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

Abstract

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.

Authors:
 [1];  [2];  [3];  [2];  [1];  [4];  [5]; ORCiD logo [3]; ORCiD logo [3];  [4];  [3]; ORCiD logo [1]; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Northwest Missouri State Univ., Maryville, MO (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. The Ohio State Univ., Columbus, OH (United States)
  5. Knoxville Periodontics, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1570133
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 37; Journal Issue: 11; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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., and Podar, Mircea. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. United States: N. p., 2019. Web. doi:10.1038/s41587-019-0260-6.
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. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. United States. doi:10.1038/s41587-019-0260-6.
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., and Podar, Mircea. Mon . "Targeted isolation and cultivation of uncultivated bacteria by reverse genomics". United States. doi:10.1038/s41587-019-0260-6.
@article{osti_1570133,
title = {Targeted isolation and cultivation of uncultivated bacteria by reverse genomics},
author = {Cross, Karissa L. and Campbell, James H. and Balachandran, Manasi and Campbell, Alisha G. and Cooper, Sarah J. and Griffen, Ann and Heaton, Matthew and Joshi, Snehal and Klingeman, Dawn and Leys, Eugene and Yang, Zamin and Parks, Jerry M. and Podar, Mircea},
abstractNote = {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.},
doi = {10.1038/s41587-019-0260-6},
journal = {Nature Biotechnology},
number = 11,
volume = 37,
place = {United States},
year = {2019},
month = {9}
}

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Works referenced in this record:

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota
journal, March 2013

  • Campbell, J. H.; O'Donoghue, P.; Campbell, A. G.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 14, p. 5540-5545
  • DOI: 10.1073/pnas.1303090110

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
journal, July 2007

  • Marcy, Y.; Ouverney, C.; Bik, E. M.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 29, p. 11889-11894
  • DOI: 10.1073/pnas.0704662104