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).

Diversity Analysis of Intestinal Bifidobacteria in the Hohhot Population.

(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.

In Vitro Evaluation of Intestinal Transport and High-Density Fermentation of Lactobacillus acidophilus.

Lactobacillus acidophilus strains have limiting factors such as low cell density and complex nutritional requirements in industrial production, which greatly restricts their industrial application. In this study, fermentation conditions for L. acidophilus were optimized and transcriptomic analysis used to understand growth mechanisms under high-density fermentation conditions. We found that L. acidophilus IMAU81186 has strong tolerance to gastrointestinal juice. In addition, its optimal culture conditions were 3% inoculum (v/v); culture temperature 37 °C; initial pH 6.5; and medium composition of 30.18 g/L glucose, 37.35 g/L soybean peptone, 18.68 g/L fish peptone, 2.46 g/L sodium citrate, 6.125 g/L sodium acetate, 2.46 g/L K2HPO4, 0.4 g/L MgSO4·7H2O,0.04 g/L MnSO4·5H2O, 0.01 g/L serine, and 0.3 g/L uracil. After optimization, viable counts of IMAU81186 increased by 7.03 times. Differentially expressed genes in IMAU81186 were analyzed at different growth stages using transcriptomics. We found that a single carbon source had limitations in improving the biomass of the strain, and terP and bfrA were significantly down-regulated in the logarithmic growth period, which may be due to the lack of extracellular sucrose. After optimizing the carbon source, we found that adding 12 g/L sucrose to the culture medium significantly increased cell density.

Comparative Genomics Analysis of Habitat Adaptation by Lactobacillus kefiranofaciens.

Lactobacillus kefiranofaciens is often found in fermented dairy products. Many strains of this species have probiotic properties, contributing to the regulation of immune metabolism and intestinal flora. This species was added to the list of lactic acid bacteria that can be added to food in China, in 2020. However, research on the genomics of this species is scarce. In this study we undertook whole genome sequencing analysis of 82 strains of L. kefiranofaciens from different habitats, of which 9 strains were downloaded from the NCBI RefSeq (National Center for Biotechnology Information RefSeq). The mean genome size of the 82 strains was 2.05 ± 0.25 Mbp, and the mean DNA G + C content was 37.47 ± 0.42%. The phylogenetic evolutionary tree for the core genes showed that all strains belonged to five clades with clear aggregation in relation to the isolation habitat; this indicated that the genetic evolution of L. kefiranofaciens was correlated to the isolation habitat. Analysis of the annotation results identified differences in the functional genes, carbohydrate active enzymes (CAZy) and bacteriocins amongst different isolated strains, which were related to the environment. Isolates from kefir grains had more enzymes for cellulose metabolism and a better ability to use vegetative substrates for fermentation, which could be used in feed production. Isolates from kefir grains also had fewer kinds of bacteriocin than isolates from sour milk and koumiss; helveticin J and lanthipeptide class I were not found in the isolates from kefir grains. The genomic characteristics and evolutionary process of L. kefiranofaciens were analyzed by comparative genomics and this paper explored the differences in the functional genes amongst the strains, aiming to provide a theoretical basis for the research and development of L. kefiranofaciens.

Gut microbiome and aging nexus and underlying mechanism.

According to the United Nations population profile, the number of individuals aged 60 and over in high-income nations is expected to rise from 302 million to over 366 million between 2019 and 2030, so there is an increasing emphasis on nutrition and health in older people. Numerous studies have demonstrated the crucial role that gut microbiota plays in maintaining human health. As a model of healthy aging, centenarians have different gut microbiota from ordinary elderly people. The core microbiome of centenarians in various countries has shown some common characteristics, which are worth further exploration. In this review, the significance of the human gut microbiota to health is briefly discussed, and the characteristics of the gut microbiota of long-lived senior persons of different ages and in different countries are described. Moreover, this review lists dietary interventions and fecal microbiota transplantation. In the end, it discusses the pros and cons of using probiotics to enhance the health of seniors through focused management of the gut microbiota. It aims to pave the way for further investigation into the nexus between gut microbiota, probiotics, and longevity, and then to reveal the underlying mechanism to promote longevity. KEY POINTS: • Gut microbial structure in different age groups and the characteristics of gut microbiota in centenarians. • Dietary interventions, fecal transplants, and probiotics target the modulation of gut microbiota for healthy aging.

[Textual research on classical prescriptions in Mongolian medicine].

Mongolians have a long history of using prescriptions, which can be classified into four stages as follows: the germination and experience accumulation stage before the 13 th century, the theoretical formation stage from the 13 th to 16 th century, the rapid development stage from the 17 th to 20 th century, and the leaping development stage from the mid-20 th century to the present. The prescriptions from the ancient classical or representative medical books have always been used by Mongolian physicians for generations, and they are still in use due to the definite curative effects. In 2008, the Notice on Issuing the Supplementary Provisions to the Registration and Management of Traditional Chinese Medicine(TCM) described that China has attached more importance to the excavation and development of classical prescriptions. As stipulated in the Law of the People's Republic of China on Traditional Chinese Medicine, the classical prescriptions should be those available in ancient TCM classics and still in wide use, with exact curative effects, distinct features, and obvious advantages. This paper expounded the historical formation and development of classical prescriptions in Mongo-lian medicine, introduced the five most influential ancient medical books revealing the formation and development of these classic prescriptions, and traced the origin of such classical prescriptions as Wenguanmu Siwei Decoction, Shouzhangshen Bawei Decoction, Jianghuang Siwei Decoction and summarized the origin, development history and characteristics of classical prescriptions in Mongolian medicine, aiming to provide a reference for their further research and development.

Comparison of Bacterial Microbiota in Raw Mare's Milk and Koumiss Using PacBio Single Molecule Real-Time Sequencing Technology.

Koumiss is a traditional fermented raw mare's milk product. It contains high nutritional value and is well-known for its health-promoting effect as an alimentary supplement. This study aimed to investigate the bacterial diversity, especially lactic acid bacteria (LAB), in koumiss and raw mare's milk. Forty-two samples, including koumiss and raw mare's milk, were collected from the pastoral area in Yili, Kazakh Autonomous Prefecture, Xinjiang Uygur Autonomous Region in China. This work applied PacBio single-molecule real-time (SMRT) sequencing to profile full-length 16S rRNA genes, which was a powerful technology enabling bacterial taxonomic assignment to the species precision. The SMRT sequencing identified 12 phyla, 124 genera, and 227 species across 29 koumiss samples. Eighteen phyla, 286 genera, and 491 species were found across 13 raw mare's milk samples. The bacterial microbiota diversity of the raw mare's milk was more complex and diverse than the koumiss. Raw mare's milk was rich in LAB, such as Lactobacillus (L.) helveticus, L. plantarum, Lactococcus (Lc.) lactis, and L. kefiranofaciens. In addition, raw mare's milk also contained sequences representing pathogenic bacteria, such as Staphylococcus succinus, Acinetobacter lwoffii, Klebsiella (K.) oxytoca, and K. pneumoniae. The koumiss microbiota mainly comprised LAB, and sequences representing pathogenic bacteria were not detected. Meanwhile, the koumiss was enriched with secondary metabolic pathways that were potentially beneficial for health. Using a Random Forest model, the two kinds of samples could be distinguished with a high accuracy 95.2% [area under the curve (AUC) = 0.98] based on 42 species and functions. Comprehensive depiction of the microbiota in raw mare's milk and koumiss might help elucidate evolutionary and functional relationships among the bacterial communities in these dairy products. The current work suffered from the limitation of a low sample size, so further work would be required to verify our findings.

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.

Characterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum.

Breast milk is the main source of nutrition for infants; it contains considerable microflora that can be transmitted to the infant endogenously or by breastfeeding, and it plays an important role in the maturation and development of the immune system. In this study, we isolated and identified lactic acid bacteria (LAB) from human colostrum, and screened 2 strains with probiotic potential. The LAB isolated from 40 human colostrum samples belonged to 5 genera: Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, and Staphylococcus. We also isolated Propionibacterium and Actinomyces. We identified a total of 197 strains of LAB derived from human colostrum based on their morphology and 16S rRNA sequence, among them 8 strains of Bifidobacterium and 10 strains of Lactobacillus, including 3 Bifidobacterium species and 4 Lactobacillus species. The physiological and biochemical characteristics of strains with good probiotic characteristics were evaluated. The tolerances of some of the Bifidobacterium and Lactobacillus strains to gastrointestinal fluid and bile salts were evaluated in vitro, using the probiotic strains Bifidobacterium lactis BB12 and Lactobacillus rhamnosus GG as controls. Among them, B. lactis Probio-M8 and L. rhamnosus Probio-M9 showed survival rates of 97.25 and 78.33% after digestion for 11 h in artificial gastrointestinal juice, and they exhibited growth delays of 0.95 and 1.87 h, respectively, in 0.3% bile salts. These two strains have the potential for application as probiotics and will facilitate functional studies of probiotics in breast milk and the development of human milk-derived probiotics.

A survey of the relationship between functional genes and acetaldehyde production characteristics in Streptococcus thermophilus by multilocus sequence typing.

Streptococcus thermophilus is an important bacterium used in the production of fermented dairy products. Yogurt with good flavor is preferred by consumers; thus, variation in flavor-formation characteristics among isolates is attracting attention. Here, acetaldehyde production characteristics of 30 isolates were evaluated in parallel with genotyping and multilocus sequence typing of key functional genes involved in acetaldehyde production. The results showed that isolates could be divided into 3 phenotypically distinct groups: high-acetaldehyde-yielding isolates (>10 mg/L), medium-acetaldehyde-yielding isolates (5-10 mg/L) and low-acetaldehyde-yielding (<5 mg/L) based on evaluation of acetaldehyde production during yogurt storage. These groups, distinguishable by phenotypic characteristics, were clustered in corresponding groups based on functional gene multilocus sequence typing analysis. Combining functional gene sequence analysis of 30 Strep. thermophilus isolates with phenotypic evaluation of their flavor-related characteristics (specifically acetaldehyde production) demonstrated that groups of isolates established using genotype data analysis corresponded with groups identified based on their phenotypic traits. Interestingly, the 30 isolates of Strep. thermophilus showed significant phylogenetic clustering in acetaldehyde content by functional gene and acetaldehyde content analysis. A corresponding relationship exists between functional gene phylogenetic clustering and acetaldehyde content variation.

Metabolomic analysis of significant changes in Lactobacillus casei Zhang during culturing to generation 4,000 under conditions of glucose restriction.

Lactic acid bacteria are being consumed more frequently as awareness of their health benefits has increased. The industrial production of lactic acid bacteria requires a comprehensive understanding of their survival stress, especially regarding changes in metabolic substances in a glucose-limited environment. In the present study, a metabolomic approach was applied to investigate Lactobacillus casei Zhang using cultures from a common ancestor that were permitted to evolve under conditions with normal or glucose-restricted media for up to 4,000 generations. Metabolomic analyses of intracellular and extracellular differential metabolites under De Man, Rogosa and Sharpe broth (2% vol/vol glucose; Oxoid Ltd., Basingstoke, UK) and glucose-restricted (0.02% vol/vol glucose in De Man, Rogosa and Sharpe broth) conditions were performed at generations 0, 2,000, and 4,000 and revealed 23 different metabolites. Myristic acid, ergothioneine, Lys-Thr, and palmitamide contents exhibited significant reductions between 0 and 4,000 generations, whereas nicotinate, histidine, palmitic acid, l-lysine, urocanate, thymine, and other substances increased. The dynamics of the pathways involved in AA metabolism, including glycine, serine, and threonine metabolism, histidine metabolism, lysine degradation, and arginine and proline metabolism, were also a focus of the present study. There were also changes in several other metabolic pathways, including vitamin B6, thiamine, nicotinate, and nicotinamide, according to generation time. Additionally, in the present study we screened for key metabolites involved in the glucose-restricted response and provided a theoretical basis for comprehensively revealing the regulatory mechanisms associated with L. casei Zhang glucose restriction at the metabolic level. These findings also provide novel ideas and methods for analyzing the glucose-restricted stress response at the metabolic level.

