Analysis | Published:

Measurement of bacterial replication rates in microbial communities

Nature Biotechnology volume 34, pages 12561263 (2016) | Download Citation

Abstract

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.

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Acknowledgements

Funding was provided by NIH grant R01AI092531 Sloan Foundation grant APSF-2012-10-05, and by the US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under award number DE-AC02-05CH11231 (Sustainable Systems Scientific Focus Area and DOE-JGI) and award number DE-SC0004918 (Systems Biology Knowledge Base Focus Area). We thank T. Raveh-Sadka, B. Brooks, and D. Burstein for helpful discussions, and M. Albertsen for comments regarding GC sequencing bias.

Author information

Affiliations

  1. Department of Plant and Microbial Biology, University of California, Berkeley, California, USA.

    • Christopher T Brown
    •  & Matthew R Olm
  2. Department of Earth and Planetary Science, University of California, Berkeley, California, USA.

    • Brian C Thomas
    •  & Jillian F Banfield
  3. Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA.

    • Jillian F Banfield
  4. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Jillian F Banfield

Authors

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Contributions

C.T.B. and J.F.B. developed the iRep and bPTR methods. M.R.O. ordered and oriented draft genome sequences for bPTR calculations and conducted kPTR analyses. C.T.B. conducted the iRep, bPTR, and kPTR comparisons, and determined the accuracy of the iRep method. J.F.B. binned the adult human metagenome and curated the Deltaproteobacterium genome, with input from C.T.B. C.T.B. implemented the iRep method. B.C.T. provided bioinformatics support. C.T.B. and J.F.B. drafted the manuscript. All authors contributed to iRep development, reviewed results, and approved the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jillian F Banfield.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7

Excel files

  1. 1.

    Supplementary Table 1

    Analysis of the impact of genome completeness on iRep replication rate measurements.

  2. 2.

    Supplementary Table 2

    Comparison of iRep, bPTR, and kPTR measurements.

  3. 3.

    Supplementary Table 3

    iRep, bPTR, and kPTR measurements for minimum genome sequencing coverage analyses.

  4. 4.

    Supplementary Table 4

    Comparison of iRep and bPTR measurements for draft-qualitygenomes ordered and oriented based on complete genome sequences.

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    Supplementary Table 5

    iRep measurements for organisms associated with prematureinfant microbiomes.

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    Supplementary Table 6

    Single copy gene inventory for genomes reconstructed from anadult human gut metagenome.

  7. 7.

    Supplementary Table 7

    iRep measurements for organisms associated with an adulthuman microbiome.

  8. 8.

    Supplementary Table 8

    kPTR values determined from the premature infantmetagenomes.

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    Supplementary Table 9

    kPTR values determined from the adult human metagenome.

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    Supplementary Table 10

    iRep measurements for Candidate Phyla Radiation (CPR)organisms.

Zip files

  1. 1.

    Supplementary Code

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DOI

https://doi.org/10.1038/nbt.3704

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