Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (L-arabinose, L-rhamnose, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restrictionmodification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.

Since dogs are part of many peoples’ lives, research and industry related to their health and longevity are becoming a rising topic. Although gut microbiota (GM) is a key contributor to host health, limited information is available for canines. Therefore, this study characterized GM according to individual signatures (e.g., breed, age, and body condition score—BCS) of dogs living in the same environment. Fresh fecal samples from 96 healthy dogs were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. The major microbial phyla were Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria, and Actinobacteria. In the comparison by breeds, relative abundance of Fusobacterium was significantly differed. Interestingly, Fusobacterium perfoetens abundance was positively correlated with age (p = 0.018), being significantly more enriched in the 6–10-year-old group (14.3%) than in the 0.5–1-year-old group (7.2%). Moreover, despite the healthy appearance of dogs in all age (0.5–10 years) and BCS (3–6) groups, the gut microbial environment may be disadvantageous in older dogs or in dogs with an abnormal BCS. These findings broaden our understanding of gut microbial ecology according to individual characteristics of dogs and may be used as a reference for providing customized-care to companion animals.

The oral cavity is the second-largest habitat for microorganisms, and a well-balanced oral microbiome contributes to preventing dental disorders caused by pathogenic bacteria. Since humans and dogs have different lifestyles and oral microbiome structures, the present study aimed to develop novel probiotics for dogs. A total 53 Lactobacillus spp. were isolated from healthy dogs, and nine isolates were identified as Lactobacillus acidophilus according to 16S rRNA gene sequencing. According to the high antimicrobial activity against the dental caries-causing bacterium Streptococcus mutans, single or three mixed strains were orally administered to dogs for 4 weeks with concentration of 108-109 CFU/day. Intraoral swab samples were collected before and after the administration, and changes of oral pathogen were analyzed using quantitative PCR. Among them, Porphyromonas gingivalis, a critical factor of periodontitis, was significantly reduced in the single-strain administered group. Based on the acid and bile salts tolerance characteristics of isolates, systemic effects were also analyzed by comparing serum immunoglobulin and reproductive ability before and after the administration. However, no significant changes were observed in the serum IgG level and sperm quality. Overall, these in vitro and in vivo results suggest that L. acidophilus isolates from dogs, especially L. acidophilus MJCD175, could be promising probiotic candidates to support oral health without systemic adverse effects in dogs.

Many Lactobacillus species are frequently isolated from dairy products, animal guts, and the vaginas of healthy women. However, sequencing-based identification of isolated Lactobacillus strain is time/cost-consuming and lobor-intensive. In this study, we developed a multiplex PCR method to distinguish six closely related species in the Lactobacillus acidophilus group (L. gasseri, L. acidophilus, L. helveticus, L. jensenii, L. crispatus, and L. gallinarum), which is based on species-specific primer sets. Altogether, 86 genomes of 9 Lactobacillus species from the National Center of Biotechnology Information (NCBI) database were compared to detect species-specific genes and design six species-specific primer sets. The PCR conditions of the individual primer sets were optimized via gradient PCR methods. A final multiplex PCR condition was also optimized for a mixture of all six primer sets mixed. When identifying a single strain, the optimized multiplex PCR method can specifically detect one of the six species, but no band was amplified at least from the other Lactobacillus and Enterococcus species. These results indicated that species-specific primer sets designed from the genome comparison could identify one strain within the six Lactobacillus species by a single PCR reaction. Using the method described here, we will be able to save time, cost, and labor during species identification and screening of commercially important probiotic lactobacilli.

Although several methods have been developed to improve male fertility and sperm quality, subfertility remains a primary clinical issue in male reproduction worldwide. The aim of this study was to determine the effects of the oral administration of three commensal Lactobacillus spp. on healthy normozoospermic dogs and the qualitative parameters of their sperm. Three weeks of supplementation induced a significant decrease of two phyla, Proteobacteria and Tenericutes, and an increase of phylum Firmicutes. At the species level, the number of Fusobacterium perfoetens and Anaerobiospirillum succiniciproducens decreased, while Limosilactobacillus reuteri increased. Parallel to these results, qualitative sperm parameters such as total and progressive motility, acrosome integrity, and other kinematic parameters were significantly enhanced after commensal lactobacilli supplementation. In addition, we showed that Firmicutes were positively correlated with sperm qualitative parameters, while Proteobacteria, F. perfoetens, and A. succiniciproducens were negatively correlated. Considering the similarities between the gut microbiome of dogs and humans, these results provide more insight into how gut microbiota regulation could improve male sperm quality in both species.

Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5 °C) versus warm (HT, 23 °C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO : 0008610, P < 0.001) and regulation of apoptotic process (GO : 0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO : 0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO : 0001666, P < 0.05), transcription regulator activity (GO : 0140110, P < 0.001) and calcium-release channel activity (GO : 0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO : 0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

Backgrounds: Hypomesus nipponensis is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming. Aim of the study: Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. Methods: We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. Results: We observed a total of 1,987 contigs, with N50 of 0.46 Gbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KO (KEGG Orthology). In the missing and gained genes analysis, we detected 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes with coverage less than 10% and for gained genes found from alignment to other species that human, zebrafish and salmon, respectively, we observed 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes with coverage less than 10% compared with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs, adjusted p-value < 0.05) were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. Conclusion: The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and be useful for better survival of the smelt and its closely related species under global warming.

Changes in the gut microbiome can be associated with diseases and affect the overall health of an individual. In the current study, the gut microbiome profile of dogs diagnosed with advanced stages of multicentric lymphoma was compared with that of healthy dogs and analyzed. For this purpose, dogs from veterinary hospitals diagnosed with lymphoma were selected and were further narrowed down to cases of stage IV multicentric lymphoma. Fecal samples from the selected sick and healthy dogs were collected and analyzed using MiSeq sequencing. The gut microbiota in the two groups of dogs was statistically analyzed and compared. The results revealed significant differences in the microbial populations present in sick and healthy dogs, particularly at the in some bacterial groups. Phylum Actinobacteria and two species (Corynebacterium amycolatum and Streptococcus lutetiensis) were found in high proportions in sick dogs and may be considered as potential biomarkers for canine stage IV multicentric lymphoma. Further investigations need to be conducted to understand the mechanisms they might be involved in.