Nat biotechnol: capture of uncultured bacteria with specific antibodies produced by reverse genetics

February 8, 2020 / BIOON / - -- bacteria and archaea constitute the vast majority of the living world, but most of them, including those closely related to human beings, have never been isolated or cultured DNA sequencing from natural microbial populations has been able to identify previously unknown taxa and, in some cases, provide detailed genomic information about these organisms However, Karsten zengler, a microbiologist at the University of California, San Diego, says having sequence data is like "having a parts list of machines." This "doesn't tell you what this machine will do." To better understand the physiology and function of microorganisms, scientists need to study living samples, or at least whole cells To this end, in a new study, Mircea podar, a microbiologist at Oak Ridge National Laboratory, and his colleagues studied the sequence data of uncultured micro-organisms (that is, those that cannot be cultured in the laboratory), so as to design tools to capture these micro-organisms The relevant research results were recently published in the journal Nature Biotechnology, with the title of "targeted isolation and culture of uncultured bacteria by reverse genetics" Picture from Nature Biotechnology, 2019, DOI: 10.1038/s41587-019-0260-6 By focusing on bacteria present in the human oral cavity, podar and his team compared available sequence data from uncultured microorganisms with previously cultured bacteria to identify potential cell surface proteins Subsequently, they used potential cell surface proteins to select as many peptide fragments specific to uncultured microorganisms as possible, injected them into rabbits to produce antibodies against them, and labeled them with fluorescent markers When these fluorescent labeled antibodies are added to microbial samples from human saliva, bacteria with corresponding surface proteins can be detected and separated by FACS The podar team isolated two different oral bacteria that could not previously be cultured: TM7 and Sr1 They cultured the two oral bacteria using a carefully chosen medium In addition to enriching the two target bacteria themselves, the antibody mediated technology also extracts specific types of bacteria that have physical relevance to TM7 and Sr1 In fact, the successful culture of TM7 and Sr1 may be partly due to the co isolation of other microorganisms needed for their growth Podar said that while in principle the technology could be applied to any bacteria, for each new target strain, one must carefully design the peptide used to produce the antibody This design is to maintain a careful balance between the similarity of known surface proteins with other microorganisms and the specificity of potential surface proteins with target microorganisms So, he said, "it will never be a toolkit." Instead, "it's a guiding way to increase your chances of success." Using this technique, called reverse genetics, scientists can acquire specific antibodies to capture previously uncultured microorganisms Zengler, who was not involved in the study, said the technology "will help us get more culturable microbes and more information about microbes that we only know from genomic fingerprints." (BIOON Com) reference: 1 KARISSA L cross et al Targeted isolation and culture of uncultured bacteria by reverse genetics Nature Biotechnology, 2019, doi:10.1038/s41587-019-0260-6 2.Genome Data Enable Capture of Elusive Microbes https://