Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

• Published in: Nature biotechnology Vol. 37; no. 11; pp. 1314 - 1321
• Main Authors: Cross, Karissa L, Campbell, James H, Balachandran, Manasi, Campbell, Alisha G, Cooper, Connor J, Griffen, Ann, Heaton, Matthew, Joshi, Snehal, Klingeman, Dawn, Leys, Eugene, Yang, Zamin, Parks, Jerry M, Podar, Mircea
• Format: Journal Article
• Language: English
• Published: United States Nature Publishing Group 01.11.2019; Springer Nature
• Subjects: Actinobacteria - classification; Actinobacteria - genetics; Actinobacteria - isolation & purification; Actinobacteria - metabolism; Analysis; Antibodies; Antibodies - metabolism; Archaea; Bacteria; Bacterial genetics; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - immunology; Bacteriology; BASIC BIOLOGICAL SCIENCES; Branches; Cell culture; Cultivation; Cultures and culture media; Dark matter; Epibionts; Genomes; Genomics; Humans; Membrane Proteins - chemistry; Membrane Proteins - genetics; Membrane Proteins - immunology; Microorganisms; Models, Molecular; Mouth - microbiology; Phylogeny; Protein Conformation; Reverse Genetics; Saccharibacteria; Sequence Analysis, DNA; Single-Cell Analysis - methods; Species; United States
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/s41587-019-0260-6

Most 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 an approach 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.