Human Gut Microbiome Response to Short-Term Bifidobacterium -Based Probiotic Treatment
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ORIGINAL RESEARCH ARTICLE
Human Gut Microbiome Response to Short-Term Bifidobacterium-Based Probiotic Treatment Natalia Naumova1 • Tatiana Alikina1 • Alexey Tupikin1 • Anna Kalmykova2 Galina Soldatova3 • Valentin Vlassov1 • Marsel Kabilov1
•
Received: 27 December 2019 / Accepted: 18 May 2020 Ó Association of Microbiologists of India 2020
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 Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12088-020-00888-1) contains supplementary material, which is available to authorized users. & Natalia Naumova [email protected] Tatiana Alikina [email protected] Alexey Tupikin [email protected] Anna Kalmykova [email protected] Galina Soldatova [email protected] Valentin Vlassov [email protected] Marsel Kabilov [email protected] 1
Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentieva 8, Novosibirsk, Russia 630090
2
Bio-Vesta LLC, Novosibirsk, Russia
3
Novosibirsk State University, Novosibirsk, Russia 630090
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. Keywords Obesity Humans Gut microbiome 16S rRNA gene sequencing Probiotic
Introduction By now there is no doubt that microbiome’s functioning is crucial for human health. Currently vast research efforts are channelled into modulating the intestinal microbiota to promote health and prevent diseases [1]. The last decade has seen a renaissance in research focusing on Actinobacteria as their role in gastrointestinal homeostasis and fighting systemic diseases became well acknowledged. Bifidobacteria have been incorporated into many food products, such as yogurt, fermented milk and dietary supplements. For decades actinobacteria have been u
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