Metabolic niche of a prominent sulfate-reducing human gut bacterium

被引:294
作者
Rey, Federico E. [1 ]
Gonzalez, Mark D. [1 ]
Cheng, Jiye [1 ]
Wu, Meng [1 ]
Ahern, Philip P. [1 ]
Gordon, Jeffrey I. [1 ]
机构
[1] Washington Univ, Sch Med, Ctr Genome Sci & Syst Biol, St Louis, MO 63108 USA
基金
美国国家卫生研究院;
关键词
artificial human gut microbiota/microbiome; determinants of microbial fitness; hydrogenotrophs; microbial foodwebs; hydrogen sulfide; CHONDROITIN SULFATE; ANAEROBIC-BACTERIA; SULFIDE; ACID; COLITIS; POPULATIONS; REDUCTION; OXIDATION; SYMBIONT; DELETION;
D O I
10.1073/pnas.1312524110
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Sulfate-reducing bacteria (SRB) colonize the guts of similar to 50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage's substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H-2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H-2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.
引用
收藏
页码:13582 / 13587
页数:6
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