Dataset Information

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.

ABSTRACT: A bottleneck for microbial community experiments with many samples and/or replicates is the fast quantification of individual taxon abundances, which is commonly achieved through sequencing marker genes such as the 16S rRNA gene. Here, we propose a new approach for high-throughput and high-quality enumeration of human gut bacteria in a defined community, combining flow cytometry and supervised classification to identify and quantify species mixed in silico and in defined communities in vitro. We identified species in a 5-species in silico community with an F1 score of 71%. In addition, we demonstrate in vitro that our method performs equally well or better than 16S rRNA gene sequencing in two-species cocultures and agrees with 16S rRNA gene sequencing data on the most abundant species in a four-species community. We found that shape and size differences alone are insufficient to distinguish species, and that it is thus necessary to exploit the multivariate nature of flow cytometry data. Finally, we observed that variability of flow cytometry data across replicates differs between gut bacterial species. In conclusion, the performance of supervised classification of gut species in flow cytometry data is species-dependent, but is for some combinations accurate enough to serve as a faster alternative to 16S rRNA gene sequencing.

SUBMITTER: van de Velde CC

PROVIDER: S-EPMC9723706 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.

van de Velde Charlotte C CC Joseph Clémence C Biclot Anaïs A Huys Geert R B GRB Pinheiro Vitor B VB Bernaerts Kristel K Raes Jeroen J Faust Karoline K

ISME communications 20220425 1

A bottleneck for microbial community experiments with many samples and/or replicates is the fast quantification of individual taxon abundances, which is commonly achieved through sequencing marker genes such as the 16S rRNA gene. Here, we propose a new approach for high-throughput and high-quality enumeration of human gut bacteria in a defined community, combining flow cytometry and supervised classification to identify and quantify species mixed in silico and in defined communities in vitro. We ...[more]

PMID: 37938658

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Dataset Information

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.

Publications

Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.

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