Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota

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

(2022) Nicholas A. Pudlo et al.   Cell Host & Microbe

Specificities and Synergistic Actions of Novel PL8 and PL7 Alginate Lyases from the Marine Fungus Paradendryphiella salina

(2021) Bo Pilgaard et al.   Journal of Fungi

DOE JGI Metagenome Workflow

(2021) Alicia Clum et al.   mSystems

A single sulfatase is required to access colonic mucin by a gut bacterium

(2021) Ana S. Luis et al.   NATURE

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

(2021) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Incidence of Celiac Disease Is Increasing Over Time

(2020) James A. King et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization

(2020) Matthew K. Schnizlein et al.   mSphere

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

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon

(2019) Caroline C. Kim et al.   ISME Journal

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

Proteomic Analysis of the Xanthan-Degrading Pathway of Microbacterium sp. XT11

(2019) Zhen Sun et al.   ACS Omega

Mannosidase mechanism: at the intersection of conformation and catalysis

(2019) Carme Rovira et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron

(2018) Matthew H. Foley et al.   MOLECULAR MICROBIOLOGY

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Structural Dynamics and Catalytic Properties of a Multimodular Xanthanase

(2018) Olga V. Moroz et al.   ACS Catalysis

Dietary trehalose enhances virulence of epidemic Clostridium difficile

(2018) J. Collins et al.   NATURE

Novel Endotype Xanthanase from Xanthan-Degrading Microbacterium sp. Strain XT11

(2018) Fan Yang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

(2018) Benoit J. Kunath et al.   ISME Journal

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions

(2018) Yunus E. Tuncil et al.   Scientific Reports

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation

(2018) Alan Cartmell et al.   Nature Microbiology

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME 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

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Samuel A. Smits et al.   SCIENCE

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

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

(2017) Qing He et al.   GigaScience

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

MET-activating Residues in the B-repeat of theListeria monocytogenesInvasion Protein InlB

(2016) Willem M. Bleymüller et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

(2015) Jun Yu et al.   GUT

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

(2015) Benoit Chassaing 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

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Alginate lyase: Review of major sources and classification, properties, structure-function analysis and applications

(2015) Benwei Zhu et al.   Bioengineered

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Characterization of an acetyl esterase from Myceliophthora thermophila C1 able to deacetylate xanthan

(2014) Marijn M. Kool et al.   CARBOHYDRATE POLYMERS

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

(2014) Johan Larsbrink et al.   NATURE

Unusual Enzymatic Glycoside Cleavage Mechanisms

(2013) Seino A. K. Jongkees et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

Comparison of xanthans by the relative abundance of its six constituent repeating units

(2013) Marijn M. Kool et al.   CARBOHYDRATE POLYMERS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

(2012) Henrik Aspeborg et al.   BMC EVOLUTIONARY BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Fold and Function of the InlB B-repeat

(2011) Maria Ebbes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analysis of a New Family of Widely Distributed Metal-independent α-Mannosidases Provides Unique Insight into the Processing ofN-Linked Glycans

(2011) Katie J. Gregg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies

(2011) P. B. Pope et al.   SCIENCE

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

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

Carbohydrate-binding domains: multiplicity of biological roles

(2009) Daniel Guillén et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS