Bifidobacteria are some of the major agents that shaped the immune system of many members of the ... more Bifidobacteria are some of the major agents that shaped the immune system of many members of the animal kingdom during their evolution. Over recent years, the question of concrete mechanisms underlying the immunomodulatory properties of bifidobacteria has been addressed in both animal and human studies. A possible candidate for this role has been discovered recently. The PFNA cluster, consisting of five core genes, pkb2, fn3, aaa-atp, duf58, tgm, has been found in all gut-dwelling autochthonous bifidobacterial species of humans. The sensory region of the species-specific serine-threonine protein kinase (PKB2), the transmembrane region of the microbial transglutaminase (TGM), and the type-III fibronectin domain-containing protein (FN3) encoded by the I gene imply that the PFNA cluster might be implicated in the interaction between bacteria and the host immune system. Moreover, the FN3 protein encoded by one of the genes making up the PFNA cluster, contains domains and motifs of cytok...
Probiotic bacteria are widely accepted as therapeutic agents against inflammatory bowel diseases ... more Probiotic bacteria are widely accepted as therapeutic agents against inflammatory bowel diseases for their immunostimulating effects. In the last decade, more evidence has emerged supporting the positive effects of probiotics on the course of neurodegenerative and psychiatric diseases. This brief review summarizes the data from clinical studies of probiotics possessing antidepressant properties and focuses on the potential genes and proteins underlying these mechanisms. Data from small-sample placebo-controlled pilot studies indicate that certain strains of bacteria can significantly reduce the symptoms of depression, especially in depressed patients. Despite the disparity between studies attempting to pinpoint the bacterial putative genes and proteins accounting for these mechanisms, they ultimately show that bacteria are a potential source of metabiotics—microbial metabolites or structural components. Since the constituents of cells—namely, secreted proteins, peptides and cell wal...
Depression is a global threat to mental health that affects around 264 million people worldwide. ... more Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclus...
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species ... more The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in th...
Here, we report the draft genome sequences of 15 Mycobacterium tuberculosis isolates of the Beiji... more Here, we report the draft genome sequences of 15 Mycobacterium tuberculosis isolates of the Beijing-B0/W-148 sublineage that carry a 7-bp insertion within the pks15 gene, which leads to the synthesis of Pks15/1 fusion protein. Pks15/1 is involved in phenolglycolipid synthesis and biofilm formation, thus potentially contributing to the B0/W-148 lineage's enhanced virulence and drug resistance. M ycobacterium tuberculosis virulence and pathogenicity are determined by a set of genes which are polymorphic in different phylogenetic lineages (1-3). The M. tuberculosis Beijing genotype has the widest spread; in Russia, it includes the "successful" clone Beijing B0/W-148, which is characterized as multidrug resistant (MDR) and highly virulent (4-6). Therefore, it is very important to analyze lineage-specific virulence and pathogenicity markers. One significant marker is the 7-bp insertion in the pks15 gene (CCGCGGC) that leads to the synthesis of an active fused Pks15/1 protein (7). Presence of the pks15/1 gene is correlated with highly virulent and drug-resistant strains of the Beijing genotype (8-10); it plays a significant role in virulence (via phenolic glycolipid synthesis) and may be involved in drug tolerance mediated by biofilm formation (7, 9, 11). Studying the genetic variability of virulence factors such as pks15/1 is essential for understanding the M. tuberculosis evolutionary process, including the evolution of host-pathogen interaction mechanisms and drug resistance. Thus, we provide the whole-genome sequencing data of 15 strains from a collection of 100 MDR M. tuberculosis Beijing-B0/W-148 strains (12) that carry a copy of the fused pks15/1 gene. M. tuberculosis was cultured in Middlebrook 7H9 medium with the addition of oleic acid-albumin-dextrose-catalase (OADC; HiMedia, India) at 37°C for 4 weeks. Genomic DNA was isolated and purified by phenol-chloroform/isoamyl alcohol extraction after enzymatic cell lysis, as described by Belisle et al. (13). The quality of DNA was checked using gel electrophoresis and a Bioanalyzer 2100 instrument (Agilent Technologies, USA). Genomic DNA libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, USA). The raw sequencing data were obtained using the HiSeq 2500 platform (Illumina, USA) in rapid run mode with a HiSeq Rapid sequencing by synthesis (SBS) kit v2 (2 ϫ100 bp; Illumina). The quality check of the reads was done using FastQC v.0.11.7 (14). Illumina reads were de novo assembled using SPAdes v.3.12.0 (15) with the-careful flag and k-mers of 21, 33, 55, and 77, while assembly metrics were calculated with QUAST v.5.0.2 with default parameters (16). Automatic functional annotation results were obtained using the NCBI Prokaryotic Genome Annotation Pipeline. Characteristics of the sequenced genomes are listed in Table 1. Data availability. The whole-genome shotgun (WGS) assemblies described here have been deposited in NCBI GenBank. The versions described in this paper are the first
The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were isola... more The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were isolated from human intestinal microbiota. Both strains synthesize gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter. Detailed genome analyses will help to understand the role of GABA in the interaction of bacteria with human intestinal cells.
Background: All living organisms experience physiological changes regulated by endogenous circadi... more Background: All living organisms experience physiological changes regulated by endogenous circadian rhythms. The main factor controlling the circadian clock is the duration of daylight. The aim of this research was to identify the impact of various lighting conditions on physiological parameters and gut microbiota composition in rats. 3 groups of outbred rats were subjected to normal light-dark cycles, darkness and constant lighting. Results: After 1 and 3 months we studied urinary catecholamine levels in rats; indicators of lipid peroxidation and antioxidant activity in the blood; protein levels of BMAL1, CLOCK and THRA in the hypothalamus; composition and functional activity of the gut microbiota. Subjecting the rats to conditions promoting desynchronosis for 3 months caused disruptions in homeostasis. Conclusions: Changing the lighting conditions led to changes in almost all the physiological parameters that we studied. Catecholamines can be regarded as a synchronization super system of split-level circadian oscillators. We established a correlation between hypothalamic levels of Bmal1 and urinary catecholamine concentrations. The magnitude of changes in the GM taxonomic composition was different for LL/LD and DD/LD but the direction of these changes was similar. As for the predicted functional properties of the GM which characterize its metabolic activity, they didn't change as dramatically as the taxonomic composition. All differences may be viewed as a compensatory reaction to new environmental conditions and the organism has adapted to those conditions.
Bifidobacteria are some of the major agents that shaped the immune system of many members of the ... more Bifidobacteria are some of the major agents that shaped the immune system of many members of the animal kingdom during their evolution. Over recent years, the question of concrete mechanisms underlying the immunomodulatory properties of bifidobacteria has been addressed in both animal and human studies. A possible candidate for this role has been discovered recently. The PFNA cluster, consisting of five core genes, pkb2, fn3, aaa-atp, duf58, tgm, has been found in all gut-dwelling autochthonous bifidobacterial species of humans. The sensory region of the species-specific serine-threonine protein kinase (PKB2), the transmembrane region of the microbial transglutaminase (TGM), and the type-III fibronectin domain-containing protein (FN3) encoded by the I gene imply that the PFNA cluster might be implicated in the interaction between bacteria and the host immune system. Moreover, the FN3 protein encoded by one of the genes making up the PFNA cluster, contains domains and motifs of cytok...
Probiotic bacteria are widely accepted as therapeutic agents against inflammatory bowel diseases ... more Probiotic bacteria are widely accepted as therapeutic agents against inflammatory bowel diseases for their immunostimulating effects. In the last decade, more evidence has emerged supporting the positive effects of probiotics on the course of neurodegenerative and psychiatric diseases. This brief review summarizes the data from clinical studies of probiotics possessing antidepressant properties and focuses on the potential genes and proteins underlying these mechanisms. Data from small-sample placebo-controlled pilot studies indicate that certain strains of bacteria can significantly reduce the symptoms of depression, especially in depressed patients. Despite the disparity between studies attempting to pinpoint the bacterial putative genes and proteins accounting for these mechanisms, they ultimately show that bacteria are a potential source of metabiotics—microbial metabolites or structural components. Since the constituents of cells—namely, secreted proteins, peptides and cell wal...
Depression is a global threat to mental health that affects around 264 million people worldwide. ... more Depression is a global threat to mental health that affects around 264 million people worldwide. Despite the considerable evolution in our understanding of the pathophysiology of depression, no reliable biomarkers that have contributed to objective diagnoses and clinical therapy currently exist. The discovery of the microbiota-gut-brain axis induced scientists to study the role of gut microbiota (GM) in the pathogenesis of depression. Over the last decade, many of studies were conducted in this field. The productions of metabolites and compounds with neuroactive and immunomodulatory properties among mechanisms such as the mediating effects of the GM on the brain, have been identified. This comprehensive review was focused on low molecular weight compounds implicated in depression as potential products of the GM. The other possible mechanisms of GM involvement in depression were presented, as well as changes in the composition of the microbiota of patients with depression. In conclus...
The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species ... more The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in th...
Here, we report the draft genome sequences of 15 Mycobacterium tuberculosis isolates of the Beiji... more Here, we report the draft genome sequences of 15 Mycobacterium tuberculosis isolates of the Beijing-B0/W-148 sublineage that carry a 7-bp insertion within the pks15 gene, which leads to the synthesis of Pks15/1 fusion protein. Pks15/1 is involved in phenolglycolipid synthesis and biofilm formation, thus potentially contributing to the B0/W-148 lineage's enhanced virulence and drug resistance. M ycobacterium tuberculosis virulence and pathogenicity are determined by a set of genes which are polymorphic in different phylogenetic lineages (1-3). The M. tuberculosis Beijing genotype has the widest spread; in Russia, it includes the "successful" clone Beijing B0/W-148, which is characterized as multidrug resistant (MDR) and highly virulent (4-6). Therefore, it is very important to analyze lineage-specific virulence and pathogenicity markers. One significant marker is the 7-bp insertion in the pks15 gene (CCGCGGC) that leads to the synthesis of an active fused Pks15/1 protein (7). Presence of the pks15/1 gene is correlated with highly virulent and drug-resistant strains of the Beijing genotype (8-10); it plays a significant role in virulence (via phenolic glycolipid synthesis) and may be involved in drug tolerance mediated by biofilm formation (7, 9, 11). Studying the genetic variability of virulence factors such as pks15/1 is essential for understanding the M. tuberculosis evolutionary process, including the evolution of host-pathogen interaction mechanisms and drug resistance. Thus, we provide the whole-genome sequencing data of 15 strains from a collection of 100 MDR M. tuberculosis Beijing-B0/W-148 strains (12) that carry a copy of the fused pks15/1 gene. M. tuberculosis was cultured in Middlebrook 7H9 medium with the addition of oleic acid-albumin-dextrose-catalase (OADC; HiMedia, India) at 37°C for 4 weeks. Genomic DNA was isolated and purified by phenol-chloroform/isoamyl alcohol extraction after enzymatic cell lysis, as described by Belisle et al. (13). The quality of DNA was checked using gel electrophoresis and a Bioanalyzer 2100 instrument (Agilent Technologies, USA). Genomic DNA libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, USA). The raw sequencing data were obtained using the HiSeq 2500 platform (Illumina, USA) in rapid run mode with a HiSeq Rapid sequencing by synthesis (SBS) kit v2 (2 ϫ100 bp; Illumina). The quality check of the reads was done using FastQC v.0.11.7 (14). Illumina reads were de novo assembled using SPAdes v.3.12.0 (15) with the-careful flag and k-mers of 21, 33, 55, and 77, while assembly metrics were calculated with QUAST v.5.0.2 with default parameters (16). Automatic functional annotation results were obtained using the NCBI Prokaryotic Genome Annotation Pipeline. Characteristics of the sequenced genomes are listed in Table 1. Data availability. The whole-genome shotgun (WGS) assemblies described here have been deposited in NCBI GenBank. The versions described in this paper are the first
The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were isola... more The genomes of Lactobacillus plantarum strain 90sk and Lactobacillus brevis strain 15f were isolated from human intestinal microbiota. Both strains synthesize gamma-aminobutyric acid (GABA), the major inhibitory neurotransmitter. Detailed genome analyses will help to understand the role of GABA in the interaction of bacteria with human intestinal cells.
Background: All living organisms experience physiological changes regulated by endogenous circadi... more Background: All living organisms experience physiological changes regulated by endogenous circadian rhythms. The main factor controlling the circadian clock is the duration of daylight. The aim of this research was to identify the impact of various lighting conditions on physiological parameters and gut microbiota composition in rats. 3 groups of outbred rats were subjected to normal light-dark cycles, darkness and constant lighting. Results: After 1 and 3 months we studied urinary catecholamine levels in rats; indicators of lipid peroxidation and antioxidant activity in the blood; protein levels of BMAL1, CLOCK and THRA in the hypothalamus; composition and functional activity of the gut microbiota. Subjecting the rats to conditions promoting desynchronosis for 3 months caused disruptions in homeostasis. Conclusions: Changing the lighting conditions led to changes in almost all the physiological parameters that we studied. Catecholamines can be regarded as a synchronization super system of split-level circadian oscillators. We established a correlation between hypothalamic levels of Bmal1 and urinary catecholamine concentrations. The magnitude of changes in the GM taxonomic composition was different for LL/LD and DD/LD but the direction of these changes was similar. As for the predicted functional properties of the GM which characterize its metabolic activity, they didn't change as dramatically as the taxonomic composition. All differences may be viewed as a compensatory reaction to new environmental conditions and the organism has adapted to those conditions.
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