Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro

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

(2020) Ching Jian et al.   PLoS One

Dynamics of Human Gut Microbiota and Short-Chain Fatty Acids in Response to Dietary Interventions with Three Fermentable Fibers

(2019) Nielson T. Baxter et al.   mBio

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

In vitro fermentation properties of pectins and enzymatic-modified pectins obtained from different renewable bioresources

(2018) Alvaro Ferreira-Lazarte et al.   CARBOHYDRATE POLYMERS

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Prevotella rara sp. nov., isolated from human faeces

(2018) Boris A. Efimov et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Phascolarctobacterium faecium abundant colonization in human gastrointestinal tract

(2017) Feifan Wu et al.   Experimental and Therapeutic Medicine

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

(2017) Ana S. Luis et al.   Nature Microbiology

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

In vitro fermentation of 12 dietary fibres by faecal inoculum from pigs and humans

(2012) Melliana C. Jonathan et al.   FOOD CHEMISTRY

Bacteria, Colonic Fermentation, and Gastrointestinal Health

(2012) George T. Macfarlane et al.   JOURNAL OF AOAC INTERNATIONAL

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

(2012) Justin M. Zook et al.   PLoS One

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

In Vitro Fermentation of Bacterial Cellulose Composites as Model Dietary Fibers

(2011) Deirdre Mikkelsen et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT