The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Structural and Spectroscopic Characterization of Iron(II), Cobalt(II), and Nickel(II) ortho-Dihalophenolate Complexes: Insights into Metal–Halogen Secondary Bonding

(2014) Timothy E. Machonkin et al.   INORGANIC CHEMISTRY

Diet, the human gut microbiota, and IBD

(2013) Gary D. Wu et al.   ANAEROBE

Emerging infectious colitis

(2013) Nejma Aboutaleb et al.   CURRENT OPINION IN GASTROENTEROLOGY

Characterization of lactic acid bacteria isolated from artisanal Travnik young cheeses, sweet creams and sweet kajmaks over four seasons

(2013) Amarela Terzic-Vidojevic et al.   FOOD MICROBIOLOGY

Bacterial ecology of PDO Coppa and Pancetta Piacentina at the end of ripening and after MAP storage of sliced product

(2013) Matteo Busconi et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

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

Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

(2013) Jonathan W. Leff et al.   PLoS One

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

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

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Cheese microbes

(2012) Julie E. Button et al.   CURRENT BIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Up-regulating the Human Intestinal Microbiome Using Whole Plant Foods, Polyphenols, and/or Fiber

(2012) Kieran M. Tuohy et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Prebiotics and the Health Benefits of Fiber: Current Regulatory Status, Future Research, and Goals

(2012) Amy M. Brownawell et al.   JOURNAL OF NUTRITION

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

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

Antibiotics, microbiota, and immune defense

(2012) Carles Ubeda et al.   TRENDS IN IMMUNOLOGY

Bovine Milk as a Source of Functional Oligosaccharides for Improving Human Health

(2012) Angela M. Zivkovic et al.   Advances in Nutrition

The intestinal microbiota dysbiosis and Clostridium difficile infection: is there a relationship with inflammatory bowel disease?

(2012) Justyna Bien et al.   Therapeutic Advances in Gastroenterology

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

(2011) T. Magoc et al.   BIOINFORMATICS

The Human Microbiome Project in 2011 and Beyond

(2011) Lita M. Proctor   Cell Host & Microbe

Role of Natural Killer and Dendritic Cell Crosstalk in Immunomodulation by Commensal Bacteria Probiotics

(2011) Valeria Rizzello et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

The Impact of a Consortium of Fermented Milk Strains on the Gut Microbiome of Gnotobiotic Mice and Monozygotic Twins

(2011) N. P. McNulty et al.   Science Translational Medicine

Microbial ecology of foodborne pathogens associated with produce

(2010) Faith J Critzer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Lag time variability in individual spores of Clostridium botulinum

(2010) S.C. Stringer et al.   FOOD MICROBIOLOGY

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

(2010) C. Manichanh et al.   GENOME RESEARCH

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity

(2009) Marie A. Hildebrandt et al.   GASTROENTEROLOGY

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Dynamics of Whole and Lysed Bacterial Cells during Parmigiano-Reggiano Cheese Production and Ripening

(2008) M. Gatti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY