Evaluation of mock community as an in situ positive control for metataxonomic studies in microbial ecology

Since the emergence of second generation sequencing technologies, metataxonomy has become the standard for investigating microbial communities, their diversity and composition. However, despite the widespread adoption of this technology, current extraction and amplifications protocols have shortcomings that could result in a biased characterization of a given microbiota. It has been suggested that the inclusion of mock communities (MC) or synthetic nucleic acids in metataxonomic experimental designs could provide positive controls for monitoring pipelines, but precise information regarding their application is limited. To close this gap of knowledge, several doses of MC were co-extracted with soil, rhizosphere, invertebrate and vertebrate samples.