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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.

The in-vitro effect of famotidine on SARS-CoV-2 proteases and virus replication

• Madeline Loffredo
• Hector Lucero
• Ali H. Munawar

In vitro efficacy of artemisinin-based treatments against SARS-CoV-2

• Yuyong Zhou
• Kerry Gilmore
• Peter H. Seeberger

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

The effectiveness of various gargle formulations and salt water against SARS-CoV-2

• Vunjia Tiong
• Pouya Hassandarvish
• Ilina Isahak

The serotonin reuptake inhibitor Fluoxetine inhibits SARS-CoV-2 in human lung tissue

• Melissa Zimniak
• Luisa Kirschner
• Jochen Bodem

Probenecid inhibits SARS-CoV-2 replication in vivo and in vitro

• Jackelyn Murray
• Robert J. Hogan
• Ralph A. Tripp

UV-C irradiation is highly effective in inactivating SARS-CoV-2 replication

• Mara Biasin
• Andrea Bianco
• Mario Clerici

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

Epidemiology and outcomes of COVID-19 in HIV-infected individuals: a systematic review and meta-analysis

• Paddy Ssentongo
• Emily S. Heilbrunn

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

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

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures

• Michael Laue
• Anne Kauter
• Andreas Nitsche

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

The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet

• Adriel Latorre-Pérez
• Marta Hernández
• Luis Collado

In vitro inactivation of SARS-CoV-2 by commonly used disinfection products and methods

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

A novel highly quantitative and reproducible assay for the detection of anti-SARS-CoV-2 IgG and IgM antibodies

• Kouki Matsuda
• Akinobu Hamada

Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load

• Mateus Nóbrega Aoki
• Bruna de Oliveira Coelho
• Lucas Blanes

Field-deployable, rapid diagnostic testing of saliva for SARS-CoV-2

• Hemant Suryawanshi
• Zev Williams

No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor

• Jarrod Shilts
• Thomas W. M. Crozier
• Gavin J. Wright

Carvacrol exhibits rapid bactericidal activity against Streptococcus pyogenes through cell membrane damage

• Niluni M. Wijesundara
• Song F. Lee
• H. P. Vasantha Rupasinghe

In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology

• Shaheen Bibi
• Inayat Ullah
• Shiquan Niu

Antiviral activity of lambda-carrageenan against influenza viruses and severe acute respiratory syndrome coronavirus 2

• Heegwon Shin
• Meehyein Kim

Nicotinamide mononucleotide production by fructophilic lactic acid bacteria

• Kazane Sugiyama
• Kana Iijima
• Nobuyuki Yoshida

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

Silicon nitride: a potent solid-state bioceramic inactivator of ssRNA viruses

• Giuseppe Pezzotti
• Francesco Boschetto

The meta-gut: community coalescence of animal gut and environmental microbiomes

• Christopher L. Dutton
• Amanda L. Subalusky
• David M. Post

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

Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

• Esther Kohl

Solar UV-B/A radiation is highly effective in inactivating SARS-CoV-2

• Fabrizio Nicastro
• Giorgia Sironi

High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings

• Emmanuel Nji
• Joseph Kazibwe
• La Thi Quynh Lien

Pupal cannibalism by worker honey bees contributes to the spread of deformed wing virus

• Francisco Posada-Florez
• Zachary S. Lamas
• Eugene V. Ryabov

Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19

• Ilario De Toma
• Mara Dierssen

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

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

Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe

• Jack M. Crook
• Ivana Murphy

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

A PCR amplicon-based SARS-CoV-2 replicon for antiviral evaluation

• Tomohiro Kotaki
• Masanori Kameoka

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

Microplastics accumulate fungal pathogens in terrestrial ecosystems

• Gerasimos Gkoutselis
• Stephan Rohrbach
• Gerhard Rambold

The lower respiratory tract microbiome of critically ill patients with COVID-19

• Paolo Gaibani
• Elisa Viciani
• Simone Ambretti

Functional profiling of COVID-19 respiratory tract microbiomes

• Niina Haiminen
• Filippo Utro
• Laxmi Parida

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

• Cristina Lazcano
• Kelly Ivors

Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2

• Yajuan Dong
• Chiyu Zhang

Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing

• Ki Wook Kim
• Ira W. Deveson
• William D. Rawlinson

UVC disinfects SARS-CoV-2 by induction of viral genome damage without apparent effects on viral morphology and proteins

• Chieh-Wen Lo
• Ryosuke Matsuura

Co-infection of SARS-CoV-2 and influenza virus causes more severe and prolonged pneumonia in hamsters

• Takaaki Kinoshita
• Kenichi Watanabe
• Jiro Yasuda

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

Neurotropic influenza A virus infection causes prion protein misfolding into infectious prions in neuroblastoma cells

• Hideyuki Hara
• Junji Chida
• Suehiro Sakaguchi

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host

• Maria J. Soto-Giron
• Gerardo Toledo

Blockade of SARS-CoV-2 spike protein-mediated cell–cell fusion using COVID-19 convalescent plasma

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

Lactobacillus reuteri AN417 cell-free culture supernatant as a novel antibacterial agent targeting oral pathogenic bacteria

• Kyung Mi Yang
• Kwang-Hak Bae

CRISPR-based transcriptional activation tool for silent genes in filamentous fungi

• László Mózsik
• Mirthe Hoekzema
• Arnold J. M. Driessen

An immortalized porcine macrophage cell line competent for the isolation of African swine fever virus

• Kentaro Masujin
• Tomoya Kitamura
• Takehiro Kokuho

The potential of COVID-19 patients’ sera to cause antibody-dependent enhancement of infection and IL-6 production

• Jun Shimizu
• Tadahiro Sasaki
• Tatsuo Shioda

Digital PCR for high sensitivity viral detection in false-negative SARS-CoV-2 patients

• Paolo Poggio
• Paola Songia
• Maurizio Pesce

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

Asymptomatic COVID-19 Adult Outpatients identified as Significant Viable SARS-CoV-2 Shedders

• Marie Glenet
• Anne-Laure Lebreil
• Laurent Andreoletti

Bacterial associations in the healthy human gut microbiome across populations

• Mark Loftus
• Sayf Al-Deen Hassouneh
• Shibu Yooseph

Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2

• Gowri Nayar
• Edward E. Seabolt
• James H. Kaufman

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

Emergence of novel SARS-CoV-2 variants in the Netherlands

• Aysun Urhan
• Thomas Abeel

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

Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions

• S. J. Meale
• D. P. Morgavi

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

Response of bacterial and fungal communities to high petroleum pollution in different soils

• Polina Galitskaya
• Liliya Biktasheva
• Svetlana Selivanovskaya

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

• Xiaofang Jia
• Xiaonan Zhang

Sensitive detection and quantification of SARS-CoV-2 in saliva

• Mustafa Fatih Abasiyanik
• Blake Flood
• Evgeny Izumchenko

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

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

Metagenomics analysis of bacteriophages and antimicrobial resistance from global urban sewage

• Josephine E. S. Strange
• Pimlapas Leekitcharoenphon
• Frank M. Aarestrup

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

Genomic evolution of antimicrobial resistance in Escherichia coli

• Markus Hans Kristofer Johansson

Outer membrane vesicles containing OmpA induce mitochondrial fragmentation to promote pathogenesis of Acinetobacter baumannii

• Varnesh Tiku
• Eric M. Kofoed
• Man-Wah Tan

Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors

• Fengju Chen
• Yiqun Zhang
• Chad J. Creighton

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

Production of bacterial cellulose using Gluconacetobacter kombuchae immobilized on Luffa aegyptiaca support

• Sameeha Syed Abdul Rahman
• T. Vaishnavi
• Sugumaran Karuppiah

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

Glucose confers protection to Escherichia coli against contact killing by Vibrio cholerae

• Cristian V. Crisan
• Holly L. Nichols
• Brian K. Hammer

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

Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19

• Martin A. Redhead
• C. David Owen
• Martin A. Walsh

Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems

• Zachary S. Ladin
• Barbra Ferrell
• K. Eric Wommack

Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

• A. K. Yadav

Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis

• Miguel Fernández-Niño
• María Juliana Rodríguez-Cubillos
• Andrés Fernando González Barrios

Isolation of viable Babesia bovis merozoites to study parasite invasion

• Hassan Hakimi
• Masahito Asada
• Shinichiro Kawazu

Incorporating human mobility data improves forecasts of Dengue fever in Thailand

• Mathew V. Kiang
• Mauricio Santillana
• Caroline O. Buckee

A rapid near-patient detection system for SARS-CoV-2 using saliva

• Noah B. Toppings
• Abu Naser Mohon
• Dylan R. Pillai

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

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

Dysbiosis of gut microbiota in Polish patients with ulcerative colitis: a pilot study

• Oliwia Zakerska-Banaszak
• Hanna Tomczak
• Marzena Skrzypczak-Zielinska

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

An ultra-portable, self-contained point-of-care nucleic acid amplification test for diagnosis of active COVID-19 infection

• Asanka Jayawardena
• Patrick Kwan

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

Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19

• Brian L. Le
• Gaia Andreoletti
• Marina Sirota

Importance of crop phenological stages for the efficient use of PGPR inoculants

• Alexandra Stoll
• Ricardo Salvatierra-Martínez
• Jaime Bravo

Isolation and screening of multifunctional phosphate solubilizing bacteria and its growth-promoting effect on Chinese fir seedlings

• Guangyu Zhao
• Ruzhen Jiao

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

Bacterial resistance to CRISPR-Cas antimicrobials

• Ruben V. Uribe
• Christin Rathmer
• Morten Otto Alexander Sommer

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

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