Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria

TLDR

Gene inventory and metagenomic techniques have enabled rapid exploration of bacterial diversity and potential physiologies within microbial communities, yet discovering environmental bacteria carrying multiple genes remains nontrivial. The study uses microfluidic digital PCR to amplify and analyze multiple genes from single environmental bacterial cells. The authors applied microfluidic digital PCR to single cells, using a symbiosis‑related gene as a hook to uncover the ribosomal RNA–based species identity of several termite gut symbionts. This approach enables systematic identification of bacteria carrying specific genes and linking multiple genes to single species in complex ecosystems, opening new research opportunities.

Abstract

Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA–based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment.