Integrated analysis of gut microbiome and host immune responses in COVID-19

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

(2021) Yun Kit Yeoh et al.   GUT

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

(2021) Yanfei Chen et al.   GUT

Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon

(2021) Atsuo Nakamura et al.   Nature Communications

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis

(2021) Charissa C. Naidoo et al.   EBioMedicine

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19

(2021) Yun Tan et al.   Cell Discovery

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

(2020) Tao Zuo et al.   GASTROENTEROLOGY

Viral and host factors related to the clinical outcome of COVID-19

(2020) Xiaonan Zhang et al.   NATURE

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

(2020) Silan Gu et al.   CLINICAL INFECTIOUS DISEASES

ALTERATIONS IN GUT MICROBIOME IN CIRRHOSIS AS ASSESSED BY QUANTITATIVE METAGENOMICS. RELATIONSHIP WITH ACUTE-ON-CHRONIC LIVER FAILURE AND PROGNOSIS

(2020) Cristina Solé et al.   GASTROENTEROLOGY

Gut microbial metabolites as multi-kingdom intermediates

(2020) Kimberly A. Krautkramer et al.   NATURE REVIEWS MICROBIOLOGY

Gut microbiota in human metabolic health and disease

(2020) Yong Fan et al.   NATURE REVIEWS MICROBIOLOGY

Polyamines and Kynurenines at the Intersection of Immune Modulation

(2020) Elisa Proietti et al.   TRENDS IN IMMUNOLOGY

Durability of neutralizing antibodies and T-cell response post SARS-CoV-2 infection

(2020) Yun Tan et al.   Frontiers of Medicine

Diagnosis of COVID-19 for controlling the pandemic: A review of the state-of-the-art

(2020) Nastaran Taleghani et al.   BIOSENSORS & BIOELECTRONICS

Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study

(2019) Clara Depommier et al.   NATURE MEDICINE

Regional Diversity of the Gastrointestinal Microbiome

(2019) Kristina Martinez-Guryn et al.   Cell Host & Microbe

Distribution of Ebp pili among clinical and fecal isolates of Enterococcus faecalis and evaluation for human platelet activation

(2018) Roya Ahmadrajabi et al.   APMIS

The gut microbiome in atherosclerotic cardiovascular disease

(2017) Zhuye Jie et al.   Nature Communications

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Activation of NAD(P)H Oxidase by Tryptophan-Derived 3-Hydroxykynurenine Accelerates Endothelial Apoptosis and Dysfunction In Vivo

(2013) Qiongxin Wang et al.   CIRCULATION RESEARCH

Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity

(2012) Michael C. Abt et al.   IMMUNITY

Priming of Natural Killer Cells by Nonmucosal Mononuclear Phagocytes Requires Instructive Signals from Commensal Microbiota

(2012) Stephanie C. Ganal et al.   IMMUNITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Clinical isolates of Enterococcus faecalis aggregate human platelets

(2010) Magnus Rasmussen et al.   MICROBES AND INFECTION

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS