Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties

Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria

(2022) Sudarshan A. Shetty et al.   npj Biofilms and Microbiomes

Blue poo: impact of gut transit time on the gut microbiome using a novel marker

(2021) Francesco Asnicar et al.   GUT

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

(2021) Doris Vandeputte et al.   Nature Communications

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

(2020) Ching Jian et al.   PLoS One

Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use

(2020) Jannike Lea Krause et al.   Gut Microbes

Macroecological dynamics of gut microbiota

(2020) Brian W. Ji et al.   Nature Microbiology

Vitamin Biosynthesis by Human Gut Butyrate-Producing Bacteria and Cross-Feeding in Synthetic Microbial Communities

(2020) Eva C. Soto-Martin et al.   mBio

Unravelling lactate‐acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics

(2020) Sudarshan A. Shetty et al.   ENVIRONMENTAL MICROBIOLOGY

Colonization of the human gut by bovine bacteria present in Parmesan cheese

(2019) Christian Milani et al.   Nature Communications

The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

(2019) Janneke Elzinga et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Community ecology as a framework for human microbiome research

(2019) Jack A. Gilbert et al.   NATURE MEDICINE

Extensive transmission of microbes along the gastrointestinal tract

(2019) Thomas SB Schmidt et al.   eLife

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans

(2019) Abigail J. Johnson et al.   Cell Host & Microbe

Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem

(2019) Racha El Hage et al.   Frontiers in Microbiology

Reconstructing functional networks in the human intestinal tract using synthetic microbiomes

(2019) Sudarshan A Shetty et al.   CURRENT OPINION IN BIOTECHNOLOGY

Drivers of human gut microbial community assembly: coadaptation, determinism and stochasticity

(2019) Kaitlyn Oliphant et al.   ISME Journal

Mutual Metabolic Interactions in Co-cultures of the Intestinal Anaerostipes rhamnosivorans With an Acetogen, Methanogen, or Pectin-Degrader Affecting Butyrate Production

(2019) Thi Phuong Nam Bui et al.   Frontiers in Microbiology

A conceptual framework for the phylogenetically constrained assembly of microbial communities

(2019) Daniel Aguirre de Cárcer   Microbiome

Evidence for a multi-level trophic organization of the human gut microbiome

(2019) Tong Wang et al.   PLoS Computational Biology

The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors

(2019) Stephanie Serena Schäpe et al.   Microorganisms

SAMSA2: a standalone metatranscriptome analysis pipeline

(2018) Samuel T. Westreich et al.   BMC BIOINFORMATICS

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses

(2018) Deepak Kumaresan et al.   Microbiome

Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut

(2018) Maria Louise Leth et al.   Nature Microbiology

Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal

(2018) Sean M. Kearney et al.   Cell Reports

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

(2018) Kevin D'hoe et al.   eLife

Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates

(2018) Emmanuelle H. Crost et al.   Frontiers in Microbiology

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts

(2018) Justin D. Silverman et al.   Microbiome

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The evolution of the host microbiome as an ecosystem on a leash

(2017) Kevin R. Foster et al.   NATURE

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts

(2017) Clara Belzer et al.   mBio

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

(2017) William Tottey et al.   Journal of Neurogastroenterology and Motility

Health and Disease Imprinted in the Time Variability of the Human Microbiome

(2017) Jose Manuel Martí et al.   mSystems

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

(2017) Marius Vital et al.   mSystems

Modulation of the human gut microbiota by dietary fibres occurs at the species level

(2016) Wing Sun Faith Chung et al.   BMC BIOLOGY

Locating rearrangement events in a phylogeny based on highly fragmented assemblies

(2016) Chunfang Zheng et al.   BMC GENOMICS

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid

(2016) Sylvia H. Duncan et al.   ENVIRONMENTAL MICROBIOLOGY

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

Structural dissection of a complexBacteroides ovatusgene locus conferring xyloglucan metabolism in the human gut

(2016) Glyn R. Hemsworth et al.   Open Biology

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

(2016) Christina Engels et al.   Frontiers in Microbiology

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

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

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

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

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

Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides

(2015) Audrey Rivière et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities

(2015) Cyrus A. Mallon et al.   ECOLOGY

Towards biome-specific analysis of meta-omics data

(2015) Youssef Darzi et al.   ISME Journal

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Synthetic microbial communities

(2014) Tobias Großkopf et al.   CURRENT OPINION IN MICROBIOLOGY

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

(2014) Nicole Reichardt et al.   ISME Journal

Molecular details of a starch utilization pathway in the human gut symbiontEubacterium rectale

(2014) Darrell W. Cockburn et al.   MOLECULAR MICROBIOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

In Vitro Continuous Fermentation Model (PolyFermS) of the Swine Proximal Colon for Simultaneous Testing on the Same Gut Microbiota

(2014) Sabine A. Tanner et al.   PLoS One

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids

(2014) S. Lukovac et al.   mBio

Timing is everything: priority effects alter community invasibility after disturbance

(2014) Celia C. Symons et al.   Ecology and Evolution

Experimental models of the gut microbiome

(2013) Koen Venema et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

(2013) Karen De Roy et al.   ENVIRONMENTAL MICROBIOLOGY

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

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

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

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

Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX

(2010) P. Van den Abbeele et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Coculture Fermentations of Bifidobacterium Species and Bacteroides thetaiotaomicron Reveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans

(2009) G. Falony et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

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

Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an Opinion

(2008) S. H. Duncan et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces

(2008) C. Liu et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY