Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It metabolizes daidzein (a soybean isoflavonoid) and produces S-equol, which has stronger estrogenic activities than daidzein. Here, we report the finished and annotated genomic sequence of this organism.The complete genomic sequence of Eggerthella sp. strain YY7918 (8) was determined by a whole-genome shotgun strategy with the Sanger method. Genomic libraries containing 2-kb inserts were constructed with pTS1 plasmids, and 36,480 sequences were generated, providing 8.1-fold coverage from both ends of the genomic clones. Sequence reads were assembled with the Phred-Phrap-Consed program (1). Remaining gaps between contigs were closed by direct sequencing of the fosmid clones. Prediction and annotation of protein-coding genes were performed by MiGAP (6).The genome of strain YY7918 consists of a circular 3,123,671-bp chromosome with 56.2% GC content and contains 2,680 predicted protein-coding sequences (CDSs) but no plasmid. It also has 2 sets of rRNA operons and 44 tRNA genes. The strain possesses two sets of clustered, regularly interspaced short palindromic repeats. Similarity at the sequence level (1,772 CDSs) was observed between strain YY7918 and the closely related type strain Eggerthella lenta VPI0255 (GenBank accession no. CP001726) (3), with overall genome synteny. However, a reciprocal BLASTP search revealed 913 (34.0%) protein-coding genes that are present in strain YY7918 but absent in E. lenta VPI0255T . The genome of strain YY7918 is 509 kb shorter than that of E. lenta VPI0255 T (circular; 3,632,260 bp) (3).The predicted CDSs were submitted to the Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server (http://www.genome.jp/tools/kaas/) (2) and the virulence factor database (VFDB) (http://www.mgc.ac.cn/VFs/) (7). We could assign 975 CDSs (36%) to known functions, 108 (4%) as conserved hypothetical genes, and 1,597 (60%) as novel hypothetical genes. As expected, strain YY7918 possesses an incomplete carbohydrate metabolic pathway in KEGG, indicating that the strain is nonsaccharolytic. By contrast, this organism posseses genes for arginine deiminase (arcA), ornithine carbamoyltransferase (argF or agI), and carbamate kinase (arcC), suggesting that the strain utilizes arginine as an important energy source, similarly to E. lenta (5). The VFDB result indicates that the strain expresses genes for streptomycin adenyltransferase (aadE) and erythromycin resistance methylase (ermB). This organism also carries antibiotic ABC transport systems, such as permease (yadH) and ATP-binding protein (yadG) genes. These results correspond with our previous report that the strain is resistant to erythromycin. However, the strain is sensitive to aminoglycoside antibiotics despite possessing aadE (7). Excluding these elements, other known virulence factors were not present.This organism also has a notable gene cluster (EGYY_15730 to EGYY_15760). Recently, Shimada et al. reported a gene that might encode NADP(H)-dependent d...

Background Bifidobacterium longum 105-A produces markedly high amounts of capsular polysaccharides (CPS) and exopolysaccharides (EPS) that should play distinct roles in bacterial–host interactions. To identify the biological function of B. longum 105-A CPS/EPS, we carried out an informatics survey of the genome and identified the EPS-encoding genetic locus of B. longum 105-A that is responsible for the production of CPS/EPS. The role of CPS/EPS in the adaptation to gut tract environment and bacteria-gut cell interactions was investigated using the ΔcpsD mutant.ResultsA putative B. longum 105-A CPS/EPS gene cluster was shown to consist of 24 putative genes encoding a priming glycosyltransferase (cpsD), 7 glycosyltransferases, 4 CPS/EPS synthesis machinery proteins, and 3 dTDP-L-rhamnose synthesis enzymes. These enzymes should form a complex system that is involved in the biogenesis of CPS and/or EPS. To confirm this, we constructed a knockout mutant (ΔcpsD) by a double cross-over homologous recombination. Compared to wild-type, the ∆cpsD mutant showed a similar growth rate. However, it showed quicker sedimentation and formation of cell clusters in liquid culture. EPS was secreted by the ∆cpsD mutant, but had altered monosaccharide composition and molecular weight. Comparison of the morphology of B. longum 105-A wild-type and ∆cpsD by negative staining in light and electron microscopy revealed that the formation of fimbriae is drastically enhanced in the ∆cpsD mutant while the B. longum 105-A wild-type was coated by a thick capsule. The fimbriae expression in the ∆cpsD was closely associated with the disappearance of the CPS layer. The wild-type showed low pH tolerance, adaptation, and bile salt tolerance, but the ∆cpsD mutant had lost this survivability in gastric and duodenal environments. The ∆cpsD mutant was extensively able to bind to the human colon carcinoma Caco-2 cell line and was phagocytosed by murine macrophage RAW 264.7, whereas the wild-type did not bind to epithelial cells and totally resisted internalization by macrophages.ConclusionsOur results suggest that CPS/EPS production and fimbriae formation are negatively correlated and play key roles in the survival, attachment, and colonization of B. longum 105-A in the gut.Electronic supplementary materialThe online version of this article (doi:10.1186/s13099-017-0177-x) contains supplementary material, which is available to authorized users.

Recent studies have shown that the gut microbiota modulates the physical and psychological functions of the host through several modes of action. One of them is mediating the production of active neurotransmitters, such as serotonin and gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the central nervous system. Here, we analyzed the relationship between fecal GABA concentration and microbial composition in more than 70 human participants. The gut microbiome composition was analyzed using next-generation sequencing based on 16S ribosomal RNA. High-performance liquid chromatography was used to evaluate the neurotransmitters GABA and glutamate. The GABA level was detected in a broad range (0–330 µg/g feces). The participants’ samples were classified into high (>100 µg/g), medium (10–100 µg/g), and low (<10 µg/g) groups, based on fecal GABA concentration. The results reveal that the microbiome of the high-GABA samples had lower alpha diversity than the other samples. Beta diversity analysis showed significant (p < 0.05) separation between the high-GABA samples and others. Furthermore, we surveyed the abundance of specific GABA producer biomarkers among the microbiomes of tested samples. The family Bifidobacteriaceae exhibited high abundance in the microbiome of the high-GABA group. This study demonstrated that Bifidobacterium abundance was associated with high fecal GABA content in healthy human subjects. These results may aid the development of potential probiotics to improve microbial GABA production, which can support the maintenance of the physical and psychiatric health of the host.

Bifidobacteria are beneficial anaerobes, and their O2 sensitivity levels differ among species as a function of unknown molecular mechanisms. Bifidobacterium longum subspecies infantis (B. infantis), a predominant colonizer of the gastrointestinal tract of infants, showed a hyper O2-sensitive growth profile with accompanying a production of H2O2. In this study, we characterized an NADPH oxidase as a key enzyme responsible for this microbe’s hyper O2 sensitivity. A dominant active elution peak of H2O2-forming NADPH oxidase activity was detected in the first step of column chromatography, and the purified NADPH oxidase (NPOX) was identified as a homolog of nitroreductase family proteins. The introduction of the gene encoding B. infantis NPOX (npoxA) into O2-tolerant Bifidobacterium minimum made the strain O2 sensitive and allowed it to produce H2O2. Knockout of the npoxA gene in B. infantis decreased the production of H2O2 and mitigated its B. infantis hyper O2 sensitivity. A transcript of B. infantis npoxA is induced by O2, suggesting that the aerobic production of toxic H2O2 is functionally conserved in B. infantis.

Background Bifidobacteria are gram-positive, probiotic, and generally regarded as safe bacteria. Techniques such as transformation, gene knockout, and heterologous gene expression have been established for Bifidobacterium, indicating that this bacterium can be used as a cell factory platform. However, there are limited previous reports in this field, likely because of factors such as the highly anaerobic nature of this bacterium. Bifidobacterium adolescentis is among the most oxygen-sensitive Bifidobacterium species. It shows strain-specific gamma-aminobutyric acid (GABA) production. GABA is a potent bioactive compound with numerous physiological and psychological functions. In this study, we investigated whether B. adolesentis could be used for mass production of GABA. Results The B. adolescentis 4–2 strain isolated from a healthy adult human produced approximately 14 mM GABA. It carried gadB and gadC, which encode glutamate decarboxylase and glutamate GABA antiporter, respectively. We constructed pKKT427::Pori-gadBC and pKKT427::Pgap-gadBC plasmids carrying gadBC driven by the original gadB (ori) and gap promoters, respectively. Recombinants of Bifidobacterium were then constructed. Two recombinants with high production abilities, monitored by two different promoters, were investigated. GABA production was improved by adjusting the fermentation parameters, including the substrate concentration, initial culture pH, and co-factor supplementation, using response surface methodology. The optimum initial cultivation pH varied when the promoter region was changed. The ori promoter was induced under acidic conditions (pH 5.2:4.4), whereas the constitutive gap promoter showed enhanced GABA production at pH 6.0. Fed-batch fermentation was used to validate the optimum fermentation parameters, in which approximately 415 mM GABA was produced. The conversion ratio of glutamate to GABA was 92–100%. Conclusion We report high GABA production in recombinant B. adolescentis. This study provides a foundation for using Bifidobacterium as a cell factory platform for industrial production of GABA.