Evaluation of Bacterial Contamination in Goat Milk Powder Using PacBio Single Molecule Real-Time Sequencing and Droplet Digital PCR.

Goat milk powder is a nutritious and easy-to-store product that is highly favored by consumers. However, the presence of contaminating bacteria and their metabolites may significantly affect the flavor, solubility, shelf life, and safety of the product. To comprehensively and accurately understand the sanitary conditions in the goat milk powder production process and potential threats from bacterial contamination, a combination of Pacific Biosciences single molecule real-time sequencing and droplet digital PCR was used to evaluate bacterial contamination in seven goat milk powder samples from three dairies. Ten phyla, 119 genera, and 249 bacterial species were identified. Bacillus, Paenibacillus, Lactococcus, and Cronobacter were the primary genera. Bacillus cereus, Lactococcus lactis, Alkaliphilus oremlandii, and Cronobacter sakazakii were the dominant species. With droplet digital PCR, 6.3 × 104 copies per g of Bacillus cereus and 1.0 × 104 copies per g of Cronobacter spp. were quantified, which may increase the risk of food spoilage and the probability of foodborne illness and should be monitored and controlled. This study offers a new approach for evaluating bacterial contamination in goat milk powder and supplies a reference for the assessment of food safety and control of potential risk, which will be of interest to the dairy industry.

A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation).

Commercially available and traditional dairy products differ in terms of their manufacturing processes. In this study, commercially available and traditionally fermented cheese, yogurt, and milk beverages were analyzed and compared. The metabolomic technique of ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF) in the MSE mode was used in combination with statistical methods, including univariate analysis and chemometric analysis, to determine the differences in metabolite profiles between commercially and traditionally fermented dairy products. The experimental results were analyzed statistically and showed that traditional and commercial dairy products were well differentiated in both positive and negative ion modes, with significant differences observed between the samples. After screening for metabolite differences, we detected differences between traditional milk beverages and yogurt and their commercial counterparts in terms of the levels of compounds such as l-lysine, l-methionine, l-citrulline, l-proline, l-serine, l-valine and l-homocysteine, and of short peptides such as Asp-Arg, Gly-Arg, His-Pro, Pro-Asn. The greatest difference between commercially available and traditional cheese was in the short peptide composition, as commercially available and traditional cheese is rich in short peptides.

Effects of microencapsulated Lactobacillus plantarum LIP-1 on the gut microbiota of hyperlipidaemic rats.

The in vivo effects of administering free and microencapsulated Lactobacillus plantarum LIP-1 cells (2·0×109 colony-forming units/d) were evaluated in high-fat-diet-induced hyperlipidaemic rats. Results from real-time quantitative PCR targeting to LIP-1 cells showed a higher colon colonisation count of LIP-1 in the rats receiving microencapsulated cells compared with free cells (P<0·05). Moreover, the microencapsulated LIP-1 treatment resulted in a more obvious lipid-lowering effect (P<0·05). Meanwhile, their faecal samples had significantly less lipopolysaccharide-producing bacteria (especially Bilophila, Sutterella and Oscillibacter) and mucosa-damaging bacteria (Bilophila and Akkermansia muciniphila), whereas significantly more SCFA-producing bacteria (P<0·05) (namely Lactobacillus, Alloprevotella, Coprococcus, Eubacterium and Ruminococcus) and bacteria that potentially possessed bile salt hydrolase activity (Bacteroides, Clostridium, Eubacterium and Lactobacillus), and other beneficial bacteria (Alistipes and Turicibacter). Further, Spearman's correlation analysis showed significant correlations between some of the modulated gut bacteria and the serum lipid levels. These results together confirm that microcapsulation enhanced the colon colonisation of LIP-1 cells, which subsequently exhibited more pronounced effects in improving the gut microbiota composition of hyperlipidaemic rats and lipid reduction.

Carbohydrate Staple Food Modulates Gut Microbiota of Mongolians in China.

Gut microbiota is a determining factor in human physiological functions and health. It is commonly accepted that diet has a major influence on the gut microbial community, however, the effects of diet is not fully understood. The typical Mongolian diet is characterized by high and frequent consumption of fermented dairy products and red meat, and low level of carbohydrates. In this study, the gut microbiota profile of 26 Mongolians whom consumed wheat, rice and oat as the sole carbohydrate staple food for a week each consecutively was determined. It was observed that changes in staple carbohydrate rapidly (within a week) altered gut microbial community structure and metabolic pathway of the subjects. Wheat and oat favored bifidobacteria (Bifidobacterium catenulatum, Bifodobacteriumbifidum, Bifidobacterium adolescentis); whereas rice suppressed bifidobacteria (Bifidobacterium longum, Bifidobacterium adolescentis) and wheat suppresses Lactobaciilus, Ruminococcus and Bacteroides. The study exhibited two gut microbial clustering patterns with the preference of fucosyllactose utilization linking to fucosidase genes (glycoside hydrolase family classifications: GH95 and GH29) encoded by Bifidobacterium, and xylan and arabinoxylan utilization linking to xylanase and arabinoxylanase genes encoded by Bacteroides. There was also a correlation between Lactobacillus ruminis and sialidase, as well as Butyrivibrio crossotus and xylanase/xylosidase. Meanwhile, a strong concordance was found between the gastrointestinal bacterial microbiome and the intestinal virome. Present research will contribute to understanding the impacts of the dietary carbohydrate on human gut microbiome, which will ultimately help understand relationships between dietary factor, microbial populations, and the health of global humans.

A Perspective Study of Koumiss Microbiome by Metagenomics Analysis Based on Single-Cell Amplification Technique.

Koumiss is a traditional fermented dairy product and a good source for isolating novel bacteria with biotechnology potential. In the present study, we applied the single-cell amplification technique in the metagenomics analysis of koumiss. This approach aimed at detecting the low-abundant bacteria in the koumiss. Briefly, each sample was first serially diluted until reaching the level of approximately 100 cells. Then, three diluted bacterial suspensions were randomly picked for further study. By analyzing 30 diluted koumiss suspensions, a total of 24 bacterial species were identified. In addition to the previously reported koumiss-associated species, such as Lactobacillus (L.) helveticus. Lactococcus lactis. L. buchneri, L. kefiranofaciens, and Acetobacter pasteurianus, we successfully detected three low-abundant taxa in the samples, namely L. otakiensis. Streptococcus macedonicus, and Ruminococcus torques. The functional koumiss metagenomes carried putative genes that relate to lactose metabolism and synthesis of typical flavor compounds. Our study would encourage the use of modern metagenomics to discover novel species of bacteria that could be useful in food industries.

Comparative genomic analysis of the genus Enterococcus.

As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced. In combination with eight complete genome sequences from the Genbank database, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. The average length of Enterococcus genomes was 3.20Mb and the average GC content was 37.99%. The core- and pan- genomes were defined based on the genomes of the 37 strains of Enterococcus. The core-genome contained 605 genes, a large proportion of which were associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism. The phylogenetic tree showed that habitat is very important in the evolution of Enterococcus. The genetic relationships were closer in strains that come from similar habitats. According to the topology of the time tree, we found that humans and mammals may be the original hosts of Enterococcus, and then species from humans and mammals made a host-shift to plants, birds, food and other environments. However, it was just an evolutionary scenario, and more data and efforts were needed to prove this postulation. The comparative genomic analysis provided a snapshot of the evolution and genetic diversity of the genus Enterococcus, which paves the way for follow-up studies on its taxonomy and functional genomics.

Characterization of Antibiotic Resistance Genes from Lactobacillus Isolated from Traditional Dairy Products.

Lactobacilli are widely used as starter cultures or probiotics in yoghurt, cheese, beer, wine, pickles, preserved food, and silage. They are generally recognized as safe (GRAS). However, recent studies have shown that some lactic acid bacteria (LAB) strains carry antibiotic resistance genes and are resistant to antibiotics. Some of them may even transfer their intrinsic antibiotic resistance genes to other LAB or pathogens via horizontal gene transfer, thus threatening human health. A total of 33 Lactobacillus strains was isolated from fermented milk collected from different areas of China. We analyzed (1) their levels of antibiotic resistance using a standardized dilution method, (2) their antibiotic resistance gene profiles by polymerase chain reaction (PCR) using gene-specific primers, and (3) the transferability of some of the detected resistance markers by a filter mating assay. All Lactobacillus strains were found to be resistant to vancomycin, but susceptible to gentamicin, linezolid, neomycin, erythromycin, and clindamycin. Their susceptibilities to tetracycline, kanamycin, ciprofloxacin, streptomycin, quinupristin/dalfopristin, trimethoprim, ampicillin, rifampicin, and chloramphenicol was different. Results from our PCR analysis revealed 19 vancomycin, 10 ciprofloxacin, and 1 tetracycline-resistant bacteria that carried the van(X), van(E), gyr(A), and tet(M) genes, respectively. Finally, no transferal of the monitored antibiotic resistance genes was observed in the filter mating assay. Taken together, our study generated the antibiotic resistance profiles of some milk-originated lactobacilli isolates and preliminarily assessed their risk of transferring antibiotic gene to other bacteria. The study may provide important data concerning the safe use of LAB.

Isolation and Identification of Lactic Acid Bacteria from Traditional Dairy Products in Baotou and Bayannur of Midwestern Inner Mongolia and q-PCR Analysis of Predominant Species.

In this study, traditional culture method and 16S rRNA gene analysis were applied to reveal the composition and diversity of lactic acid bacteria (LAB) of fermented cow milk, huruud and urum from Baotou and Bayannur of midwestern Inner Mongolia. Also, the quantitative results of dominant LAB species in three different types of dairy products from Baotou and Bayannur were gained by quantitative polymerase chain reaction (q-PCR) technology. Two hundred and two LAB strains isolated from sixty-six samples were identified and classified into four genera, namely Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, and twenty-one species and subspecies. From these isolates, Lactococcus lactis subsp. lactis (32.18%), Lactobacillus plantarum (12.38%) and Leuconosto mesenteroides (11.39%) were considered as the dominated LAB species under the condition of cultivating in MRS and M17 medium. And the q-PCR results revealed that the number of dominant species varied from samples to samples and from region to region. This study clearly shows the composition and diversity of LAB existing in fermented cow milk, huruud and urum, which could be considered as valuable resources for LAB isolation and further probiotic selection.

Investigating bacterial population structure and dynamics in traditional koumiss from Inner Mongolia using single molecule real-time sequencing.

Koumiss is considered as a complete dairy product high in nutrients and with medicinal properties. The bacterial communities involved in production of koumiss play a crucial role in the fermentation cycle. To reveal bacterial biodiversity in koumiss and the dynamics of succession in bacterial populations during fermentation, 22 samples were collected from 5 sampling sites and the full length of the 16S ribosomal RNA genes sequenced using single molecule real-time sequencing technology. One hundred forty-eight species were identified from 82 bacterial genera and 8 phyla. These results suggested that the structural difference in the bacterial community could be attributed to geographical location. The most significant difference in bacterial composition occurred in samples from group D compared with other groups. The sampling location of group D was distant from the city and maintained the primitive local nomadic life. The dynamics of succession in bacterial communities showed that Lactobacillus helveticus increased in abundance from 0 to 9h and reached its peak at 9h and then decreased. In contrast, Enterococcus faecalis, Enterococcus durans, and Enterococcus casseliflavus increased gradually throughout the fermentation process, and reached a maximum after 24h.