Measurement of bacterial replication rates in microbial communities

被引:266
作者
Brown, Christopher T. [1 ]
Olm, Matthew R. [1 ]
Thomas, Brian C. [2 ]
Banfield, Jillian F. [2 ,3 ,4 ]
机构
[1] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA
[2] Univ Calif Berkeley, Dept Earth & Planetary Sci, Berkeley, CA 94720 USA
[3] Univ Calif Berkeley, Dept Environm Sci Policy & Management, Berkeley, CA 94720 USA
[4] Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA
关键词
GENOME SEQUENCES; REVEALS; METABOLISM; RECONSTRUCTION; IDENTIFICATION; CHROMOSOMES; ORGANISMS; COVERAGE; PHYLUM; RARE;
D O I
10.1038/nbt.3704
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication. We apply this method to show that microbial replication rates increase after antibiotic administration in human infants. We also show that uncultivated, groundwater-associated, Candidate Phyla Radiation bacteria only rarely replicate quickly in subsurface communities undergoing substantial changes in geochemistry. Our method can be applied to any genome-resolved microbiome study to track organism responses to varying conditions, identify actively growing populations and measure replication rates for use in modeling studies.
引用
收藏
页码:1256 / 1263
页数:8
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