Measurement of bacterial replication rates in microbial communities.
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.
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
Christopher T
http://orcid.org/0000-0002-7758-6447
CT
Brown
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.
Matthew R
MR
Olm
Department of Earth and Planetary Science, University of California, Berkeley, California, USA.
Brian C
BC
Thomas
Department of Earth and Planetary Science, University of California, Berkeley, California, USA.|Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA.|Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Jillian F
JF
Banfield
D000465:Algorithms; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D058491:Bacterial Load / Q000235:genetics* / Q000379:methods*; D049109:Cell Proliferation / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics; D059013:Microbial Consortia / Q000502:physiology*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity