Absolute quantitation of microbiota abundance in environmental samples.

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PubMed ID: 29921326

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Tkacz A, Hortala M, Poole PS

Microbiome. Jun 2018. doi: 10.1186/s40168-018-0491-7

COMMENT: The environmental microbial community has multiple components that are normally abundant and are typically investigated by PCR amplification of marker genes. However, for most studies, only one microbiota domain, such as bacteria, is investigated. Furthermore, most microbiota studies are limited by the production of PCR amplicons (amplified genes from an  individual environmental sample) using domain-specific primers. This in turn leads to loss of quantitative comparison between any two or more groups of PCR amplicons. However, in order to unravel the real complexity of the gut, soil and other environments, the quantitative relations between major microbial groups must be determined.

In this article, the authors describe the development oa an absolute quantitation of amplicon families using synthetic chimeric DNA spikes. Synthetic spikes were added directly to environmental samples, co-isolated and PCR-amplified, allowing calculation of the absolute abundance of amplicon families (e.g. prokaryotic 16S, eukaryotic 18S and fungal ITS per unit mass of sample). Spikes can be adapted to any amplicon-specific group including rhizobia from soils, Firmicutes and Bifidobacteria from human gut or Enterobacteriaceae from food samples. Crucially, using highly complex soil samples, the authors show that the absolute abundance of specific groups can remain steady or increase, even when their relative abundance decreases. 

Quantification of the active microbiota will contribute to a better understanding of functional groups in environmental microbiology and can help in producing better microbiota interactions models. Such quantification has widespread application to microbiota/metagenome-wide association studies linked to disease or soil productivity.


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Javier Velasco