Evolutionary relationships among bifidobacteria and their hosts and environments

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Unveiling genomic diversity among members of the Bifidobacterium pseudolongum species, a widely distributed gut commensal of the animal kingdom.

(2019) Gabriele Andrea Lugli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolutionary and Ecological Consequences of Gut Microbial Communities

(2019) Nancy A. Moran et al.   Annual Review of Ecology Evolution and Systematics

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Emergence of Soil Bacterial Ecotypes Along a Climate Gradient

(2018) Alexander B. Chase et al.   ENVIRONMENTAL MICROBIOLOGY

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

(2018) Vikas Sharma et al.   Genes

Human milk oligosaccharides and infant gut bifidobacteria: Molecular strategies for their utilization

(2017) Pamela Thomson et al.   FOOD MICROBIOLOGY

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life

(2017) Christian Milani et al.   ISME Journal

Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity

(2017) Eirin Esaiassen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

(2017) Mathieu Groussin et al.   Nature Communications

bcgTree: automatized phylogenetic tree building from bacterial core genomes

(2016) Markus J. Ankenbrand et al.   GENOME

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

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

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Cospeciation of gut microbiota with hominids

(2016) A. H. Moeller et al.   SCIENCE

Glycoside Hydrolases across Environmental Microbial Communities

(2016) Renaud Berlemont et al.   PLoS Computational Biology

Genomics of the Genus Bifidobacterium Reveals Species-Specific Adaptation to the Glycan-Rich Gut Environment

(2015) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Starch and starch hydrolysates are favorable carbon sources for Bifidobacteria in the human gut

(2015) Songling Liu et al.   BMC MICROBIOLOGY

The Role of Microbial Amino Acid Metabolism in Host Metabolism

(2015) Evelien Neis et al.   Nutrients

Comparative Genomic Analysis of 45 Type Strains of the Genus Bifidobacterium: A Snapshot of Its Genetic Diversity and Evolution

(2015) Zhihong Sun et al.   PLoS One

Genomic Encyclopedia of Type Strains of the Genus Bifidobacterium

(2014) Christian Milani et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Investigation of the Evolutionary Development of the Genus Bifidobacterium by Comparative Genomics

(2014) Gabriele Andrea Lugli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

The Ability of Bifidobacteria To Degrade Arabinoxylan Oligosaccharide Constituents and Derived Oligosaccharides Is Strain Dependent

(2013) Audrey Rivière et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Variation in Consumption of Human Milk Oligosaccharides by Infant Gut-Associated Strains of Bifidobacterium breve

(2013) Santiago Ruiz-Moyano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fiber and Prebiotics: Mechanisms and Health Benefits

(2013) Joanne Slavin   Nutrients

Human milk oligosaccharides: Every baby needs a sugar mama

(2012) L. Bode   GLYCOBIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Bacterial Genomes: Habitat Specificity and Uncharted Organisms

(2012) Francisco Dini-Andreote et al.   MICROBIAL ECOLOGY

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Bifidobacterium asteroides PRL2011 Genome Analysis Reveals Clues for Colonization of the Insect Gut

(2012) Francesca Bottacini et al.   PLoS One

How to measure and test phylogenetic signal

(2012) Tamara Münkemüller et al.   Methods in Ecology and Evolution

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Evolutionary Glycomics: Characterization of Milk Oligosaccharides in Primates

(2011) Nannan Tao et al.   JOURNAL OF PROTEOME RESEARCH

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

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

(2011) B. D. Muegge et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genomics and ecological overview of the genus Bifidobacterium

(2010) Francesca Turroni et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Isolation of Bifidobacteria from Breast Milk and Assessment of the Bifidobacterial Population by PCR-Denaturing Gradient Gel Electrophoresis and Quantitative Real-Time PCR

(2008) R. Martin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY