Olga V. Averina

Identification and characterization of WhiB-like family proteins of the Bifidobacterium genus

Bifidobacteria are strictly anaerobic bacteria, that are an important component of human microbiote due to their probiotic characteristics. They are frequently exposed to a variety of stresses, therefore, identification of genes implicated in stress responses in bifidobacteria is critical for biomedicine and maintenance of industrial strains. The WhiB-like family proteins unique for Actinobacteria are transcriptional regulators involved in major cellular processes, including stress responses. The aim of this study was the identification of WhiB-like family proteins of the Bifidobacterium genus of the Actinobacteria class and functional characterization of conservative whiB-like genes. The DNA sequence database of 36 strains revealed a family of WhiB-encoding genes. It were identified the wblE orthologs in all Bifidobacteria species and the whiB2 orthologs in all bifidobacterial strains except of all strains of Bifidobacterium animalis subsp. lactis and Bifidobacterium gallicum. Some strains, in particular, those of the Bifidobacterium longum group, contain additional whiB-like genes of different length and a low degree of similarity in sequences. The wblE and whiB2 genes of the Bifidobacterium genus are evolutionary conservative and ancient genes. The real-time PCR analysis showed that transcription of wblE is induced by a variety of stress conditions such as heat shock, osmotic, oxidative stresses, by antibiotic tetracycline and bile salt treatment, the nutrient starvation and entry into late stationary phase. The wblE gene may play a significant role in general stress responses in bifidobacteria.

Distribution of genes of toxin-antitoxin systems of MazEF and RelBE families in bifidobacteria from human intestinal microbiota

The in silico analysis of 36 sequenced genomes of bacteria of the Bifidobacterium genus determined the presence of 19 genes of toxin-antitoxin (TA) system that belong to the MazEF and RelBE families, including five mazF and two relE genes that encode toxins and 12 relB genes that encode antitoxins. A high level of gene (at the level of nucleotide changes) and genomic (presence or absence of genes in distinct genomes) polymorphism in the investigated genes was revealed. The highest level of polymorphism was observed in strains of the Bifidobacterium longum species, primarily in relB1-relB10 genes. Gene and genomic polymorphism might be used to identify the strain of B. longum species. PCR analysis of genomic DNA of 30 bifidobacteria strains belonging to the three species, B. longum, B. adolescentis, and B. bifidum, isolated from the intestinal microbiota of astronauts demonstrated the presence of mazF and relB genes. The observed polymorphism of TA genes indicates the presence of differences in bifidobacteria strains isolated from the intestinal microbiota of astronauts before and after space flight and the control group.

Genetic instability of probiotic characteristics in the Bifidobacterium longum subsp. longum B379M strain during cultivation and maintenance

The stability of inheritance of several genes in the Russian commercial strain Bifidobacterium lon-gum subsp. longum B379M during cultivation and maintenance under laboratory conditions has been studied. The examined genes code for probiotic characteristics, such as utilization of several sugars (lacA2 gene, encoding β-galactosidase; ara gene, encoding arabinosidase; and galA gene, encoding arabinogalactan endo-β-galactosidase); synthesis of bacteriocins (lans gene, encoding lanthionine synthetase); and mobile gene tet(W) of resistance to the antibiotic tetracycline. The other gene families studied include the genes responsible for signal transduction and adaptation to stress conditions in the majority of bacteria (serine/threonine protein kinases and the toxin-antitoxin systems of MazEF and RelBE families) and transcription regulators (genes encoding WhiB family proteins). Genomic DNA was analyzed by PCR using specially selected primers. A loss of the genes galA and tet(W) has been shown. It is proposed to expand the requirements on probiotic strains, namely, to control retention of the key probiotic genes using molecular biological methods.

Identification and characterization of the serine/threonine protein kinases in Bifidobacterium

Abstract Six genes encoding the bifidobacterial Hanks-type (eukaryote-like) serine/threonine protein kinases (STPK) were identified and classified. The genome of each bifidobacterial strain contains four conserved genes and one species-specific gene. Bifidobacterium longum and Bifidobacterium bifidum possess the unique gene found only in these species. The STPK genes of Russian industrial probiotic strain B. longum B379M were cloned and sequenced. The expression of these genes in Escherichia coli and bifidobacteria was observed. Autophosphorylation of the conserved STPK Pkb5 and species-specific STPK Pkb2 was demonstrated. This is the first report on Hanks-type STPK in bifidobacteria.

Draft Genome Sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150: Focusing on the Genes Potentially Involved in the Gut-Brain Axis

ABSTRACT The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150 strains isolated from the human intestinal microbiota are reported. Both strains are able to produce gamma-aminobutyric acid (GABA). Detailed genomes analysis will help to understand the role of GABA in the functioning of gut-brain axis.

Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains

ABSTRACT In this study, we report the first completely annotated genome sequence of the Russian-origin Bifidobacterium longum subsp. longum strain GT15. We discovered 35 unique genes (UGs) which were detected from only the B. longum GT15 genome and were absent from other B. longum strain genomes (not of Russian origin).

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota

A great amount of attention has been paid to the study of the microbiota–gut–brain axis in recent years. Gut microbiota can affect development and functioning of the brain through synthesis of various neuroactive metabolites, such as neurotransmitters, hormones, and other compounds. In the present study, the presence and distribution are analyzed for the genes controlling the synthesis of enzymes involved in production of neuroactive compounds in 147 gut metagenomes of healthy people from Human Microbiome Project database and synthetic metagenome artificially assembled from 508 bacterial genomes. The analysis is conducted using the collected catalog of orthologs for 17 key enzymes and an algorithm developed for their search. As a result of analyses of genomic and metagenomic data of healthy people, seven bacterial genera containing the greatest number of enzyme genes and 8 enzymes out of 17 that are observed the most frequently are chosen. It is assumed that the selected “core” genera and enzymes form a metagenomic signature reflecting the neurometabolic potential of the human intestinal microbiota in the norm.

Neuropeptides in the microbiota-brain axis and feeding behavior in autism spectrum disorder

A combination of altered social and feeding behaviors is common in children with autism spectrum disorder (ASD); however, the underlying mechanisms are unknown. Nevertheless, it has been established that several specific neuropeptides are critically involved in the regulation of both feeding and social behavior, such as α-melanocyte-stimulating hormone (α-MSH) and oxytocin, respectively. Moreover, recent data implicated gut microbiota in regulation of host feeding and emotion and revealed its dysbiosis in ASD, suggesting a mechanistic role of altered microbiota-brain axis in ASD. In this review, we discuss how gut microbiota dysbiosis may alter hunger and satiety peptide hormones as well as brain peptidergic pathways involved in the regulation of host feeding and social behaviors and hence may contribute to the ASD pathophysiology. In particular, we show that interactions between α-MSH and oxytocin systems in the brain can provide clues for better understanding of the mechanisms underlying altered feeding and social behaviors in ASD and that the origin of such alterations can be linked to gut microbiota.