Human Microbiome Handbook Preview

The
Human
Microbiome
Handbook
Edited by
Jason A. Tetro
Visiting Scientist
Department of Molecular and Cellular Biology
University of Guelph
Emma Allen-Vercoe, Ph.D.

Associate Professor
Department of Molecular and Cellular Biology
University of Guelph
The Human Microbiome Handbook
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Preface
T HE term “microbiome” has been in use for over 50 years but only in
the last 15 years has it gained popularity in the health community.
The word describes the totality of microorganisms in and on a particular
environment. In humans, this totality includes the gastrointestinal tract
(including the mouth), the skin, the respiratory tract, the genitalia, and
even the ocular surface. But while this singular concept has garnered
significant attention, our understanding of the scope in terms of public
health and medicine continues to be enigmatic.
For over a century we have known microbes play a role in our lives,
although for the majority of this span, the focus has been on infec-
tion or, ecologically speaking, parasitism. We now know the number of
pathogens amounts to only a tiny fraction of the entirety of the micro-
bial species on earth and less than one-tenth of the microbes associated
with the human body. The rest have been primarily studied outside of
the realm of human health with discoveries limited to journals focusing
on microbiology rather than medicine.
Over the last 40 years, we have seen a burgeoning increase in the
number of scientific articles examining the interaction of microbes and
humans in terms of “commensalism” as well as “mutualism”; ecologi-
cal terms that now also apply in the field of medicine and public health
because of a deeper appreciation of the microbial ecology of the body.
We are not solely made up of 37 trillion human cells; we also have
microbes totalling up to three times that number. Through observation
at the lab bench, in animal models, and clinical trials, we are learning
how these two very different organisms—mammal and microbe—in-
ix
x Preface
teract. More importantly, we have a growing understanding of how

this interkingdom interface affects acute as well as chronic health out-
comes.
The Human Microbiome Handbook was conceived as an examina-
tion of our knowledge about the microbial influence in public health.
Though the amount of data continues to increase at a staggering rate,
many trends of microbe-human interaction have become solidified.
These are duly explored within the pages of this book. The range of
topics encompasses many branches of medicine from gastroenterology
to metabolism to immunology and mental health. In each chapter, the
authors, all of whom are experts in their individual microbiome fields,
provide the latest findings and, where applicable, mechanism-based ex-
planations. All told, this compilation will provide any medical or health
professional with the necessary knowledge and applicable references to
ensure a well-rounded appreciation of the microbiome and its impact
on our health.
Many health professionals have only a rudimentary understanding of
the microbiome. This book has been designed to ensure all individuals
can access the most pertinent information in the field. This has been ac-
complished by separating the book into three sections, beginning with
a general overview of the microbiome and gradually moving to specific
mechanisms, including discussions on disease and possible therapeu-
tics. In this way, it is our hope that any reader, regardless of academic
background, will be able to gain enough information for use in their
future work and practice.
The first section provides an introductory perspective on the microbi-
ome in which a more general observation of the knowledge is provided.
Chapter 1, by one of the pioneers of microbiome research, Sydney Fi-
negold, is historical in nature, taking us through his journey in the field
over five decades. Chapter 2, by Dutch researchers Kaludyna Borewicz
and Hauke Smidt, provides an overview of the microbiome as a part of
the human body. This chapter also introduces the concept of ecology in
which microbial populations, not solely singular species, are now the
focus of research. The final section provides an overview of the concept
of our microbiome as more than a static entity. Chapter 3, headed by
Paul O’Toole from Ireland, provides a longitudinal examination of the
nature of the gut microbiome from birth to death.
The second section of this book examines the trends of microbial
influence on our bodily processes. Vicky De Preter and Kristin Ver-
beke from Belgium examine first the microbial side of the interaction.
Preface xi
Chapter 4 takes a look at the life cycle of bacteria and how certain by-
products can act not as waste but as useful stimuli for several associated
biological systems. The effect of microbes and mental health is next ex-
amined in Chapter 5 by Canadian scientists, Aadil Bharwani, John Bi-
enenstock, and Paul Forsythe. These researchers are forging the path to
our understanding of how microbes in the gastrointestinal tract can af-
fect our mental state and influence pathologies such as depression. The
key to this may lie in immune system interactions, and Chapter 6 by
Leando Lobo, Rosana Ferreira, and Caetano Antunes, from Brazil, ex-
plores this concept. Although much has already been learned as a result
of traditional, infection-based work, incorporation of the microbiome
into this field of study may lead to the development of microbially-me-
diated immune therapies. Finally in Chapter 7, Tinting Ju, Jiaying Li,
and Benjamin Willing, from Canada, provide an examination of how
microbes can modulate our metabolism. In the context of human health,
microbes have a significant influence and may be the key to several
chronic illnesses such as obesity, diabetes, and cardiovascular disease.
The third section deals specifically with disease and therapies. The
theme in this section is “balance”. As in all ecological environments,
equilibrium of species is needed in order to attain harmony, and when
this balance is disrupted, problems may ensue. We now understand the
same applies to the human body and several diseases once thought to
be mysteries have been elucidated on the basis of this lack of ecological
balance. In addition, when the ecology is restored, balance can be re-
established and health can be returned.
In Chapter 8, Spanish researchers, Claudia Herrera, Virginia Robles-
Alonso, and Francisco Guarner examine the effects of microbes on our
gastrointestinal health and how a change in ecology may lead to chronic
health problems including inflammatory bowel disease, liver diseases,
and antibiotic-mediated illnesses. In Chapter 9, Holly Ganz and Dawn
Kingsbury, from the United States, explore one of the most hotly de-
bated topics in microbiome research: epigenetics. Though this field is
still relatively new, we are beginning to appreciate how microbes are
not only influencing our cellular world, but also our genes. This chapter
will examine what is already known and as well will explore several
hypotheses to explain potential mechanisms behind some of our most
problematic diseases.
In contrast to disease, Rowena Almeida and Elaine Petrof, from Can-
ada, provide an in-depth look at one of the most discussed medical pro-
cedures today. Known as fecal microbiota transplantation, or FMT, this
xii Preface
process of restoring a balanced ecology in the gastrointestinal tract has

of late gained significant notoriety. Chapter 10 will unveil the mecha-
nisms, reveal the benefits and drawbacks, and dispel the myths. Apart
from FMT, the other major interest for health professionals is the realm
of probiotics. Canadian scientist Gregor Reid, in Chapter 11, will pro-
vide an examination of the nature of probiotics—what they are, what
they are not—and will explore the beneficial properties of these special
microbes. He will also provide a critical perspective on questions asso-
ciated with their use and where gaps in our understanding may be filled.
The end of this book offers a positive outlook for the future. We are
still only beginning to understand the scope of microbial influence on
our health and illness. As we continue to explore the once-hidden ecol-
ogy within our bodies, we will unveil even more incredible mechanisms
and possibly routes to novel and perhaps even revolutionary therapies.
Although we have come far in the short period of time since Lederberg
introduced the microbiome terminology to the world, we also know the
journey will extend long into the future and change the face of health
practice. The Human Microbiome Handbook will enable anyone to join
the journey, if only as a witness, and to gain awareness and readiness for
the marvels that undoubtedly will come. For those in pursuit of medical
and health degrees or simply wishing to learn more about the involve-
ment of microbes in their field, understanding the impact of the micro-
biome now will make for an even richer practice down the road.
We wish you a good read and a very balanced microbiome.
JASON TETRO
EMMA ALLEN-VERCOE
CHAPTER 1
Some Historical Notes on

Bowel Microflora
SYDNEY M. FINEGOLD, M.D., MACP, D (ABMM)
S INCE so much of the bowel flora is anaerobic, it makes sense to start

with what was known about anaerobic bacteria in the “olden days”.
I graduated from UCLA in 1943 as a Bacteriology major. This school
is one of good reputation. Still, I learned virtually nothing about anaer-
obes; just that clostridia were anaerobic bacteria and were responsible
for some serious and often fatal infections, or intoxications, such as
tetanus, botulism, and gas gangrene. There were laboratory sessions
for most of the courses we took as bacteriology majors, but we didn’t
do anything with any clostridia and did not even see pictures of these
organisms or of the serious clinical illnesses related to them in our text-
books. There might well have been concern about handling such bacte-
ria in the laboratory since penicillin was only available for the military
in 1943 and was in such short supply that urine was saved from patients
receiving it so that penicillin could be recovered from it and used again,
but there are many benign anaerobes that could have been used in col-
lege courses. (As a Navy Corpsman assigned to the clinical microbiolo-
gy lab at Long Beach Naval Hospital from 1943 to 1945, I was assigned
the task of collecting all urine from patients treated with penicillin.)
In medical school (1945 to 1949), I worked part time in the surgi-
cal research laboratory of Dr. Edgar Poth who was well known for his
studies on so-called “intestinal sulfonamides”, used prophylactically in
patients having bowel surgery. These compounds were tested initially
in dogs and my job was to obtain fecal samples and study the fecal
flora using a protocol that was set up previously. For anaerobic flora,
we used Brewer plates (special Petri dishes whose lids came down to a
1
2 SOME HISTORICAL NOTES ON BOWEL MICROFLORA
very short distance from the agar surface so that the air space was quite
limited) with Brewer thioglycollate agar which supported the growth of
many anaerobes. What was not known at that time (and I didn’t know
until sometime later) was that virtually all clinically significant aerobic
and microaerophilic bacteria are facultative and grow well (often bet-
ter) under anaerobic conditions. We did not know to test all organisms
recovered on these Brewer agar plates for the ability to grow under
nonanaerobic conditions. In fact, there was no identification of anything
growing on those plates; we simply determined the “anaerobic counts”
by counting colonies on these plates, not even counting different colony
types. They had used these procedures for many years before I was
involved.
In my postgraduate work in Minneapolis I worked with Dr. Wesley
Spink and Dr. Wendell Hall. There was no specialty of Infectious Dis-
eases yet, but I chose their program because they worked with brucel-
losis and other bacterial infections and I was still very interested in
microbiology. During my clinical training, I had a patient with pleural
empyema. I removed purulent pleural fluid by thoracentesis; it was pu-
trid and I was surprised when the laboratory told me they didn’t grow
any bacteria from it. I looked at the Gram stain with the Chief of the
Clinical Microbiology Laboratory and we couldn’t decide that there
were any bacteria present, just pink-staining pleomorphic “globs”. I
presented this patient at a conference attended by Faculty and students
from several teaching hospitals in the city and no one had any sugges-
tions as to what the cause of this infection was. Finally, one of my col-
league Fellows, Gordon Riegel, from the University and VA hospitals
in Minneapolis, timidly asked whether this might be an anaerobic em-
pyema. Gordon had trained earlier at Johns Hopkins and remembered
one professor talking about anaerobic infections and noting that the
discharges were often foul smelling and it was difficult to grow these
organisms. No one knew how to respond to the Fellow. I discussed the
case further with the head of the Clinical Microbiology Lab and she had
no other suggestions.
I had another period in military service from 1951 to 1953. Then I
got my first real faculty position 62 years ago as a staff physician at the
VA Hospital in Los Angeles and on the faculty of the UCLA School of
Medicine in the Department of Medicine and the Department of Micro-
biology, Immunology, and Molecular Genetics. As luck would have it,
we had another case of putrid empyema which did not grow any organ-
isms. I recalled the patient from Minneapolis and I discussed the two
Some Historical Notes on Bowel Microflora 3
cases with Vera Sutter, Ph.D., head of the Clinical Microbiology Lab
at the VA hospital where the patient was being treated. We looked at
the Gram stains together and found the same questionable pleomorphic
bacteria. This time I decided I needed to pursue these anaerobes. Vera
said she remembered seeing an anaerobic jar in the basement some-
where and searched until she found it. We again cultured pus from this
patient, both on plates in the anaerobic jar and on aerobic plates. We
again grew no aerobes but recovered two different gram-negative an-
aerobic bacilli from the plates incubated in the anaerobic jar. I was very
lucky that no bacteria grew from either of the two putrid empyema pa-
tients. Anaerobic infections very commonly are mixed with aerobes as
well as anaerobes. For that reason, anaerobic infections are often over-
looked because the aerobic bacteria grow and the infection is attributed
to them. I was also unlucky because if there had been gram-positive
anaerobes (cocci, for example) present, I would have seen them on the
Gram stain and with negative cultures I would have realized there was
some kind of fastidious organism present.
I was finally launched on a many-years-long study of anaerobic bac-
teria. This was no easy task as it required classification, optimum meth-
ods of growing and preserving cultures, unique features of the bacteria,
and clinical presentations of anaerobic infections. I was amazed to find
anaerobes in so many different settings. Early on I found a small green
book by Louis D.S. Smith of Montana on nonspore-forming anaerobic
bacteria and their activities. As I got into literature searches, I became
aware of centuries-old studies by French and German microbiologists
in particular; I was amazed at how much they knew in the 1800s. I
published Anaerobic Bacteria in Human Disease in 1977 summarizing
our studies and those of others. My laboratory, with some outside col-
laborators, published the Wadsworth Anaerobic Bacteriology Manual
in 1972, now in its sixth edition and called the Wadsworth-KTL Anaero-
bic Bacteriology Manual.
Early in my academic career, and overlapping my new-found major
interest in anaerobic bacteria, I also became interested in bowel flora.
Neomycin was a newly introduced antibiotic and it was noted that there
was little absorption by the oral route, so the levels achieved in the gut
were relatively huge. This led to an interest in using this and similar
drugs for preoperative preparation of patients for bowel surgery. With
my background from Dr. Poth’s laboratory, I was very much interested
in studying this compound. I started by determining what the impact of
oral neomycin was on the bowel microflora. This was so early in my
career that I still was not using the anaerobic jar routinely. I made se-
rial 10-fold dilutions of feces and planted them onto various agar plates
that would permit recovery of various known colonic bacteria and also
planted them into a set of thioglycollate broths. The appearance of the
cultures at 48 hours was really striking. There was no growth on any
of the plates incubated aerobically, but the thioglycollate broths were
turbid all the way out to 1012/ml! Aerobic subcultures from these broths
were sterile, but subcultures incubated in anaerobic jars yielded many
anaerobic bacteria of various types.
We subsequently learned about other systems for growing anaerobes,
including watch glasses placed on the surface of inoculated plates by
Professor Haenel of Potsdam, East Germany. These watch glasses were
close to the agar surface and early growth of aerobes soon converted
the space to an anaerobic environment. It was tedious working with this
setup but Haenel managed to do excellent studies of bowel flora with it.
Initially we used line gas (methane) in our anaerobic jars; fortunately, it
was not so toxic to anaerobes in Los Angeles and we could grow some
of them (but didn’t know what we might be missing). Later, commer-
cial kits to provide an anaerobic atmosphere with carbon dioxide in jars
became available, as did catalysts to remove traces of oxygen. We ulti-
mately switched to anaerobic chambers when these became available,
and to tanks of pure nitrogen, hydrogen, and carbon dioxide gases, in-
dividually and in appropriate mixtures. Learning to identify anaerobes,
even by the crude techniques available at that time, was a problem. Ini-
tially, we called them “gray colonies” (the Bacteroides fragilis group,
it turned out), “clear colonies” (some of these were Fusobacterium we
later found out), and brown or black “pigmented” colonies on blood or
hemoglobin-containing media.
In comparison to the rapid, wide spectrum of analyses performed
on a day-to-day basis, this work may seem minimal. Yet, back then,
everything was. Take the mere concept of sharing results and/or com-
municating with colleagues. Today, the communication possibilities are
great and one can phone or e-mail anyone and expect to usually get
responses that are very helpful and save much time. At present, one
can usually easily arrange to visit other laboratories briefly or even ar-
range to spend several months or even years studying with someone
who has perfected techniques and procedures to deal with problems you
have not yet coped with yourself. And textbooks and current literature
are presently readily available. One can travel to scientific meetings to
listen to and even meet leaders in various fields that may be of inter-
est. When I was starting out, these communication benefits were not so
readily available. I did write to and subsequently briefly visited several
leaders in the United Kingdom, France, and Germany when I had the
opportunity to do so. I was fortunate to meet such notable Professors as
Garrod, Beerens, and the grand master of anaerobes, Professor André
Prévot, who unfortunately was ill on the day I met him and couldn’t
meet with me for more than half an hour. But in that short period of
time, one could gain a wealth of knowledge and even find a direction
for future work. Also, it is so much more personable than any electronic
media; you have to exist in order to communicate.
Of course, a half-hour talk does little in the context of the second
generation systems currently used to study the microbiome. Using a
machine such as the Illumina permits rapid detection and identification
of complex microbial floras. These can then be catalogued in databases
and analyzed using a number of different software methods. This has
indeed helped us to better understand the microbes such as those seen in
the human colon. But we were able to do many important studies older
methods combined with a DNA sequencer and real-time PCR machine.
I will comment on some of these studies in the remainder of Chapter 1.
We studied small bowel fluid from a patient with blind loop syn-
drome and found six different anaerobes and a total anaerobic count
one log higher than the total aerobic count. We developed and evaluated
several selective media; we improved gas liquid chromatographic pro-
cedures for quantitation of fatty acids and alcohols; and we compared
the efficiency of anaerobic jars, the Anoxomat system, and anaerobic
chambers. We found that antibiotic susceptibility patterns of various
anaerobes were useful as guides to classification and characterization
of certain anaerobes and studied these patterns with various anaerobes
as a guide to therapy of infections with these organisms. We studied
the effect of various antimicrobial drugs on the normal bowel flora
of patients. We studied the toxins of Clostridium difficile and the epi-
demiology of disease due to this organism in the hospital setting. We
studied an outbreak of enterocolitis in our hospital due to phage type
54 staphylococci resistant to kanamycin, neomycin, paromomycin, and
chloramphenicol. We studied the normal flora of ileostomy and trans-
verse colostomy effluents and the flora of the maternal cervix and the
newborn’s gastric fluid and conjunctivae.
We were the first to isolate Acidaminococcus fermentans and
Megasphaera elsdenii from normal human feces. Our group studied the
bacteriology of infections in patients undergoing head and neck cancer
surgery that provided guidance for the type of antimicrobial prophy-

laxis that would be most effective in prophylaxis for such patients. We
studied the impact of a partially chemically defined diet on the bowel
flora of humans. We also had the opportunity to study stool specimens
from two patients presenting with d-lactic acidosis; one patient had pre-
viously had most of the small bowel removed because of mesenteric
thrombosis and the other patient had previously undergone a jejunoileal
bypass. The stool flora of both patients was quite abnormal on admis-
sion with predominantly gram-positive anaerobic bacilli, Eubacterium,
Lactobacillus, and Bifidobacterium, which produced primarily d-lactic
acid. The patients responded well to oral vancomycin therapy.
A very important study that we did in collaboration with Dr. Ernst
Drenick, an internist and nutritionist, and Dr. Edward Passaro, Jr., a
general surgeon, concerned patients undergoing jejunoileal bypass sur-
gery for obesity. The really unique approach of this study was to obtain
specimens from patients in the operating room who did not receive any
preoperative antimicrobial prophylaxis. Specimens were obtained dur-
ing surgery from the proximal jejunum and distal ileum. The plan was to
obtain similar specimens from any patients who might require surgery
for complications relating to the original surgical procedure. We could
also compare the data from patients who had only specimens from after
the bypass procedure since they were all processed in the same way.
Among eight patients from whom we had baseline studies, the proxi-
mal jejunum was sterile in five. The other three had a predominantly
aerobic flora with low counts. Only one patient had anaerobes in the
jejunum and counts were low. Ileal contents were sterile in two patients;
the other six had variable counts. The ileal contents had higher counts
than the jejunal contents; the flora resembled fecal flora qualitatively
but with lower counts and a higher ratio of aerobes to anaerobes. Only
one of the original patients required repeat surgery; he had a sterile jeju-
num at the first surgery but at re-operation the functioning small bowel
was colonized with fecal-type organisms with a total count of 107.5/ml.
Looking at the three patients with no baseline studies, one had a
high total bacterial count of >109/ml., another had Fusobacterium var-
ium outnumbering the B. fragilis group in both the functioning small
bowel and in the blind loop. The third case yielded only E. coli from
the excluded loop. This latter patient, despite a sparse flora, had severe
complications suggesting that perhaps toxin production or metabolic
behavior might account for some complications. The various complica-
tions that may be seen in these bypass patients include an inflamma-
tory bypass enteritis, pneumatosis cystoides intestinalis, impaired liver

function, and even fatal hepatic coma, polyarthritis, skin lesions, eye
complications, etc. Metronidazole typically was quite effective thera-
peutically.
We also did microbiology studies in 10 patients undergoing so-called
biliopancreatic bypass (Scopinaro procedure). Collection of specimens,
only from the bypassed segment (biliopancreatic bowel segment), was
done in the operating room at the start of the procedure and with no
antibiotic bowel preparation preoperatively. Counts of organisms re-
covered were relatively low (102 to 107/ml. Three subjects developed
diarrhea that was moderate to severe which responded promptly to met-
ronidazole given orally.
The final notable study we performed was a comparison of bowel
flora in different populations with different incidences of colon can-
cer—Japanese with their traditional diet, Seventh Day Adventists with
variable incidences of meat consumption, people on the standard Amer-
ican or Western diet, and people with colonic polyps. This study went
on for years thorough bacteriologic studies on their stools as we could
in the 1970s. This important study, however, really should be done
again with second generation sequencing techniques.
In the past 15 years, we have been studying the fecal flora of children
with regressive autism,of autistic children in comparison with that of
normal control children, and with that of their siblings. Our first pub-
lication (with Sandler et al. 2000) was a small open-label study of oral
vancomycin but it was important because of the dramatic improvement
in virtually all the 10 children treated. All the subjects relapsed after the
short treatment course was stopped, but this study established that the
clostridia recovered from their stools played a key role in the disease.
A study published in Clin. Infect. Dis. in 2002 showed the impor-
tance of clostridia and included small bowel aspirates as well as stool.
We documented the presence of clostridia by quantitative culture, real-
time PCR, and analysis of 16-23 S space region. Bacteria found that
were much more frequently found in autistic children than in the control
patients were Clostridium bolteae, sp. nov., and perhaps some closely
related species. A pyrosequencing study was performed and published
in 2010. This study led to recognition of five Desulfovibrio spedies as
role players in autism, the findng that Bifidobacterium counts were low
in stools of autistic children as compared to controls. We have con-
firmed the work of others as to the importance of certain Sutterella spe-
cies in autism and of a protective role for Akkermansia, as well as Bifi-
dobacterium, but have not published this as yet. We have recently found
that an unusual clostridial toxin plays a role in autism.
As to where we stand with the colon and indeed the microbiome, even
after all the years of work, I have realized we are only at the beginning.
Our laboratory has detected a number of novel taxa and studied, named,
and reported them, with various colleagues. Included were: Bilophila
wadsworthia, Sutterella wadsworthensis, Clostridium bolteae, Ceto-
bacterium somerae, Anaerotruncus colihominis, Anaerofustus stercori-
hominis, Clostridium bartlettii, Porphyromonas uenonis, Bacteroides
nordii, Bacteroides salyersae, Fastidiosipila sanguinis, Parabacteroi-
des goldsteinii, Porphyromonas somerae, Alistipes onderdonkii, Alis-
tipes, shahii, Peptoniphilus duerdenii, Peptoniphilus koeneneniae, Pep-
toniphilus gorbachii, Peptoniphilus olsenii, Anaerococcus murdochii,
Blautia wexlerae, Porphyromonas bennonis, Murdochiella asaccharo-
lytica, Gemella asaccharolytica, and Corynebacterium pyruviprodu-
cens. Along with Paul Lawson and others, we have even recommended
reclassification of a few organisms, notably the Ruminococcus group.
This group is now being regarded as one of the three major enterotypes
of the gut microbiome. That means all this work is only one-third of
the information we have now. As we continue to learn more with even
higher levels of analysis, this fraction may diminish even further. Al-
though this may appear at first to be disheartening after over six decades
of work, I am happy. While the microbiome continues to expand in its
scope, much of which will be discussed in this book, it all started with
a general look at the colon and the belief there was much more to the
picture. As we continue to learn, that picture is larger than we might
have ever imagined.
CHAPTER 2
Ecology of the Human Microbiome

KALUDYNA BOREWICZ and HAUKE SMIDT
2.1. OVERVIEW
R ECENT technological and conceptual developments in culture

independent approaches targeting bacterial 16S ribosomal RNA
(rRNA) genes have offered a new way of looking at microbial eco-
systems. This in turn has contributed to the current expansion in the
number of research projects aiming at characterizing microbiota com-
position and function in health and disease. Healthy human microbi-
ota is composed of many complex and diverse microbial ecosystems,
with estimated 1014 microbial cells inhabiting the human body (Savage
1977). These microbial ecosystems are also unique between different
body sites and between individuals, and this variation in microbial com-
position can be attributed to many factors including host genetics, en-
vironment, diet, and early life microbial exposure (Human Microbiome
Project 2012). Despite taxonomic differences in microbial community
structure, the core metabolic and functional pathways carried out by
these ecosystems seem to be relatively stable, suggesting that the role
of microbiota in health and disease may be largely due to disturbances
in microbial function, rather than changes in microbiota composition
alone (Human Microbiome Project 2012).
2.2. MICROBIOTA OF THE GASTROINTESTINAL TRACT
The human gastrointestinal (GI) tract is by far the most densely colo-
nized and best studied microbial ecosystem found in the human body. It
9
10 ECOLOGY OF THE HUMAN MICROBIOME
is estimated that 1,000–1,500 species of bacteria can inhabit an average

adult GI tract, but this number could be even higher (DiBaise 2008).
Each person carries approximately 160 bacterial species and about 10
million microbial genes, which give each individual a unique microbial
make up (Li 2014). Host genetics may contribute to these individual
variations in microbiota, and it has been shown to be an important fac-
tor affecting bacterial community composition and function (Moreno-
Indias 2014).
Microbial colonization of the GI tract in healthy humans starts at
birth and is influenced mainly by the mode of delivery (vaginal versus
Caesarean section) and the method of feeding (breast milk versus for-
mula) during infancy (Moreno-Indias 2014). An adult-like microbiota
becomes established with introduction of solid foods and begins to re-
semble microbiota of adults during the first year of life, after which it
remains relatively stable throughout adulthood. Diet, infections, anti-
biotic use, and other environmental conditions can temporarily disturb
the normal gut microbial ecosystem, however, these disturbances tend
to be temporary and in most cases, the microbiota is able to recover
back to its former state. Microbial composition changes in elderly, as
the diversity and stability of gut microbiota decrease with age (Moreno-
Indias 2014).
Despite the individual variation in microbial composition, the ma-
jority of bacterial species found in the human gut belong to two phy-
la: Bacteroidetes and Firmicutes (Mariat et al. 2009). Most species in
the phylum Bacteroidetes belong to the class Bacteroidetes, and more
specifically to the genera Bacteroides and Prevotella. Most species in
the phylum Firmicutes belong to Clostridium clusters IV and XIVa,
which include genera Clostridium, Eubacterium, and Ruminococcus.
Other detected phyla include Proteobacteria, Actinobacteria, Fusobac-
teria, Spirochaetes, Verrucomicrobia, and Lentisphaerae (Gerritsen et
al. 2009). In addition to bacterial groups, Archaea (methanogens) and
eukaryotic microorganisms (fungi) are also part of healthy human gut
microbiota.
Metagenomic sequencing data suggests that even with individual
differences in microbiota composition, the metabolic pathways remain
stable in the GI tract of healthy subjects (Human Microbiome Project
2012). This collection of microbes forms a dynamic ecosystem which is
known to exert important metabolic, physiological, and immunological
functions on its host, as well as to provide protection from pathogens
through so-called colonization resistance (Wade 2013). The host, on
Microbial Composition in the GI Tract of Healthy Adults 11
the other hand, offers the microbes a stable environment and nutrients
necessary for their survival. The general understanding of the micro-
bial ecosystem function has increased tremendously in the recent years,
however, the details are still largely unknown. It is becoming clear that
the network of interactions, whether these are positive or negative, is
very complex and we are now only at the beginning of understanding
the roles of different bacterial groups, and how their functions influence
the host.
In order to understand how microbial ecosystems contribute in health
and disease, we should first know which microbes comprise the healthy
human microbiota. More importantly, we need to ascertain the specific
roles they perform and how their presence can impact the host. In the
following sections we will first give an overview of the key microbial
groups and their functions in different regions of a GI tract of healthy
adults. Later, we will discuss how changes in microbiota correlate with
selected types of diseases.
2.3. MICROBIAL COMPOSITION IN THE GI TRACT OF

HEALTHY ADULTS
The human GI tract can be divided in anatomical regions, each char-

acterized by a different set of physicochemical conditions which create
a unique environment for microbial growth. The most important factors
influencing intestinal microbiota include pH, redox potential, nutrient
content, motility, and presence of host secretions such as digestive en-
zymes, bile, and mucus. The environment at each anatomical region can
be further divided into the luminal content and the mucosal layer. The
mucosal layer forms a lining along the GI tract and consists of a single
sheet of epithelial cells and an irregular coating of mucus that protects the
cells from direct action of host secretions, food, and pathogens found in
the lumen. The mucosal layer also provides a site of attachment for com-
mensal microbiota. In the following sections, we will describe microbial
ecosystems with respect to different regions of the GI tract.
2.3.1. The Oral Cavity
The oral cavity comprises many different niches that provide unique
conditions for microbial growth. Most microbes are associated with the
mucosal surfaces on the cheeks or tongue, and hard surfaces of teeth,
braces, or dentures, and there is no resident microbiota in the lumen,
because the passage time of food in the mouth is very short. The oral
microbial ecosystem is very diverse, with about 1012 bacterial cells of
about 1,000 different species belonging to phyla Actinobacteria, Bac-
teroidetes, Firmicutes, Proteobacteria, Spirochaetes, Synergistetes,
and Tenericutes, candidate phylum TM7, and the uncultured divisions
GN02 and SR1 (Wade 2013; Tlaskalova-Hogenova et al. 2011; Soro
et al. 2014; He et al. 2015). The relative distribution of each micro-
bial phylum differs between individuals and between location in the
mouth (Zaura et al. 2009). The most predominant genera include Ac-
tinomyces, Streptococcus, Neisseria, Veillonella, Porphyromonas, and
Selenomonas. In addition, viruses, protozoa, fungi, and a small number
of methanogenic Archaea are also members of the normal microbiota.
The microbial composition at the species level is highly variable be-
tween individuals and can be influenced by factors such as age, diet,
oral health, and hygiene (Wade 2013).
2.3.2. The Upper Gastrointestinal Tract
The upper gastrointestinal tract includes the esophagus, stomach,

and duodenum. In humans, microbial ecosystem composition and func-
tion in the upper GI tract are still largely unknown, due to poor acces-
sibility of these areas and the need for invasive procedures to obtain
samples. In the surveys on microbiota of the distal esophagus, members
of six phyla, namely Firmicutes, Bacteroides, Actinobacteria, Proteo-
bacteria, Fusobacteria, and TM7, were found in the mucosal layer, and
most common genera included Streptococcus, Prevotella, and Veillon-
ella (Pei et al. 2004; Fillon et al. 2012). Research shows that the distal
esophagus is inhabited by a complex but conserved microbial commu-
nity, with composition resembling the oral microbiota of the host (Pei
et al. 2004). Similar to the oral cavity, food does not stay in the esoph-
agus long enough to allow for establishment of resident microbiota.
The stomach is the first part of the GI tract that holds food for longer
periods of time. Thus, the microbial distribution in the stomach, and in
the descending regions of the GI tract, is spatially specific, with differ-
ent microbes associated with the gastric content and with the mucosal
layer (Wang and Yang 2013). Because of its low pH which can only be
tolerated by certain acid-resistant bacteria, the bacterial counts in the
stomach content are generally low, with about 103–104 bacterial cells
per mL (Tlaskalova-Hogenova et al. 2011). The microbiota of gastric
content can vary depending on diet or influx of bacteria from the mouth,
esophagus, and duodenum, however, these factors affect to a lesser de-

gree the mucosa-associated microbiota which is protected in the mu-
cus and much more stable (Wang and Yang 2013). Culture indepen-
dent studies on stomach microbiota showed that in the mucosal layer
Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the
most abundant phyla, and Streptococcus, Prevotella, Porphyromonas,
Neisseria, Haemophilus, and Veillonella were common genera, but the
distribution of taxa at genus level was highly variable between indi-
viduals (Stearns et al. 2011; Bik et al. 2006; Li et al. 2009). One of the
important, and certainly most well-studied species found in about 50%
of the human population is Helicobacter pylori, which has been associ-
ated with gastric diseases such as gastritis and cancer (Wang and Yang
2013). The duodenum is the last part of the upper GI tract and the first
part of the small intestine, and it is discussed in Section 2.3.3.
2.3.3. The Small Intestine
The small intestine is the site where most of the host enzymatic diges-
tion and absorption of nutrients, in particular lipids and simple carbo-
hydrates, takes place. Studies on microbial composition are again very
limited with the majority of findings being based on biopsy specimens
in association with various GI disorders. The duodenal lumen forms a
unique environment characterized by a low pH, fast passage time, and
the presence of antimicrobial bile and digestive enzymes, making it an
unfavourable place for microbial growth. No culture independent stud-
ies up to date focused on resident microbiota in human duodenal con-
tent. On the other hand, biopsy samples provided insight in microbiota
in the duodenal mucosa. In a recent study using 16S rRNA gene-target-
ed HITChip analysis of duodenal biopsies from children, 13 phylum-
like level bacterial groups were detected, and Proteobacteria, Bacilli,
and Bacteroidetes were the most abundant taxa, with each individual
subject showing a different and unique microbial profile (Jing Cheng et
al. 2013). The predominant genus-like groups included Sutterella wad-
sworthensis et rel., Streptococcus mitis et rel., Aquabacterium, Strepto-
coccus intermedius et rel., and Prevotella melaninogenica et rel. (Jing
Cheng et al. 2013). In a study using sequencing of 16S rRNA gene clone
libraries, the most abundant phyla detected in biopsies from children and
adult subjects were Firmicutes, Proteobacteria, Bacteroidetes, and also
Actinobacteria, Fusobacteria, and Deinococcus-Thermus (Nistal et al.
2012). Most sequences were classified as Streptococcus and Prevotella
spp. in both age groups, and 5% of sequences that were found only in
healthy children could not be assigned to any known genus. Bacterial
community richness was higher in the adult group as compared to the
juvenile group, with members of Veillonella, Neisseria, Haemophilus,
Methylobacterium, and Mycobacterium present in adult mucosa. It is
interesting to note that overall duodenal microbiota composition seems
to resemble the microbiota found in the oral cavity and esophagus, and
less so the microbiota found in the lower GI tract (Wacklin et al. 2013).
The number of bacterial cells and diversity increase along the intestine,
and it is estimated that the jejunum harbors 105–106 bacteria per mL of
content (Tlaskalova-Hogenova et al. 2011). An earlier study examining
mucosa biopsies of human jejunum showed that Streptococcus and Pro-
teobacteria were the most abundant taxa and contributed respectively
to 68% and 13% of all microbiota detected (Wang et al. 2005). A more
recent study showed that ileostomy effluent samples can provide a good
representation of microbial composition in the human jejunum/prox-
imal-ileum without the need for invasive sampling (Zoetendal 2012).
The most predominant (common core) taxa in ileostoma-effluent and
in jejunum included Bacilli (Streptococcus spp.), Clostridium cluster
IX (Veillonella spp.), Clostridium cluster XIVa, and Gammaproteo-
bacteria (Zoetendal 2012). Similar findings came from an earlier study
on ileostoma-effluent where the most abundant species were members
of the Lactobacillales and Clostridiales, mainly Streptococcus bovis-
related species and the Veillonella group, as well as species belong-
ing to Clostridium cluster I and Enterococcus (Booijink et al. 2010).
However, the ileum-associated Bacteroidetes and Clostridium clusters
III, IV, and XIVa were reduced in ileostoma-effluent samples. Bacterial
numbers increase to about 108–109 cells per mL of ileal digesta. Biop-
sies and catheter-collected lumen samples revealed that the bacterial
community in the human ileum is dominated by species belonging to
Bacteroidetes and Clostridium clusters IV and XIVa and resembles the
microbiota found in the colon (Tlaskalova-Hogenova et al. 2011; Wang
et al. 2005). Similar to the ileostomy-effluent samples, ileum microbio-
ta is also characterized by short and long term fluctuations in microbial
profiles within individuals and large interindividual variability between
patients (Booijink et al. 2010).
2.3.4. The Large Intestine
The large intestine is separated from the small intestine by the il-
eocecal valve, and it can be divided into the cecum; the ascending,
transversing, and descending colon; the rectum, and the anal canal. The
cecum is the first region of the large intestine that receives food from
the small intestine. It is also connected with the appendix—a small
and rudimentary projection, which in humans has no function in food
digestion, but it may play an important role as a reservoir of micro-
biota and in stabilizing and restoring the colon microbial ecosystem,
especially after disturbance, for example due to antibiotic use (Laurin
et al. 2011; Bollinger et al. 2007). Unlike the small intestine, micro-
bial composition and function of the human large intestine has been
studied to great extent, mostly because of the ease of collecting fecal
samples, and because of the high density of microbial cells, estimated
to be around 1011–1012 per mL (Tlaskalova-Hogenova et al. 2011). The
most predominant microbial groups found in the human large intestine
include Bacteroides, members of the various Clostridium clusters, Bi-
fidobacterium, Enterobacteriaceae, and Eubacterium. Even though the
large intestine can be divided into five anatomical regions, the micro-
bial composition is very uniform, and fecal material seems to represent
well the microbiota in the entire region (Gerritsen et al. 2011). How-
ever, just like in other parts of the GI tract, in the large intestine there
is a large difference between microbial ecosystems found in the lumen
and mucosal layer. Fecal samples represent the luminal fraction only,
and the mucosal layer is much less explored due to the need for more
invasive methods in collecting biopsy samples. Large intestinal micro-
biota is very diverse, highly unique to each individual, and relatively
stable over time (Lahti et al. 2014). Factors such as age, disease, or
the use of antibiotics may permanently alter the microbial composition
(Lahti et al. 2014). Recent studies utilizing large cohorts of subjects
suggested that the fecal microbiota composition in healthy adults can be
categorized into three major enterotypes dominated by different bacte-
rial populations, in particular Bacteroides, Prevotella, and Ruminococ-
cus (Arumugam et al. 2011; Benson et al. 2010). These enterotypes are
independent of age, ethnicity, gender, and body mass. However, this
division is still controversial, and some studies failed to detect presence
of enterotypes in both the elderly (Claesson 2012) and in adult research
populations (Huse et al. 2012).
Another large study suggested an alternative to the enterotype theory
(Lahti et al. 2014). The authors noted that in fecal samples of Western
adults, certain bacterial groups, namely Dialister spp., Bacteroides fra-
gilis, Prevotella melaninogenica, P. oralis, and two groups of uncultured
Clostridiales cluster I and II, were bimodally distributed in the healthy

human population, representing so called “tipping elements” (Lahti et
al. 2014). These bistable bacterial groups were either very abundant
or almost absent, and unstable at their intermediate abundance levels
(Lahti et al. 2014). In addition, the condition of the bistable groups,
especially the Bacteroides and Prevotella, seemed to correlate with the
shifts in other bacteria, and as a result they were believed to be driv-
ing the overall composition of the colonic ecosystem towards specific
enterotypes (Lahti et al. 2014).
2.4. MICROBIAL ECOSYSTEM FUNCTION IN THE

GI TRACT OF HEALTHY ADULTS
Metagenomic studies provide insight on the functional potential of

microbiota by analyzing microbial genes, collectively known as the mi-
crobiome. A recent study reported that each person carries about 10
million bacterial genes in their GI tract, the majority of which are in-
volved in bacterial metabolism (Li et al. 2014; Turnbaugh et al. 2009).
Additional information about microbial activity can be obtained from
metatranscriptomics, metabolomics, and metaproteomics analyses.
These approaches provide insight about microbial gene regulation and
expression, as well as the production of metabolites, proteins, vita-
mins, and regulatory elements. Similar to compositional diversity, there
is a large functional variation in different microbial ecosystems, but
the core metabolic and functional pathways carried out by the same
types of ecosystems seem to be relatively conserved and stable (Human
Microbiome Project 2012). It is also common for the same metabolic
functions to be carried out by different bacterial groups, meaning that
correlating the compositional and functional changes in the ecosystem
maybe less straightforward because changes in the composition and the
function of a given microbial ecosystem can be independent from each
other (Zoetendal 2008).
2.4.1. The Oral Cavity
The oral cavity is the first point of contact between microbiota, diet,
and host. Despite regular influx of food ingested by the host, the major-
ity of nutrients for the oral commensal microbes are derived from gly-
coproteins present in saliva and gingival crevicular fluid (Homer et al.
1999). Complete breakdown of these glycoproteins requires coopera-
Microbial Ecosystem Function in the GI Tract of Healthy Adults 17
tion between different species of bacteria. For example, oral streptococ-

ci (e.g., S. oralis, S. sangiunis) remove oligosaccharide side chains and
break down the protein core by their proteolytic, endopeptidase, and
glycosidic activity, while other Gram-negative anaerobes (e.g., Porphy-
romonas gingivalis, Prevotella intermedia, Prevotella nigrescens, and
Peptostreptoccus micros) further break down proteins into peptides and
amino acids (Homer et al. 1999; Wickstrom et al. 2009; Bao et al. 2008).
Amino acids can then be fermented to short chain fatty acids (SCFA),
including branched chain fatty acids, which are further degraded by
other bacteria and by methanogenic Archaea (Wade 2013). Certain food
components, such as gluten or nitrate can also be degraded/transformed
by microbial enzymes, and the processes and products are crucial for
the health and well-being of the host, while breakdown of these func-
tions can be linked with host diseases (Hezel and Weitzberg 2013; Hel-
merhorst 2010; Zamakhchari 2011). As already mentioned, the mouth
is an open environment and commensal bacteria create a barrier against
colonisation with transient microbes and any opportunistic pathogens
that can enter with food or water. An in vitro study on oral microbiota
from mice provided a good illustration of how the cooperation of differ-
ent commensal species can leverage a community response to pathogen
invasion. The study proposed that cooperation of three different species
of oral streptococci were involved, with S. saprophyticus sensing the
presence of an invader, and initiating the defence pathway, S. infantis
acting as a mediator, and S. sanguinis producing hydrogen peroxide
and acting as a killer (He et al. 2014). Besides colonization resistance,
oral microbiota plays an important role in maintaining host-microbe
homeostasis, by interacting with host mucosal cells and training the
host’s immune system to recognize and destroy pathogens, while down-
regulating the proinflammatory immune response towards the commen-
sal bacteria normally present in the mouth (Srinivasan 2010).
2.4.2. Upper Gastrointestinal Tract
Upper gastrointestinal tract microbiota function is still not well un-

derstood, and most studies to date focused on specific pathogens and
their role in the aetiology of different diseases and to a lesser extent on
the microbial interactions in a healthy ecosystem. Little is known about
the ecology of microbiota inhabiting the esophagus and stomach, but its
role in colonization resistance and protection from pathogens is likely
to be an important one. Normal microbiota generates a microenviron-
ment that can inhibit growth of pathogens by competing for substrates

and binding sites, stimulating host immune responses against invaders
and production of antimicrobial substances. For example, in vitro and
in vivo studies using animal models showed that stomach colonization
with H. pylori is inhibited by the normal commensal microbiota and
by probiotic strains of Lactobacillus, Bifidobacterium, and Saccharo-
myces, suggesting the importance of microbial interaction in pathogen
resistance (Wang and Yang 2013). Other studies using human biopsy
samples also reported changes in intestinal microbiota associated with
gastric cancer, however, the exact function and causality of this associa-
tion is still being investigated (Tlaskalove-Hogenova 2011). It is likely
that microbial metabolites, bacterial lipopolysaccharides (LPS), lipo-
proteins, lipoteichoeic acids (LTA), flaggellins, and bacterial nucleic
acids can interfere with the normal function of gastric mucosa, caus-
ing chronic inflammation, changes in mucin production, metaplasia,
and eventually can lead to diseases (Tlaskalove-Hogenova 2011; Jing
Cheng et al. 2013). The functions of the microbiota in the duodenum
are still not well understood, but changes in microbial composition be-
tween Celiac disease patients and healthy controls suggest that the mi-
crobiota plays a role in immune response, inflammation, and maintain-
ing gut homeostasis (Jing Cheng et al. 2013; Wacklin et al. 2013). The
homeostasis of gut epithelia relies to a large extent on adequate activa-
tion of toll-like receptors (TLRs), which recognize microbe-associated
motifs, regulate the immune response to pathogens, and affect the epi-
thelial barrier by regulating the expression of tight junction proteins,
mucin, and antimicrobial peptides by the host’s intestinal cells (Jing
Cheng et al. 2013).
2.4.3. The Small Intestine
The small intestine is the site where most of the host enzymatic di-
gestion and absorption of energy from the diet takes place. Thus, diet is
an important factor modulating microbial function, by selecting bacte-
rial groups that are better equipped to break down different dietary sub-
strates (Moreno-Indias 2014). For example, certain Lactobacillus spp.
found in duodenum and jejunum have been associated with weight gain
and leanness, and differ in their metabolic capacities to break down
dietary carbohydrates and fats supplied by the host (Moreno-Indias
2014). The transit time in the small intestine is very short, and Strepto-
coccus and Veillonella spp., which dominate the microbial ecosystem
Microbial Ecosystem Function in the GI Tract of Healthy Adults 19
in the jejunum and ileum, are well adapted to quickly metabolize a vari-
ety of available carbohydrates, first to lactate (Streptococcus) and then
to acetate and propionate (Veillonella) (Booijink et al. 2010). Recent
metatranscriptome analysis of the ileostoma effluent confirmed a high
abundance of genes involved in the transport and metabolism of diet-
derived simple carbohydrates and linked the task mainly to Streptococ-
cus groups (Aidy et al. 2015). In addition to its function in carbohydrate
metabolism, it was concluded that small intestine microbiota could also
play a key role in immune system development and homeostasis. For
example, the ileum is connected with a large mass of gut associated
lymphoid tissue (GALT) and Peyer’s patches, and commensal bacteria,
such as different strains of streptococci, were shown to induce specific
immune responses in the host (Aidy et al. 2015). The close contact be-
tween the microbiota and the host cells in the small intestine underlines
the current hypothesis that microbially derived metabolites or toxins
also modulate gene expression via the gut-brain neural circuit and may
influence endocrine function (e.g., secretion of glucagon and incretins)
and even show an effect on mood or behavior of the host (Moreno-
Indias 2014; Aidy et al. 2015).
2.4.4. The Large Intestine
Large intestine microbial ecosystem function has been well studied,

mainly due to the ease of collecting fecal samples, but also because it
has been known for a long time that colonic microbial processes play
an important role in human health. The most direct role is in the diges-
tion and metabolism, as the large intestinal microbiota breaks down
indigestible food components and provides the host with an otherwise
inaccessible source of energy. It also produces SCFA which are the
main source of energy for colonocytes (Leser and Molbak 2009). In ad-
dition, the colonic microbiota is a main source of vitamins K and B12,
it prevents colonization by pathogens, and it plays an important role
in regulating the host’s immune responses (Moreno-Indias et al. 2014;
Leser and Molbak 2009). A study on the fecal microbiome of healthy
Japanese subjects was among the first to explore microbial ecosystem
function in the human colon using culture-independent methods. The
study revealed that a high proportion of genes present were related to
carbohydrate metabolism and transport. The authors also noted an en-
richment of peptidases and enzymes for anaerobic pyruvate metabolism
and reduction in genes involved in fatty-acid metabolism. There were
also high levels of enzymes involved in energy storage, antimicrobial

peptide transport, and multidrug efflux pump peptides (Kurokawa et
al. 2007). The authors concluded that these enzymes may help certain
commensal microbes to compete with each other and thus may be es-
sential for maintenance of ecosystem balance. Enzymes for DNA repair
were also enriched. On the other hand, there was a low abundance of
genes involved in biosynthesis of flagella and chemotaxis and in oxy-
gen take-up (Kurokawa et al. 2007). Interestingly, these patterns in gene
distribution were not observed in unweaned infants, suggesting that in-
fant microbiota is less complex and thus microbial ecosystem function
is less stable, more dynamic, and highly adaptable. In adult microbiota
a higher diversity of bacterial species exists with large interindividual
variability in microbial composition, yet there is a shared functional
core, which is believed to be stable and much more uniform between
individuals (Turnbaugh et al. 2009; (Kurokawa et al. 2007). Recently,
more in depth analyses showed that there could be functional differenc-
es correlating with different enterotypes found in the colon (Arumugam
et al. 2010). For example, the Bacteroides-rich type has more bacterial
species that are capable of producing vitamins C, B2, B5, and H. This
group is dominated by species that utilize carbohydrate fermentation as
the main energy source. On the other hand, the Prevotella type showed
higher numbers of species producing vitamin B1 and folic acid, and
included species that use mucin glycoproteins as a source of energy,
similarly to the Ruminococcus type (Arumugam et al. 2010).
One of the important functions of colonic microbiota that received
a lot of attention in recent years is the production of SCFA, and in par-
ticular butyrate, by bacteria from Clostridium clusters IV and XIVa.
The main butyrate-producing species are believed to be Eubacterium
rectale and Faecalibacterium prausnitzii, in addition to others in the
genera Coprococcus and Roseburia (Louis and Flint 2009). The pro-
cess provides a great example of synergic interaction between diet, mi-
crobes, and host, and the presence of butyrate producers in the colon
has been shown to be negatively correlated with functional dysbiosis,
reduction of the risk of infections with opportunistic pathogens, and
the decrease in oxidative stress (Moreno-Indias et al. 2014). Butyrate
producers can respond to different environmental conditions, such as
diet or pH, and engage different fermentation pathways in which the
final products are lactate, formate, hydrogen, and carbon dioxide. It
has been shown that cross-feeding between bifidobacteria and butyrate
producers is also possible: bifidobacteria break down polysaccharides
CHAPTER 12
Considering the Microbiome as

Part of Future Medicine and
Nutrition Strategies
EMMA ALLEN-VERCOE
12.1. INTRODUCTION
T HE purpose of The Human Microbiome Handbook is to provide

an overview of current knowledge as it pertains to the human mi-
crobiome. It demonstrates that a few areas of health research have re-
ceived such a surge in interest over the last decade. Moreover, while
this handbook provides a current review of our understanding, the field
is advancing at an astonishingly rapid rate. These are undoubtedly ex-
citing times, since until recently modern medicine has considered hu-
man beings to be strictly human; our microbial passengers have been
ignored—or worse—persecuted. It is my hope that this book has high-
lighted the very many aspects of our human biology and physiology
that are influenced—or even controlled—by our microbial symbionts.
This chapter considers the current outlook for microbiome research,
particularly as it pertains to the gut microbial ecosystem, and predicts
areas where this research will be leveraged to benefit health in the near
future.
12.2. MINING THE HUMAN MICROBIOTA FOR

NEW DRUGS
What defines a healthy gut and why do some people seem to be more
susceptible to GI infection than others? It is well known that people
who have recently suffered microbial ecosystem depletion through, for
example, antibiotic use or acute enteroviral infection are more suscep-
347
348 CONSIDERING THE MICROBIOME AS PART OF FUTURE MEDICINE
tible to further gut infection during their convalescence (Croswell et al.

2009; Stecher et al. 2010). There are several reasons for this suscepti-
bility, but the reduced ability for competitive exclusion of pathogens by
a depleted microbiota has always been considered as a primary cause
(Malago 2014). However, more recently there has been a growing ap-
preciation for the role of the gut microbiota in maintaining homeostasis
in the GI tract, through protective effects that include the secretion of
chemical signals that modify pathogen behavior.
Microbes within an ecosystem interact dynamically and ecosystem
cohesion may rely on microbial chemical “conversations” that inform
ecosystem members of, for example, food substrate availability or type,
and cross-feeding availability (El Aidy et al. 2013). Such chemical sig-
nals may also act as a signal for pathogens—both autochthonous op-
portunistic species as well as allochthonous species—to refrain from
expression of virulence determinants, since this energetically expensive
exercise is less likely to be fruitful for these pathogens in the face of an
intact, protective microbial ecosystem. Antunes et al. (2014), demon-
strated this principle recently by screening members of the normal gut
microbiota for antvirulence activity against the well-studied food-borne
pathogen, Salmonella enterica. By measuring expression of the S. en-
terica virulence global regulator, hilA, it was found that the spent cul-
ture supernatants of particular members of the Lachnospiraceae family
in particular had repressive activity that was afforded by the secretion
of an as-yet uncharacterized small molecule metabolite by these com-
mon gut microbial species.
This finding likely only scratches the surface of the potentially pro-
phylactic chemical repertoire secreted by the healthy human microbio-
ta, a pharmacopeia that is as-yet relatively untapped. The major barrier
to this area of drug discovery lies in a general inability to culture many
of our microbial symbionts; however, there are now several efforts un-
derway to both bring recalcitrant species into in vitro study (reviewed in
Allen-Vercoe 2013). In the future, we should expect to see an expansion
in the development of drugs mined from gut microbial ecosystems.
12.3. PROTECTING THE GUT MICROBIOTA

FROM COLLATERAL DAMAGE DURING
ANTIBIOTIC EXPOSURE
The overuse of antimicrobial drugs has received a lot of recent atten-

tion, from the point of view that the targeted pathogens have evolved
Protecting the Gut Microbiota from Collateral Damage 349
widespread resistance to these drugs, minimizing their effectiveness

and creating fears of a return to the preantibiotic era when a simple
puncture wound could lead to a life-threatening infection (Barriere
2015). Unfortunately, antibiotic resistance is not the only consequence
of antimicrobial overuse, and there is now a growing realization that the
collateral damage inflicted on the microbiota during antibiotic therapy
is taking a toll on our health. Several studies have now conclusively
shown that the gut microbial ecosystem changes profoundly during
antibiotic administration, and that there may not be a recovery to the
preantibiotic state, particularly if broad-spectrum antibiotics, or com-
binations of such, are used (Antunes et al. 2011; Arboleya et al. 2015;
Cotter et al. 2012; Iapichino et al. 2008; Jernberg et al. 2007; Mangin
et al. 2010; O’Sullivan et al. 2013). The missing microbiota hypothesis,
as set out by Blaser and Falkow, also posits that because some aspects
of the microbiota are inherited (through, for example, the processes of
birth and breastfeeding), the ecosystem damage wreaked by antimicro-
bial use may compound over generations (2009).
The solution to both antibiotic resistance and collateral damage is-
sues is to simply stop the use of antimicrobials; however, antibiotics are
life-saving drugs when used appropriately, and an important weapon in
the fight against infectious disease. Another strategy, therefore, is to find
ways to protect the healthy microbiota during treatment. Many broad-
spectrum antibiotics are given as oral preparations, and this fact as well
as their pharmacology means that the gut microbiota, of all the host-as-
sociated microbes, is usually under the greatest threat during treatment.
This is well illustrated by the common onset of diarrhea during a course
of oral, broad-spectrum antimicrobials, which reflects a sudden change
to the microbial ecology of the gut microbiota and a concomitant upset
of the normal physiological homeostasis (Varughese et al. 2013). Part
of the issue is that, if pharmacology allows, it is convenient to supply
most antimicrobials by mouth for systemic absorption; however, most
targeted infections are not found in the gut itself. Another problem is
that for some infections where pathogenic biofilms are a component of
the disease, such as otitis media, antibiotic doses have to be higher than
the minimum inhibitory concentrations to be effective (Belfield et al.
2015), with potentially even greater collateral damage.
In the future, antibiotic administration will be much more careful-
ly targeted. For example, treatment of ear or tooth infections may be
carried out using topical applications of drugs that are less likely to
accumulate to damaging concentrations in the GI tract (Dohar et al.
2006; Purucker et al. 2001). The necessity for prophylactic treatment as

a routine part of surgical procedures will be more carefully evaluated
(Young and Khadaroo 2014). Broad spectrum antimicrobials may be
used only in emergency situations, with greater attention paid to rapid
diagnostics allowing more targeted, narrow-spectrum antibiotics to be
used (Spellbuerg et al. 2015). Alternatively, broad-spectrum antibiotics
may be delivered orally in conjunction with compounds designed to
maintain the antimicrobial in an inactive form until absorbed, to reduce
damage to the gut microbiota from direct contact.
12.4. MICROBIAL ECOSYSTEM THERAPEUTICS
A greater understanding of the role of a damaged gut microbiota in

disease has led to a surge in interest in the use of probiotics, defined as
“live micro-organisms which, when administered in adequate amounts,
confer a health benefit on the host,” (Hill et al. 2014). There are many
probiotics now on the market, although only a minority has had pro-
posed beneficial effects clinically proven, and even then the effects are
moderate at best (McFarland 2014). Eventually, probiotics may prove
to be very useful, for example in extending remission in some types of
inflammatory bowel disease, or for reducing the severity of traveler’s
diarrhea (Ghouri et al. 2014; Sarowska et al. 2013). Yet there are limita-
tions to their effectiveness because, from an ecology point of view, the
addition of a single or small group of similar species to the enormous
diversity of the human gut is unlikely to have a dramatic effect on the
ecosystem as a whole. Furthermore, because the gut microbiota is a
cohesive ecosystem that can be thought of as a microbial “organ”, the
addition of incidental microbes in the form of probiotics does not add
to the ecosystem; probiotics are unable to colonize the gastrointestinal
tract and have an effect on the host only while they transit through the
gut (Gonzalez-Rodriguez et al. 2013; Mills et al. 2011).
The principle of probiotic use is sound, and because the practice is
generally regarded as safe, there is little reason for patients not to try it.
But to view probiotics solely as a therapeutic regimen for one particular
indication may exclude a greater potential. With the combined knowl-
edge shared in The Human Microbiome Handbook, we have become
aware of the ecological nature of the human microbiome. One particu-
lar direction involves using the combination of experimental and clini-
cal evidence to identify the steps in development of an ecosystem rich
in beneficial microbes. Alternatively, in the future, we could leverage
Microbial Ecosystem Therapeutics 351
the accumulating knowledge of the human gut microbiota to discover

novel probiotic species or to create whole probiotic ecosystems. We are
only beginning to understand how this is possible. Perhaps we should
turn our attention to the microbiotas of individuals from varied geo-
graphical and cultural backgrounds, which traditionally are considered
to be very healthy, often with higher than globally average numbers of
centenarians. An expansion of the concept of probiotic use will require
both time and further experimentation, yet more importantly, may result
in a shift of the microbial-based medical mindset from one of treat and
cure to adapt and restore.
To a certain extent, steps have already been made toward this goal.
In the treatment of recurrent Clostridium difficile infection, where fecal
transplant is rapidly emerging as an effective intervention (as discussed
Chapter 3), concerns about the safety of using stool as medicine have
driven us to try to determine the microbial components that are missing
from the colons of patients, and then to effect a treatment by replacing
these components in a defined way (Lawley et al. 2012; Perez-Cobas et
al. 2014; Petrof et al. 2013; Shahinas et al. 2012; Shankar et al. 2014).
Our prototype therapeutic, “RePOOPulate”, or Microbial Ecosystem
Therapeutic (MET)-1 is an example of this approach, where a 33-strain
ecosystem, rich in Firmicutes, was applied to C. difficile patients (Petrof
et al. 2013). C. difficile infection is known to correlate with a reduction
in Firmicutes and a concomitant increase in Proteobacteria (Fuentes et
al. 2014), and thus our defined ecosystem was introduced to try to re-
dress this balance. Although only a pilot study, MET-1 rapidly cured
two patients with severe, recurrent C. difficile infection; furthermore,
16S rRNA gene profiling of patient stool during the 6-month period
after treatment revealed signatures that identified with MET-1 compo-
nents, indicating that, unlike traditional probiotics, the delivered eco-
system was able to colonize for at least this long in the patients (Petrof
et al. 2013). MET-1 was designed with microbial ecology in mind; the
33-strain mixture was derived from a single healthy donor (Petrof et al.
2013). We believe this to be important because these selected strains
had formed part of a cohesive ecosystem in the donor. In other words,
the gut environment of the donor had selected a groups of strains that
could work together efficiently. Further work is underway to create
more complex ecosystems from a series of different healthy donors
with differing lifestyles (for example, various dietary practices), recog-
nizing that different ecosystems may be optimal for diverse recipients.
Studies of the gut microbiotas of individuals from cultural back-
grounds not typically exposed to widespread antibiotic exposure may

help us to determine diversity loss in the Western world (Grzeskowiak
et al. 2012; Schnorr et al. 2014) and could be instrumental in develop-
ing METs to restore the “missing microbiota”. Understanding the host-
microbiota cross talk that allows a given microbial ecosystem to work
optimally within its host is a current research goal, and already bioin-
formatics approaches are being used to try to understand microbiota
function in the context of disease (Collison et al. 2012). In the future,
this stream of research will allow for the rational design of METs for
use in the gut as well as other body sites. With accumulated knowledge,
we may discover treatment or prevention regimens for a wide range of
diseases.
12.5. PREDICTING THE INFLUENCE OF XENOBIOTICS ON

THE HUMAN MICROBIOTA
Diet, so far, is the greatest known modulator of the gut microbiota

(Dore and Blottiere 2015); microbes come into contact with and are
influenced by the food we eat during the process of digestion, and the
colon is essentially a specialized chamber where food substrates that
are indigestible through the actions of human enzymes and processes
can be broken down by the microbiota through anaerobic fermentation,
a highly complex activity (Louis et al. 2007). As such, the food that we
eat is more than food for our human selves, and we should consider our
gut microbiota as an organ that takes part in the digestive process.
Recently, however, research on the effects of certain food additives
on the colonic microbiota has brought to light some disturbing over-
sights. While xenobiotics such as food additives are rigorously tested
for safety, in the past these toxicity assays have rarely, if ever, taken
into account the effects of these additives on the gut microbiota. Some
artificial food additives, such as sweeteners and emulsifying agents,
have now been shown to affect the balance of microbes within the gut
(Chassaing et al. 2015; Palmnas et al. 2014; Suez et al. 2014), and in
the case of some sweeteners, may actually contribute to a microbiota
reminiscent to that seen in metabolic disease (Palmnas et al. 2014; Suez
et al. 2014).
In the same way that food additives have been overlooked as gut
microbiota modulators, many of the drugs we consume have likewise
rarely been tested for their effects on the gut microbiota (Li and Jia
2013). Pharmaceutical companies invest billions of dollars in drug
Leveraging Microbiome Knowledge to Optimize Nutrition Strategies 353
discovery, and the added burden of testing for microbiome-associated

effects (where every individual may be different) seems like an impos-
sible achievement. However, drugs such as metformin, used to treat
people with type-2 diabetes, serve as a good example of the role of the
gut microbiota in modulation of pharmacological effects—this drug has
been shown to directly affect the metabolic pathways of the microbiota,
influencing the growth of some microbes over others, perhaps explain-
ing why some individuals cannot tolerate the medication because of
diarrheal side-effects (Lee and Ko 2014).
In the future, food additives and drugs will require more vigorous
safety profiling, with predictions of effects on microbiota types from
a wide range of individuals in addition to standard toxicology assess-
ments. This will allow much more accurate assessments of detriment
versus benefit and may alter the way that new and existing food addi-
tives and drugs are used or introduced.
12.6. LEVERAGING MICROBIOME KNOWLEDGE TO

OPTIMIZE NUTRITION STRATEGIES
Simplistically, gaining nutrition from foods takes place via two path-
ways: (1) directly, through the actions of human enzymes and bind-
ing factors on the food and subsequent absorption of the breakdown/
bound products through the gut; and (2) indirectly, through the actions
of the microbiota on foods to yield host-absorbable substrates and me-
tabolites. Until fairly recently, the second pathway has been generally
ignored, however, there are important consequences of this pathway to
nutrition.
At its most extreme, the gut microbiota is associated with malnutri-
tion in both infancy and old age, with changes in the microbiota corre-
lating with poor absorption of nutrients (Claesson et al. 2012; Ghosh et
al. 2014; Kane et al. 2015; Lakshminarayanan et al. 2014; Subramanian
et al. 2014). In childhood malnutrition, poor development of the gut mi-
crobiota, perhaps because of lack of exposure to a diverse diet, has been
implicated in the disease (Subramanian et al. 2014). The gut microbial
ecosystem becomes resistant to compositional change as successions
in various taxa naturally decrease with age (Valles et al. 2014), and
therefore a poorly developed microbial ecosystem may persist through
childhood and contribute to malnutrition even in the face of dietary
intervention.
At the other end of the scale, obesity and metabolic syndrome are
now understood to be associated with the microbial content of the gut,

and studies of identical twins discordant to obesity implicate certain
microbial taxa in the disease (Goodrich et al. 2014). Two recent stud-
ies highlight the importance of the gut microbial ecosystem in obesity.
The first of these was a trial of the effectiveness of fecal transplant, as
donated from a healthy, lean individual, on metabolic disease in obese
men (Vrieze et al. 2012). In this study, a reduction in insulin depen-
dence was noted in the obese recipients who received the lean donor’s
stool, compared to those who received their own stool back as a control.
The second study is a case report of a woman of average BMI who re-
ceived a stool transplant from her obese daughter to treat a C. difficile
infection, and though this patient was cured of her infection, she went
on to gain significant weight in the months following the procedure,
potentially as a consequence of receiving an obese-type microbiota (Al-
ang and Kelly 2015).
In the future, the use of microbiome-modulating therapies to treat
these conditions may become a reality, with a greater understanding
of the development of the microbiota, as well as the influence of diet
on these microbes. Such therapies may range from directed prebiotic
therapy, using food starches targeted to specific microbial groups to
stimulate their growth and effect more efficient digestion (Scott et al.
2015), to full MET strategies as above, to replace or modify ecosystems
that are contributing to metabolic disease or malnutrition.
Future nutritional therapies need not be confined to disease manage-
ment. Along with a dawning recognition that everyone has a unique gut
microbial ecosystem, there is an opportunity for food manufacturers to
capitalize on personalized nutrition. For example, it may become pos-
sible to determine optimal prebiotic foods from an assessment of gut
microbiota profiles on an individual basis; armed with this knowledge,
a person may be able to select food at the supermarket that is compat-
ible with his or her gut microbiota, and to understand which food sub-
strates might be the most optimal for their microbial symbionts.
12.7. SUMMARY
As was predicted thousands of years ago with the advent of Chinese

traditional medicine, wellbeing originates in the gut (Li et al. 2009).
This was echoed over 100 years ago by Élie Metchnikoff who postu-
lated that microbes may be key to a longer and healthier life. Although
much time has passed, we are now playing a form of catch-up to best
References 355
understand and appreciate the involvement of our trillions of microbial

passengers. Thankfully, this revolution is not limited to microbiology
but is now widespread in medicine and incorporating numerous studies
once considered unimaginable. As this book was published, research-
ers began to demonstrate the use of microbes to alleviate allergies to
peanuts as well as in the remediation of psychiatric conditions. While
the data is still scant and more work needs to be performed, these two
studies alone demonstrate how microbes have transcended their initial
denouncements as solely pathogens, and have become an integral part
of our health and medicine. In the future, greater attention will be paid
to our microbial symbionts and leverage their beneficial activities. In
doing so, it is anticipated that our view of health will be expanded such
that we no longer focus on our human selves, but rather on ourselves
as human/microbial superorganisms that can maintain our wellbeing
through support of all our biological systems, physiological, metabolic,
immunological, neurological, endocrinological, and finally, microbial.
12.8. REFERENCES
Alang, A. and C. Kelly. 2015. Weight Gain After Fecal Microbiota Transplantation.
Open Forum Infectious Diseases 2, 1–2.
Allen-Vercoe, E. 2013. Bringing the gut microbiota into focus through microbial cul-
ture: recent progress and future perspective. Current opinion in microbiology 16,
625–629.
Antunes, L.C., et al. 2011. Effect of antibiotic treatment on the intestinal metabolome.
Antimicrobial agents and chemotherapy 55, 1494–1503.
Antunes, L.C., et al. 2014. Antivirulence activity of the human gut metabolome. mBio
5, e01183-01114.
Arboleya, S., et al. 2015. Intestinal Microbiota Development in Preterm Neonates and
Effect of Perinatal Antibiotics. The Journal of pediatrics 166, 538–544.
Barriere, S.L. 2015. Clinical, economic and societal impact of antibiotic resistance.
Expert opinion on pharmacotherapy 16, 151–153.
Belfield, K., R. Bayston, J.P. Birchall, and M. Daniel. 2015. Do orally administered
antibiotics reach concentrations in the middle ear sufficient to eradicate planktonic
and biofilm bacteria? A review. International journal of pediatric otorhinolaryngol-
ogy 79, 296–300.
Blaser, M.J., and S. Falkow. 2009. What are the consequences of the disappearing hu-
man microbiota? Nature reviews. Microbiology 7, 887–894.
Chassaing, B., et al. 2015. Dietary emulsifiers impact the mouse gut microbiota pro-
moting colitis and metabolic syndrome. Nature 519, 92–96.
Claesson, M.J., et al. 2012. Gut microbiota composition correlates with diet and health
in the elderly. Nature 488, 178–184.
Collison, M., et al. 2012. Data mining the human gut microbiota for therapeutic targets.
Briefings in bioinformatics 13, 751–768.
Cotter, P.D., C. Stanton, R.P. Ross, and C. Hill. 2012. The impact of antibiotics on the
gut microbiota as revealed by high throughput DNA sequencing. Discovery medicine
13, 193–199.
Croswell, A., E. Amir, P. Teggatz, M. Barman, and N.H. Salzman. 2009. Prolonged
impact of antibiotics on intestinal microbial ecology and susceptibility to enteric
Salmonella infection. Infection and immunity 77, 2741–2753.
Dohar, J., et al. 2006. Topical ciprofloxacin/dexamethasone superior to oral amoxicil-
lin/clavulanic acid in acute otitis media with otorrhea through tympanostomy tubes.
Pediatrics 118, e561–569.
Dore, J. and H. Blottiere. 2015. The influence of diet on the gut microbiota and its con-
sequences for health. Current opinion in biotechnology 32C, 195–199.
El Aidy, S., P. Van den Abbeele, T. Van de Wiele, P. Louis, and M. Kleerebezem. 2013.
Intestinal colonization: how key microbial players become established in this dy-
namic process: microbial metabolic activities and the interplay between the host and
microbes. BioEssays: news and reviews in molecular, cellular and developmental
biology 35, 913–923.
Fuentes, S., et al. 2014. Reset of a critically disturbed microbial ecosystem: faecal
transplant in recurrent Clostridium difficile infection. ISME J 8, 1621–1633.
Ghosh, T.S., et al. 2014. Gut microbiomes of Indian children of varying nutritional
status. PLoS One 9, e95547.
Ghouri, Y.A., et al. 2014. Systematic review of randomized controlled trials of probiot-
ics, prebiotics, and synbiotics in inflammatory bowel disease. Clinical and experi-
mental gastroenterology 7, 473–487.
Grzeskowiak, L., et al. 2012. Distinct gut microbiota in southeastern African and
northern European infants. Journal of pediatric gastroenterology and nutrition 54,
812–816.
Gonzalez-Rodriguez, I., L. Ruiz, M. Gueimonde, A. Margolles, and B. Sanchez. 2013.
Factors involved in the colonization and survival of bifidobacteria in the gastrointes-
tinal tract. FEMS Microbiol Lett 340, 1–10.
Goodrich, J.K., et al. 2014. Human genetics shape the gut microbiome. Cell 159, 789–
799.
Hill, C., et al. 2014. Expert consensus document. The International Scientific Associa-
tion for Probiotics and Prebiotics consensus statement on the scope and appropri-
ate use of the term probiotic. Nature reviews. Gastroenterology & hepatology 11,
506–514.
Iapichino, G., et al. 2008. Impact of antibiotics on the gut microbiota of critically ill
patients. Journal of medical microbiology 57, 1007–1014.
Jernberg, C., S. Lofmark, C. Edlund, and J.K. Jansson. 2007. Long-term ecological
impacts of antibiotic administration on the human intestinal microbiota. ISME J 1,
56–66.
Kane, A.V., D.M. Dinh, and H.D. Ward. 2015. Childhood malnutrition and the intestinal
microbiome. Pediatric research 77, 256–262.
References 357
Lakshminarayanan, B., C. Stanton, P.W. O’Toole, and R.P. Ross. 2014. Compositional
dynamics of the human intestinal microbiota with aging: implications for health. The
journal of nutrition, health & aging 18, 773–786.
Lawley, T.D., et al. 2012. Targeted restoration of the intestinal microbiota with a sim-
ple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.
PLoS Pathog 8, e1002995.
Lee, H. and G. Ko. 2014. Effect of metformin on metabolic improvement and gut mi-
crobiota. Appl Environ Microbiol 80, 5935–5943.
Li, H., M. Zhou, A. Zhao, and W. Jia. 2009. Traditional Chinese medicine: balancing
the gut ecosystem. Phytotherapy research: PTR 23, 1332–1335.
Li, H. and W. Jia. 2013. Cometabolism of microbes and host: implications for drug
metabolism and drug-induced toxicity. Clinical pharmacology and therapeutics 94,
574–581.
Louis, P., K.P. Scott, S.H. Duncan, and H.J. Flint. 2007. Understanding the effects of
diet on bacterial metabolism in the large intestine. Journal of applied microbiology
102, 1197–1208.
Malago, J.J. 2014. Contribution of microbiota to the intestinal physicochemical barrier.
Beneficial microbes, 1–17.
Mangin, I., A. Suau, M. Gotteland, O. Brunser, and P. Pochart. 2010. Amoxicillin treat-
ment modifies the composition of Bifidobacterium species in infant intestinal micro-
biota. Anaerobe 16, 433–438.
McFarland, L.V. 2014. Use of probiotics to correct dysbiosis of normal microbiota fol-
lowing disease or disruptive events: a systematic review. BMJ open 4, e005047.
Mills, S., C. Stanton, G. F. Fitzgerald, and R.P. Ross. 2011. Enhancing the stress re-
sponses of probiotics for a lifestyle from gut to product and back again. Microbial
cell factories 10 Suppl 1, S19.
O’Sullivan, O., et al. 2013. Alterations in intestinal microbiota of elderly Irish subjects
post-antibiotic therapy. The Journal of antimicrobial chemotherapy 68, 214–221.
Palmnas, M.S., et al. 2014. Low-dose aspartame consumption differentially affects gut
microbiota-host metabolic interactions in the diet-induced obese rat. PLoS One 9,
e109841.
Perez-Cobas, A.E., et al. 2014. Structural and functional changes in the gut microbiota
associated to Clostridium difficile infection. Frontiers in microbiology 5, 335.
Petrof, E.O., et al. 2013. Stool substitute transplant therapy for the eradication of Clos-
tridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 1, 3.
Purucker, P., H. Mertes, J.M. Goodson, and J.P. Bernimoulin. 2001. Local versus sys-
temic adjunctive antibiotic therapy in 28 patients with generalized aggressive peri-
odontitis. Journal of periodontology 72, 1241–1245.
Sarowska, J., I. Choroszy-Krol, B. Regulska-Ilow, M. Frej-Madrzak, and A. Jama-
Kmiecik. 2013. The therapeutic effect of probiotic bacteria on gastrointestinal dis-
eases. Advances in clinical and experimental medicine: Official organ Wroclaw
Medical University 22, 759–766.
Schnorr, S.L., et al. 2014. Gut microbiome of the Hadza hunter-gatherers. Nature com-
munications 5, 3654.
Scott, K.M., J.M. Antoine, T. Midtvedt, and S. van Hemert. 2015. Manipulating the
gut microbiota to maintain health and treat disease. Microbial ecology in health and
disease 26, 25877.
Shahinas, D., et al. 2012. Toward an understanding of changes in diversity associated
with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.
mBio 3.
Shankar, V., et al. 2014. Species and genus level resolution analysis of gut microbiota
in Clostridium difficile patients following fecal microbiota transplantation. Micro-
biome 2, 13.
Spellberg, B., J. Bartlett, R. Wunderink, and D.N. Gilbert. 2015. Novel approaches are
needed to develop tomorrow’s antibacterial therapies. American journal of respira-
tory and critical care medicine 191, 135–140.
Stecher, B., et al. 2010. Like will to like: abundances of closely related species can pre-
dict susceptibility to intestinal colonization by pathogenic and commensal bacteria.
PLoS Pathog 6, e1000711.
Subramanian, S., et al. 2014. Persistent gut microbiota immaturity in malnourished
Bangladeshi children. Nature 510, 417–421.
Suez, J., et al. 2014. Artificial sweeteners induce glucose intolerance by altering the gut
microbiota. Nature 514, 181–186.
Valles, Y., et al. 2014. Microbial succession in the gut: directional trends of taxonom-
ic and functional change in a birth cohort of Spanish infants. PLoS genetics 10,
e1004406.
Varughese, C.A., N.H. Vakil, and K.M. Phillips. 2013. Antibiotic-associated diarrhea:
a refresher on causes and possible prevention with probiotics--continuing education
article. Journal of pharmacy practice 26, 476–482.
Young, P.Y., and R.G. Khadaroo. 2014. Surgical site infections. The Surgical clinics of
North America 94, 1245–1264.
Vrieze, A., et al. 2012. Transfer of intestinal microbiota from lean donors increases
insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143,
913–916 e917.
Index
16S rRNA, 9, 13, 30, 33, 39, 44–46, 60, Adenosine diphosphate (ADP), 236
63, 65, 71, 218, 220, 233, 243, 254, Adenosine triphosphate (ATP), 75, 78,
278, 315, 320, 323, 338, 351, 358 88, 200, 254
3, 5, 3′-triiodothyronine, 187 Adipocytes, 80, 176, 178, 181, 194–195,
4-ethylphenylsulfate (4EPS), 116, 238 197, 204, 211–212, 242, 297
4-hydroxyphenylacetate, 83 Adipose tissues, 105, 176–177, 179,
4-hydroxyphenyllactate, 83 180–181, 187, 195–196, 198,
4-hydroxyphenylpropionate, 83 200–201, 205, 207, 211, 312
4- hydroxyphenylpyruvate, 83 Afferent neurons, 111, 119, 120, 126,
4-ethylphenol, 83 128, 223
5-bromocytosine, 247 Akkermansia, 7, 45–47, 51, 198, 204,
5-chlorocytosine, 247 284, 306
5-halocystosine, 247 Akkermansia spp, 284
5-methylcytosine, 247 Alistipes, 8, 36, 44–46
7-α-dehydroxylase, 77, 321 Alkaline phosphatase, 199, 201–202,
Acetate, 19, 21, 43, 74–76, 78–80, 82, 204, 206–208
83, 86, 103, 147–149, 157, 172– Alkaliphilus, 46
173, 175–177, 181, 190, 205–206, Allergy, 29, 33, 68–69, 157, 160,
210–212, 237–239, 283 162–163, 167, 169, 257–258,
Acetylation, 80–81, 107, 122, 175, 210, 265, 335–336, 342–345
236, 239, 245, 265 Ammonia, 43, 82, 89, 98–99, 101,
Acidaminococcus fermentans, 5 103, 106–107, 215, 228, 265,
Acinetobacter lwoffii F78, 245 290, 297
Acquapendente, Fabricus, 271 Amphiregulin, 240
ACTH, 116 Anaerobic bacteria, 1, 3–4, 184
Actinobacteria, 10, 12–13, 22, 36, 51, Anaerococcus, 8, 192
54, 73, 189, 192, 220, 227, 229, Anaerotruncus, 8, 45, 58, 284
239, 287, 289, 292 Anaerotruncus coliohominis, 284
Actinomycetales, 25 Angiogenesis, 137, 321
359
360 Index
Anthocyanin, 92, 94, 98 B cells, 119, 132, 134, 140, 143–145,

