Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population

Koliada et al. BMC Microbiology (2020) 20:100 https://doi.org/10.1186/s12866-020-01786-8 RESEARCH ARTICLE Open Access Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population Alexander Koliada1, Vladyslav Moseiko2, Mariana Romanenko1, Liubov Piven1, Oleh Lushchak3, Nadiia Kryzhanovska4, Vitaly Guryanov5 and Alexander Vaiserman1* Abstract Background: Gut microbiota composition is known to depend on environmental (diet, day length, infections, xenobiotic exposure) and lifestyle (alcohol/drug intake, physical activity) factors. All these factors fluctuate seasonally, especially in areas with highly variable climatic conditions between seasons. Seasonal microbiota changes were reported in several previous studies. The purpose of our study was to investigate whether there is a seasonal variability in the gut microbiota composition in Ukrainian population. In contrast to previous studies performed on small-size samples using a longitudinal design, we used cross-sectional design with a large sample size (n = 769). Determination of microbial composition at the level of major microbial phyla was performed by qRTPCR. Results: The relative abundance of major taxonomic groups of gut microbiota was found to be affected by month of sampling. Actinobacteria were more abundant and Bacteroidetes were less abundant in summer-derived samples compared to those obtained during other seasons, whereas Firmicutes content was seasonally independent. The Firmicutes to Bacteroidetes (F/B) ratio was significantly higher in summer-derived samples than in winter-derived ones. Odds to have F/B > 1 were 3.3 times higher in summer samples and 1.9 times higher in autumn samples than in winter ones; neither age, nor sex were significant confounding factors. Conclusions: Seasonality of sampling could influence results of human microbiome research, thereby potentially biasing estimates. This factor must be taken into consideration in further microbiome research. Keywords: Gut microbiota composition, Seasonality of sampling, Diet, Lifestyle factors Background The term “gut microbiota” generally refers to a dynamic community of about 100 trillion microbial cells harbored within the human gastrointestinal tract, and the term “human microbiome” refers to the about 3 million genes (mostly from bacteria) harbored by these microbial cells [1–3]. The most common human intestinal bacteria are members of the gram-negative Bacteroidetes and the * Correspondence: 1 Institute of Gerontology, Vyshgorodskaya st. 67, Kyiv 04114, Ukraine Full list of author information is available at the end of the article gram-positive Firmicutes phyla, and also some other phyla, such as Actinobacteria, Fusobacteria and Verrucomicrobia, that are present at subdominant levels [4]. It is becoming increasingly clear now that most microbes inhabiting our body are critically involved in the organism’s vital functions. The microbiota contains far more important metabolic genes than have been discovered in the human genome and provides the host organism with essential enzymes and biochemical pathways. The metabolic processes regulated by intestinal microbial communities are substantially contributed to both nutrient © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Koliada et al. BMC Microbiology (2020) 20:100 acquisition and xenobiotic processing, including the metabolism of undigested carbohydrates and vitamin biosynthesis [5, 6]. Moreover, the microbiota provides a barrier protecting the host against infections through production of antimicrobial compounds and competitive exclusion of pathogens [7]. The unbalanced state of the gut microbiota composition (dysbiosis) can result in adverse health outcomes including not only intestinal diseases but also extra-intestinal pathological conditions such as atherosclerosis, metabolic syndrome, diabetes mellitus and cancer [8–10]. The composition of microbiota is known to depend on both host genetic background and lifestyle/environmental factors, although recent evidence suggest that exogenous determinants dominate over host genetics in shaping the human gut microbiota [11]. Dietary factors certainly play a central role in these processes [12, 13], although environmental (day length, infections, xenobiotic exposure) and lifestyle (alcohol/drug intake, physical activity) factors are undoubtedly of great importance as well [14, 15]. All these variables obviously fluctuate with season, especially in areas with highly variable climatic conditions between seasons. Given this, it is not surprising that seasonal changes in the intestinal microbiota composition have been reported in several studies. Most of these findings were obtained from isolated religious groups or autochthonous hunter-gatherer communities. Such variations were found, for example, in the study by Davenport et al. conducted in a population of Hutterites, members of an ethno-religious anabaptist group having similar lifestyles due to their communal life [16]. In particular, since they live and eat together, their dietary patterns are practically the same across individuals and very stable throughout the year, with the exception of availability of fresh fruits and vegetables throughout the summer and autumn months. Although overall gut microbiome stability was observed within individuals over time, the significant and consistent population-wide shifts in their gut microbiome composition have been evident across seasons. More specifically, significantly increased ratios of Bacteroidetes and decreased ratios of Actinobacteria and Firmicutes were found in summer compared to winter fecal samples. Subsequently, seasonal variations in the gut microbiota composition were observed in this population by using a genome-wide association study (GWAS) approach [17]. At least eight bacterial taxa have been identified whose seasonal abundance was associated with single nucleotide polymo (...truncated)