A dataset of four probiotic Bifidobacterium strains genome assemblies.

A dataset of four draft genome sequences of Bifidobacterium strains is presented. All four genome assemblies are high-quality drafts characterized by high completeness and low contamination levels. GC content of the genomes varied in the range between 59.27% and 62.77%. Genome sequences were annotated for further functional and taxonomical analyses of the respective Bifidobacterium strains. Genetic determinants of probiotic capabilities, including the genes, related to utilization of human milk oligosaccharides and mucin, as well as the genes, encoding bile salt hydrolase were identified. The genome of B. bifidum VKPM=Ac-1784 has been shown to possess two bacteriocin gene clusters. The dataset expands knowledge on genomic diversity of probiotic strains of Bifidobacterium genus. The dataset is available under PRJNA656137 accession number in NCBI database and under zyv26t6x5r accession number in Mendeley Data repository.

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project.

Personalized nutrition is of increasing interest to individuals actively monitoring their health. The relations between the duration of diet intervention and the effects on gut microbiota have yet to be elucidated. Here we examined the associations of short-term dietary changes, long-term dietary habits and lifestyle with gut microbiota. Stool samples from 248 citizen-science volunteers were collected before and after a self-reported 2-week personalized diet intervention, then analyzed using 16S rRNA sequencing. Considerable correlations between long-term dietary habits and gut community structure were detected. A higher intake of vegetables and fruits was associated with increased levels of butyrate-producing Clostridiales and higher community richness. A paired comparison of the metagenomes before and after the 2-week intervention showed that even a brief, uncontrolled intervention produced profound changes in community structure: resulting in decreased levels of Bacteroidaceae, Porphyromonadaceae and Rikenellaceae families and decreased alpha-diversity coupled with an increase of Methanobrevibacter, Bifidobacterium, Clostridium and butyrate-producing Lachnospiraceae- as well as the prevalence of a permatype (a bootstrapping-based variation of enterotype) associated with a higher diversity of diet. The response of microbiota to the intervention was dependent on the initial microbiota state. These findings pave the way for the development of an individualized diet.