Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Abstract

Most microorganisms from all taxonomic levels are uncultured. Single-cell genomes and metagenomes continue to increase the known diversity of Bacteria and Archaea, but while 'omics can be used to infer physiological or ecological roles for species in a community, most of those 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 Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Methane oxidation and methylotroph population dynamics in groundwater mesocosms

“…Cross et al . () showed that related SN01 bacteria may be isolated by immuno‐targeting cell surface proteins used by SN01 for attachment to prey bacteria. The blooming of these bacteria during famine periods indicates they may at least benefit from the demise of other populations.…”

“…Among CPR Bacteria, Gracilibacteria have been shown to use a different genetic code and are believed to survive through a highly syntrophic or parasitic lifestyle (Hanke et al, 2014;Anantharaman et al, 2016;Probst et al, 2018). Cross et al (2019) showed that related SN01 bacteria may be isolated by immuno-targeting cell surface proteins used by SN01 for attachment to prey bacteria. The blooming of these bacteria during famine periods indicates they may at least benefit from the demise of other populations.…”

“…Furthermore, groundwater flow and gas migration in the subsurface are not homogeneous and therefore, environmental conditions are partially unknown, adding uncertainty to statistical inferences about relationships between environmental conditions and the occurrence of bacteria of interest. Groundwater microbial communities harbor members of the Candidate Phyla Radiation and other unknown bacteria that may affect the fitness of methylotrophs by antagonistic ecological interactions (Brown et al ., ; Anantharaman et al ., ; Cross et al ., ). In the present study, we address these issues using laboratory mesocosms inoculated with groundwater from our previous field injection experiment (Cahill et al ., ).…”

“…Groundwater microbial communities harbor members of the Candidate Phyla Radiation and other unknown bacteria that may affect the fitness of methylotrophs by antagonistic ecological interactions (Brown et al, 2015;Anantharaman et al, 2016;Cross et al, 2019). In the present study, we address these issues using laboratory mesocosms inoculated with groundwater from our previous field injection experiment .…”

Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system

“…In addition to this wealth of information, one of the most beneficial outcomes of shotgun metagenomic projects is the ability to assemble high quality, complete or nearly-complete, genomes from organisms not yet amenable to cultivation practices (Tyson et al , 2004;Luo et al , 2012) . And indeed, such metagenome-assembled-genomes (MAGs) have provided information leading to the cultivation of organisms of interest (Gutleben et al , 2018;Cross et al , 2019;Imachi et al , 2019) , along with the discoveries of new metabolic processes (Daims et al , 2015) , novel insights into the ecology and evolution of globally abundant groups (Delmont et al , 2018) , and uncovering a wide diversity of novel Phylum-level lineages that have restructured the current understanding of the tree of life (Brown et al , 2015;Hug et al , 2016) .…”