Antibiotic-associated diarrhoea (AAD), 168, 180, 240, 244
48–49 Bacterial vaginosis, 331, 339, 342–343
Antibiotics, 15, 35, 42, 48–49, 57, 59, Bacterial vaginosis (BV), 331
61–62, 90, 135, 147, 155, 157, 159, Bactericidal/permeability increasing
162, 184, 191, 199–200, 215–217, protein (BPI), 199
219, 225, 230, 233–234, 255, 268, Bacteriology, 1, 3, 205, 258
272–275, 277–278, 281, 286, 288, Bacteroides fragilis, 4, 15, 44, 53, 141,
290–291, 293, 297, 303–304, 307, 225, 238, 253, 290
313, 319, 328–329, 334, 339–342, Bacteroides thetaiotaomicron, 36, 72
345, 349–350, 355–356 Bacteroidetes, 10, 12, 13, 14, 22, 24, 26,
Antigen presenting cells (APCs), 141 31, 36, 39, 44, 46, 50, 51, 52, 53,
Antimicrobial, 5, 6, 13, 18, 20–21, 54, 57, 58, 73, 94, 95, 174, 189,
27, 41, 74, 94–95, 113, 132, 135, 192, 217, 220, 225, 227, 228, 229,
137–139, 161, 164, 166, 168–170, 255, 276, 284, 287, 289, 292, 293,
188, 215, 272, 277, 280, 293, 296, 294
321, 328–329, 331, 342, 344–345, Balb/c mice, 113, 115, 316
348–350, 355, 357 Barrett’s oesophagus, 27, 294, 324
Antimicrobial—associated molecular β-glucosidase, 77
patterns (MAMPs), 135 β-glucuronidase, 77
Antimicrobial peptides, 21, 132, 135, Bifidobacterium, 6–7, 15, 18, 23–26, 32,
161, 164, 166 36, 40, 68–69, 81, 92, 94, 128, 184,
Antimicrobial peptides (AMPs), 132 225, 234, 268, 271, 280, 284, 329,
Anxiety, 28–29, 54, 111–113, 115–116, 333, 342–343, 357
118, 122, 124–128, 238 Bifidobacterium animalis, 23, 31, 314
Apoptosis, 25, 80, 196, 203, 239, 248, Bifidobacterium breve, 100, 337
251, 256, 259–260, 291, 324 Bifidobacterium infantis, 126, 141, 288,
Arabinogalactan, 76 332, 336–337
Arabinoxylan, 76, 99, 105–106 Bifidobacterium lactis, 336, 339, 341,
Archaea, 10, 12, 17, 241, 254, 260, 267 345
Archaed, 55 Bifidobacterium longum, 41, 64, 67, 125,
Arginine, 236, 262 128, 288, 291, 337
Aryl hydrocarbon receptor (AhR), 151, Bile Acid Metabolism, 171, 188, 285
238–240 Bilophila wadsworthia, 8, 188, 221,
Atherosclerosis, 90, 102, 189–193, 224–225
201, 205–207, 210, 244–245, 259, Body Mass Index (BMI), 47, 76, 354
261–262, 266 Borrelia burgdorferi, 244
Atlas, Ron, 329, 339 Botulism, 1
Atopic dermatitis, 68, 154, 166, 332 Brain derived neurotrophic factor
Atopobium, 40 (BDNF), 114–115, 122, 127
Autism, 7–8, 28, 31, 109, 115, 124–125, Branched-chain fatty acids (BCFA), 83
127, 237, 255–256, 258, 261–262, Breast cancer, 240
264–265 Breast milk, 10, 41, 67, 287
Autism Spectrum Disorder (ASD), Butyrate, 20–21, 24–25, 31–32, 36, 43,
115–116, 307, 312 47, 50–53, 55, 64, 67, 75–83, 88,
Autoimmunity, 32, 132, 161, 202, 269 98–101, 103–107, 122, 128, 147,
Avenanthramides, 92 149–150, 156, 163–164, 168–169
Index 361
Butyrate (continued), 171–175, 177–181, Cecum, 15, 67, 74, 184, 215
204, 207–208, 212, 237–239, 249, Centers for Disease Control and Preven-
254, 256–259, 261, 270, 279, tion (CDC), 217
283–285, 289, 305, 307, 314, 340 Cephalosporins, 49, 272
Butyrivibrio, 44, 47, 147 c-Fos, 121
Butyrivibrio fibrisolvens, 147 Chemokine receptor, 141
Butyrovibrio crossotus, 284 Chemotaxis, 20, 137, 180
Butyrylation, 236 Chenodeoxycholic acid, 182–183
Chinese Hamster Ovary (CHO), 81
Caco-2, 101, 152 Chlamydia psittaci, 244
Cadaverine, 90 Chloramphenicol, 5
Campylobacter, 21, 126, 244 Cholesterol, 44, 78, 95, 136, 151, 167,
Candida albicans, 96, 100 173, 181–182, 189–191, 193, 197,
Capnocytophaga gingivalis, 242 207, 240
Capsaicinoids, 92 Cholic acid, 182, 189
carbohydrate response element binding Chromatin, 99, 122, 129, 175, 235–237,
protein (ChREBP), 297 239, 247, 257
Carboxylation, 90, 237 Chromosomes, 235, 247
Carcinogenesis, 30, 88, 100, 102, 105, Chylomicrons, 181
248, 258, 260, 264, 266, 290–292, Cirrhosis, 89, 208, 227–231, 234,
309, 313, 316, 319 295–296, 300, 303, 310, 321,
Carcinogenic N-nitroso compounds 324
(NOC), 91, 106 Citrobacter, 139
Carcinoma, 181, 200, 240, 242–243, Citrobacter rodentium, 81, 127, 139,
246–257, 259–260, 262–263, 289, 269, 324
292–294, 301–302, 306, 309, 312 Citrullination, 236, 262
CARD15, 22 c-Jun N-terminal kinase (JNK), 195
CARD9, 158 Clarithromycin, 48
Cardiovascular , 22, 27, 49, 87, 90–91, Claudin-1, 198
97, 99, 103, 106–107, 172, 190, Claudin-3, 198
193, 210–211, 226, 239, 244–245, Clindamycin, 49, 272
249, 259–261, 323 Clostridial toxins (tcdA, TcdB), 274–275,
Cardiovascular Disease (CVD), xi, 22, 321
49, 87, 90, 97, 172, 244, 249 Clostridium, 23, 25, 66, 83, 184, 192,
Carnitine, 90–91, 102, 189–193, 206, 229–230, 269, 280, 296, 300, 304
209, 245, 261 Clostridium bolteae, 7–8
Catenibacterium, 44, 46 Clostridium clostridioforme, 57, 284
Cathelicidins, 137, 139, 161, 165–166, Clostridium cluster, 10, 14–15, 20, 24,
170 43–44, 46, 58, 268, 274, 276, 285
CCL8, 157 Clostridium coccoides, 293, 295
CD14, 50, 198, 207 Clostridium difficile, 5, 41, 48, 66,
CD39, 253–254, 261, 265 69, 215–216, 272, 300, 302–303,
CD4 T-cells, 82, 132, 134, 137, 140–141, 305–315, 317–324, 334, 343–345,
149, 167, 236, 245, 252–253, 256, 351, 356–358
259, 263, 306 Clostridium histolyticum, 158, 255
CD41, 245 Clostridium leptum, 53, 94, 221, 321
CD8 T-cells, 134, 140, 142, 252, 260, 263 Clostridium lituseburense, 158
362 Index
Clostridium perfringens, 287 Defensins, 136–139, 160–163, 167–168,

Coabundance gene groups, 222 280, 296
Coagulase negative staphylococci, 40 Dendritic cells (DCs), 82, 111, 119, 134,
Colitis, 112, 138–139, 141–142, 148, 141, 163, 166, 194, 251, 263, 270,
167–168, 180, 203, 207, 216, 221, 304, 319, 321
230, 273, 290–291, 299, 301–302, Deoxycholic acid, 183, 187, 238
304, 307, 310–311, 317, 320, 322, Dermitis, 332
324, 343, 345–355 Desulfitobacterium, 192
Colitogenic bacteria, 53 Desulfomonas, 25, 87
Collinsella, 192 Desulfomonas spp, 87
Colon, 5, 7, 8, 14–15, 19–20, 24, 42–43, Desulfovibrio, 7, 25, 46, 51, 57, 87, 192,
59, 64, 73, 76–80, 82–83, 87–88, 201, 205, 231, 238, 279, 319
90–91, 97–98, 100–106, 138, 148, Desulfovibrio alaskensis, 192
157–158, 162–163, 169, 172, 175, Desulfovibrio desulfuricans, 192, 201,
181, 184, 200, 212, 214–215, 229, 205
248, 256, 259, 262, 265, 288, Desulfovibrio spp, 87
290–291, 305, 308, 310, 316–317 Diabetes, 23–24, 30–32, 44, 49–51, 62,
Colon cancer, 31, 78, 80, 103, 175, 212, 65–66, 68–69, 74, 105–106, 125,
257–258, 262, 288, 290, 306, 317 155–156, 160–161, 163–164, 166,
Colonocytes, 19, 21, 77–78, 88–89, 103, 168–169, 172, 175, 179, 181–182,
173 187, 193–194, 196, 201–206,
Colorectal cancer, 24, 29–30, 33, 91, 208–211, 217, 237, 242, 249, 263,
101–102, 128, 257, 262, 265, 288– 282–284, 295, 299, 302, 307, 312,
289, 301, 303–304, 308, 314–315, 318, 323, 353
322–324 Dimethylamine (DMA), 90
Colorectal carcinoma (CRC), 289 Dopamine, 111, 201
Coping Checklist (CCL), 118 Duodenum, 12–13, 18, 42, 214, 345
Coprobacillus, 45, 58 Dysbiosis, 20–23, 25–28, 35–36, 38,
Coriobacteridae, 289 40–41, 49, 53, 59, 62, 116, 120,
Corynebacterium, 8, 27, 41 163, 168, 177, 225–226, 228–229,
C-reactive protein (CRP), 56, 58, 282 231–232, 234, 255, 265, 281, 286,
Crohn’s disease, 21, 28, 31–32, 52, 67, 295, 301, 304, 308, 311–313, 320,
70, 105, 138, 161, 163, 166–167, 324, 330, 357
169, 212, 219, 221–222, 231–234,
238, 278–280, 301, 304, 306–307, Eczema, 27, 332, 336, 345
311, 313, 316–317, 320, 324, 332, ELDERMET, 58
339, 344 Endocannabinoid system, 50, 66,
Crohn’s disease (CD), 44, 53, 138, 219, 68
221, 278–280, 332 Endotoxemia, 24, 50, 62, 64–65, 197,
Crotonylation, 236 201–202, 204, 206–209, 232, 283,
C-type lectin, 137–138 285, 296, 299–300, 302, 310, 316
Cyclic adenosine monophosphate , 254 Enterobacter cloacae, 144
CYP7A1, 183–186 Enterobacteriaceae, 15, 21, 26, 221–222,
Cystathionine beta-synthase, 89 225, 229, 273, 278, 280–281, 288,
Cystathionine gamma lyase, 89 291
Cysteine, 87, 89, 137, 251, 279 Enterococcus, 94
Cytokine, 137 Enterococcus faecium, 39, 310
Index 363
Enterocolitis, 5, 27, 32, 40, 70, 285–286, Fibroblast growth factor (FGF),
298, 300, 302–305, 308–310, 312, 185–186, 201, 206
314–316, 322, 329, 331, 336, 340 Firmicutes, 10, 12, 13, 21–22, 24–26, 31,
Entero-pathogens, 48 36, 39, 43–46, 50, 53–54, 57–58,
Enterotype, 8, 15–16, 20, 28, 42, 44, 46, 73, 94–95, 156, 158, 174, 184, 189,
51, 60, 72, 97, 234, 256, 324 192, 221, 225, 227, 229, 238–239,
Epigenetic, 80, 110, 122, 124, 127–129, 254–255, 276, 278–279, 284, 289,
175, 200, 202, 209, 235–246, 292–294, 351
248–252, 254–266, 270 Flavin mono-oxygenase (FMO), 90, 189,
Epigenome, 235, 237, 252, 261, 263 279
Epinephrine, 117 Fluorescent in situ hybridisation (FISH),
Epiregulin, 240 54
Erysipelotrichales, 222 Fluoroquinolones, 49, 272
Erysipelotrichi, 298 Foam cell, 90, 191
Escherichia coli, 6, 21, 25–26, 31, 39, 41, Food and Drug Administration (FDA),
51, 77, 92, 99, 117, 150, 158, 161, 328, 330, 335
184, 221–222, 230, 238, 271, 278, Formyl peptide receptors (FPRs), 148
280, 284, 287, 289, 310, 315, 320, Formylation, 236–237
333, 343 Free Fatty Acid Receptor (FFA), 79–82,
Esophagitis, 27, 30, 294, 324 102–103, 106, 148, 176, 187, 206,
Eubacterium, 6, 10, 15, 25, 36, 43, 45, 208–210, 261–262, 306
58, 92–93, 184, 192, 238–239, 248, Functional gastrointestinal disorders
268, 311 (FGIDs), 52–54
Eubacterium aerofaciens, 248 Fusobacteria, 12–13, 39, 222, 228, 294
Eubacterium hallii, 285 Fusobacteriaceae, 222
Eubacterium ramulus, 93 Fusobacterium, 4, 279, 290, 312, 333
Eubacterium rectale, 20, 24, 44–46, 50, Fusobacterium nucleatum, 27, 290, 302,
55, 238, 239 321
Eubacterium spp, 91 Fusobacterium varium, 6, 221, 223,
316
Faecalibacterium prausnitzii, 20, 21,
33, 43, 53, 57, 70, 72, 77, 158, Gamma aminobutyric acid (GABA),
162, 167, 169, 220–221, 233–234, 113–114, 121, 123, 125, 164, 238
238–239, 279, 284, 320, 322 Gas gangrene, 1
Farnesoid X Receptor (FXR), 151, 184, Gemella, 292
185–187, 209 Gemella asacchrolytica, 8
Fast-acting-induced adipocyte factor GLP-1, 79–80, 102, 176, 178, 180,
(FIAF), 176, 181, 242, 297 187–188, 198, 208, 212
Fecal microbiota transplantation (FMT), Glucagon-like peptide-1 (GLP-1), 178
267–268, 270–278, 281–282, 285, Gluconeogenesis, 78, 173, 180
288, 291, 298, 335 Glucose transporter type 4 (GLUT4),
Fermentation, 20, 39, 42–43, 50, 54–55, 196
58–59, 66–67, 71, 74–77, 82–83, Glutamine, 58, 89
87, 89, 91–92, 94, 95, 99, 101, Glutathione, 279
103–107, 111, 122, 125, 127, 156, Glycans, 64, 72, 95, 283, 290
162, 169, 171, 177, 189, 201, 205, Glycine, 90, 184, 190, 245, 320
215, 227, 230, 262, 327, 334, 352 Glycoside hydrolases, 92, 172
364 Index
Glycosylation, 236 Hydrogen sulfide (H2S), 21, 25, 87–88,

Gnotobiotic mice, 32–33, 43, 72, 262, 97–100, 102–104, 137, 221, 225,
342 233, 284, 290
GPR109a, 80, 82, 99, 105–106, 148, 169 Hydroxylation, 33, 95, 103, 183, 229,
GPR41, 23, 79, 98, 102, 106–107, 148, 236, 274, 309, 323
161, 176–180, 182, 201, 206, Hydroxymethylation, 237
208–210, 212 Hygiene hypothesis, 27, 33, 155, 251
GPR43, 23, 79, 98, 102, 148–149, 161, Hyperlipidaemia, 242
166, 176–182, 201, 206, 208, 210, Hypersensitivity, 223, 230
212, 314 Hypertension, 27, 89, 98, 242, 249
GR-1, 331 Hypobromous acid, 247
Graft-versus-hostdisease (GVHD), 138 Hypochlorous acid, 247
Guar gum, 76, 104 Hypothalamic-pituitary-adrenal (HPA),
Gut-associated lymphoid tissue (GALT), 116
19, 132, 134–135, 137, 139, Hypothalamic-pituitary-adrenal axis
140–141, 143, 145, 269 (HPA), 110, 116–117, 123
Gut-brain axis, 53, 109–111, 116–121, Hypoxia, 240, 248
123–125
IEC-6 cells, 78
Hadza, 36–38, 70, 357 IFN-γ-inducible protein 10 (IP-10), 153
Hall, Wendel, 2 IFN-γ-inducible protein 10 (IP-10), 153
HDL, 198 IgA, 70, 119, 132, 134–135, 140, 143–
Health Canada, 330, 334, 341 144, 145, 161–164, 167–168, 270
Helicobacter, 334 IgE, 144, 157, 162–163
Helicobacter hepaticus, 269, 291, 316 IgG, 132, 144
Helicobacter pylori, 13, 31, 244–245, Interleukin 12, 81, 236, 253, 310, 332
257–265, 289, 299, 301, 304–306, Interleukin 13, 153
309, 313–314, 316–317, 319–321, Interleukin 17, 142, 155, 308–309
323, 334, 340 Interleukin 1β, 81, 152–153, 196, 306
Hemostasis, 328 Interleukin 4, 153, 236, 253
Hepatic encephalopathy, 89, 98, 106, Interleukin 5, 153
228, 230, 296–297, 300, 318 Interleukin 6, 56, 58, 81, 153, 179, 194,
High fat diet, 64, 91, 194, 197 236, 240, 253, 259, 280, 294
Histamine, 137, 157 Interleukin 8 receptor, 158
Histidine, 236 Interleukin 18, 56
Histone, 80–81, 99, 105, 107, 122, 128, Interleukin 22, 142, 151, 270, 325
175–176, 202, 210–211, 235–239, Interleukin 23 receptor, 158
245, 249, 256, 258, 262–263 Ileum, 6, 14, 19, 77, 89, 183, 185, 214,
Histone deacetylases (HDAC), 80–81, 221, 229, 280
122, 175–176, 180, 202, 239 Immunoglobulin, 134, 144, 161,
Histone deacetylases acetylation 168–169, 269, 296
(HDAC), 175 Indican, 86
Homocysteine, 245 Indirubin, 239
Hospital Anxiety and Depression Scale Indole, 83, 86–87, 99, 104, 150–151,
(HADS), 118–119 160, 165–166, 238–239
HT-29 cell line, 87–88, 259 Inducible nitric oxide synthase (iNOS),
Human Microbiome Project, 9–10, 16, 30 132
Index 365
Inflammation, 18, 22, 24–27, 29, 36, L cells, 102, 178

38, 47, 50, 53, 55–56, 58, 62, Lachnospiraceae, 52
64–66, 68, 71, 81–82, 88, 101, Lachnospiraceae, 52, 228, 254, 273–274,
103, 105–106, 112, 121, 125, 132, 281, 348
140–142, 148–152, 154–155, Lactic acid, 330
157–158, 160–161, 163–169, 176, Lactobacillus, 6, 8, 24–25, 28, 32, 40,
178–179, 185, 188–189, 194–199, 46, 54, 83, 92, 94, 112, 125, 184,
201, 203–206, 208–212, 217, 221, 225, 227, 238, 268, 294–295, 306,
224, 226, 228, 230, 232, 238–239, 316, 327, 339, 341–342, 344–345
241, 243, 247–249, 251, 253–254, Lactobacillus acidophilus, 106, 248,
258–259, 261, 264–265, 269–270, 261–262, 337
278–281, 283, 285, 296, 289–290, Lactobacillus brevis, 27, 32
293, 295–296, 298, 300, 307, 311, Lactobacillus casei, 100, 280, 291, 309,
313, 318–320, 324, 331, 333 313, 333, 337, 341, 343, 344
Inflammatory Bowel Disease (IBD), Lactobacillus delbrueckii, 337
21–22, 52–53, 70, 134, 142, 150, Lactobacillus gasseri, 284, 290, 302
152, 155, 157–159, 217, 219–221, Lactobacillus helveticus, 128, 333,
231, 278–282, 301, 306–307, 341
310–311, 313, 320–321, 324, Lactobacillus johnsonii, 156, 166, 169,
331–333 291, 333
Insulin sensitivity, 176–78, 181–182, Lactobacillus plantarum, 336–337,
184–185, 187–188, 196, 198, 201, 344
204, 211, 285, 307, 322, 358 Lactobacillus reuteri, 23, 31–32, 156,
Interferon gamma (IFN-γ), 80, 105, 138, 336, 342–343
153, 155, 196, 236, 245, 253, 280 Lactobacillus rhamnosus, 113, 120–121,
Interferon regulatory factor (IRF), 195 128, 323, 329, 336–337, 340–342
Intestinal gluconeogenesis (IGN), 180 Lactococcus, 227, 295
Intestinal intraepithelial lymphocytes Lactose, 23, 76, 107
(IELs), 142 Lactulose, 76, 97, 297
Intraepithelial lymphocytes (IEL), 129, Lamina propria, 21, 81, 119, 132, 134,
132, 134, 142, 161–162, 164, 313 140–141, 143, 198, 200, 270, 304,
Irritable Bowel Syndrome (IBS), 27, 29, 314, 321, 323
31, 52–55, 65, 67–70, 74, 76, 82, L-carnitine, 90
101, 103, 107, 120, 208, 223–225, LDL, 95, 181, 190–191, 197–198,
230, 232, 263, 271, 301, 308, 332, 227
336, 341, 345 Leptotrichia, 41
Isoleucine, 83 Leuconostoc, 227, 279, 295
IκB kinase (IKK), 195 Leuconostocaceae, 279
Lipogenesis, 78, 173, 181, 205
Jejunum, 6, 14, 18–19, 214 Lipolysis, 176, 181, 197, 204–205, 208,
Junctional adhesion molecule 1 275, 317
(JAM-1), 198 Lipopolysaccharide (LPS), 18, 24,
50, 81, 136–138, 153, 157, 178,
Kanamycin, 5 194–199, 201, 207, 235, 240, 251,
Keratinocytes, 154 283, 290, 294
Klebsiella, 158, 192, 287 Lipoprotein lipase (LPL), 181, 226, 242,
Klebsiella oxytoca, 26 297
366 Index
Lipoproteins, 18, 95, 104, 106, 181, 190, Methionine, 87, 242, 245, 264
226–227, 231, 242, 275, 297–298, Methylation, 80, 122, 176, 236–238,
310, 317 242–249, 255–257, 259, 261–262,
Listeria monocytogenes, 138 264–266
Lithocholic acid, 169, 187, 290 Methylcellulose, 76
Low-density lipoprotein–cholesterol Methyltransferase, 88, 104, 236,
(LDL), 95 244–245, 247
Lymphocytes, 149 Methyltransferase, 88, 104, 236,
Lysine, 80, 236 244–245, 247
Microbial-associated molecular patterns
M cells, 119 (MAMP), 135, 138
Macrophage Inflammatory Protein microRNA (miRNA), 237, 242, 244,
(MIP-1α), 148 252, 257, 262–264
Macrophage inflammatory protein 1α Monocarboxylate transporter (MCT),
(MIP-1α), 148 77, 101
Major Hostological Complex (MHC), 139 Monocyte chemoattractant protein 1
Malonylation, 236 (MCP-1), 153
Maternal Immune Activation (MIA), Monocytes, 137, 194, 203, 319
115 Morganella morganii, 145
Megacolon, 216 MUC1, 247
Megasphaera, 5, 228 MUC19, 157
Megasphaera elsdenii, 5 Mucin, 18, 20–21, 46, 51, 82, 87–88,
Mesenchymal, 240 135, 142, 162, 198, 204, 231, 247,
Mesenteric lymph nodes, 120, 141, 285, 306, 310, 338
144–145, 198, 296 Multiple sclerosis, 28, 251, 254–255,
Metabolism, 16, 19, 23, 25, 27, 29, 258, 260–262
31, 33, 41–42, 46, 49–52, 58, 60, Muricholic acid (MCA), 182, 209
62–63, 66–68, 74–75, 78–79, Mycobacterium, 14
83–86, 89–90, 92–93, 95, 97, Myeloid differentiation primary response
99–107, 151, 153, 162–163, 171, gene 88 (MyD88), 156, 254
176–185, 187–194, 196, 200–201,
203, 206–212, 227, 234, 237, Necrotizing, 329, 331
239–240, 244–245, 249, 255, Necrotizing enterocolitis (NEC), 286
258, 261–262, 264, 266, 268, Neisseria, 12–14
274, 279, 282–285, 291, 297, Neomycin, 3, 5, 113
305, 312, 316, 318, 323, 357 Neonatal, 329
Metabolomics, 16, 90, 152, 262, 265, Neuroinflammation, 253, 265
278, 282, 338 Neutrophils, 135, 137, 142, 148, 169,
Metagenomic, 10, 16, 22, 30, 33, 39, 179, 243, 247, 270
43, 50–52, 60, 67, 69, 71, 104, Nitric oxide, 27, 29, 30, 99–100, 132,
142, 161, 166, 206, 232, 233, 290, 306
267, 278–279, 282, 284, 306, Nitrosamine, 90
318, 338 N-nitroso compounds (NOC), 91
Metaproteomics, 16, 306 NOD, 22, 29, 31, 128, 138, 141,
Metatranscriptomics, 16 144–145, 158, 161, 165, 182–183,
Metchnikoff, Elie, 270–271, 315, 209, 244, 269, 280, 290–291, 296,
327–328, 354 301, 303–304, 316–317, 320
Index 367
NOD2, 138 PBMC cells, 81, PCR-denaturing gradi-

Nonalcoholic steatohepatitis, 49, 51, ent gel electrophoresis (PCR-DG-
72, 194, 202, 205, 209, 225, 232, GE), 54, 67
233–234, 295, 299, 306, 322, 325 p-cresol, 58, 83, 86–87, 97–98, 100,
Nonalcoholic fatty liver disease 103–104
(NAFLD), 49, 51–52, 60, 68, 91, Penicillin, 1, 135, 184
97, 99, 187, 208, 225–227, 229, Peptide YY (PYY), 23, 79, 176, 178–180,
232, 294, 315, 318, 340 198
Nonalcoholic Steatohepatitis A, 49, Peptidoglycan, 137–138, 164, 254, 283,
51, 194, 197–198, 225, 227, 229, 290, 303
295–298 Peroxisome proliferator activated recep-
noncoding RNAs (ncRNA), 237, 242 tor γ (PPAR- γ), 29, 36, 48, 78, 181,
Norepinephrine (NE), 114 187, 197–198, 298–299, 311, 327
Nuclear Factor Kappa B (NF-κB), Peroxisome proliferator activated recep-
55–56, 69, 81, 96, 105, 115, 138, tor γ (PPARγ), 181
148, 150, 153, 166, 179–180, 188, Peroxisome proliferator-activated recep-
194–197, 200–211, 240, 244, 280, tor gamma coactivator (PGC)-1α,
294, 307, 314, 345 181
Obesity, 6, 22–23, 28–29, 31–34, 42, Peyer’s patches, 19, 119, 132, 134, 141,
49–51, 56, 62–64, 66, 68, 70–71, 145, 163, 269
79, 80, 95, 103, 105, 155, 172–175, Pharmacopeia, 348
178–179, 181–182, 185, 187, Phascolarctobacterium, 279
193–194, 198–199, 201–212, 217, Phenotype, 36, 50, 95, 100, 113, 115,
219, 226, 230, 232, 234, 242, 249, 121–122, 149, 163, 165, 172, 174,
257, 264, 282–285, 295, 298, 302, 189, 191, 200, 202–203, 219, 221,
306, 308, 312–313, 315, 318–323, 230, 234–235, 237, 240, 245, 252,
353–354 259, 268, 285, 305–306
Odoribacter, 279 Phenylacetate, 83
Oligofructose, 76, 100, 107 Phenylacetyglutamine, 58
Oligosaccharides, 83 Phenylalanine, 83, 85
Phenyllactate, 83
p38 mitogen-activated protein kinase Phenylpropionate, 83
(MAPK), 153, 195, 250 Phenylpyruvate, 83
Palmitate, 78 Phosphatidylcholine, 90–91, 106–107,
Pancreatic β-cell, 24, 178 189, 210–211, 227, 244, 323
Paneth cells, 135, 137–138, 160–163, Phosphoinositide 3-kinase, 197, 254
167, 169, 280, 296, 321 Phospholipase A2, 138, 166
Parabacteroides, 8, 44–46, 58 Phospholipid, 136, 190, 231, 233, 310
Paraprevotella, 44, 46 Phosphorylation, 188, 195, 199, 201,
Paraventricular nucleus (PVN), 111 236, 248, 252, 313
Paromomycin, 5 Piperidine, 90
Pasteur, Louis, 26, 131, 167 piwi-interacting RNA (piRNA), 237
Pasteurellacaea, 222 Placebo, 332–333
Pasteurization, 155 Planck, Max, 327–328
Pathogens, 328–329, 331 Platelet derived growth factor, 240
Pattern Recognition Receptors (PRR), Polycystic ovarian disease, 242
119, 253, 290 Polyphenols, 43, 74, 92–98, 100–106
368 Index
Polysaccharide A, 121, 141, 253 RePOOPulate, 277, 335, 351

Porphyromonas, 8, 12–13, 17, 26, 242, Resveratrol, 92, 95, 99
257, 260–262 Riboflavin, 279
Post-transcriptional modification, 235 Ribosylation, 236
Poth, Edgar, 1, 3 Rice, 63, 76, 125, 154, 164, 202, 228,
Prebiotics, 43, 61, 101, 111, 125, 225, 307, 331, 336, 343
302, 304, 308, 319, 341, 343, 356 Riegel, Gordon, 2
Pregnane X receptor (PXR), 151, 169 Rifaximin, 276, 278, 296–297, 310
Prevotella, 10, 12–13, 15–17, 20–21, 24, RNase 7, 154
26, 40, 41, 44, 46– 47, 50–51, 57, Rome criteria, 54
192, 220, 228, 242, 255, 260, 268, Roseburia, 20–21, 25, 43–46, 55, 58, 77,
292, 294, 296 192, 221, 228, 238–239, 268, 279,
Probiotics, 327, 329–330, 332, 335 284, 297, 305
Proinflammatory, 17, 21, 24, 49, 55, Roseburia intestinalis, 285
81, 112, 121, 137–138, 142, 153, Ruminococcus, 8, 10, 15, 20, 36, 46,
158, 162, 170, 175–176, 180, 188, 221
194–195, 199, 203, 240, 252, 283,
293, 297, 317 Saccharomyces, 18, 333–334
Prophylaxis, 6, 302, 328, 334, 340–341 Saccharomyces boulardii, 271, 339–340,
Proprionate, 19, 43, 75–80, 82–83, 86, 342–343
98, 103, 122, 147, 149, 157, 161, Saccharomyces cerevisiae, 333, 337
172–181, 201, 205, 207, 211, 237, S-adenosylhomocysteine, 245
238, 261, 283 S-adenosylmethionine, 245
Proprionylation, 236 Saliva, 16, 26–27, 33, 262, 331,
Prostaglandin, 153 336–337, 340
Proteobacteria, 10, 12–14, 22, 24, 26, Salmonella, 71, 77, 96, 153, 163,
36, 39, 41–42, 51–52, 54, 73, 192, Salmonella enterica, 56, 348, 356
220, 228, 238–239, 255, 276, 278, Salmonella typhimurium, 25, 48, 161
281, 287, 289, 292, 294, 298, 351 Sarcopenia, 55
Proteus, 184, 192, 287, 297 SCFA, 17, 19–21, 23, 25, 32, 43, 47, 58,
Providencia, 192 70, 74–82, 89, 94, 96, 105, 122,
Pseudomembranous colitis, 271, 272, 146–150, 157, 172–182, 209–210,
305 215, 237–239, 242, 249, 255,
Pseudomonas, 184, 287 269–270, 279, 283, 289–290, 320,
psoriasin, 154 338
Putrescine, 90 Segmented filamentous bacteria (SFB),
Pyrrolidine, 90 145
Selenomonas, 12
Qsec sensor kinase, 117 Sepsis, 40, 67, 168, 202, 321
Serine, 195, 236
Ralstonia, 287 Serotonin, 111, 127–128, 238–239, 257
Reg IIIα, 138 Short heterodimer partner (SHP), 185
Regulatory T-cell (Treg), 60, 70, 82, 106, short interfering RNA, 237
140–142, 149, 151, 155, 157–158, Signal transducer and activator of
168, 210, 216, 236, 251–254, transcription 3 (STAT3), 236, 244,
261–263, 269–270, 300, 320–321 247–248
RelA/p50, 240 Silencing RNA, 179, 237
Index 369
skatole, 83, 107, 165 Thiol S-methyltransferase (TMT), 88

SLC5A8, 78, 99, 103, 106 Thiosulfate sulfurtransferase (TST), 88
SMCT-1, 78 Threonine, 236
Smith, Louis D.S., 3 Thyroxine, 187
Specific pathogen free (SPF) mice, 113, TLR3, 154
117 TMAO, 90–91, 189–193, 244–245
Spink, Wesley, 2 Toll-Like Receptor, 18, 22, 26, 148,
Spirochaetes, 10, 12, 294 153–154, 157, 194–198, 203–204,
Squamous cell carcinoma, 240, 242–243, 240–241, 244, 253–256, 265, 286,
259–260, 262–263 290, 298, 307, 310, 319
Staphylococcus aureus, 23, 27, 154, 162, Transcription, 53, 69, 80–82, 141, 151,
254 166, 175, 180–181, 185, 195–196,
Staphylococcus aureus δ-toxin, 154 235, 237–240, 244, 247, 250–255,
Staphylococcus epidermidis, 26–27, 39, 257, 261, 280, 297, 317
154 Translation, 237, 250, 256, 262, 343
Streptococcus, 12–14, 18–19, 25–28, Translocation, 21, 50, 81, 118, 138, 143,
31–32, 39, 41, 243, 284, 289, 292, 145, 197–199, 205, 208, 226, 228,
294, 301, 331, 336–337, 340 230, 240, 262, 283, 295–296, 306,
Streptococcus bovis, 15, 25, 27–28, 289 316, 321, 324
Streptococcus gallolyticus, 25, 28, 289, Treponema, 27, 44, 47
301 Trimethylamine (TMA), 90–91, 189,
Streptococcus mitis, 13, 27, 106, 243 202, 212, 227, 244, 298
Streptococcus salivarius, 27, 331, Trimethylamine-N-oxide (TMAO), 90
336–337, 340 Tryptamine, 151, 238–239
Streptomycin, 48, 152, 184 Tryptophan, 86, 107, 150–151, 163, 165,
Succinylation, 236 170, 238–240, 260, 265–266
Sulfurtransferase, 88 Tumour necrosis factor-alpha (TNF- α),
Sulphur-reducing Bacteria, 87 56, 58, 81, 138, 148, 150, 153,
Sumoylation, 236 179, 194, 196–197, 240, 250, 280,
Sutterella, 7, 8, 13 293–294, 297–298, 307, 339
Tyrosine, 83–84, 236, 246, 252
T cell receptor (TCR), 139, 252
T cells, 331 Ubiquitination, 236, 246
T helper 1 (Th1), 81, 100, 102, 104, 106, Ulcerative colitis, 21, 28, 33, 52, 99–102,
140, 142, 149, 155–156, 166, 236, 104–105, 139, 164, 220, 231–234,
252, 253, 256, 262, 269, 310, 332, 278, 299, 301–302, 310, 314,
335 316–317, 319–320, 322, 333, 343
T helper 2 (Th2), 140–141, 153, 157, Ulcers, 21, 27
170, 236, 252–253, 262 Urea, 89, 215, 246, 330
T helper 17 (Th17), 140–142, 149, 155– Uremia, 87
156, 166, 236, 252–253, 258–259, Urinary Track Infection (UTI), 331
261, 269, 309, 313, 316 Urogenital, 239, 243, 249, 328–330, 336,
Taurocholic acid, 203, 230, 274 344
Tauromuricholic acid, 185
Tempol, 185, 201–202 Vaccination, 155, 299, 328
Tenericutes, 12, 39, 243 Vagus nerve, 111, 120–122, 125
TGR5, 184, 187–188, 206, 208, 210, 212 Valine, 83
370 Index
Valproic acid (VPA), 115 Vitamin D Receptor (VDR), 151

van Leeuwenhoek, Antoine, 327 Vulvovaginal candidiasis, 331, 342
Vancomycin, 6–7, 48, 184, 211, 264,
274–276 Western Diet, 7, 22, 268, 290
Vascular endothelial growth factor, 195, Wheat dextrins, 76, 101, 104
240
Vegetarian diet, 44, 46, 280, 325 X receptor, 151
Veillonella, 12–14, 18–19, 23, 41, 54, Xenobiotic, 51, 217, 240, 243, 352
222, 228, 255, 294 Xylanibacter, 44, 47, 268
Veillonellaceae, 222, 255
Verrucomicrobia, 10, 36, 227 Yokenella, 192
Very low-density lipoproteins (VLDL),
181 Zona occuldens (ZO), 198

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The

Emma Allen-Vercoe, Ph.D.

DEStech Publications, Inc.

Copyrig ht © 2016 by DEStech Publications, Inc.

No part of this pub licati on may be reprodu ced, sto red in a

Prin ted in the United States of Ameri ca

Library of Congress Catalog Card No. 2016933594

teract. More importantly, we have a growing understanding of how

process of restoring a balanced ecology in the gastrointestinal tract has

Some Historical Notes on

S INCE so much of the bowel flora is anaerobic, it makes sense to start

surgery that provided guidance for the type of antimicrobial prophy-

tory bypass enteritis, pneumatosis cystoides intestinalis, impaired liver

Ecology of the Human Microbiome

R ECENT technological and conceptual developments in culture

2.2. MICROBIOTA OF THE GASTROINTESTINAL TRACT

is estimated that 1,000–1,500 species of bacteria can inhabit an average

2.3. MICROBIAL COMPOSITION IN THE GI TRACT OF

The human GI tract can be divided in anatomical regions, each char-

2.3.1. The Oral Cavity

2.3.2. The Upper Gastrointestinal Tract

The upper gastrointestinal tract includes the esophagus, stomach,

esophagus, and duodenum, however, these factors affect to a lesser de-

2.3.3. The Small Intestine

2.3.4. The Large Intestine

Clostridiales cluster I and II, were bimodally distributed in the healthy

2.4. MICROBIAL ECOSYSTEM FUNCTION IN THE

Metagenomic studies provide insight on the functional potential of

2.4.1. The Oral Cavity

tion between different species of bacteria. For example, oral streptococ-

2.4.2. Upper Gastrointestinal Tract

Upper gastrointestinal tract microbiota function is still not well un-

ment that can inhibit growth of pathogens by competing for substrates

2.4.3. The Small Intestine

2.4.4. The Large Intestine

Large intestine microbial ecosystem function has been well studied,

also high levels of enzymes involved in energy storage, antimicrobial

Considering the Microbiome as

T HE purpose of The Human Microbiome Handbook is to provide

12.2. MINING THE HUMAN MICROBIOTA FOR

tible to further gut infection during their convalescence (Croswell et al.

12.3. PROTECTING THE GUT MICROBIOTA

The overuse of antimicrobial drugs has received a lot of recent atten-

widespread resistance to these drugs, minimizing their effectiveness

2006; Purucker et al. 2001). The necessity for prophylactic treatment as

12.4. MICROBIAL ECOSYSTEM THERAPEUTICS

A greater understanding of the role of a damaged gut microbiota in

the accumulating knowledge of the human gut microbiota to discover

grounds not typically exposed to widespread antibiotic exposure may

12.5. PREDICTING THE INFLUENCE OF XENOBIOTICS ON

Diet, so far, is the greatest known modulator of the gut microbiota

discovery, and the added burden of testing for microbiome-associated

12.6. LEVERAGING MICROBIOME KNOWLEDGE TO

now understood to be associated with the microbial content of the gut,

As was predicted thousands of years ago with the advent of Chinese

understand and appreciate the involvement of our trillions of microbial

Anthocyanin, 92, 94, 98 B cells, 119, 132, 134, 140, 143–145,

Clostridium perfringens, 287 Defensins, 136–139, 160–163, 167–168,

Glycosylation, 236 Hydrogen sulfide (H2S), 21, 25, 87–88,

Inflammation, 18, 22, 24–27, 29, 36, L cells, 102, 178