Omics in gut microbiome analysis

Infection trains the host for microbiota-enhanced resistance to pathogens

(2021) Apollo Stacy et al.   CELL

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

(2021) Ceylan Tanes et al.   Cell Host & Microbe

Longitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance

(2021) Hyun Sik Kim et al.   Nature Communications

Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages

(2021) Tae Woong Whon et al.   mSystems

DeepMicro: deep representation learning for disease prediction based on microbiome data

(2020) Min Oh et al.   Scientific Reports

High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease

(2020) Jee-Yon Lee et al.   Cell Host & Microbe

Mucosal or systemic microbiota exposures shape the B cell repertoire

(2020) Hai Li et al.   NATURE

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Gut microbiome, big data and machine learning to promote precision medicine for cancer

(2020) Giovanni Cammarota et al.   Nature Reviews Gastroenterology & Hepatology

The human gut archaeome: identification of diverse haloarchaea in Korean subjects

(2020) Joon Yong Kim et al.   Microbiome

Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

(2020) Frederic D. Bushman et al.   Cell Host & Microbe

The Nubeam reference-free approach to analyze metagenomic sequencing reads

(2020) Hang Dai et al.   GENOME RESEARCH

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function

(2020) Lior Lobel et al.   SCIENCE

Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD

(2020) Giljae Lee et al.   Nature Communications

Gut Microbiome Contributes to Liver Fibrosis Impact on T Cell Receptor Immune Repertoire

(2020) Qing Liang et al.   Frontiers in Microbiology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Human gut microbiome: hopes, threats and promises

(2018) Patrice D Cani   GUT

Lysogeny is prevalent and widely distributed in the murine gut microbiota

(2018) Min-Soo Kim et al.   ISME Journal

Microbial symbionts regulate the primary Ig repertoire

(2018) Yuezhou Chen et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier

(2018) Eric C. Martens et al.   NATURE REVIEWS MICROBIOLOGY

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography

(2018) Mélanie Deschasaux et al.   NATURE MEDICINE

Species-level functional profiling of metagenomes and metatranscriptomes

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

Ménage à trois in the human gut: interactions between host, bacteria and phages

(2017) Mohammadali Khan Mirzaei et al.   NATURE REVIEWS MICROBIOLOGY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro

(2017) James W. Marsh et al.   Frontiers in Microbiology

Droplet digital PCR quantifies host inflammatory transcripts in feces reliably and reproducibly

(2016) Jennifer Stauber et al.   CELLULAR IMMUNOLOGY

Lytic to temperate switching of viral communities

(2016) B. Knowles et al.   NATURE

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology

(2016) Sarah K. Hilton et al.   Frontiers in Microbiology

The vocabulary of microbiome research: a proposal

(2015) Julian R. Marchesi et al.   Microbiome

Insect Gut Bacterial Diversity Determined by Environmental Habitat, Diet, Developmental Stage, and Phylogeny of Host

(2014) Ji-Hyun Yun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Epithelial Cell Shedding and Barrier Function

(2014) J. M. Williams et al.   VETERINARY PATHOLOGY

An increase in theAkkermansiaspp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice

(2013) Na-Ri Shin et al.   GUT

Transcriptomic fingerprinting ofPseudomonas putidaunder alternative physiological regimes

(2013) Juhyun Kim et al.   Environmental Microbiology Reports

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Phage–bacteria infection networks

(2012) Joshua S. Weitz et al.   TRENDS IN MICROBIOLOGY

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY