Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer

(2020) Farnaz Fouladi et al.   ISME Journal

Candida albicans Morphogenesis Programs Control the Balance between Gut Commensalism and Invasive Infection

(2019) Jessica N. Witchley et al.   Cell Host & Microbe

Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans

(2019) Jack Guinan et al.   Scientific Reports

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

(2019) Berk Aykut et al.   NATURE

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Secondary bile acids inhibit Candida albicans growth and morphogenesis

(2018) Jack Guinan et al.   Pathogens and Disease

Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome

(2018) Kang Kang et al.   Cell Reports

Enterobacteriaceae are essential for the modulation of colitis severity by fungi

(2018) Bruno Sovran et al.   Microbiome

Response to Fungal Dysbiosis by Gut-Resident CX3CR1+ Mononuclear Phagocytes Aggravates Allergic Airway Disease

(2018) Xin Li et al.   Cell Host & Microbe

Exploring the Gut Fungi-Lung Allergy Axis

(2018) Akira Shibuya et al.   Cell Host & Microbe

Species-level functional profiling of metagenomes and metatranscriptomes

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

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

(2018) Helle Krogh Pedersen et al.   Nature Protocols

High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage

(2018) Akintunde Emiola et al.   Nature Communications

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Roseburia spp.: a marker of health?

(2017) Zohreh Tamanai-Shacoori et al.   Future Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Gas chromatography – mass spectrometry data processing made easy

(2017) Lea G. Johnsen et al.   JOURNAL OF CHROMATOGRAPHY A

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Strain profiling and epidemiology of bacterial species from metagenomic sequencing

(2017) Davide Albanese et al.   Nature Communications

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning

(2017) Christopher Staley et al.   Microbiome

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

Comparative genomics of Clostridium bolteae and Clostridium clostridioforme reveals species-specific genomic properties and numerous putative antibiotic resistance determinants

(2016) Pierre Dehoux et al.   BMC GENOMICS

Immunological Consequences of Intestinal Fungal Dysbiosis

(2016) Matthew L. Wheeler et al.   Cell Host & Microbe

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

(2016) Li Zhang et al.   ISME Journal

Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota

(2016) Albert Palleja et al.   Genome Medicine

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

(2016) Henrik M. Roager et al.   Nature Microbiology

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

The initial state of the human gut microbiome determines its reshaping by antibiotics

(2015) Frédéric Raymond et al.   ISME Journal

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

(2015) Samuel C. Forster et al.   NUCLEIC ACIDS RESEARCH

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

(2015) Hyun S. Gweon et al.   Methods in Ecology and Evolution

Editorial: the changing faces of glutathione, a cellular protagonist

(2015) Alfonso Pompella et al.   Frontiers in Pharmacology

Gut Dysbiosis Promotes M2 Macrophage Polarization and Allergic Airway Inflammation via Fungi-Induced PGE2

(2014) Yun-Gi Kim et al.   Cell Host & Microbe

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment

(2013) Serena Dollive et al.   PLoS One

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Gut microbiome composition is linked to whole grain-induced immunological improvements

(2012) Inés Martínez et al.   ISME Journal

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

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy

(2011) Yuanqing Chao et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Interplay between the Gastric Bacterial Microbiota and Candida albicans during Postantibiotic Recolonization and Gastritis

(2011) Katie L. Mason et al.   INFECTION AND IMMUNITY

Sodium butyrate inhibits pathogenic yeast growth and enhances the functions of macrophages

(2011) L. N. Nguyen et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Blocking of Candida albicans biofilm formation by cis-2-dodecenoic acid and trans-2-dodecenoic acid

(2011) Y. Zhang et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

(2011) P. Frey-Klett et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

DBETH: A Database of Bacterial Exotoxins for Human

(2011) Abhijit Chakraborty et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Medically important bacterial–fungal interactions

(2010) Anton Y. Peleg et al.   NATURE REVIEWS MICROBIOLOGY

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY