4.6 Article

The Role of Intestinal Microbiota in Regulating the Metabolism of Bile Acids Is Conserved Across Vertebrates

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine

Jia Wen et al.

Summary: Key components of hepatic bile salt synthesis and ileal transport pathways in zebrafish are conserved and controlled by Fxr. Zebrafish bile salts primarily consist of a C-27 bile alcohol and a C-24 bile acid, which undergo microbial modifications. Fxr plays significant roles in transcriptional and differentiation programs in zebrafish intestinal epithelium.

SCIENCE ADVANCES (2021)

Article Biochemistry & Molecular Biology

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Michael Y. Galperin et al.

Summary: The COG database, created in 1997 and most recently updated in 2014, includes extensive information on bacterial and archaeal genomes. The current version introduces new features and plans for future expansion and refinement of annotations.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

UniProt: a worldwide hub of protein knowledge

Alex Bateman et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The Pfam protein families database in 2019

Sara El-Gebali et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Gastroenterology & Hepatology

Microbiota-induced obesity requires farnesoid X receptor

Ava Parseus et al.

Article Biochemical Research Methods

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

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Fisheries

The influence of diet on the grass carp intestinal microbiota and bile acids

Jing Zhang et al.

AQUACULTURE RESEARCH (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Mihaela Pertea et al.

NATURE PROTOCOLS (2016)

Article Biochemical Research Methods

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

Brendan J. Kelly et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

Prokka: rapid prokaryotic genome annotation

Torsten Seemann

BIOINFORMATICS (2014)

Article Biochemical Research Methods

STAMP: statistical analysis of taxonomic and functional profiles

Donovan H. Parks et al.

BIOINFORMATICS (2014)

Review Cell Biology

Pleiotropic Roles of Bile Acids in Metabolism

Thomas Q. de Aguiar Vallim et al.

CELL METABOLISM (2013)

Article Biotechnology & Applied Microbiology

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Morgan G. I. Langille et al.

NATURE BIOTECHNOLOGY (2013)

Article Biochemical Research Methods

UCHIME improves sensitivity and speed of chimera detection

Robert C. Edgar et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

FLASH: fast length adjustment of short reads to improve genome assemblies

Tanja Magoc et al.

BIOINFORMATICS (2011)

Article Multidisciplinary Sciences

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

J. Gregory Caporaso et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Systemic gut microbial modulation of bile acid metabolism in host tissue compartments

Jonathan R. Swann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biotechnology & Applied Microbiology

Metagenomic biomarker discovery and explanation

Nicola Segata et al.

GENOME BIOLOGY (2011)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Letter Biochemical Research Methods

QIIME allows analysis of high-throughput community sequencing data

J. Gregory Caporaso et al.

NATURE METHODS (2010)

Article Microbiology

The seasonal structure of microbial communities in the Western English Channel

Jack A. Gilbert et al.

ENVIRONMENTAL MICROBIOLOGY (2009)

Article Biochemical Research Methods

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

Review Physiology

Role of Bile Acids and Bile Acid Receptors in Metabolic Regulation

Philippe Lefebvre et al.

PHYSIOLOGICAL REVIEWS (2009)

Review Microbiology

Worlds within worlds: evolution of the vertebrate gut microbiota

Ruth E. Ley et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Review Microbiology

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

Harry J. Flint et al.

NATURE REVIEWS MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

KEGG for linking genomes to life and the environment

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Differential regulation of bile acid homeostasis by the farnesoid X receptor in liver and intestine

Insook Kim et al.

JOURNAL OF LIPID RESEARCH (2007)

Article Multidisciplinary Sciences

An obesity-associated gut microbiome with increased capacity for energy harvest

Peter J. Turnbaugh et al.

NATURE (2006)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Review Biochemistry & Molecular Biology

Bile salt biotransformations by human intestinal bacteria

JM Ridlon et al.

JOURNAL OF LIPID RESEARCH (2006)

Article Multidisciplinary Sciences

Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota

JF Rawls et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Multidisciplinary Sciences

The gut microbiota as an environmental factor that regulates fat storage

F Bäckhed et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

The Gene Ontology (GO) database and informatics resource

MA Harris et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

The TIGRFAMs database of protein families

DH Haft et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)