• Comparative genomic analyses of Lactobacillus rhamnosus isolated from Chinese subjects

      Huang, Dan; Yang, Bo; Chen, Yang; STANTON, CATHERINE; Ross, R Paul; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; National First-Class Discipline Program of Food Science and Technology; et al. (Elsevier, 2020-08-31)
      Lactobacillus rhamnosus has been found in many niches, including human intestine, vagina, mouth and dairy products. To intensively investigate the genomic diversity of this species, draft genomes of 70 L. rhamnosus strains isolated from different Chinese subjects were sequenced and further investigated. The pan-genome of L. rhamnosus was open. And gene-trait matching (GTM) was done to explore the carbohydrate utilization ability and antibiotic resistance, and to establish a pattern of gene existence/absence and growth/absence. There were no significant correlations between genetic diversity of the strains and the age or region of the donors. The current results extend the understanding of L. rhamnosus, which could be used as a reference for subsequent research as well as mining and application of the species.
    • Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches

      Wang, Shuo; Yang, Bo; Ross, R. Paul; STANTON, CATHERINE; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; Jiangsu Province; 31771953; et al. (MDPI AG, 2020-01-08)
      Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.
    • Comparative genomics and gene-trait matching analysis of Bifidobacterium breve from Chinese children

      Liu, Rui; Yang, Bo; STANTON, CATHERINE; Ross, Paul; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; National First-Class Discipline Program of Food Science and Technology; the Fundamental Research Funds for the Central Universities; et al. (Elsevier BV, 2020-08)
      Bifidobacterium breve is one of the dominant Bifidobacterial species in children. In the current work, 46 strains of B. breve isolated from fecal samples of Chinese children were analyzed using whole-genome sequencing and comparative genomics to explore their genetic diversity, as well as genotype and phenotype analysis for carbohydrate utilization and antibiotic tolerance. The phylogenetic tree was independent of region, age and feeding mode, and without any regularity in the clustering of carbohydrates and antibiotics at the genetic level. Based on genotypic-phenotypic correlation analysis, the diversity of glycosyl hydrolases and the ability of strains to metabolize carbohydrates corroborated the predominance of B. breve in the children's intestines. Simultaneously, the sensitivity of strains to antibiotics increased the understanding of its genetic features and provided a potential basis for safety evaluation.
    • Diversity of Gut Microbiota and Bifidobacterial Community of Chinese Subjects of Different Ages and from Different Regions

      Yang, Bo; Yan, Shuang; Chen, Yang; Ross, R. Paul; STANTON, CATHERINE; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; National First-Class Discipline Program of Food Science and Technology; et al. (MDPI AG, 2020-07-24)
      Gut microbiota composition and functionality are closely linked to host health. In this study, the fecal microbiota and bifidobacterial communities of 111 healthy volunteers from four regions of China of varying age profiles (Child, 1–5 years; Young, 18–50 years; Elder, 60–80 years; Longevity, ≥90 years) were investigated via high-throughput sequencing. Canonical analysis revealed that the gut microbiota, as well as bifidobacteria profiles of the subjects, clustered according to their regions and age. Eight genera were shared among all subjects, however, certain genera distributed differently in subjects grouped by region and age. Faecalibacterium was enriched in samples from Zhongxiang, unclassified Ruminococcaceae and Christensenellaceae were enriched in the Longevity group, and Bifidobacterium was enriched in Child. Within Bifidobacterium, B. longum was the most abundant species in almost all samples except for Child, in which B. pseudocatenulatum was the most abundant. Additionally, the abundances of B. adolescentis and B. dentium were lower in Child. In conclusion, our results suggest that geography and age affect the structure of the gut microbiota, as well as Bifidobacterium composition, and this variation may greatly associate with the metabolic and immune changes that occur during the process of aging.
    • Lactobacillus acidophilus JCM 1132 Strain and Its Mutant with Different Bacteriocin-Producing Behaviour Have Various In Situ Effects on the Gut Microbiota of Healthy Mice

      Wang, Gang; Yu, Yunxia; Garcia-Gutierrez, Enriqueta; Jin, Xing; He, Yufeng; Wang, Linlin; Tian, Peijun; Liu, Zhenmin; Zhao, Jianxin; Zhang, Hao; et al. (MDPI AG, 2019-12-25)
      The production of bacteriocin is considered to be a probiotic trait of lactic acid bacteria (LAB). However, not all strains of LAB harbour bacteriocin genes, even within the same species. Moreover, the effects of bacteriocins on the host gut microbiota and on host physiological indicators are rarely studied. This study evaluated the effects of the bacteriocin-producing Lactobacillus acidophilus strain JCM1132 and its non-producing spontaneous mutant, L. acidophilus CCFM720, on the physiological statuses and gut microbiota of healthy mice. Mice that received the bacteriocin-producing strain JCM1132 exhibited reduced water and food intake. Furthermore, the administration of these strains induced significant changes in the compositional abundance of faecal microbiota at the phylum and genus levels, and some of these changes were more pronounced after one week of withdrawal. The effects of CCFM720 treatment on the gut microbiota seemed to favour the prevention of metabolic diseases to some extent. However, individuals that received JCM1132 treatment exhibited weaker inflammatory responses than those that received CCFM720 treatment. Our results indicate that treatment with bacteriocin-producing or non-producing strains can have different effects on the host. Accordingly, this trait should be considered in the applications of LAB.