Under-detection of endospore-forming Firmicutes in metagenomic data

• DOI: 10.1016/j.csbj.2015.04.002
• Publication Date: 2015-04-26T05:26:00Z
• Authors: Sevasti Filippidou; Thomas Junier; Tina Wunderlin; Chien-Chi Lo; Po-E Li; Patrick S. Chain; Pilar Junier
• Keywords: Amplicon

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is fact that not all microorganisms are equally well detected, questioning universality this approach. Firmicutes known to be a dominant bacterial group. Several species endospore formers and property makes them hardy in potentially harsh conditions, thus likely present wide variety environments, even as residents functional players. While libraries can expected contain formers, endospores resilient many traditional methods DNA isolation undetectable. In study we evaluated representation endospore-forming 73 published datasets using two molecular markers unique group (spo0A gpr). Both were notably absent well-known habitats such soil, with spo0A found only three mammalian gut microbiomes. A tailored extraction method resulted detection large endospore-formers amplicon 16S rRNA genes. shotgun classification was still poor minor fraction community assigned Firmicutes. Thus, removing specific bias workflow improves sequencing, but it insufficient overcome limitations for detecting whole-genome metagenomics. conclusion, highlights importance understanding methodological biases contribute improve approaches.