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Human Gut Microbiome Response to Short-Term Bifidobacterium-Based Probiotic Treatment

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Abstract

Gut microbiota is believed to play a crucial role in modulating obesity in humans, and probiotics affecting gut microbiota can alleviate some of the obesity-related health complications. The study was aimed to investigate changes in the composition of the gut microbiome in obese humans due to short-term (2 weeks) treatment of obese patients with a probiotic preparation containing Bifidobacterium longum. Faecal microbiome diversity was studied using the 16S amplicon sequencing by Illumina MiSeq. Bioinformatic analysis showed distribution across 14 phyla (with Firmicutes and Bacteroidetes dominating), 21 class, 125 genera and 973 OTUs. The probiotic treatment decreased relative abundance of Bacteroidetes (Prevotellaceae and Bacteroidaceae), while increasing that of Actinobacteria (Bifidobacteriaceae and Coriobacteriaceae), and Firmicutes (Negativicutes: Veillonellaceae and Clostridia: Peptostreptococcaceae). The probiotic treatment decreased total blood sugar and increased patients’ assessment of their physical and mental health. Thus even the short-term Bifidobacterium-based probiotic treatment brought significant compositional changes in the 16S rRNA gene diversity in faecal bacterial assemblages by increasing beneficial and decreasing pathogenic or opportunistic bacteria; the related shifts in life quality assessment necessitate further research into the causal relationships involved.

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Availability of Data and Material

The read data were deposited in GenBank under the sequence read archive (SRA) accession No. SRP194142.

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Funding

This research was funded by the Russian Ministry of Science and Higher Education, the projects (2018−2020) Nos. 0309-2018-0004 and AAAA-A17-117020210021-7.

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentieva 8, Novosibirsk, Russia, 630090

    Natalia Naumova, Tatiana Alikina, Alexey Tupikin, Valentin Vlassov & Marsel Kabilov

  2. Bio-Vesta LLC, Novosibirsk, Russia

    Anna Kalmykova

  3. Novosibirsk State University, Novosibirsk, Russia, 630090

    Galina Soldatova

Authors
  1. Natalia Naumova
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  2. Tatiana Alikina
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  3. Alexey Tupikin
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  4. Anna Kalmykova
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  5. Galina Soldatova
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  6. Valentin Vlassov
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  7. Marsel Kabilov
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Contributions

Conceptualization, G.S. and A.K.; methodology, T.A.; software, M.K.; validation, N.N.; formal analysis, M.K.; investigation, T.A. and G.S.; resources, V.V.; data curation, A.T. and N.N.; writing—original draft preparation, N.N.; writing−review and editing, V.V.; supervision, V.V.; project administration, M.K.; and funding acquisition, A.K. and V.V.

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Correspondence to Natalia Naumova.

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Conflict of interest

Author A.K. is an employee of Bio-Vesta LLC. Any opinions or scientific interpretations expressed in this manuscript are those of the author and do not necessarily reflect the position or policy of Bio-Vesta LLC. Otherwise the authors declare that they have no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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All patients were duly informed and gave their consent to the study.

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Naumova, N., Alikina, T., Tupikin, A. et al. Human Gut Microbiome Response to Short-Term Bifidobacterium-Based Probiotic Treatment. Indian J Microbiol 60, 451–457 (2020). https://doi.org/10.1007/s12088-020-00888-1

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  • DOI: https://doi.org/10.1007/s12088-020-00888-1

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