Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

DOE JGI Metagenome Workflow

(2021) Alicia Clum et al.   mSystems

The carbohydrate-active enzyme database: functions and literature

(2021) Elodie Drula et al.   NUCLEIC ACIDS RESEARCH

Laminarin is a major molecule in the marine carbon cycle

(2020) Stefan Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

(2020) Guillaume Déjean et al.   mBio

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

(2019) Grzegorz M. Boratyn et al.   BMC BIOINFORMATICS

Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group

(2019) Liliane Costa Conteville et al.   Frontiers in Microbiology

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity

(2019) Guillaume Déjean et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biochemical characterization of an ulvan lyase from the marine flavobacterium Formosa agariphila KMM 3901T

(2018) Lukas Reisky et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets

(2018) Darryl R. Jones et al.   Biotechnology for Biofuels

An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont

(2018) Benjamin Pluvinage et al.   Nature Communications

Ancient acquisition of “alginate utilization loci” by human gut microbiota

(2018) Sophie Mathieu et al.   Scientific Reports

Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

(2018) Lennart Kappelmann et al.   ISME Journal

Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal

(2018) Sean M. Kearney et al.   Cell Reports

Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation

(2018) Greta Reintjes et al.   ISME Journal

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention

(2017) Ruixin Liu et al.   NATURE MEDICINE

Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

(2017) David Kamanda Ngugi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence

(2017) Yunus E. Tuncil et al.   mBio

Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment

(2017) Yanyun Gu et al.   Nature Communications

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

(2017) Elizabeth Ficko-Blean et al.   Nature Communications

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients

(2017) Qing He et al.   GigaScience

Novel sulfated xylogalactoarabinans from green seaweed Cladophora falklandica : Chemical structure and action on the fibrin network

(2016) Paula X. Arata et al.   CARBOHYDRATE POLYMERS

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

The gut microbiome of healthy Japanese and its microbial and functional uniqueness

(2016) Suguru Nishijima et al.   DNA RESEARCH

Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease

(2016) Darrell W. Cockburn et al.   JOURNAL OF MOLECULAR BIOLOGY

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

(2015) Jun Yu et al.   GUT

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae

(2014) Jan-Hendrik Hehemann et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes

(2014) Eric C. Martens et al.   JOURNAL OF MOLECULAR BIOLOGY

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

(2014) Johan Larsbrink et al.   NATURE

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

Dynamic responses ofBacteroides thetaiotaomicronduring growth on glycan mixtures

(2013) Theresa E. Rogers et al.   MOLECULAR MICROBIOLOGY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides

(2012) François Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

Analysis of Keystone Enzyme in Agar Hydrolysis Provides Insight into the Degradation (of a Polysaccharide from) Red Seaweeds

(2012) Jan-Hendrik Hehemann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes

(2012) J.-H. Hehemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution

(2012) Eva Heinz et al.   PLoS Pathogens

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

β-d-(1→4), β-d-(1→3) ‘mixed linkage’ xylans from red seaweeds of the order Nemaliales and Palmariales

(2011) Adriano G. Viana et al.   CARBOHYDRATE RESEARCH

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces

(2010) M. Kitahara et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

(2008) Nicole M. Koropatkin et al.   STRUCTURE