Quantitative microbiome profiling links gut community variation to microbial load

Water activity does not shape the microbiota in the human colon

(2017) Doris Vandeputte et al.   GUT

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD

(2016) João Sabino et al.   GUT

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines

(2016) Mireia Valles-Colomer et al.   Journal of Crohns & Colitis

Flow cytometry analysis of the microbiota associated with the midguts of vector mosquitoes

(2016) Tibebu Habtewold et al.   Parasites & Vectors

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Brief Report:Dialisteras a Microbial Marker of Disease Activity in Spondyloarthritis

(2016) Raul Y. Tito et al.   Arthritis & Rheumatology

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

(2016) Frank Stämmler et al.   Microbiome

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

Gut microbiota composition associated with stool consistency

(2015) E F Tigchelaar et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

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

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

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

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular Studies Neglect Apparently Gram-Negative Populations in the Human Gut Microbiota

(2013) P. Hugon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method

(2013) E.I. Prest et al.   WATER RESEARCH

Crohn's Disease Patients Have More IgG-Binding Fecal Bacteria than Controls

(2012) Hermie J. M. Harmsen et al.   Clinical and Vaccine Immunology

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Identification of Pathogen and Host-Response Markers Correlated With Periodontal Disease

(2009) Christoph A. Ramseier et al.   JOURNAL OF PERIODONTOLOGY

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

(2008) Cindy J. Smith et al.   FEMS MICROBIOLOGY ECOLOGY

Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes

(2007) Frederik Hammes et al.   WATER RESEARCH