Concepedia

The ‘<i>in vivo</i> lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice

Jason M. Ridlon, Saravanan Devendran, João M. P. Alves, Heidi L. Doden, Patricia G. Wolf, Gabriel Vasconcelos Pereira, Lindsey K. Ly, Alyssa Volland, Hajime Takei, Hiroshi Nittono,

Gut Microbes · 2019 · 141 citations · 65 references

DOIFull text

Open access

Concepts

Abstract

suggest fermentation of simple sugars and utilization of amino acids glycine and proline as electron acceptors. Genes predicted to be involved in trimethylamine (TMA) formation were also expressed.

References

65

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · Bioinformatics · 2009 · 44.5K citations · Full text

, , +14

Search and clustering orders of magnitude faster than BLAST

R. C. Edgar · Bioinformatics · 2010 · 21.7K citations · Full text

, , +14

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink, Chao Xie, Daniel H. Huson · Nature Methods · 2014 · 15.2K citations

, , +8

Diversity of the Human Intestinal Microbial Flora

Paul B. Eckburg, Elisabeth M. Bik, Çharles N. Bernstein et al. · Science · 2005 · 7.8K citations · Full text

, , +17

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

Daniel McDonald, Morgan N. Price, Julia K. Goodrich et al. · The ISME Journal · 2011 · 5.3K citations · Full text

, , +17