Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris

(2020) Sou Miyake et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome

(2019) Nielsen T. Baxter et al.   mSphere

Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family

(2019) Ilias Lagkouvardos et al.   Microbiome

Acarbose improves health and lifespan in aging HET3 mice

(2019) David E. Harrison et al.   AGING CELL

Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice

(2019) Byron J Smith et al.   BMC MICROBIOLOGY

Nonmicrobicidal Small Molecule Inhibition of Polysaccharide Metabolism in Human Gut Microbes: A Potential Therapeutic Avenue

(2018) Anthony D. Santilli et al.   ACS Chemical Biology

Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Primer for Internists

(2018) Gaurav Syal et al.   AMERICAN JOURNAL OF MEDICINE

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

(2018) Liping Zhao et al.   SCIENCE

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

On the Road to Strain-Resolved Comparative Metagenomics

(2018) Nicola Segata   mSystems

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Ten years of CAZypedia: a living encyclopedia of carbohydrate-active enzymes

(2017)   GLYCOBIOLOGY

Polysaccharide Utilization Loci: Fueling Microbial Communities

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

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial

(2017) Xiuying Zhang et al.   Diabetes Therapy

Effects of Acarbose on the Gut Microbiota of Prediabetic Patients: A Randomized, Double-blind, Controlled Crossover Trial

(2017) Xiuying Zhang et al.   Diabetes Therapy

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Longer lifespan in male mice treated with a weakly estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer

(2016) Randy Strong et al.   AGING CELL

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

(2016) Matthew H. Foley et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization

(2016) Vincent Valk et al.   Scientific Reports

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals

(2016) Kate L. Ormerod et al.   Microbiome

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron

(2015) Alicia Lammerts van Bueren et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

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

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Acarbose, 17-α-estradiol, and nordihydroguaiaretic acid extend mouse lifespan preferentially in males

(2013) David E. Harrison et al.   AGING CELL

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

α-Amylase: an enzyme specificity found in various families of glycoside hydrolases

(2013) Štefan Janeček et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

Dynamic responses ofBacteroides thetaiotaomicronduring growth on glycan mixtures

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Molecular Evidence of Lateral Gene Transfer in rpoB Gene of Mycobacterium yongonense Strains via Multilocus Sequence Analysis

(2013) Byoung-Jun Kim et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Bacteroides thetaiotaomicronVPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions

(2012) Young-Min Kim et al.   FEBS Journal

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance

(2012) Robert A. Britton et al.   TRENDS IN MICROBIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Consolidation of glycosyl hydrolase family 30: A dual domain 4/7 hydrolase family consisting of two structurally distinct groups

(2010) Franz J. St John et al.   FEBS LETTERS

Rapamycin, But Not Resveratrol or Simvastatin, Extends Life Span of Genetically Heterogeneous Mice

(2010) Richard A. Miller et al.   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

SusG: A Unique Cell-Membrane-Associated α-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules

(2010) Nicole M. Koropatkin et al.   STRUCTURE

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

(2008) Patrick D Schloss et al.   BMC BIOINFORMATICS

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria

(2008) Obaidur Rahman et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY