In terms
of cellular biology the facts mentioned earlier constitute an important set of differences but not the
most important one, especially in the context of the wildly diversified prokaryotic cells. Archaea
and Bacteria have more in common than not: transformation and conjugation, although mediated
by different effectors, are instances of direct HGT and occur in both these groups (whatever their
name and status) and in these two groups only (Garcı́a-Aljaro et al., 2017; Stingl and Koraimann,
2017), creating a network of lineages and sequences rather than a phylogenetic tree (Toussaint and
Chandler, 2012). Interestingly, transkingdom conjugation seems to set the tune for reconsidering
(Lacroix and Citovsky, 2016) the exclusivity of autonomous HGT outside the Eukarya domain/empire.
HGTs are nuclear (sensu lato) and genetic, but not genomic, events, implicating cellular
mechanisms exclusive to prokaryotic organisms. Transduction, an indirect HGT event taking place
through sequential viral infections, is a complex nuclear and cellular event (Touchon et al., 2017).
This process is applicable in all three domains (Touchon et al., 2017; Hashemi et al., 2018), but
there are viral strains that infect both Bacteria and Archaea (Fuchsman et al., 2017), a cross-
domain flexibility in host specificity and selection not observed with viruses infecting Eukarya:
eukaryote-specific viruses infect neither Bacteria nor Achaea. In cellular terms, Bacteria and
Archaea are even closer, which resulted in their being brigaded together as Prokaryota (or Monera)
since genomic differences were not considered paramount in principle (although at the time, some
of them had not been identified). Instead, they were viewed as significant variations within an
extremely diverse kingdom. Cell structure, size, and basic physiology were considered much more
important, a view giving precedence to “hardware” over “software” in modern parlance. The obser-
vation that Archaea and Bacteria may very well form polymicrobial biofilms (Probst et al., 2014),
being thus perfectly capable of cooperating in a far more integrated manner, similar (or precedent)
to multicellular structures/tissues, has been downplayed due to the fact that fungi and bacteria can
also participate in the same biofilm as elaborated in Chapter 3 (Ghannoum, 2016; Hoarau et al.,
2016). Still, the latter is a transkingdom event, whereas the domain system makes the former case
of far greater impact, since it escalates to a transdomain integration, or, actually, a chimera.
Even more perplexing has been a couple of uneasy observations. The first was that the domain
Eukarya was comprised of organisms which had undergone two (plants), or one (fungi and animals)
symbiotic events (Dolezal et al., 2005), an evolutionary distance of considerably greater magnitude
and significance compared to some chemical differences in lipids and some DNA sequences and
material (Woese et al., 1990). The second was the observation that prokaryotic cells could sponsor
either one cell membrane (monoderms), which is the case with all Gram-positive Bacteria and
Archaea, or, among Gram-negative Bacteria, a very intriguing two-membrane envelope (diderms).
This difference in cell structure is far more prominent than its consequences in cell motility, cell
wall thickness and permeability, drug and pest resistance, and sporulation efficiency (Gupta, 2011).
As a conclusion, the actual, genome-centric opinion is that bacteriome and archaeome are two dif-
ferent and distinct biomes within a microbiome, but the case that the archaeome is actually a part
of the bacteriome is not as thoroughly discarded as the sponsors of the genome-centric opinion
would like to hold.
HABITATS, SETTINGS, AND FORMATS

Studies on the bacteriome, either as such or in its guise as microbiome, highlighted two basic
issues. The first is the massive interactions among its members, which are cooperating, competing,
or indifferent to each other. The actual status of interactions may change by the slightest alteration
in any one out of a large number of factors relating to the environment. Such are temperature or
living in an abiotic environment, the existence of host(s) or factors directly related with the biota,
like age, fitness, population density, and gene transfer (Deshpande et al., 2018; Izhar and Ben-Ami,
2015; Egert et al., 2017; Miller and Bassler, 2001). The second issue refers to the collective interac-
tions of bacteriome’s members with the host or the abiotic habitat (Foster et al., 2017; Gould et al.,
2018; Marrero et al., 2015). These two issues are actually one and the same if taken into consider-
ation in a more relaxed perspective and from the point of view of the bacteria—an approach defi-
nitely heretical a decade or so earlier (Turnbaugh et al., 2007; Ley et al., 2007). Actually, although
biomedicine simply detested the idea, it is true that for any metabolically active microbe a biocom-
partment of a human, animal or plant multicellular organism is simply a potentially toxic but rich
in nutrients environment (de Oliveira et al., 2017; Foster et al., 2017). An environment character-
ized also by potentially destructive and abrupt changes in temperature and chemical composition,
as well as fraught with enemies and predators (including, without being restricted to, natural killer
cells and phagocytes respectively).
This unified view of possible interactions with both biotic and abiotic elements implied in its
turn a number of interesting projections: to start with, the bacteriome could have repercussions
extending much further than its actual position. Microbiomes hosted in gut may affect the cardio-
vascular system or the brain (Liu et al., 2019; Ordovas and Mooser, 2006). In addition, a micro-
biome could be used positively to shape different environments according to needs and wishes; the
acidification of fruit juice to alcoholic beverages (brewing) is an example, and the use of bacteria
for biomining (Banerjee et al., 2017; Donati et al., 2016; Marrero et al., 2015) or for bioremediation
(Verma and Sharma, 2017) are additional ones. Furthermore, by extending the latter thought, it is
possible to use communal relationships so as not only to postpone or avert adverse effects caused
by (members of) the bacteriome (Tanaka and Itoh, 2019)—thus limiting it to neutrality as a best
case scenario—but also to actually mobilize it for supporting or restoring good health (Huang
et al., 2019).
Within a bacteriome, multiple interactions can be dissected to very few baseline events. The
first, most probably in importance if not in occurrence, is antagonism, sometimes causing unilateral
extinction of one of the antagonists. The antagonistic setup, where one or more bacterial strains
forestall the development or impede the survival of usually one homogenous population, or some-
times more than one (Johnson and Foster, 2018) whether similar or widely different to each other,
offers considerable leverage for shaping bacteriomes at will, usually through either the production
of specialized antimicrobial substances, such as, but not restricted to, antibiotics; or extreme com-
petition for resources such as nutrients (Egert et al., 2017).
The other baseline interaction is cooperation (Coyte et al., 2015). In that case, (some of) the
constituent microbiota enhance the development, fitness and/or survival of others, with different
degrees of reciprocity. The more advanced cooperative condition, synergy, implies a mutually, or
rather omnilaterally beneficial set of interactions, for all (minimum, two) participant microbiotes
HABITATS, SETTINGS, AND FORMATS 15
(Troselj et al., 2018; Miller and Bassler, 2001). Different ranges and scopes accommodate
cognitively the unilaterally neutral (commensalistic) versus the mutually beneficial (mutualistic)
interaction, although such terms usually describe symbiotic relations which are directional, with a
symbiont and a host, not mere interactive coexistence formats, which are better described by the
term “syntrophy.” The latter may expand to more complicated association networks than the rather
straightforward host symbiont pairs (Dimijian, 2000).
Similar relationships are observed among different biomes of microbiota. The truth is that
viruses are practically the ultimate predators and different strains plague prokaryota (Fuchsman
et al., 2017), and eukaryota (Li et al., 2010). However, the bacteriome demonstrates a more com-
plex relationship with the mycobiome, from joint polymicrobial biofilms (Probst et al., 2014)
through bipartite serial metabolic reactions as in the production of acetate from carbohydrates and
all the way to the production of antibiotics (Mishra et al., 2017; Petatán-Sagahón et al., 2011).
Symbiosis is a different breed of interactions and concerns the relationship, on a comparative bene-
ficial basis, between one or many microbiota and their host. If a whole microbiome is investigated,
the host can be considered an all-biotic environment, usually extremely homogenous (single-host,
in terms of individuals), but the idea can be expanded to consider multihost setups, usually limited
in a spatiotemporal and/or host-type context. In other words, identical or similar hosts being colo-
nized by one or by the same community of symbionts within the same space, whatever its defini-
tion, or within a time unity, whatever its length or its period. In the context of prokarya, such
interactions may be beneficial (mutualism), neutral (commensalism), or negative (parasitism) for
the host, while they are, at their basic setup, beneficial for the symbiont. Parasitic events usually
lead to infections of multicellular hosts, mostly animals, plants, and occasionally fungi (especially
mushrooms). Mutualistic events are highlighted by bacteriomes in insects, benign gut bacteria in
various animals (Egert et al., 2017; Ipci et al., 2017) or cyanolichens consisting of cyanobacterium
and fungus (Henskens et al., 2012). Nonharmful symbionts, commensals sensu lato, are endophytic
and epiphytic bacteria residing in/on host plants (Balsanelli et al., 2019), a great number of animal
gut-residing microbiota and skin-colonizing microbiota (Christensen and Brüggemann, 2014; Egert
et al., 2017). The dynamic balance in commensalism may be upset by the relative dominance (sur-
vival or overgrowth) of a specific symbiont (Egert et al., 2017; Weiss and Hennet, 2017), by the
arrival and propagation of a virulent strain (Ipci et al., 2017; Weiss and Hennet, 2017) or due to a
drastic alteration of host immunocompetence (de Oliveira et al., 2017), be it immunocompromiza-
tion (Egert et al., 2017) or derailment to allergy or autoimmunity (de Oliveira et al., 2017; Ipci
et al., 2017). All these factors derail symbioses to dysbioses, initiate the pathophysiology of infec-
tion, and, possibly cause, as a consequence, disease. Although the latter may be of other, noninfec-
tious etiology, dysbiosis may still participate in the process (Weiss and Hennet, 2017). Many
bacteria show an effort, or at least a tendency to evolve into multicellular organisms (Meysman,
2018; Risgaard-Petersen et al., 2015), which is a step further from colonial organization. Different
to common knowledge, a bacterial colony will not expand indefinitely even if substrate is available;
under the quorum sensing concept, there are different suppression signals, including, but not
restricted to, catabolism by-products of toxic effect (Chacón et al., 2018; Miller and Bassler, 2001).
The notion of continuous cultures includes many more intrinsic factors subject to rebooting by the
presence of the dynamic, influx efflux processes than the simple supplementation with additional
quantities of nutrients. Among them are the efflux of biomass to keep cells as young as possible
and—the most vital—stirring. The latter not only distributes evenly nutrients and toxins (preventing
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is to say, four-fifths of all these steamers will belong to England. This
will give to us a fleet of ocean steamers outnumbering those of all
the rest of the world combined; and these will always be at our
disposal for, to say the least, the transport of troops, and of the
materials of war. Of the remaining fifth a large proportion will be built
in this country, as our resources and arrangements for the
construction of iron ships and marine engines are superior to those
of any other country.
If, then, it should prove that this forecast of the advantages of the
Canal to us in war is correct, it would seem to follow that, in time of
war, we should be under the necessity of holding it ourselves; or, at
all events, of occupying its two extremities. We should be obliged to
take care that neither an enemy blocked it up, nor a friend permitted
it to go out of repair.
CHAPTER LX.
CONCLUSION.
Beatus qui intelligit.—Book of Psalms, Vulg.
No one can see anything in Egypt except what he takes with him
the power of seeing. The mysterious river, the sight of which carries
away thought to the unknown interior of the great Continent, where
solar heat, evaporation, and condensation are working at their
highest power, giving birth abundantly to forms of vegetable and
animal life with which the eye of civilized man has yet to be
delighted, and instructed; the lifeless desert which has had so much
effect in shaping, and colouring, human life in that part of the world;
the grand monuments which embody so much of early thought and
earnestness; the contrast of that artistically grand, morally purposed,
and wise past with the Egypt of to-day; the graceful palm, and the
old-world camel, so unlike the forms of Europe; the winter climate
without a chill, and almost without a cloud; all these are certainly
inducements enough to take one to Egypt; but how differently are
they seen and interpreted at the time by the different members of the
same party of travellers; and with what widely different after-thoughts
in each!
And just as many of us are dissatisfied with life’s journey itself, if
we can find no object in it, so are we with the travel to which a
fraction of it may have been devoted, if it be resultless. Should we,
when we look back upon it, be unable to see that it has had any
issues which reach into our future thought and work, it seems like a
part of life wasted. For, whatever a man may have felt at the time, he
cannot, afterwards, think it is enough that he has been amused,
when the excitement of passing through new scenes is over, and he
is again in his home,—that one spot on earth where he becomes
most conscious of the divinity that is stirring within and around him,
and finds that he must commune closely with it.
But as to particulars: that which is most on the surface of what
Egypt may teach the English traveller is the variety of Nature. It has
not the aspects of the tropics, in which the dark primæval forest, and
tangly jungle, are the predominant features; yet its green palmtufted
plain, and drab life-repelling desert, are a great contrast to our still
hedge-divided corn-fields, and meadows; to our downs, and heaths,
and hills, and streams; and so are its clear sky, and dry atmosphere
to our clouds and humidity. To see, and understand something about
such things ought, in these days, to be part of the education of all
who can afford the time and money requisite for making themselves
acquainted with the riches of Nature; which is the truest, indeed the
only, way to make them our own. In saying this, I do not at all wish to
suggest the idea that in variety, and picturesqueness of natural
beauty, the scene in Egypt is superior to what we have at home. The
reverse is, emphatically, the case. Every day I look upon pleasanter
scenes than any Egypt can show: scenes that please the eye, and
touch the heart more. Nature’s form and garb are both better here.
So, too, is even the colour of her garb. To have become familiar,
then, with the outer aspects of Egypt, is not only good in itself, as an
addition to our mental gallery of the scenes of Nature, but it is good
also in the particular consequence of enabling us to appreciate more
highly the variety and the beauty of our own sea-girt home.
Of course, however, the source of deepest interest in any scene is
not to be found in its outer aspect, but in its connexion with man. If
we regard it with the thought of the way in which man has used,
modified, and shaped it, and of how, reversely, it has modified, and
shaped man, how it has ministered to his wants, and affected the
form, and character of his life; or if we can in any way associate it
with man, then we contemplate it from quite another point of view,
and with quite different feelings. Indeed it would almost seem as if
this was the real source of the interest we take even in what we call
the sublime and beautiful in nature. Man was only repelled from
snow-capped mountains, and stormy oceans, till he had learnt to
look upon them as the works of Intelligent Mind akin to his own.
Conscious of intelligence within himself, he began to regard as grand
and beautiful, what he had at length come to believe Supreme
Intelligence had designed should possess these characteristics. This
is, perhaps, the source of the sentiments of awe, and admiration,
instead of the old horror, and repugnance, with which we now
contemplate cold and inaccessible barrier Alps, and angry dividing
Seas. To Homer’s contemporaries, who believed not that the gods
had created the visible scene, but that, contrariwise, they were
posterior to it, and in some sort an emanation from it, the ocean was
only noisy, pitiless, and barren. And the modern feeling on these
subjects has, of late, been greatly intensified, and become almost a
kind of religion, since men have come to think that they have
discovered that these grand objects were brought into being by the
slow and unfailing operation of certain general laws which they have
themselves ascertained. So that now, to some extent, they have
begun to feel as though they had themselves assisted at their
creation: they stood by, in imagination, as spectators, knowing,
beforehand, the whole process by which Alps and Oceans were
being formed. That they were able to discover the laws and the steps
by which Omnipotent Intelligence had brought it all about, alone and
sufficiently demonstrates the kindredness of their own intelligence. It
is the association of these ideas with natural objects that causes the
present enthusiastic feeling—almost a kind of devotion—they
awaken within us, and which would have been incomprehensible to
the ancients, and even, in a great measure, to our forefathers. They
seem like our own works. They were formed by what is, in human
degree and fashion, within ourselves. We know all about them;
almost as if we had made them ourselves.
Regarded, then, in this way, it is not the object itself merely that
interests, but the associations connected with it. Not so much what is
seen, as what is suggested by what is seen. The object itself affects
us little, and in one way; the interpretation the mind puts upon it
affects us much, and in quite a different way. In this view there are
reasons why the general landscape here, at home, should be more
pleasing to us than it is in Egypt. It is associated with hope, and with
the incidents and pictures of a better life than there is, or ever has
been, in Egypt. I have already said that the natural features are not
so varied and attractive there as here; their value to us, in this
respect, consisting in their difference. But what I now have in my
mind is the thought of the landscape as associated with man; and in
this other respect also I think the inferiority of Egypt great.
The two pre-eminently grand and interesting scenes on this kind in
Egypt, where our Egyptian associations with man’s history
culminate, I have already endeavoured to present to the imagination
of the reader. They are the scene that is before the traveller when he
stands somewhere to the south-east of the Great Pyramid, looking
towards Memphis, and commanding the Necropolis in which the old
Primæval Monarchy is buried, the green valley, the river, and the two
bounding ranges; or, to take it reversely, as it appears when looked
at from the Citadel of Cairo; and the scene, for this is the other one,
which is presented to the eye, again acting in combination with the
historical imagination, from the Temple-Palace of the great Rameses
at Thebes, where you have around and before you the Necropolis,
and the glories of the New Monarchy.
What, then, are the thoughts that arise in the mind at the
contemplation of these scenes? That is precisely the question I have
been endeavouring to answer throughout the greater part of the
preceding pages. My object now, as I bring them to a close, is
somewhat different; it is to look at what we have found is to be seen
in Egypt from an English point of view; with the hope that we may
thus be brought to a better understanding, in some matters, both of
old Egypt and of the England of to-day. This will best be done by
comparing with the Egyptian scenes, which are now familiar to us,
the English scene which in its historical character, and the elements
of human interest it contains, occupies, at this day, a position
analogous to that which they held formerly. These are subjects that
are made interesting, and we may say intelligible, more readily and
completely by comparisons of this kind than by any other method.
Anatomical and philological comparisons do this for anatomy and
philology, and historical comparisons will do the same for history. We
shall come to understand Egypt not by looking at Egypt singly and
alone, but by having in our minds, at the time we are looking at it, a
knowledge of Israel, Greece, Rome, and of the modern world. Each
must be set by the side of Egypt.
We will come to ourselves presently. We will take Israel first. It
proposed to itself the same object as Egypt, that of building up the
State on moral foundations, only it had to do its work under
enormous disadvantages. Considering, however, the circumstances,
it attained its aims with astonishing success. We must bear in mind
how in the two the methods of procedure differed. So did their
respective circumstances. Egypt had the security which enabled it
freely and fully to develop and mature its ideas and its system. This
precious period of quiet was no part of the lot which fell to Israel. It
had to maintain itself and grow up to maturity under such crushing
disadvantages as would have extinguished the vitality of any other
people, except perhaps of the Greeks, the periods, however, of
whose adolescence and manhood were also very different from
those of Israel. At those epochs of their national life they had
freedom, sunshine, and success. Israel, on the contrary, had then,
and almost uninterruptedly throughout, storm and tempest;
overthrows and scatterings. The people never were long without
feeling the foot of the oppressor on their necks. Still they held on
without bating one jot of hope or heart; and by so doing made the
world their debtors, just as did the Egyptians, the Greeks, and the
Romans. Regarding the point historically, we cannot say that one did
this more than another; for, where all are necessary, it would be
illogical to affirm that one is greater or less than another. Neither the
seeing nor the hearing, we are told, can boast that it is of more
importance than the other; for, were it not for the seeing, where
would be the hearing? and, were it not for the hearing, where would
be the seeing? In the progress of man the ideas, and principles, and
experience contributed by each of these constituent peoples of
humanity were necessary: and if the contribution of any one had
been wanting, we should not be what actually we are; and that
something that we should be then would be very inferior to what we
are now. We could not dispense with the gift of any one of the four.
Egypt gave letters, and the demonstration of the fact that morality
can, within certain limits, be deliberately and designedly shaped and
made instinctive. Greece taught the value of the free development of
the intellect. Rome contributed the idea of the brotherhood of
mankind, not designedly, it is true, but only incidentally, though yet
with a glimmering that this was its mission. Without Rome we might
not yet have reached this point. Israel taught us that, if the aims of a
State are distinctly moral, morality may then be able to maintain
itself, no matter how great the disadvantages, both from within and
from without, under which the community has to labour; and even
when morality is unsustained by the thought of future rewards and
punishments: a lesson which has thrown more light on the power the
moral sentiments have over man’s heart than perhaps any other fact
in the history of our race.
I bow down before the memory of the old Israelite with every
feeling of the deepest respect, when I remember that he abstained
from evil from no fear of future punishment, and that he laid down his
life for truth and justice without any calculation of a future heaven. In
this view the history of the world can show no such single-minded,
self-devoted, heroic teachers as the long line of Hebrew Prophets.
They stand in an order quite by themselves. Socrates believed that it
would be well with him hereafter. They did not touch that question.
Sufficient unto them was the consciousness that they were
denouncing what was false and wrong, and that they were
proclaiming and doing what was true and right.
We will now turn to the Greeks. The interest with which they
contemplated the antique, massive, foursquare wisdom of Egypt is
well worthy of consideration. It is true they did not get much from
Egypt, either in the sphere of speculation or of practice: still for them
it always possessed a powerful attraction. The reason why it was so
is not far to seek. The Egyptians had done great things; and they
had a doctrine, a philosophy of human life. This was that
philosopher’s stone the Greek mind was in search of. And they
inferred from the great things done by the Egyptians (and this was
not a paralogism) that there must be something in their doctrine. In
fact, however, they learnt little from Egypt: for if it was the cradle,
Greece itself was the Holy Land of Mind. Nor was it possible that
they could learn much from it, for the two peoples looked upon
society and the world from quite different points of view. Greece
acted on the idea that in political organization, and in the well-being
of the individual, man is the arbiter and the architect of his own
fortune. Egypt acted on the supposition that these things rested on
an once-for-all heaven-ordained system. Greece believed that truth
was to be discovered by man himself, and that it would, when
discovered, set all things right; and that freedom, investigation, and
discussion were the means for enabling men to make the needed
discovery. Egypt thought that truth had been already communicated;
and that freedom, investigation, and discussion could only issue in
its overthrow. What Greece regarded as constructive, Egypt
regarded as destructive. It could not therefore learn much from
Egypt.
Rome we will now set by the side of Egypt. It will bring the two into
one view sufficiently for our purpose, if we endeavour to make out
what Germanicus must have thought of old Egypt, when he was at
Thebes. He must often have compared it with Rome; in doing which
he could, of course, only view it with the eyes of a Roman. And the
time for such a comparison had arrived, for the work of Rome, and
the form and pressure of that work upon the world, were then
manifesting themselves with sufficient distinctness. What he was in
search of was light that would aid him in governing the Roman world.
Probably he came to the conclusion that the wisdom of Egypt could
be but of very little use to him. The aim of Egypt had been all-
embracing social order, maintained by morality, compacting the
whole community into a single organism, in which every individual
had his allotted place and work, neither of which he could see any
possibility of his ever abandoning, or even feel any desire to
abandon. Egyptian society had thus been brought, through every
class and member, to do its work with the regularity, the smoothness,
the ease, the combined action of all its parts, and the singleness of
purpose of a machine. I need hardly repeat that they had understood
that the morality by which their social order was to be maintained
must be instinctive, and that they had made it so. The difference
between them and other people in this matter was, that they had
understood distinctly both what they wanted for their purpose, and
how to create what they had wanted. Germanicus must have been
aware, if he had seen this point clearly, that no government could
frame the general morality of the Roman Empire; and that the single
moral instinct upon which he would have to depend, if he could
create it, must be the base and degrading one of obedience and
submission brought about by fear. No attempt could be made, in the
world he expected to be called to govern, to cultivate an all-
embracing scheme of noble and generous, or even of serviceable,
morality. Much, indeed, of what was best would have to be
repressed, and stamped out, as hostile and subversive; as, for
instance, the sentiment of freedom, and the consciousness that the
free and full development of a mans inner being (in a sense the
Athenian and the Christian idea) is the highest duty. He would have
to provide not for what would encourage his future subjects to think
for themselves, and to make themselves men, but for what would
indispose them to think for themselves, and would make them only
submissive subjects. He had to consider how many abundant and
virulent elements of disorder, discontent, and corruption could be
kept down: under such a system an impossible task. These evil
growths of society had, each of them, been reduced to a
manageable minimum, spontaneously, by the working of the
Egyptian system; but, under the circumstances of the Roman world,
they were inevitably fostered and developed. The application,
however, of the Egyptian system to that world was out of the
question and inconceivable. So, here, Egypt could give him no help.
It could not show him how he could eliminate or regulate these evils.
He would not be able to get rid of the elements of discord and
discontent in the Egyptian fashion, by creating such instincts of order
and submission as would dispose every man to accept the position
in which he found himself as the irreversible appointment of Nature.
Nor, again, would he be able to counteract social corruption, in the
Egyptian fashion, by making virtue the aim of the state, of religion,
and of human life.
There were also two other problems to the solution of which he
would have to attend. How was the ring of barbarians that
beleaguered the Empire to be kept in check? and how was the
enormous military force that must be maintained for the internal, as
well as the external, defence of the Empire to be prevented from
knowing, at all events from using for its own purposes, its irresistible,
unbalanceable power? For doing every thing of every kind he had to
do, he had but one instrument, and that was force, law being
degraded into the machinery through which that force was to act;
and being also itself at discord with much that was becoming the
conscience of mankind, that is, at discord with its own proper object.
He could make no use of the Egyptian instruments, those, namely, of
general morality, of religion, and of fixed social order. The task,
therefore, that was before him, however strong the hand and clear
the head might be which would have to carry it out, was ultimately
hopeless. For one of two things must happen: either men must rebel
against the order he would have to maintain, and overthrow it, or it
must corrupt and degrade men. For, in the long run, nothing but law
and religion, both in conformity with right reason, and aiming at
moral growth, can govern men; that is to say, government must aim
at human objects, to be attained by human means. Men, of course,
can be controlled otherwise, as, for instance, by armed force, the
only means that would be at the disposal of Germanicus; but then
the product is worthless. Egypt, therefore, could give him no
assistance. It could only tell him that the task before him was to him
an unattainable one. It was not the one the Egyptians had taken in
hand, nor could it be carried out by Egyptian means. A great fight
had to be fought out in the bosom of Roman society, and under such
conditions that its progress and issue would be the ruin and
overthrow of society, as then constituted.
We all know that the man who, in a period of dearth, withholds his
corn for a time, is thinking only of himself, though it eventually turns
out that what he did was done unintentionally for the benefit of the
community: a law, above and beyond him, had been working through
him, and shaping his selfish act so that it should contribute to the
general good. So was it with the Roman Empire. It subjugated and
welded together all people merely to satisfy its own greed, but in so
doing it had further unfolded and advanced the world-drama of
human history. When it had played out its part, it was seen that that
part could not have been dispensed with, because, though so hard
for those times, it was essential to the great plot, for it was that that
had given birth to, and brought to maturity, the sentiment of the unity
and brotherhood of mankind.
And now at last we come to ourselves. All, including Egypt, have
become teachers to us. We are the inheritors of the work of all. To us
—and how pleasant is it to know this—the wisdom even of old Egypt
is not quite a Dead Sea apple, something pretty to look at, but inside
only the dust of what had been the materials of life. We can feel our
connexion with Egypt, and that we are in its debt; and we shall not
be unworthy of the connexion, and of the debt (a true debt, for we
are benefited through what they did), if we so make use of them as
that those who shall come after us shall have reason to feel that
they, too, are, in like manner, debtors to ourselves. Inquiries of this
kind enable us to discover what are the historical, which means the
natural and actual, bases of our own existing civilization.
What we now have to do is to compare ourselves with old Egypt.
Things of this kind become more intelligible when made palpable to
sense by being taken in the concrete. We have looked on the scenes
in Egypt which are invested with an interest that can never die,
because it is an interest that belongs to the history of humanity. By
the side of them we must set the scene in the England of to-day,
which holds the analogous position. Of course it must be in London.
And as it must be in London I know no better point at which we can
place ourselves than on the bridge over the Serpentine, with our
back upon Kensington, so that we may look over the water, the
green turf, and the trees to the towers of the old Abbey and of the
Palace of Westminster. The view here presented to us is one which
obliges us, while looking at it, to combine with what is actually seen
what we know is lying behind and beyond it. It is not a scene for
which an otiose glance will suffice, because it is precisely the
connexion between what is before the eye, and what is to be
understood, that gives it its distinguishing interest.
What is immediately before you, in its green luxuriance of turf and
leaf, is peculiarly English; you might imagine yourself miles away
from any city, and yet you are standing in the midst of the largest
collection of human beings ever brought together upon the earth:
what is around you is hardly more the capital of England than of the
world. Strange is it to find yourself in the midst of such an
incomprehensible mass of humanity, and yet at the same time in the
midst of a most ornate scene of natural objects—water, trees, turf.
Just as in the Egyptian scenes, where the interests of its history are
brought to a focus, the preponderant objects presented to the eye
are graves and temples in the desert, which tell us of how religious
and sombre a cast was the thought of the Egyptians, who could see
nothing in the world but God, and could regard life only in connexion
with death; so here, too, we find, as we take our stand in the midst of
this English world-capital, that we can see nothing of it; that it is hid
from our eyes by the country enclosed within it. This alone tells us
something about the people. It intimates to us that those who have
built this world-wonder have not their heart in it; that it is against the
grain for them to be here: they do not love it: they do not care to
make it beautiful: that, unlike their Latin neighbours, they are not a
city-loving people; that the first and strongest of their affections are
for the green fields, the wavy trees, and the running streams; and
that they have, therefore, reproduced them, as far as they could, in
the midst of the central home of their political life, to remind them of
what they regard as the pleasanter and the better life. But it is
strange that this very fondness for rural life is one of the causes that
have contributed to the greatness of this city. It has been the love of
Nature, and the hardihood of mind and body the people have
acquired in their country life, which have disposed them to go forth to
occupy the great waste places of the earth; and so have helped in
enabling the Nature-and-country-loving English race to build up an
Empire, out of which has grown this vast, but from the spot where we
are standing in the midst of it invisible, city.
Each also of the two great buildings, whose towers are seen
above the trees, has much to tell us about ourselves. There is the
old Abbey, reminding us of the power religion has had and will ever
have over us, though not now in the Egyptian fashion of something
that has been imposed upon us, but rather of something that is
accepted by us; and of our determination that it shall not be
constructed out of the ideas and fixed for ever in the forms which
belong to ages that, in comparison with our own really older and
riper times, had something to learn, and not everything to teach. It is
precisely the attempt to invest Christianity with Egyptian aims and
claims, fixity and forms, which is arraying men’s minds and hearts
against it; and, in some parts of Christendom, making the action of
society itself hostile to it. It is this attempt which is in a great measure
depriving it of the attractiveness and power it possessed in its early
days when it was rightly understood: though then it was, necessarily,
not only a private care, but one that had also to strive hard to
maintain its existence against the fierce and contemptuous
antagonism of the collective force of the old pagan form and order of
society. If men are now turning away from what they once gladly
received, it can only be because what is now offered to them has
ceased to be what it was then—the interpretation, and expression,
and the right ordering, of all that they knew, and of the aspirations of
their better nature. The phenomenon is explained, if we have reason
for believing that men then regarded Christianity as an honest
organization of knowledge, thought, and morality, for the single
purpose of raising and bettering human life, but now regard it as, in
some measure, their priestly organization for the purpose, primarily,
of maintaining priestly domination, through the maintenance of a
system which was the growth of widely different times and
circumstances.
It cannot be seen too clearly, or repeated too often, that
Christianity did not originate in any sense in priestly thought, but
was, on the contrary, a double protest against it, first in its own actual
inception, which included a protest against priest-perverted Judaism,
and antecedently in the primary conception of the previous
dispensation, which included a protest against priestly Egyptianism;
so that neither in itself, nor in its main historical source, could it
originally have had any priestly or ecclesiastical, but only broadly
human and honestly moral aims.
This will, by the way, assist us in forming a right estimate of the
character of that argumentum ad ignorantiam we have heard so
much of lately, that Protestantism is only a negation of truth, and an
inspiration of the Principle of Mischief. Looking back along the line of
our own religion, we find that Moses, speaking historically, was the
first Protestant; and that the Saviour of the World was, in this respect
also, like unto him. As, indeed, have been, and will be, more or less,
in the corrupt, but though corrupt, yet still, on the whole, advancing
currents of this world, all who are wise and good, and who have the
courage of their wisdom and goodness. It will also assist us to
understand that religion does not mean systematic Theology and
organized priestly domination, which are its degeneration, and into
which the ignorance and carelessness of the mass of mankind, and
the short-sightedness of some, and self-seeking of others, of its
constituted expounders are tending always to corrupt it; but that it
means, above all things, the ideal theory of perfect morality and
virtue, combined with the attempt to work it out practically in human
life, so far as is possible, under the difficulties and hindrances of this
world, supported by the good hope of its actual complete realization
in a better world to come.
The history of old Egypt is very much the history of the character,
working, and fate of the priestly perversion (as we must regard it
now) of religion, even when the attempt is made, as it was in that
case, honestly, and without any violation or contradiction of the
original principles and aims of the religion. As respects the modern
world, the lamentable and dangerous consequences of this
perversion of religion are to be traced, in some form or other, in the
actual moral and intellectual condition of perhaps every part of
Christendom. We see indications of them amongst ourselves in
individuals, and even in classes. The legitimate action of religion has
been in many cases not merely neutralized and lost, but directly
reversed. It ought to generate the instincts that contribute to the
order, the unity, the building up of society; whereas, by aiming at
ecclesiasticism, and endeavouring to retain what is at variance with
its own true purpose, it has given rise to unavowed repugnances, to
fierce antagonisms, to repulsion of class from class, and even
among some of hatred to the very order of Society; that is to say, it
has produced instincts that contribute, and that most energetically, to
disorder, disunion, and the overthrow of Society; proving the truth of
the saying that nothing is so bad as the corruption of that which is
best. Religion is the summa philosophia which interprets,
harmonizes, systematizes, and directs to the right ordering of
Society, and of the individual, all knowledge from whatever source
derived, all true and honest thought, all noble aspirations, all good
affections. Development and growth ever have been, and ever must
be, a law of its existence: nothing else can maintain its continuity.
And as, notwithstanding this necessity of development, its end and
aim must all the while, and for ever, be one and the same,
development and growth do not and cannot mean the overthrow of
religion, as some have told us, and will continue to tell us, but, on the
contrary, the enlargement and strengthening of its foundations, and
the better ordering and furnishing of the superstructure.
The very name of the building before us—The Abbey—reminds us
that, as far as we ourselves are concerned, we have accepted and
acted on the principle of development, adaptation, and correction in
our religion. The old name, belonging to a past order of things, is
evidence that this principle has once been applied; and so it supplies
us with a ground for hope that it will be applied again, whenever a
similar necessity may arise. History, indeed, assures us that this
must be done always, sooner or later, for in all ages and places the
religion of any people has ever been, in the end, what the knowledge
of the people made it; but it makes a great difference whether what
has to be done be done soon, or whether it be done late. If the
former, then the continuity of growth and development is not
interrupted. If the latter, then there intervenes a long period of
intellectual and moral anarchy, of religious and irreligious conflict.
The consequences and the scars of the conflict are seen in what is
established eventually. It is found that some things that were good
have perished; and that some that are not good have become
inevitable.
By the side of the old Abbey rise the towers of the Palace of
Westminster—a new structure on an old site. That which first occurs
to the beholder, who has old Egypt in his thoughts, is its inferiority in
artistic effect to the stupendous but simple grandeur of the Egyptian
Priests’ House of Parliament in the hypostyle Hall of Karnak, with its
entourage of awe-inspiring temples, its vast outer court, and its lofty
propylons. In that hall he had felt that its great characteristic was not
so much its grandeur as its truthfulness to its purpose, of which there
is not one trace to be found in the home of our great National
Council, which one might survey carefully, both internally and
externally, without obtaining the slightest clue for enabling him to
guess for what purpose it was designed. But how grand, I hesitate to
say how much grander, is the history which the site, at all events, of
the building we are looking at brings into our thoughts. It has not
indeed numbered the years of the Egyptian Panegyries. They might
have counted theirs by thousands, while our Assembly counts its by
hundreds. And we must also remember that they assisted at the
birth, and watched by the cradle, of political wisdom. True they
swathed the infant in the bands of a fixed religious system; but, then,
they could not have done otherwise; and what they did, under the
restrictions and limitations which times and circumstances imposed
upon them, was, notwithstanding, good and precious work; and we
comparing that work of theirs with much that has since been done,
and is now doing, see that, though it was crippled and distorted at
every step by their evil necessities, it was done wisely, and well, by
men who clearly understood what they wanted to do, and how it was
to be done. Our Parliament had to do its work under very different
and even opposite conditions. This island—indeed, this part of the
world—was not an Egypt where none but corporations of priests and
despotic rulers could be strong. We could not, on the contrary, be
without chieftains’ strongholds, and strong towns, too. While,
therefore, with us the armed possessors of these strong places
accepted religion, they could resist and forbid ecclesiastical
encroachments, and could thus save Society, through saving the
State, from ecclesiastical domination. They were strong and free,
and so could nurture freedom, instead of standing by and looking on
while it was strangled and buried out of sight. They were, too, the
heirs of Israelite, Greek, Roman, and German traditions; and these
they could keep alive, even without quite understanding them, until
the day came when they might be carried out more fully and
harmoniously; and more might be made of them than had been
possible even in the days, and in the countries, which had given
them birth. That has been the slow but glorious rôle in human history
of these English Parliaments, of which that Palace of Westminster at
which you are looking is the shrine: a spot most sacred in human
history, and which will be closely interesting to the generations that
are to come when time shall have forgot the great Hall of the
Panegyries of Egypt; for the History of the freedom of Religion, of
Speech, and of the Press, of Commerce, and of political and almost
of human freedom itself, is the History of these English Parliaments.
The History, then, of these two buildings throws much useful light
on the history of the later phases of the progressive relations to each
other of the State and of the Church; and of the rights, the duties, the
proper field, and the legitimate work of each. The questions involved
in these points have been answered very differently at different
times, in accordance with the varying conditions of society: but the
answers given have, on the whole, been such as to assist us in
understanding two particulars of importance: first, that the character
of the relation of the two to each other among any given people, and
at any given time, is dependent on the conditions of society, then
and there; on the point knowledge has reached; the degree to which
it has been disseminated; and on the course antecedent events have
taken. (The relation, at any time established, does, of course, re-act
on the conditions which gave rise to it, and so has some effect in
shaping, and colouring, their character in the proximate future.) And,
in the second place, that there is observable, throughout History, if
its whole range be included in our view, a regular evolution and ever-
growing solution of the great question itself.
All the peculiarities, and particulars of the history, of these two
buildings, such, for instance, as that they stand side by side, and yet
are quite distinct from one another; that the Ecclesiastical building is
very old, very ornate, and imposing, and was very costly; and that
the Civil building is modern, but on an old site; that it too was costly,
and is very ornate and imposing, and in its ornamentation and
aspects affects somewhat the Ecclesiastical style; that they are in
the hands of distinct orders of men belonging to the same
community; that the work carried on in them is quite distinct, and yet
that ultimately their respective work is meant to contribute, by
different paths, and with different sanctions, to the same end, that is
to say, the bettering of man’s estate—all this symbolizes with
sufficient exactness the history and character of the conflicts, and of
the relations, past and present, of the Church and of the State
amongst ourselves.
I am here taking the word Church in its widest, most intelligible,
and only useful sense—and which is the interpretation history puts
on the phenomena the word stands for—that of the conscious
organization of the moral and intellectual forces and resources of
humanity for a higher life than that which the State requires and
enforces. It is untrue, and as mischievous as untrue, to talk of
Religion—that is, the effect on men’s lives of the doctrine which the
Church has elaborated—as if it were something apart, something
outside the natural order of things, something up in the air,
something of yesterday, which has no root in man’s nature, and the
history of which is, therefore, not coincident with the history of man.
Like every thing else of which we have any knowledge, it is the result
of certain causes. And in the case of this effect, of which the Church
is the personal embodiment, the affiliation is distinct and palpable.
Poetry and Philosophy are as much manifestations of it, as what we
call Religion, when we are employing the word in its popular,
restricted signification. They do, indeed, so entirely belong to it that
there could be no advance in Religion, I might almost say no
Religion at all, without them. And, conversely, Religion supplies to
the bulk of mankind all the Poetry and Philosophy that will ever be
within their reach. Poetry (which uses Art as one of its instruments of
expression), dealing with things both objectively, as they appear to
address themselves to us, and subjectively, as they are seen
through the medium of our own sentiments; and Philosophy, dealing
with the ensemble of things as they are in themselves—the two,
working in these ways, and endeavouring to organize sentiment and
knowledge, or, in other words, human thought and the world of
external facts, for the sovereign purpose of nurturing and developing
our moral being, if they do not give rise to Religion, yet have, at all
events, largely contributed towards expanding, purifying, and
shaping it. Every one can see how Philosophy and Poetry
contributed each its part to the construction of the Old Dispensation.
It is equally plain that Christianity originally rested on a profoundly
philosophical view of the Old Dispensation, considered in connexion
with the then new conditions of the world. And it was, precisely,
because the view taken was so profound, because it went so
completely to the bottom of all that then and there had to be dealt
with, that it was felt and seen to be thoroughly true. For the same
reason it was as simple as it was true. And it was because it was so
entirely in accord with man’s nature and history, and with the
conditions on which the world had then entered, that it was
understood to be, and received as, a Revelation from God. This was
the internal evidence. And in the old Classic world, which we can
now contemplate ab extra, and without prepossession, we see that
the only teachers of Religion were first Poetry, and then Philosophy:
at first mainly the former, and afterwards mainly the latter. And thus
were they the means by which the outer world, at all events, was
prepared for Christianity.
If, then, we take the word Church in the sense I am now proposing
(and I am concerned here only with the interpretation History gives of
the phenomenon), it will help us to understand how it happens that
every Church, at certain stages in its career, comes into conflict with
the State, or the State with the Church; and, too, how it happens
that, at certain conjunctures, the action of the State, as it is, is to
restrict and to thwart the action of the Church, as it should be; and
why it is that, in the end, the latter must always carry the day. It will
also lead us to think that in the future the Clergy will not have the
entire decision of religious questions; but that, strange as it may
sound to us, the Poet, the Historian, and the Philosopher will, sooner
or later, be able to make their ideas felt in the discussion and
shaping of these matters. It has been so in the past; and we may
suppose that it will be so again in the future. Even now the lay
Prophet has no insignificant auditory, and it is one that it is growing
rapidly in every element of influence. We have no reason for
believing that the world will be content to leave, for ever, its own
highest affair in the hands of those only whose function, as
understood and interpreted, at present, by the majority of
themselves, is to witness to what were the thoughts of their own
order, in an age when that order thought for mankind; and did so,
sometimes, not in complete accordance with the common heart,
conscience, and aspirations of mankind, certainly not with what they
are now, but rather with what the Church supposed would complete
and strengthen its own system; at all events, always in accordance
with the insufficient knowledge, sometimes even with the mistaken
ideas, of times when the materials supplied by the then existing
conditions of society, and by the then state of knowledge, for the
solution of the problem, were not the same as those supplied by our
own day.
In old Egypt—under the circumstances it could not possibly have
been otherwise—the Church administered, and was, the State: the
State was contained within it. The distinction between things civil and
things religious had not emerged yet. This fact deeply modified the
whole being of the Church. Its resultant colour thus came to be
compounded of its own natural colour and of that of the State. This
primæval phase can never again recur. The increase and
dissemination of knowledge; the idea and the fact of civil as opposed
to ecclesiastical, we may almost say of human as opposed to divine
legislation, and the now thoroughly well ascertained advantage of
the maintenance of civil order by civil legislation, have made the
primæval phase, henceforth, impossible among Europeans, and all
people of European descent. We may add, that it has, furthermore,
become impossible now on account of the higher conception that
has been formed of the duty and of the work of the Church itself.
The Middle Ages present to our contemplation the curious and
instructive picture of a long-sustained effort, made under
circumstances in many respects favourable to the attempt, and
which was attended by a very considerable amount of success, to
revert to and to re-establish the old Egyptian unspecialized identity of
the two. This effort was in direct contradiction to the relation in which
the early Christian Church had placed itself to the State; though, of
course, it was countenanced, apparently, by the early history of the
Hebrew Church, which, like that of Egypt, had necessarily embraced,
and contained within itself, the State, in the form and fashion that
had belonged to the requirements of those times. That it had been
so with it, however, only shows, when we regard the fact, as we can
now, historically, that society, there and then, was in so rudimentary
a condition, that its two great organs of order, progress, and life had
not yet been specialized; the ideas and means requisite for this
advance not having been at that time, among the Hebrews, in
existence.

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Microbiomics: Dimensions,

Applications, and Translational

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Environment and Development. Basic Principles, Human

Diabetic Bone Disease: Basic and Translational Research

The Human Dimensions of Forest and Tree Health Julie

Societal dimensions of environmental science: global

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Exploring the Dimensions of Human Sexuality Jerrold S.

Digital Geoarchaeology: New Techniques for

Copyright © 2020 Elsevier Inc. All rights reserved.

For Information on all Academic Press publications

Publisher: Andre Gerhard Wolff

Typeset by MPS Limited, Chennai, India

List of Contributors ............................................................................................................................ xiii

CHAPTER 1 Introduction: The Microbiome as a Concept: Vogue

PART I CLASSES AND KINDS OF MICROBIOMES ..................................... 5

CHAPTER 3 Myc(et)obiome: The Big Uncle in the Family .................................... 29

Remote Effects, Communication, and Control Functions of Mycobiomes ............ 47

CHAPTER 4 Virome: The Prodigious Little Cousin of the Family.......................... 53

PART II THE STUDY OF MICROBIOTA AND MICROBIOMES.................... 75

Conclusion: A Peek of the Future............................................................................ 90

CHAPTER 6 Panmicrobial Microarrays .................................................................. 95

CHAPTER 7 Metagenomics in Microbiomic Studies ........................................... 121

Ribosomal RNA Genes rrs and rrl ........................................................................ 133

CHAPTER 8 Culturomics: The Alternative From the Past .................................... 155

Roche 454 Pyrosequencing ............................................................................... 178

PART III NOVEL AND LEGACY FIELDS OF MICROBIAL

CHAPTER 11 A Prerequisite for Health: Probiotics............................................... 225

CHAPTER 12 Microbiomic Prospects in Fermented Food and Beverage

CHAPTER 13 Legacy and Innovative Treatment: Projected Modalities for

CHAPTER 14 Electromagnetism and the Microbiome(s)....................................... 299

The New Generation of Electrostimulation: WMCS-NCCT............................ 315

CHAPTER 15 Microbiomics: A Focal Point in GCBR and Biosecurity................... 333

CHAPTER 16 Epilogue............................................................................................. 361

Index .................................................................................................................................................. 367

BACTERIOME AND ARCHAEOME:

Microbiomics. DOI: https://doi.org/10.1016/B978-0-12-816664-2.00002-5

THE PIONEERS, THEIR VISION AND THEIR MEANS

HABITATS, SETTINGS, AND FORMATS

Beatus qui intelligit.—Book of Psalms, Vulg.

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