Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut

Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate

(2020) Jiayi Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A transaldolase-dependent sulfoglycolysis pathway in Bacillus megaterium DSM 1804

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Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

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A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia

(2019) Spencer C. Peck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Radical-mediated C-S bond cleavage in C2 sulfonate degradation by anaerobic bacteria

(2019) Meining Xing et al.   Nature Communications

Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut

(2019) Andrew Bell et al.   Nature Microbiology

Hydrogen sulfide: an agent of stability at the microbiome-mucosa interface

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An exclusive metabolic niche enables strain engraftment in the gut microbiota

(2018) Elizabeth Stanley Shepherd et al.   NATURE

HMMER web server: 2018 update

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Human Gut Microbiome: Function Matters

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Metatranscriptome of human faecal microbial communities in a cohort of adult men

(2018) Galeb S. Abu-Ali et al.   Nature Microbiology

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Discovering radical-dependent enzymes in the human gut microbiota

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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Structural and Biochemical Insights into the Function and Evolution of Sulfoquinovosidases

(2018) Palika Abayakoon et al.   ACS Central Science

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

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

(2018) Chirag Jain et al.   Nature Communications

Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model

(2018) Anna Burrichter et al.   Frontiers in Microbiology

Faecalibacterium Prausnitzii Prevents Tumorigenesis in a Model of Colitis-Associated Colorectal Cancer

(2017) Yun Tian et al.   GASTROENTEROLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

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Persistent microbiome alterations modulate the rate of post-dieting weight regain

(2016) Christoph A. Thaiss et al.   NATURE

YihQ is a sulfoquinovosidase that cleaves sulfoquinovosyl diacylglyceride sulfolipids

(2016) Gaetano Speciale et al.   Nature Chemical Biology

The Role of Hydrogen Sulfide in Evolution and the Evolution of Hydrogen Sulfide in Metabolism and Signaling

(2016) Kenneth R. Olson et al.   PHYSIOLOGY

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

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

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

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Entner–Doudoroff pathway for sulfoquinovose degradation inPseudomonas putidaSQ1

(2015) Ann-Katrin Felux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon

(2015) Noortje Ijssennagger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A protein trisulfide couples dissimilatory sulfate reduction to energy conservation

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

(2015) Craig W. Herbold et al.   Frontiers in Microbiology

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

(2015) Dongwan D. Kang et al.   PeerJ

Sulfur as a Signaling Nutrient Through Hydrogen Sulfide

(2014) Omer Kabil et al.   Annual Review of Nutrition

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

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Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle

(2014) Karin Denger et al.   NATURE

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

(2014) David Berry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10 −/− mice

(2012) Suzanne Devkota et al.   NATURE

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Physiological Implications of Hydrogen Sulfide: A Whiff Exploration That Blossomed

(2012) Rui Wang   PHYSIOLOGICAL REVIEWS

Hydrogen sulfide (H2S) metabolism in mitochondria and its regulatory role in energy production

(2012) M. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

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Microbial pathways in colonic sulfur metabolism and links with health and disease

(2012) Franck Carbonero et al.   Frontiers in Physiology

Hydrogen Sulfide: Redox Metabolism and Signaling

(2011) Ruma Banerjee   ANTIOXIDANTS & REDOX SIGNALING

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

2,3-Dihydroxypropane-1-sulfonate degraded by Cupriavidus pinatubonensis JMP134: purification of dihydroxypropanesulfonate 3-dehydrogenase

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

(2010) Jan-Hendrik Hehemann et al.   NATURE