Microbiota associated with caries and apical periodontitis: A next-generation sequencing study.

Aim: This study investigated the correlation between microbiota of caries-free enamel and caries-affected dentine biofilms and that of root canals with primary apical periodontitis, by using an Illumina MiSeq platform.

Methodology: Biofilm from caries-free enamel surface (Biofilm-C) or caries-affected dentine (Biofilm-E) and root canal paper point samples (Canal) were collected from 31 teeth with primary apical periodontitis. Microbial composition was analysed by amplicon sequencing that targeted the V3-V4 region of 16S rRNA gene.

. nov., isolated from the gut of a Korean limpet, .

A novel bacterium, designated strain JHSY0214, was isolated from the gut of a Korean limpet, . Cells of strain JHSY0214 were Gram-stain-negative, strictly aerobic, yellow-pigmented, non-spore-forming, non-motile and showed a rod-coccus growth cycle. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus , and was most closely related to KCTC 12764 (98.

Arginine-mediated gut microbiome remodeling promotes host pulmonary immune defense against nontuberculous mycobacterial infection.

Nontuberculous mycobacterial pulmonary diseases (NTM-PDs) are emerging as global health threats with issues of antibiotic resistance. Accumulating evidence suggests that the gut-lung axis may provide novel candidates for host-directed therapeutics against various infectious diseases. However, little is known about the gut-lung axis in the context of host protective immunity to identify new therapeutics for NTM-PDs.

Host phylogeny, habitat, and diet are main drivers of the cephalopod and mollusk gut microbiome.

Background: Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota and the determining factors is essential for understanding their symbiotic mechanism. Cephalopods are invertebrates that have similar biological properties to vertebrates such as closed circulation system, an advanced nervous system, and a well-differentiated digestive system.

Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish.

Three aerobic, Gram-negative, and rod-shaped bacterial strains, designated strains G4M1, SM13, and L12M9, were isolated from the gut of Batillaria multiformis, Cellana toreuma, and Patinopecten yessoensis collected from the Yellow Sea in South Korea. All the strains grew optimally at 25°C, in the presence of 2% (w/v) NaCl, and at pH 7. These three strains, which belonged to the genus Polaribacter in the family Flavobacteriaceae, shared < 98.

sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease.

Cultivation and isolation of gut bacteria are necessary for understanding their role in the intestinal ecosystem. We isolated a novel bacterium, designated strain BG01, from the faeces of a patient with Crohn's disease. Strain BG01 was a strictly anaerobic, rod-shaped, Gram-variable and endospore-forming bacterium.

Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds.

Phenotypic and genomic analyses were performed to characterize two novel species, H23M54 and AMA3305, isolated from the faeces of the Oriental stork (Ciconia boyciana) and the cinereous vulture (Aegypius monachus), respectively. Strains H23M54 and AMA3305 showed the highest similarities of 16S rRNA gene sequences and complete genome sequences with Ornithinimicrobium cavernae CFH 30183 (98.5% of 16S rRNA gene sequence similarity and 82.

Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome.

Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model.

sp. nov., isolated from the gut of the freshwater mussel .

A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18, was isolated from the gut of the freshwater mussel collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus . Strain 2T18 formed a monophyletic clade with KCTC 42982, KACC 11706 and KCTC 23839, with sequence similarities of 98.

sp. nov., isolated from the intestine of the dark diving beetle , and sp. nov., isolated from the intestine of the diving beetle .

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, designated as HDW11 and HDW19, isolated from intestine samples of the dark diving beetle and the diving beetle , respectively. Both isolates were Gram-stain-positive, facultatively anaerobic and non-motile. Strain HDW11 grew optimally at 30 °C, pH 8 and in the presence of 1% (w/v) NaCl.

sp. nov., isolated from the gut of the Korean turban shell, .

A novel Gram-stain-negative, coccus-shaped, aerobic and motile bacterial strain, designated S12M18, was isolated from the gut of the Korean turban shell, . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S12M18 belonged to the genus and had the highest 16S rRNA gene sequence similarity twith HDW-19 (98.63 %).

Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus.

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17A and HDW17B, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.

Male castration increases adiposity via small intestinal microbial alterations.

Castration of young males is widely used in the cattle industry to improve meat quality, but the mechanism linking hypogonadism and host metabolism is not clear. Here, we use metataxonomic and metabolomic approaches to evaluate the intestinal microbiota and host metabolism in male, castrated male (CtM), and female cattle. After pubescence, the CtM cattle harbor distinct ileal microbiota dominated by the family Peptostreptococcaceae and exhibit distinct serum and muscle amino acid profiles (i.

sp. nov., isolated from the faeces of the oriental stork, .

A novel Gram-stain-positive, non-motile, non-spore-forming, coccobacillus-shaped, strictly aerobic bacterium, designated strain H23T48, was isolated from the faecal sample of an oriental stork collected from the Seoul Grand Park Zoo in Seoul, Republic of Korea. Optimal growth of strain H23T48 was observed at 30-37 °C, pH 8 and with 3 % (w/v) NaCl. 16S rRNA gene sequence-based phylogenetic analysis revealed that strain H23T48 was closely related to the genus , with 97.

sp. nov., isolated from the faeces of an Oriental stork.

A novel, Gram-stain-positive, non-spore-forming, facultatively anaerobic bacterium, designated strain H21T32, was isolated from the faeces of an Oriental stork, . Cells formed cocci grouped in pairs, tetrads or conglomerates, and colonies on solid medium were pale yellow. Strain H21T32 belonged to the genus , family , order and class .

sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, .

A novel Gram-negative, obligately aerobic, rod-shaped and non-motile bacterium, designated strain K13M18, was isolated from the intestinal tract of a Korean indigenous fish, oily bitterling (). Strain K13M18 formed creamy-pink colonies on a marine agar plate. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain K13M18 was most closely related to DRYC-M-16, sharing 97.

sp. nov., isolated from the gut of the Korean scallop, .

A novel Gram-stain-negative, aerobic, rod-shaped, reddish-orange-coloured, gliding bacterial strain, designated L12M1, was isolated from the gut of the Korean scallop, . Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain L12M1 formed a monophyletic clade with the strains in the genus and showed highest 16S rRNA gene sequence similarity to YS10 (98.66 %).

sp. nov., isolated from Korean shiner intestine.

A novel Gram-stain-negative, non-spore-forming, obligate aerobic, motile, rod-shaped, and flagellated bacterium, designated S11R28, was isolated from the intestinal tract of a Korean shiner, . Based on 16S rRNA gene sequences, strain S11R28 was identified as member of the genus in class , and was closely related to DSM 23061 (98.49 %).

sp. nov., a bacterium isolated from feces of oriental stork, .

A novel Gram-stain-negative, facultatively anaerobic, non-motile, non-violet-pigmented, rod-shaped bacterium, designated strain H11R3, was isolated from the feces of Oriental stork, , collected from Seoul Grand Park Zoo, Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that H11R3 formed a monophyletic clade with DSM 3764, DSM 100243, and DSM 103822, with sequence similarities of 98.8, 98.

Phenotypic and Genomic Properties of sp. nov. and sp. nov.

Two strains, VM2412 and VR2415, were isolated from the feces of an Andean condor () living in Seoul Grand Park, Gyeonggi-do, South Korea. Cells of both strains were observed to be Gram-stain positive, non-motile, aerobic, catalase positive and oxidase negative. Growth was found to occur at 10-30°C, showing optimum growth at 30°C.

Oceanisphaera avium sp. nov., isolated from the gut of the cinereous vulture, Aegypius monachus.

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, rod-shaped, flagellated bacterial strain, designated AMac2203, was isolated from the gut of the cinereous vulture, Aegypiusmonachus, collected from the Seoul Grand Park Zoo, Republic of Korea. Strain AMac2203 grew optimally at 15-25 °C, pH 7-8 and in the presence of 3-5 % (w/v) NaCl. Phylogenetic analysis revealed 97.