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Open AccessArticle

Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota

1
Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia
2
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
3
Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
4
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
5
Faculty of Ecology, International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Toxins 2020, 12(6), 388; https://doi.org/10.3390/toxins12060388
Received: 6 May 2020 / Revised: 8 June 2020 / Accepted: 10 June 2020 / Published: 12 June 2020
(This article belongs to the Section Bacterial Toxins)
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM. View Full-Text
Keywords: toxin-antitoxin systems; metagenomes; gut microbiota; strain identification toxin-antitoxin systems; metagenomes; gut microbiota; strain identification
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Klimina, K.M.; Voroshilova, V.N.; Poluektova, E.U.; Veselovsky, V.A.; Yunes, R.A.; Kovtun, A.S.; Kudryavtseva, A.V.; Kasianov, A.S.; Danilenko, V.N. Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota. Toxins 2020, 12, 388.

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