Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

Colorectal Cancer—Recent Advances and Future Challenges

(2020) John Inadomi et al.   GASTROENTEROLOGY

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth

(2020) Elena Zagato et al.   Nature Microbiology

Interaction between microbiota and immunity in health and disease

(2020) Danping Zheng et al.   CELL RESEARCH

Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer

(2020) Clélia Coutzac et al.   Nature Communications

MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics

(2020) Zhiqiang Pang et al.   Metabolites

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

(2019) Takeshi Tanoue et al.   NATURE

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Tumor mutation burden: from comprehensive mutational screening to the clinic

(2019) Francesca Galuppini et al.   Cancer Cell International

Intestinal microbiota and colorectal cancer: changes in the intestinal microenvironment and their relation to the disease

(2019) Sandra Aparecida dos Reis et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Commensal microbiota drive the functional diversification of colon macrophages

(2019) Byunghyun Kang et al.   Mucosal Immunology

Intestinal microbiota and colorectal carcinoma: Implications for pathogenesis, diagnosis, and therapy

(2019) Ana Montalban-Arques et al.   EBioMedicine

Tumor Mutational Burden and Efficacy of Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis

(2019) Jong Yeob Kim et al.   Cancers

Gut microbiome–mediated bile acid metabolism regulates liver cancer via NKT cells

(2018) Chi Ma et al.   SCIENCE

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

(2018) Vyara Matson et al.   SCIENCE

Mutation load estimation model as a predictor of the response to cancer immunotherapy

(2018) Guan-Yi Lyu et al.   npj Genomic Medicine

Host-Microbiota Interactions Shape Local and Systemic Inflammatory Diseases

(2017) John B. Grigg et al.   JOURNAL OF IMMUNOLOGY

Nivolumab in patients with metastatic DNA mismatch repair-deficient or microsatellite instability-high colorectal cancer (CheckMate 142): an open-label, multicentre, phase 2 study

(2017) Michael J Overman et al.   LANCET ONCOLOGY

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

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

(2017) Claire Duvallet et al.   Nature Communications

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

(2017) Marius Vital et al.   mSystems

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Correction: Diversity of Intestinal Clostridium coccoides Group in the Japanese Population, as Demonstrated by Reverse Transcription-Quantitative PCR

(2016) Takashi Kurakawa et al.   PLoS One

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Species–function relationships shape ecological properties of the human gut microbiome

(2016) Sara Vieira-Silva et al.   Nature Microbiology

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing

(2016) Emily Vogtmann et al.   PLoS One

Lowering of Large Bowel Butyrate Levels in Healthy Populations Is Unlikely to Be Beneficial

(2015) Michael A Conlon et al.   JOURNAL OF NUTRITION

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Complete genome sequence of a novel human papillomavirus identified by metagenomic analysis from a child with diarrhea in China

(2014) Jie-mei Yu et al.   ARCHIVES OF VIROLOGY

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

(2014) Manon D. Schulz et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976

(2012) Emma Allen-Vercoe et al.   ANAEROBE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

(2012) Weiguang Chen et al.   PLoS One

High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

(2011) Tobias Fuhrer et al.   ANALYTICAL CHEMISTRY

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers

(2011) Tingting Wang et al.   ISME Journal

Improvement of phylum- and class-specific primers for real-time PCR quantification of bacterial taxa

(2011) Tristano Bacchetti De Gregoris et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Lifestyle as risk factor for cancer: Evidence from human studies

(2010) Naghma Khan et al.   CANCER LETTERS

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

(2010) Nadja Larsen et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii

(2008) Carlett Ramirez-Farias et al.   BRITISH JOURNAL OF NUTRITION