Streptococcus hohhotensis sp. nov., isolated from the breast milk of a healthy woman.

Human breast milk contains lactic acid bacteria (LAB), which have an important influence on the composition of the intestinal microbia of infants. In this study, one strain of an α-hemolytic species of the genus Streptococcus, IMAU99199T, isolated from the breast milk of a healthy nursing mother in Hohhot city PR China, was studied to characterise its taxonomic status using phenotypic and molecular taxonomic methods. The results indicated that it represented a member of the mitis-suis clade, pneumoniae subclade of the genus Streptococcus. It is a Gram-stain-positive, catalase-negative and oxidase-negative bacterium, and the cells are globular, paired or arranged in short chains. The results of a phylogenetic analysis of its 16S rRNA gene and two housekeeping genes (gyrB and rpoB) placed it in the genus Streptococcus. A phylogenetic tree based on 135 single-copy genes sequences indicated that IMAU99199T formed a closely related branch well separated from 'Streptococcus humanilactis' IMAU99125, 'Streptococcus bouchesdurhonensis' Marseille Q6994, Streptococcus mitis NCTC 12261T, 'Streptococcus vulneris' DM3B3, Streptococcus toyakuensis TP1632T, Streptococcus pseudopneumoniae ATCC BAA-960T and Streptococcus pneumoniae NCTC 7465T. IMAU99199T and 'S. humanilactis' IMAU99125 had the highest average nucleotide identity (93.7 %) and digital DNA-DNA hybridisation (55.3 %) values, which were below the accepted thresholds for novel species. The DNA G+C content of the draft genome of IMAU99199T was 39.8 %. The main cellular fatty acids components of IMAU99199T were C16 : 0 and C16 : 1ω7. It grew at a temperature range of 25-45 °C (the optimum growth temperature was 37 °C) and a pH range of 5.0-8.0 (the optimum growth pH was 7.0). These data indicate that strain IMAU99199T represents a novel species in the genus Streptococcus, for which the name Streptococcus hohhotensis sp. nov. is proposed. The type strain is IMAU99199T (=GDMCC 1.1874T=KCTC 21155T).

Targeted Deletion of Glycoprotein B Gene by CRISPR/Cas9 Nuclease Inhibits Gallid herpesvirus Type 3 in Dually Infected Marek's Disease Virus-Transformed Lymphoblastoid Cell Line MSB-1.

Marek's disease virus (MDV) is a member of the genus Mardivirus in the subfamily Alphaherpesvirinae. There are three different serotypes of MDV designated as MDV-1 (Gallid herpesvirus type 2), MDV-2 (Gallid herpesvirus type 3), and MDV-3 (Meleagrid herpesvirus 1, herpesvirus of turkeys, HVT). MDV-1 is the only serotype that induces Marek's disease (MD), a lymphoproliferative disorder resulting in aggressive T-cell lymphomas and paralytic symptoms. In the lymphomas and lymphoblastoid cell lines (LCL) derived from them, MDV establishes latent infection with limited viral gene expression. The latent viral genome in LCL can be activated by co-cultivation with chicken embryo fibroblast (CEF) monolayers. MSB-1, one of the first MDV-transformed LCL established from the splenic lymphoma, is distinct in harboring both the oncogenic MDV-1 and non-oncogenic MDV-2 viruses. Following the successful application of CRISPR/Cas9 editing approach for precise knockdown of the MDV-1 genes in LCL, we describe here the targeted deletion of MDV-2 glycoprotein B (gB) in MSB-1 cells. Due to the essential nature of gB for infectivity, the production of MDV-2 plaques on CEF was completely abolished in the MDV-2-gB-deleted MSB-1 cells. Our study has demonstrated that the CRISPR/Cas9 system can be used for targeted inactivation of the co-infecting MDV-2 without affecting the MDV-1 in the MSB-1 cell line. Successful inactivation of MDV-2 demonstrated here also points toward the possibility of using targeted gene editing as an antiviral strategy against pathogenic MDV-1 and other viruses infecting chickens. IMPORTANCE Marek's disease (MD) is a lymphoproliferative disease of chickens characterized by rapid-onset lymphomas in multiple organs and by infiltration into peripheral nerves, causing paralysis. Lymphoblastoid cell lines (LCL) derived from MD lymphomas have served as valuable resources to improve understanding of distinct aspects of virus-host interactions in transformed cells including transformation, latency, and reactivation. MDV-transformed LCL MSB-1, derived from spleen lymphoma induced by the BC-1 strain of MDV, has a unique feature of harboring an additional non-pathogenic MDV-2 strain HPRS-24. By targeted deletion of essential gene glycoprotein B from the MDV-2 genome within the MSB-1 cells, we demonstrated the total inhibition of MDV-2 virus replication on co-cultivated CEF, with no effect on MDV-1 replication. The identified viral genes critical for reactivation/inhibition of viruses will be useful as targets for development of de novo disease resistance in chickens to avian pathogens.

Phylogenomics of the Liquorilactobacillus Genus.

The genus Liquorilactobacillus is a new genus commonly found in wine and plants. Despite its significance, previous studies on Liquorilactobacillus are primarily focused on phenotypic experiments, with limited genome-level studies. This study used comparative genomics to analyze 24 genomes from the genus Liquorilactobacillus, including two novel sequenced strains (IMAU80559 and IMAU80777). A phylogenetic tree of 24 strains was constructed based on 122 core genes and divided into two clades, A and B. Significant differences in GC content were observed between the two clades (P = 10e-4). Additionally, change revealed to suggests that clade B has more exposure to prophage infection having an upgraded immune system. Further analysis of functional annotation and selective pressure suggests that clade A was subjected to greater selection pressure than B clade (P = 3.9e-6) and had higher number of functional types annotated than clade B (P = 2.7e-3), while clade B had a lower number of pseudogenes than clade A (P = 1.9e-2). The findings suggest that differently prophages and environmental stress may have influenced the common ancestor of clades A and B during evolution, leading to the development of two distinct clades.

Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts.

BACKGROUND: The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics. RESULTS: A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine. CONCLUSIONS: These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.

Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product.

Two lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to Lentilactobacillus rapi. However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from L. rapi DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA-DNA hybridization values between IMAU80584T and L. rapi DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from L. rapi DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1 ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2 ω6c and/or C18 : 2 ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species L. rapi with the proposed name Lentilactobacillus rapi subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).

The efficacy and safety of esketamine in the treatment of major depressive disorder with suicidal ideation: study protocol for a randomized controlled trial.

BACKGROUND: Major depressive disorder (MDD) is a high risk factor for suicide, with up to 20% of MDD patients attempting suicide during their lifetime. Current treatments for MDD are slow onset of action, low efficiency, and the inability to control suicidal behaviors quickly and effectively. Intravenous ketamine has been shown to have a rapid but transient antidepressant effect, but there is still lack evidence on the efficacy and safety of intravenous esketamine in reducing suicidal ideation and depressive symptoms in MDD patients with suicidal ideation. We designed a study to investigate the effect of short-term repeated intravenous infusion of esketamine three times in MDD patients with suicidal ideation. METHODS: This study features a randomized, double-blind, placebo-controlled trial (RCT) comparing short-term repeated intravenous infusions of esketamine with placebo as a supplement to conventional antidepressants with an intervention period of 6 days and one infusion every other day, followed by 4 weeks of follow-up. These methods support the examination of the efficacy, safety, tolerability, and mechanism of action of short-term repeated intravenous infusions of esketamine in MDD patients with suicidal ideation. DISCUSSION: This is the first RCT to explore the efficacy and safety of short-term repeated infusion of esketamine on suicidal ideation and depressive symptoms in MDD patients with suicidal ideation. If proven effective and tolerated, it will provide evidence for rapid and effective treatment of suicidal ideation and depressive symptoms in MDD individuals with suicidal ideation. TRIAL REGISTRATION: Chinese Clinical Trial Register, ChiCTR2000041232 . Registered 22 December 2020.

Comparative genomics of in vitro and in vivo evolution of probiotics reveals energy restriction not the main evolution driving force in short term.

Probiotics have attracted much attention because of their health-promoting effects, but little is known about the in vivo evolution of probiotics. This study analyzed the genome adaptation of the probiotic Lactiplantibacillus plantarum P-8 strain cultivated in ordinary and glucose restrictive growth media. Then, this study re-analyzed genomes of P-8 isolates recovered from the gut contents of subjects in two feeding trials (in rat and human). The sampling time points were similar to that of the in vitro evolution experiment, which might give parallel comparison of the in vitro and in vivo evolution processes. Our results showed that intra-individual specific microbial genomic variants of the original strain were detected in all human and some rat subjects. The divergent patterns of evolution within the host gastrointestinal tract suggested intra-individual-specific environmental adaptation. Based on comprehensive analysis of adapted-isolates recovered from these experiments, our results showed that the energy restriction was not the main driving force for evolution of probiotics. The individual-specific adaptation of probiotics might partially explain the varying extent of health effects seen between different individuals after probiotic consumption. In addition, the results suggest that probiotics should not only adapt to the environment of the birth canal, but also adapt to other species in the gut, revealing the Red Queen hypothesis in the process of intestinal flora.

Characterization and association of bacterial communities and nonvolatile components in spontaneously fermented cow milk at different geographical distances.

In the ecosystem of spontaneously fermented cow milk, the characteristics and relationship of bacterial communities and nonvolatile components at different scales of geographical distances (provincial, county, and village levels) are unclear. Here, 25 sampling sites from Xin Jiang and Tibet, 2 provinces of China, were selected based on the distribution of spontaneously fermented cow milk and used for metagenomic and metabolomic analysis. At the provincial geographical distance, the same predominant species, Lactobacillus delbrueckii ssp. bulgaricus and Streptococcus thermophilus, were detected in Xin Jiang and Tibet. Further, the richness of the bacterial composition of samples from Tibet was higher than those from Xin Jiang; specifically, at the species level, 28 species were identified in Tibet samples but only 7 species in Xin Jiang samples. At the provincial geographical level, we detected significant differences in bacterial structure, shown in principal coordinate analysis plots, and significant differences (Simpson index) in bacterial diversity were also detected. However, at the county and village levels, no significant differences were detected in bacterial communities and diversity, but a difference in bacterial compositions was detectable. This indicates that bacterial communities and diversity of spontaneously fermented milk dissimilarity significantly increased with geographic distance. For the nonvolatile component profiles, the partial least squares discriminant analysis plot (R2Y > 0.5 and Q2 > 0.5 for the goodness-of-fit and predictive ability parameter, respectively) showed that samples from different geographical distances (provincial, county, and village) were all separated, which indicated that all the discriminations in nonvolatile components profiles were from different geographical distances. Investigating relationships between lactic acid bacteria and discriminatory nonvolatile components at the county level showed that 9 species were positively correlated with 16 discriminatory nonvolatile components, all species with low abundance rather than the predominant species L. delbrueckii ssp. bulgaricus and Strep. thermophilus, which indicates the importance of the selection of autochthonous nonpredominant bacteria.

Exploring the industrial potential of Lactobacillus delbrueckii ssp. bulgaricus by population genomics and genome-wide association study analysis.

Lactobacillus delbrueckii ssp. bulgaricus is one of the most commonly used starter cultures for yogurt production. However, how its genetic background affects acid production capacity is unclear. This study investigated the industrial potential of L. delbrueckii ssp. bulgaricus using population genomics and GWAS analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced L. delbrueckii ssp. bulgaricus strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation results with sucrose-fortified reconstituted skim milk revealed a significant association between l-lactate dehydrogenase (lldD; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of L. delbrueckii ssp. bulgaricus by identifying potential targets for further research, development, and use of lactic acid bacteria in the dairy industry.

Changes in physico-chemical characteristics and viable bacterial communities during fermentation of alfalfa silages inoculated with Lactobacillus plantarum.

This study investigated the effect of inoculating Lactobacillus (L.) plantarum PS-8 in fermentation of alfalfa silages. We monitored the fermentation characteristics and bacterial population dynamics during the ensiling process. PacBio single molecule real time sequencing was combined with propidium monoazide (PMA) treatment to monitor the viable microbiota dynamics. We found that inoculating L. plantarum PS-8 may improve the silage quality by accelerating acidification, reducing the amounts of clostridia, coliform bacteria, molds and yeasts, elevating the protein and organic acid contents (except butyrate), and enhancing lactic acid bacteria (LAB) while suppressing harmful microorganisms. Some significant differential abundant taxa were found between the PMA-treated and non-treated microbiota. For example, the relative abundances of L. brevis, L. plantarum, and Pediococcus pentosaceus were significantly higher in the PMA-treated group than the non-PMA-treated group, suggesting obvious differences between the viable and non-viable microbiota. It would thus be necessary to distinguish between the viable and non-viable microbial communities to further understand their physiological contribution in silage fermentation. By tracking the dynamics of viable microbiota in relation with changes in the physico-chemical parameters, our study provided novel insights into the beneficial effects of inoculating L. plantarum PS-8 in silage fermentation and the physiological function of the viable bacterial communities.

Profiling of koumiss microbiota and organic acids and their effects on koumiss taste.

BACKGROUND: Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. RESULTS: A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami. CONCLUSIONS: Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.

Lactobacillus enshiensis sp. nov., a novel arsenic-resistant bacterium.

A lactic acid bacterial strain, HBUAS57009T, isolated from traditionally fermented food (Zha-Chili) in China, was characterized to clarify its taxonomic status using a polyphasic approach. Strain HBUAS57009T was phylogenetically closely related to Lactobacillus koreensis DCY50T, Lactobacillus fujinensis 218-6T, Lactobacillus mulengensis 112-3T, Lactobacillus cerevisiae TUM BP 140423000-2250T, Lactobacillus tongjiangensis 218-10T and Lactobacillus yonginensis THK-V8T with sequence similarities of 98.6-99.3 %. The genome-to-genome distance and average nucleotide identity values between the genomes of strain HBUAS57009T and type strains of closely related Lactobacillus species were less than 32.0 and 86.0 %, respectively; this is below the threshold for species boundaries. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1 ω9c and iso-C19 : 0. The G+C content of the genomic DNA of strain HBUAS57009T was 47.8 mol%. Examination of the functional categories of the genome revealed that strain HBUAS57009T could perform both homolactic and heterolactic fermentation processes to produce lactic acid via complete glycolysis and the pentose phosphate pathway. The putative biosynthesis pathway of butane-2,3-diol and acetoin, two important flavour compounds in the food industry, were identified using kegg mapper analysis. Based on its genotypic and phenotypic features, strain HBUAS57009T (=GDMCC 1.1664T=KACC 21424T) is designated as the type strain of a novel species, for which the name Lactobacillus enshiensis sp. nov. is proposed.

Lactobacillus casei protects dextran sodium sulfate- or rapamycin-induced colonic inflammation in the mouse.

PURPOSE: Human colon inflammation is associated with changes in the diverse and abundant microorganisms in the gut. As important beneficial microbes, Lactobacillus contributes to the immune responses and intestinal integrity that may alleviate experimental colitis. However, the mechanisms underlying probiotic benefits have not been fully elucidated. METHODS: Dextran sodium sulfate or rapamycin-challenged mice were used as model for colon inflammation evaluation. Histological scores of the colon, levels of colonic myeloperoxidase, serum tumor necrosis factor-α and interleukin-6 were assessed as inflammatory markers and the gut microbiota profiles of each mouse were studied. RESULTS: We found that Lactobacillus casei Zhang (LCZ) can prevent experimental colitis and rapamycin-induced inflammation in intestinal mucosa by improving histological scores, decreasing host inflammatory cytokines, modulating gut-dominated bacteria, enhancing cystic fibrosis transmembrane conductance regulator (CFTR) expression and downregulating the expression of p-STAT3 (phosphorylated signal transducer and activator of transcription 3) or Akt/NF-κB (AKT serine/threonine kinase and nuclear factor kappa B). CONCLUSION: Our results suggest that LCZ may provide effective prevention against colitis.

Comparative genomic analysis revealed great plasticity and environmental adaptation of the genomes of Enterococcus faecium.

BACKGROUND: As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments. RESULTS: In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium. CONCLUSIONS: This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.

Facile Generation of Thermally Activated Delayed Fluorescence and Fabrication of Highly Efficient Non-Doped OLEDs Based on Triazine Derivatives.

A series of donor-acceptor-donor triazine-based molecules with thermally activated delayed fluorescence (TADF) properties were synthesized to obtain highly efficient blue-emitting OLEDs with non-doped emitting layers (EMLs). The targeted molecules use a triazine core as the electron acceptor, and a benzene ring as the conjugated linker with different electron donors to alternate the energy level of the HOMO to further tune the emission color. The introduction of long alkyl chains on the triazine core inhibits the unwanted intermolecular D-D/A-A-type π-π interactions, resulting in the intermolecular D-A charge transfer. The weak aggregation-caused quenching (ACQ) effect caused by the suppressed intermolecular D-D/A-A-type π-π interaction further enhances the emission. The crowded molecular structure allows the electron donor and acceptor to be nearly orthogonal, thereby reducing the energy gap between triplet and singlet excited states (ΔEST ). As a result, blue-emitting devices with TH-2DMAC and TH-2DPAC non-doped EMLs showed satisfactory efficiencies of 12.8 % and 15.8 %, respectively, which is one of the highest external quantum efficiency (EQEs) reported for blue TADF emitters (λpeak <475 nm), demonstrating that our tailored molecular designs are promising strategies to endow OLEDs with excellent electroluminescent performances.

Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili.

Strain HBUAS52074T is a Gram-positive staining, aerobic bacterium that was isolated from Zha-Chili, a traditional fermented food made in China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HBUAS52074T is a member of the genus Lactobacillus and closely related to Lactobacillus nantensis DSM 16982T (98.9 %), Lactobacillus heilongjiangensis DSM 28069T (98.8 %), Lactobacillus formosensis NBRC 1095009T (98.6 %), Lactobacillus futsaii JCM 17355T (98.5 %), Lactobacillus farciminis KCTC 3681T (98.5 %), Lactobacillus musae NBRC 112868T (98.5 %) and Lactobacillus crustorum LMG 23699T (98.4 %). The DNA G+C content is 36.3 mol%. The major cellular fatty acids are C16 : 0 (28.2 %), C18 : 1ω9c (30.5 %) and summed feature 7 (C19 : 1ω6c, and/or C19 : 1ω7c; 14.9 %). Average nucleotide identity and DNA-DNA hybridization (GGDC) values based on genomic comparisons between HBUAS52074T and related type species showed that the bacterium was significantly different from its closest relatives. Using polyphasic taxonomic analysis, we have shown that strain HBUAS52074T is a new species in the genus Lactobacillus, for which we propose the name Lactobacilluszhachilii sp. nov. The type strain is HBUAS52074T (=GDMCC 1.1417T=KCTC 21106T).

Vibrio zhugei sp. nov., a moderately halophilic bacterium isolated from pickling sauce.

Strain HBUAS61001T was isolated from the pickling sauce used to make a traditional fermented food product, datoucai, in China. The strain belonged to the genus Vibrio, but was placed in a clade separate from any known Vibrio species based on the 16S rRNA gene and MLSA results. The genome consisted of two chromosomes: chromosome I was 2 901 449 bp long with a G+C content of 45.4 mol%; and chromosome II was 1 107 930 bp long with a G+C content of 45.5 mol%. The most abundant fatty acids were C16 : 0 (28.1 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 29.4 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 10.1 %). The isoprenoid quinones detected were Q7 and Q8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Strain HBUAS61001T could grow in the presence of up to 17 % NaCl. The calculated average nucleotide identity and in silico DNA-DNA hybridization (GGDC) values of the strain against the closest related type strains were all lower than 95 and 70 %, respectively. Putative genes in the genome associated with survival under high salinity stress were identified. Based on whole genome sequence analysis and phenotypic characteristics, strain HBUAS61001T is a new species in the genus Vibrio, and the name Vibrio zhugei (=GDMCC 1.1416T=KCTC 62784T) is proposed.

Halobasidium xiangyangense gen. nov., sp. nov., a new xylose-utilizing yeast in the family Cystobasidiaceae, isolated from the pickling sauce used to make Datoucai, a high-salt fermented food.

In this study, we describe a new genus and species of yeast with high-salt tolerance. The strain was isolated from the pickling sauce used to make Datoucai, a traditional fermented food made from Brassica juncea in Xiangyang, China. Phylogenetic analysis of sequences from the D1/D2 region of the LSU rRNA gene and from the ITS region demonstrated that the strain, reference HBUAS51001T, was most closely related to members of the genera Occultifur and Cystobasidium. However, the greatest similarities between the D1/D2 and ITS nucleotide sequences of strain HBUAS51001T and the most closely related type strains from Occultifur and Cystobasidium were only 91 and 92 %, respectively. This suggests that strain HBUAS51001T does not belong to any currently described species. Strain HBUAS51001T grew readily on media in which xylose was the sole carbon source. The major ubiquinone was Q9. The genome of strain HBUAS51001T was 42.42 Mb with a G+C content of 53.93 mol%. Three candidate genes associated with xylose metabolism were identified. On the basis of genotypic and phenotypic data, strain HBUAS51001T can be considered as both a new species and a new genus, for which the name Halobasidium xiangyangense gen. nov., sp. nov. is proposed. The type strain is HBUAS51001T (=KCTC27810T=GDMCC 2.231T=CCTCC AY 2018002T).

Comparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations.

BACKGROUND: Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins. RESULTS: Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes. CONCLUSION: These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.

Analysis of the Gut Microbial Diversity of Dairy Cows During Peak Lactation by PacBio Single-Molecule Real-Time (SMRT) Sequencing.

BACKGROUND: The gut microbes of dairy cows are strongly associated with their health, but the relationship between milk production and the intestinal microbiota has seldom been studied. Thus, we explored the diversity of the intestinal microbiota during peak lactation of dairy cows. METHODS: The intestinal microbiota of nine dairy cows at peak lactation was evaluated using the Pacific Biosciences single-molecule real-time (PacBio SMRT) sequencing approach. RESULTS: A total of 32,670 high-quality 16S rRNA gene sequences were obtained, belonging to 12 phyla, 59 families, 107 genera, and 162 species. Firmicutes (83%) were the dominant phylum, while Bacteroides (6.16%) was the dominant genus. All samples showed a high microbial diversity, with numerous genera of short chain fatty acid (SCFA)-producers. The proportion of SCFA producers was relatively high in relation to the identified core intestinal microbiota. Moreover, the predicted functional metagenome was heavily involved in energy metabolism. CONCLUSIONS: This study provided novel insights into the link between the dairy cow gut microbiota and milk production.