Targeted isolation and cultivation of uncultivated bacteria by reverse genomics.
Karissa L CrossJames H CampbellManasi BalachandranAlisha G CampbellConnor J CooperAnn GriffenMatthew HeatonSnehal JoshiDawn KlingemanEugene LeysZamin YangJerry M ParksMircea PodarPublished in: Nature biotechnology (2019)
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.
Keyphrases
- single cell
- rna seq
- endothelial cells
- high throughput
- induced pluripotent stem cells
- induced apoptosis
- pluripotent stem cells
- healthcare
- gene expression
- microbial community
- genome wide
- genetic diversity
- risk assessment
- mental health
- human health
- cancer therapy
- endoplasmic reticulum stress
- cell proliferation
- cell death
- amino acid
- cell fate