Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota

(2018) Carolina Tropini et al.   CELL

Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

(2018) Łukasz Krych et al.   JOURNAL OF MICROBIOLOGICAL METHODS

In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing—A Proof-of-Principle Study

(2018) Elena Herrmann et al.   Nutrients

Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS)

(2018) Sophie A. Poeker et al.   Scientific Reports

Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue

(2018) Yu Tahara et al.   Scientific Reports

Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

(2017) Leyuan Li et al.   JOURNAL OF PROTEOME RESEARCH

Dietary capsaicin and antibiotics act synergistically to reduce non-alcoholic fatty liver disease induced by high fat diet in mice

(2017) Jingjuan Hu et al.   Oncotarget

Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing

(2017) Elena Herrmann et al.   Frontiers in Microbiology

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

Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants

(2017) Van T. Pham et al.   Scientific Reports

Production of Butyrate from Lactate by a Newly Isolated Clostridium sp. BPY5

(2016) Yong Tao et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Microbiota-Produced Succinate Improves Glucose Homeostasis via Intestinal Gluconeogenesis

(2016) Filipe De Vadder et al.   Cell Metabolism

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

The mouse gut microbiome revisited: From complex diversity to model ecosystems

(2016) Thomas Clavel et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities

(2016) Philipp Rausch et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

(2016) Kimberly A. Krautkramer et al.   MOLECULAR CELL

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

(2016) Sandrine Brugiroux 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

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

Integrated multi-scale strategies to investigate nutritional compounds and their effect on the gut microbiota

(2015) Christophe Lacroix et al.   CURRENT OPINION IN BIOTECHNOLOGY

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model

(2015) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A catalog of the mouse gut metagenome

(2015) Liang Xiao et al.   NATURE BIOTECHNOLOGY

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon

(2015) Sophie Fehlbaum et al.   PLoS One

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro

(2015) A. Dostal et al.   mBio

Entrainment of mouse peripheral circadian clocks to

(2015) Yutaro Hamaguchi et al.   Scientific Reports

Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

(2015) Jacob Bak Holm et al.   PLoS One

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

(2014) Amir Zarrinpar et al.   Cell Metabolism

SynbioticLactobacillus acidophilusNCFM and cellobiose does not affect human gut bacterial diversity but increases abundance of lactobacilli, bifidobacteria and branched-chain fatty acids: a randomized, double-blinded cross-over trial

(2014) Gabriella C. van Zanten et al.   FEMS MICROBIOLOGY ECOLOGY

Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity

(2014) Amandine Everard et al.   ISME Journal

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

Commercially available avian and mammalian whole prey diet items targeted for consumption by managed exotic and domestic pet felines: Macronutrient, mineral, and long-chain fatty acid composition

(2014) Katherine R. Kerr et al.   ZOO BIOLOGY

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Linking the gut microbiota to human health

(2013) Virginia Robles Alonso et al.   BRITISH JOURNAL OF NUTRITION

Carbohydrates and the human gut microbiota

(2013) Christophe Chassard et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Three-stage continuous culture system with a self-generated anaerobia to study the regionalized metabolism of the human gut microbiota

(2013) David Feria-Gervasio et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Re-print of “Intestinal luminal nitrogen metabolism: Role of the gut microbiota and consequences for the host”

(2013) Anne-Marie Davila et al.   PHARMACOLOGICAL RESEARCH

Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

(2013) Annina Zihler Berner et al.   PLoS One

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

Gut Microbiota Composition Is Correlated to Grid Floor Induced Stress and Behavior in the BALB/c Mouse

(2012) Katja Maria Bangsgaard Bendtsen et al.   PLoS One

The blessings and curses of C57BL/6 substrains in mouse genetic studies

(2011) Camron D. Bryant   Annals of the New York Academy of Sciences

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Starch Characteristics and Their Influences onIn Vitroand Pig Prececal Starch Digestion

(2011) Tzu-Tai Lee et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Advances and perspectives in in vitro human gut fermentation modeling

(2011) Amanda N. Payne et al.   TRENDS IN BIOTECHNOLOGY

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

Family relationship of female breeders reduce the systematic inter-individual variation in the gut microbiota of inbred laboratory mice

(2010) M R Hufeldt et al.   LABORATORY ANIMALS

Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

(2010) M. Rajilic-Stojanovic et al.   MICROBIOLOGY-SGM

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic background determines metabolic phenotypes in the mouse

(2008) Marie-France Champy et al.   MAMMALIAN GENOME