Scientific Reports

Collection 10 March 2022

Top 100 in Microbiology

This collection highlights our most downloaded* microbiology papers published in 2021. Featuring authors from around the world, these papers showcase valuable research from an international community.

*Data obtained from SN Inights, which is based on Digital Science's Dimensions.

1-25

The in-vitro effect of famotidine on SARS-CoV-2 proteases and virus replication
- Madeline Loffredo
- Hector Lucero
- Ali H. Munawar
ArticleOpen Access8 Mar 2021 Scientific Reports
In vitro efficacy of artemisinin-based treatments against SARS-CoV-2
- Yuyong Zhou
- Kerry Gilmore
- Peter H. Seeberger
ArticleOpen Access16 Jul 2021 Scientific Reports
Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America
- Elena Delgado
- Aurora Fernández-García
- Michael M. Thomson
ArticleOpen Access1 Jun 2021 Scientific Reports
The effectiveness of various gargle formulations and salt water against SARS-CoV-2
- Vunjia Tiong
- Pouya Hassandarvish
- Ilina Isahak
ArticleOpen Access15 Oct 2021 Scientific Reports
The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue
- Melissa Zimniak
- Luisa Kirschner
- Jochen Bodem
ArticleOpen Access15 Mar 2021 Scientific Reports
Probenecid inhibits SARS-CoV-2 replication in vivo and in vitro
- Jackelyn Murray
- Robert J. Hogan
- Ralph A. Tripp
ArticleOpen Access10 Sep 2021 Scientific Reports
UV-C irradiation is highly effective in inactivating SARS-CoV-2 replication
- Mara Biasin
- Andrea Bianco
- Mario Clerici
ArticleOpen Access18 Mar 2021 Scientific Reports
Diagnostic performance of rapid antigen tests (RATs) for SARS-CoV-2 and their efficacy in monitoring the infectiousness of COVID-19 patients
- John G. Routsias
- Maria Mavrouli
- Athanasios Tsakris
ArticleOpen Access24 Nov 2021 Scientific Reports
Epidemiology and outcomes of COVID-19 in HIV-infected individuals: a systematic review and meta-analysis
- Paddy Ssentongo
- Emily S. Heilbrunn
- Ping Du
ArticleOpen Access18 Mar 2021 Scientific Reports
Temporal dynamics of viral load and false negative rate influence the levels of testing necessary to combat COVID-19 spread
- Katherine F. Jarvis
- Joshua B. Kelley
ArticleOpen Access28 Apr 2021 Scientific Reports
Nasopharyngeal SARS-CoV-2 viral loads in young children do not differ significantly from those in older children and adults
- Sharline Madera
- Emily Crawford
- Joseph L. DeRisi
ArticleOpen Access4 Feb 2021 Scientific Reports
Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures
- Michael Laue
- Anne Kauter
- Andreas Nitsche
ArticleOpen Access10 Feb 2021 Scientific Reports
Glycan reactive anti-HIV-1 antibodies bind the SARS-CoV-2 spike protein but do not block viral entry
- Dhiraj Mannar
- Karoline Leopold
- Sriram Subramaniam
ArticleOpen Access14 Jun 2021 Scientific Reports
The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet
- Adriel Latorre-Pérez
- Marta Hernández
- Luis Collado
ArticleOpen Access10 Nov 2021 Scientific Reports
In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods
- Guo Xiling
- Chen Yin
- Xu Yan
ArticleOpen Access28 Jan 2021 Scientific Reports
Methylene Blue has a potent antiviral activity against SARS-CoV-2 and H1N1 influenza virus in the absence of UV-activation in vitro
- Valeria Cagno
- Chiara Medaglia
- Caroline Tapparel
ArticleOpen Access12 Jul 2021 Scientific Reports
A novel highly quantitative and reproducible assay for the detection of anti-SARS-CoV-2 IgG and IgM antibodies
- Kenta Noda
- Kouki Matsuda
- Akinobu Hamada
ArticleOpen Access4 Mar 2021 Scientific Reports
Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load
- Mateus Nóbrega Aoki
- Bruna de Oliveira Coelho
- Lucas Blanes
ArticleOpen Access27 Apr 2021 Scientific Reports
Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2
- Shan Wei
- Hemant Suryawanshi
- Zev Williams
ArticleOpen Access9 Mar 2021 Scientific Reports
No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor
- Jarrod Shilts
- Thomas W. M. Crozier
- Gavin J. Wright
ArticleOpen Access11 Jan 2021 Scientific Reports
Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage
- Niluni M. Wijesundara
- Song F. Lee
- H. P. Vasantha Rupasinghe
ArticleOpen Access15 Jan 2021 Scientific Reports
In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology
- Shaheen Bibi
- Inayat Ullah
- Shiquan Niu
ArticleOpen Access13 Jan 2021 Scientific Reports
Antiviral activity of lambda-carrageenan against influenza viruses and severe acute respiratory syndrome coronavirus 2
- Yejin Jang
- Heegwon Shin
- Meehyein Kim
ArticleOpen Access12 Jan 2021 Scientific Reports
Nicotinamide mononucleotide production by fructophilic lactic acid bacteria
- Kazane Sugiyama
- Kana Iijima
- Nobuyuki Yoshida
ArticleOpen Access7 Apr 2021 Scientific Reports
Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects
- Lucas L. Maldonado
- Andrea Mendoza Bertelli
- Laura Kamenetzky
ArticleOpen Access18 Feb 2021 Scientific Reports

26-50

Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses
- Giuseppe Pezzotti
- Francesco Boschetto
- Osam Mazda
ArticleOpen Access3 Feb 2021 Scientific Reports
The meta-gut: community coalescence of animal gut and environmental microbiomes
- Christopher L. Dutton
- Amanda L. Subalusky
- David M. Post
ArticleOpen Access30 Nov 2021 Scientific Reports
Ingestion of probiotic (Lactobacillus helveticus and Bifidobacterium longum) alters intestinal microbial structure and behavioral expression following social defeat stress
- Katherine A. Partrick
- Anna M. Rosenhauer
- Kim L. Huhman
ArticleOpen Access12 Feb 2021 Scientific Reports
Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction
- Shan Wei
- Esther Kohl
- Zev Williams
ArticleOpen Access28 Jan 2021 Scientific Reports
Solar UV-B/A radiation is highly effective in inactivating SARS-CoV-2
- Fabrizio Nicastro
- Giorgia Sironi
- Mario Clerici
ArticleOpen Access20 Jul 2021 Scientific Reports
High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings
- Emmanuel Nji
- Joseph Kazibwe
- La Thi Quynh Lien
ArticleOpen Access9 Feb 2021 Scientific Reports
Pupal cannibalism by worker honey bees contributes to the spread of deformed wing virus
- Francisco Posada-Florez
- Zachary S. Lamas
- Eugene V. Ryabov
ArticleOpen Access26 Apr 2021 Scientific Reports
Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19
- Ilario De Toma
- Mara Dierssen
ArticleOpen Access21 Jan 2021 Scientific Reports
MRC5 cells engineered to express ACE2 serve as a model system for the discovery of antivirals targeting SARS-CoV-2
- Kentaro Uemura
- Michihito Sasaki
- Akihiko Sato
ArticleOpen Access8 Mar 2021 Scientific Reports
A descriptive analysis of antimicrobial resistance patterns of WHO priority pathogens isolated in children from a tertiary care hospital in India
- Vijayalaxmi V. Mogasale
- Prakash Saldanha
- Vittal Mogasale
ArticleOpen Access4 Mar 2021 Scientific Reports
Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe
- Jack M. Crook
- Ivana Murphy
- Diana Bell
ArticleOpen Access19 Jul 2021 Scientific Reports
Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples
- Mohammad Javad Gharavi
- Javad Zarei
- Niloufar Rashidi
ArticleOpen Access12 Jan 2021 Scientific Reports
A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation
- Tomohiro Kotaki
- Xuping Xie
- Masanori Kameoka
ArticleOpen Access26 Jan 2021 Scientific Reports
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities
- Denise M. O’Sullivan
- Ronan M. Doyle
- Jim F. Huggett
ArticleOpen Access19 May 2021 Scientific Reports
Microplastics accumulate fungal pathogens in terrestrial ecosystems
- Gerasimos Gkoutselis
- Stephan Rohrbach
- Gerhard Rambold
ArticleOpen Access15 Jul 2021 Scientific Reports
The lower respiratory tract microbiome of critically ill patients with COVID-19
- Paolo Gaibani
- Elisa Viciani
- Simone Ambretti
ArticleOpen Access12 May 2021 Scientific Reports
Functional profiling of COVID-19 respiratory tract microbiomes
- Niina Haiminen
- Filippo Utro
- Laxmi Parida
ArticleOpen Access19 Mar 2021 Scientific Reports
The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions
- Cristina Lazcano
- Eric Boyd
- Kelly Ivors
ArticleOpen Access4 Feb 2021 Scientific Reports
Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2
- Yajuan Dong
- Xiuming Wu
- Chiyu Zhang
ArticleOpen Access3 Feb 2021 Scientific Reports
Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing
- Ki Wook Kim
- Ira W. Deveson
- William D. Rawlinson
ArticleOpen Access16 Feb 2021 Scientific Reports
UVC disinfects SARS-CoV-2 by induction of viral genome damage without apparent effects on viral morphology and proteins
- Chieh-Wen Lo
- Ryosuke Matsuura
- Yoko Aida
ArticleOpen Access5 Jul 2021 Scientific Reports
Co-infection of SARS-CoV-2 and influenza virus causes more severe and prolonged pneumonia in hamsters
- Takaaki Kinoshita
- Kenichi Watanabe
- Jiro Yasuda
ArticleOpen Access28 Oct 2021 Scientific Reports
Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2
- Ewelina Weglarz-Tomczak
- Jakub M. Tomczak
- Stanley Brul
ArticleOpen Access11 Feb 2021 Scientific Reports
Neurotropic influenza A virus infection causes prion protein misfolding into infectious prions in neuroblastoma cells
- Hideyuki Hara
- Junji Chida
- Suehiro Sakaguchi
ArticleOpen Access12 May 2021 Scientific Reports
The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host
- Maria J. Soto-Giron
- Ji-Nu Kim
- Gerardo Toledo
ArticleOpen Access15 Dec 2021 Scientific Reports

51-75

Blockade of SARS-CoV-2 spike protein-mediated cell–cell fusion using COVID-19 convalescent plasma
- Ling Wang
- Juan Zhao
- Zhi Q. Yao
ArticleOpen Access10 Mar 2021 Scientific Reports
Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
- Santiago Justo Arevalo
- Daniela Zapata Sifuentes
- Roberto Pineda Chavarría
ArticleOpen Access7 Sep 2021 Scientific Reports
Lactobacillus reuteri AN417 cell-free culture supernatant as a novel antibacterial agent targeting oral pathogenic bacteria
- Kyung Mi Yang
- Ji-Sun Kim
- Kwang-Hak Bae
ArticleOpen Access15 Jan 2021 Scientific Reports
CRISPR-based transcriptional activation tool for silent genes in filamentous fungi
- László Mózsik
- Mirthe Hoekzema
- Arnold J. M. Driessen
ArticleOpen Access13 Jan 2021 Scientific Reports
An immortalized porcine macrophage cell line competent for the isolation of African swine fever virus
- Kentaro Masujin
- Tomoya Kitamura
- Takehiro Kokuho
ArticleOpen Access26 Feb 2021 Scientific Reports
The potential of COVID-19 patients’ sera to cause antibody-dependent enhancement of infection and IL-6 production
- Jun Shimizu
- Tadahiro Sasaki
- Tatsuo Shioda
ArticleOpen Access9 Dec 2021 Scientific Reports
Digital PCR for high sensitivity viral detection in false-negative SARS-CoV-2 patients
- Paolo Poggio
- Paola Songia
- Maurizio Pesce
ArticleOpen Access22 Feb 2021 Scientific Reports
Natural variants in SARS-CoV-2 Spike protein pinpoint structural and functional hotspots with implications for prophylaxis and therapeutic strategies
- Suman Pokhrel
- Benjamin R. Kraemer
- Daria Mochly-Rosen
ArticleOpen Access23 Jun 2021 Scientific Reports
Asymptomatic COVID-19 Adult Outpatients identified as Significant Viable SARS-CoV-2 Shedders
- Marie Glenet
- Anne-Laure Lebreil
- Laurent Andreoletti
ArticleOpen Access18 Oct 2021 Scientific Reports
Bacterial associations in the healthy human gut microbiome across populations
- Mark Loftus
- Sayf Al-Deen Hassouneh
- Shibu Yooseph
ArticleOpen Access2 Feb 2021 Scientific Reports
Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2
- Gowri Nayar
- Edward E. Seabolt
- James H. Kaufman
ArticleOpen Access26 Apr 2021 Scientific Reports
Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp
- Laxmi Sharma
- Ravinder Nagpal
- Prashant Singh
ArticleOpen Access8 Feb 2021 Scientific Reports
Emergence of novel SARS-CoV-2 variants in the Netherlands
- Aysun Urhan
- Thomas Abeel
ArticleOpen Access23 Mar 2021 Scientific Reports
Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients
- Eric C. Rouchka
- Julia H. Chariker
- Donghoon Chung
ArticleOpen Access3 Aug 2021 Scientific Reports
Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions
- S. J. Meale
- M. Popova
- D. P. Morgavi
ArticleOpen Access4 Feb 2021 Scientific Reports
The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds
- Kazunori Sawada
- Hitoshi Koyano
- Takuji Yamada
ArticleOpen Access19 Jan 2021 Scientific Reports
Response of bacterial and fungal communities to high petroleum pollution in different soils
- Polina Galitskaya
- Liliya Biktasheva
- Svetlana Selivanovskaya
ArticleOpen Access8 Jan 2021 Scientific Reports
A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification
- Xiaofang Jia
- Lvyin Hu
- Xiaonan Zhang
ArticleOpen Access23 Feb 2021 Scientific Reports
Sensitive detection and quantification of SARS-CoV-2 in saliva
- Mustafa Fatih Abasiyanik
- Blake Flood
- Evgeny Izumchenko
ArticleOpen Access14 Jun 2021 Scientific Reports
Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa
- Idowu B. Olawoye
- Jessica N. Uwanibe
- Christian T. Happi
ArticleOpen Access30 Aug 2021 Scientific Reports
The SARS-CoV-2 viral load in COVID-19 patients is lower on face mask filters than on nasopharyngeal swabs
- Agnieszka Smolinska
- David S. Jessop
- Marc P. van der Schee
ArticleOpen Access29 Jun 2021 Scientific Reports
Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage
- Josephine E. S. Strange
- Pimlapas Leekitcharoenphon
- Frank M. Aarestrup
ArticleOpen Access15 Jan 2021 Scientific Reports
Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19
- Graham J. Britton
- Alice Chen-Liaw
- Jeremiah J. Faith
ArticleOpen Access25 Jun 2021 Scientific Reports
Genomic evolution of antimicrobial resistance in Escherichia coli
- Pimlapas Leekitcharoenphon
- Markus Hans Kristofer Johansson
- Frank M. Aarestrup
ArticleOpen Access23 Jul 2021 Scientific Reports
Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii
- Varnesh Tiku
- Eric M. Kofoed
- Man-Wah Tan
ArticleOpen Access12 Jan 2021 Scientific Reports

76-100

Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors
- Fengju Chen
- Yiqun Zhang
- Chad J. Creighton
ArticleOpen Access28 Jan 2021 Scientific Reports
Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa
- Mojisola C. Hosu
- Sandeep D. Vasaikar
- Teke Apalata
ArticleOpen Access29 Mar 2021 Scientific Reports
Production of bacterial cellulose using Gluconacetobacter kombuchae immobilized on Luffa aegyptiaca support
- Sameeha Syed Abdul Rahman
- T. Vaishnavi
- Sugumaran Karuppiah
ArticleOpen Access3 Feb 2021 Scientific Reports
An efficient direct screening system for microorganisms that activate plant immune responses based on plant–microbe interactions using cultured plant cells
- Mari Kurokawa
- Masataka Nakano
- Toshiki Furuya
ArticleOpen Access1 Apr 2021 Scientific Reports
Glucose confers protection to Escherichia coli against contact killing by Vibrio cholerae
- Cristian V. Crisan
- Holly L. Nichols
- Brian K. Hammer
ArticleOpen Access3 Feb 2021 Scientific Reports
Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2
- Georgina I. López-Cortés
- Miryam Palacios-Pérez
- Marco V. José
ArticleOpen Access22 Sep 2021 Scientific Reports
Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19
- Martin A. Redhead
- C. David Owen
- Martin A. Walsh
ArticleOpen Access24 Jun 2021 Scientific Reports
Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
- Zachary S. Ladin
- Barbra Ferrell
- K. Eric Wommack
ArticleOpen Access15 Jan 2021 Scientific Reports
Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India
- J. Singh
- A. K. Yadav
- S. Singh
ArticleOpen Access10 Nov 2021 Scientific Reports
Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis
- Miguel Fernández-Niño
- María Juliana Rodríguez-Cubillos
- Andrés Fernando González Barrios
ArticleOpen Access21 Apr 2021 Scientific Reports
Isolation of viable Babesia bovis merozoites to study parasite invasion
- Hassan Hakimi
- Masahito Asada
- Shinichiro Kawazu
ArticleOpen Access20 Aug 2021 Scientific Reports
Incorporating human mobility data improves forecasts of Dengue fever in Thailand
- Mathew V. Kiang
- Mauricio Santillana
- Caroline O. Buckee
ArticleOpen Access13 Jan 2021 Scientific Reports
A rapid near-patient detection system for SARS-CoV-2 using saliva
- Noah B. Toppings
- Abu Naser Mohon
- Dylan R. Pillai
ArticleOpen Access28 Jun 2021 Scientific Reports
In vitro and in vivo inhibition of malaria parasite infection by monoclonal antibodies against Plasmodium falciparum circumsporozoite protein (CSP)
- Merricka C. Livingstone
- Alexis A. Bitzer
- Sheetij Dutta
ArticleOpen Access5 Mar 2021 Scientific Reports
Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences
- Juliana Carneiro Gomes
- Aras Ismael Masood
- Wellington Pinheiro dos Santos
ArticleOpen Access2 Jun 2021 Scientific Reports
Dysbiosis of gut microbiota in Polish patients with ulcerative colitis: a pilot study
- Oliwia Zakerska-Banaszak
- Hanna Tomczak
- Marzena Skrzypczak-Zielinska
ArticleOpen Access25 Jan 2021 Scientific Reports
Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations
- Jacquelyn Jones
- Stacey N Reinke
- Claus T. Christophersen
ArticleOpen Access7 Jul 2021 Scientific Reports
An ultra-portable, self-contained point-of-care nucleic acid amplification test for diagnosis of active COVID-19 infection
- Hao Deng
- Asanka Jayawardena
- Patrick Kwan
ArticleOpen Access26 Jul 2021 Scientific Reports
Oral hygiene and oral microbiota in children and young people with neurological impairment and oropharyngeal dysphagia
- Luiz Fernando Fregatto
- Isabela Bazzo Costa
- Paula Cristina Cola
ArticleOpen Access10 Sep 2021 Scientific Reports
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19
- Brian L. Le
- Gaia Andreoletti
- Marina Sirota
ArticleOpen Access10 Jun 2021 Scientific Reports
Importance of crop phenological stages for the efficient use of PGPR inoculants
- Alexandra Stoll
- Ricardo Salvatierra-Martínez
- Jaime Bravo
ArticleOpen Access1 Oct 2021 Scientific Reports
Isolation and screening of multifunctional phosphate solubilizing bacteria and its growth-promoting effect on Chinese fir seedlings
- Jiaqi Chen
- Guangyu Zhao
- Ruzhen Jiao
ArticleOpen Access27 Apr 2021 Scientific Reports
Persimmon-derived tannin has antiviral effects and reduces the severity of infection and transmission of SARS-CoV-2 in a Syrian hamster model
- Ryutaro Furukawa
- Masahiro Kitabatake
- Toshihiro Ito
ArticleOpen Access8 Dec 2021 Scientific Reports
Bacterial resistance to CRISPR-Cas antimicrobials
- Ruben V. Uribe
- Christin Rathmer
- Morten Otto Alexander Sommer
ArticleOpen Access26 Aug 2021 Scientific Reports
First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core
- Victoria I. Paun
- Paris Lavin
- Cristina Purcarea
ArticleOpen Access12 Jan 2021 Scientific Reports

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