Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection

Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome

(2022) Qin Liu et al.   GUT

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19

(2021) Yun Kit Yeoh et al.   GUT

6-month consequences of COVID-19 in patients discharged from hospital: a cohort study

(2021) Chaolin Huang et al.   LANCET

Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma

(2021) Jason Behary et al.   Nature Communications

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults

(2021) Rong Xu et al.   Communications Biology

Six-month follow-up of gut microbiota richness in patients with COVID-19

(2021) Yanfei Chen et al.   GUT

Post-acute COVID-19 syndrome

(2021) Ani Nalbandian et al.   NATURE MEDICINE

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

(2021) Tao Zuo et al.   Microbiome

SARS-CoV-2 cell tropism and multiorgan infection

(2021) Jia Liu et al.   Cell Discovery

Dynamics of the Upper Respiratory Tract Microbiota and its Association with Mortality in COVID-19

(2021) Lili Ren et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Recent advances in Clp protease modulation to address virulence, resistance and persistence of MRSA infection

(2021) Yuan Ju et al.   DRUG DISCOVERY TODAY

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

Long covid—mechanisms, risk factors, and management

(2021) Harry Crook et al.   BMJ-British Medical Journal

Is There a Connection Between Gut Microbiome Dysbiosis Occurring in COVID-19 Patients and Post-COVID-19 Symptoms?

(2021) Kai Hilpert et al.   Frontiers in Microbiology

Gut Microbiome Alterations in COVID-19

(2021) Tao Zuo et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization

(2021) Yongjian Wu et al.   npj Biofilms and Microbiomes

Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

(2020) Zijie Shen et al.   CLINICAL INFECTIOUS DISEASES

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

RNA sequencing by direct tagmentation of RNA/DNA hybrids

(2020) Lin Di et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

(2020) Furong Qi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

(2020) Carly G.K. Ziegler et al.   CELL

Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization

(2020) Tao Zuo et al.   GASTROENTEROLOGY

SARS‐CoV‐2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens

(2020) Liang Peng et al.   JOURNAL OF MEDICAL VIROLOGY

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

(2020) Waradon Sungnak et al.   NATURE MEDICINE

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings

(2020) Marcela França Dias et al.   WATER RESEARCH

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection

(2020) Xin Zou et al.   Frontiers of Medicine

Alterations of the Gut Microbiota in Patients With Coronavirus Disease 2019 or H1N1 Influenza

(2020) Silan Gu et al.   CLINICAL INFECTIOUS DISEASES

MINERVA: A Facile Strategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples

(2020) Chen Chen et al.   MOLECULAR CELL

Streptococcus gordonii: Pathogenesis and Host Response to Its Cell Wall Components

(2020) Ok-Jin Park et al.   Microorganisms

Bacterial and viral respiratory tract microbiota and host characteristics in children with lower respiratory tract infections: a matched case-control study

(2019) Wing Ho Man et al.   Lancet Respiratory Medicine

The role of short-chain fatty acids in microbiota–gut–brain communication

(2019) Boushra Dalile et al.   Nature Reviews Gastroenterology & Hepatology

PERFect: PERmutation Filtering test for microbiome data

(2018) Ekaterina Smirnova et al.   BIOSTATISTICS

Redirection of metabolism in response to fatty acid kinase in Staphylococcus aureus

(2018) Zachary R. DeMars et al.   JOURNAL OF BACTERIOLOGY

Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

(2018) Soner Yildiz et al.   Microbiome

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia

(2018) Shigeo Hanada et al.   Frontiers in Immunology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

The microbiota of the respiratory tract: gatekeeper to respiratory health

(2017) Wing Ho Man et al.   NATURE REVIEWS MICROBIOLOGY

Secondary Bacterial Infections Associated with Influenza Pandemics

(2017) Denise E. Morris et al.   Frontiers in Microbiology

Disordered oropharyngeal microbial communities in H7N9 patients with or without secondary bacterial lung infection

(2017) Hai-feng Lu et al.   Emerging Microbes & Infections

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Emerging pathogenic links between microbiota and the gut–lung axis

(2016) Kurtis F. Budden et al.   NATURE REVIEWS MICROBIOLOGY

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell–dependent inflammation

(2014) Jian Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Links between diet, gut microbiota composition and gut metabolism

(2014) Harry J. Flint et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

SatR Is a Repressor of Fluoroquinolone Efflux Pump SatAB

(2013) Jose Antonio Escudero et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Comparing thousands of circular genomes using the CGView Comparison Tool

(2012) Jason R Grant et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fluoroquinolone Efflux in Streptococcus suis Is Mediated by SatAB and Not by SmrA

(2011) Jose Antonio Escudero et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Spread of Pseudomonas fluorescens Due to Contaminated Drinking Water in a Bone Marrow Transplant Unit: Table 1.

(2011) Vanessa Wong et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Solution structure of GSP13 from Bacillus subtilis exhibits an S1 domain related to cold shock proteins

(2009) Wenyu Yu et al.   JOURNAL OF BIOMOLECULAR NMR

Halomonas, a Newly Recognized Human Pathogen Causing Infections and Contamination in a Dialysis Center

(2009) David A. Stevens et al.   MEDICINE

RseA, the SigE specific anti-sigma factor ofMycobacterium tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2 proteolysis

(2009) Subhasis Barik et al.   MOLECULAR MICROBIOLOGY