Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Cross, Karissa L.; Campbell, James H.; Balachandran, Manasi; Campbell, Alisha G.; Cooper, Sarah J.; Griffen, Ann; Heaton, Matthew; Joshi, Snehal; Klingeman, Dawn; Leys, Eugene; Yang, Zamin; Parks, Jerry M.; Podar, Mircea

doi:10.1038/s41587-019-0260-6

Title: Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Journal Article · Mon Sep 30 00:00:00 EDT 2019 · Nature Biotechnology

DOI:https://doi.org/10.1038/s41587-019-0260-6· OSTI ID:1570133

Cross, Karissa L. ^[1]; Campbell, James H. ^[2]; Balachandran, Manasi ^[3]; Campbell, Alisha G. ^[2]; Cooper, Sarah J. ^[1]; Griffen, Ann ^[4]; Heaton, Matthew ^[5];

^[3];

^[3]; Leys, Eugene ^[4]; Yang, Zamin ^[3];

^[1];

^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Northwest Missouri State Univ., Maryville, MO (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
The Ohio State Univ., Columbus, OH (United States)
Knoxville Periodontics, Knoxville, TN (United States)

The majority of microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea; however, while ’omics can be used to infer physiological or ecological roles for species in a community, most of these hypothetical roles remain unvalidated. Here, we report a technique to capture specific microorganisms from complex communities into pure cultures using genome-informed antibody engineering. We apply our reverse genomics approach to isolate and sequence single cells and to cultivate three different species-level lineages of human oral Saccharibacteria (TM7). Using our pure cultures, we show that all three Saccharibacteria species are epibionts of diverse Actinobacteria. We also isolate and cultivate human oral SR1 bacteria, which are members of a lineage of previously uncultured bacteria. Reverse-genomics-enabled cultivation of microorganisms can be applied to any species from any environment and has the potential to unlock the isolation, cultivation and characterization of species from as-yet-uncultured branches of the microbial tree of life.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1570133

Journal Information:: Nature Biotechnology, Vol. 37, Issue 11; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 136 works

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