Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil

Description of Olsenella kribbiana sp. nov., an anaerobic bacterium isolated from pig faeces

A short-rod-shaped, obligate anaerobic, Gram-stain-positive bacterium isolated from the faeces of a pig was designated as the strain YH-ols2221T. The analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Olsenella phocaeensis DSM 103159T, Olsenella urininfantis KCTC 25755T and Olsenella absiana KCTC 25800T with 96.6-96.7% similarities. The multi-locus sequence tree revealed that the isolate formed a cluster adjacent to O. absiana KCTC 25800T. The average nucleotide identity and the digital DNA-DNA hybridization values for the isolate and the most closely related strains were 71.7-74.1% and 19.9-23.0%, respectively. The main fatty acids identified were C14 : 0, C16 : 0 DMA and C18 : 0  ω9c DMA. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The end products of the fermentation were lactic acid and acetic acid. Given the chemotaxonomic, phenotypic and phylogenetic properties, YH-ols2221T (=KCTC 25801T=NBRC 116679T) represents a novel taxon. The name Olsenella kribbiana sp. nov. was proposed.

Description of Veillonella absiana sp. nov., isolated from pig faeces

Two Gram-stain-negative cocci anaerobes were isolated from pig faeces and designated as strains YH-vei2232T and YH-vei2233. Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates were most closely related to Veillonella rogosae KCTC 5967T, with 97.0% similarity. Analysis of housekeeping gene sequences (rpoB) revealed the strain formed a sub-cluster within the genus Veillonella. The average nucleotide identities between the two isolates and the most closely related strains within genus Veillonella were <75.0%. The major fatty acids were Summed Feature 8 and C16 : 1  ω9c. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major metabolic end products of isolates were propionic and acetic acids. The genomic DNA G+C contents of both strains were 40.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-vei2232T (=KCTC 25748T=NBRC 116427T) and YH-vei2233 (=KCTC 25749=NBRC 116428) suggest that they represent a novel species of the genus Veillonella, for which the name Veillonella absiana sp. nov. is proposed.

Aerococcus kribbianus sp. nov., a facultatively anaerobic bacterium isolated from pig faeces

Two cocci-shaped, facultatively anaerobic, Gram-positive bacteria isolated from the faeces of a pig were designated as strains YH-aer221T and YH-aer222. Analysis of the 16S rRNA gene sequences revealed that the isolates were most closely related to Aerococcus suis JCM 18035T with 96.6 % similarity. The multi-locus sequence tree revealed that the isolates formed a sub-cluster adjacent to A. suis JCM 18035T. The average nucleotide identity values for the isolates and their most closely related strains were 71.8 and 71.7 %, respectively; and the digital DNA-DNA hybridization values for the isolates and their most closely related strains were 25.6 and 25.5 %, respectively. The main fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 0. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The two isolates shared the same metabolic pathways. Isolates YH-aer221T and YH-aer222 harboured the same CRISPR array with 33 and 46 spacers, respectively. Single-genome vs. metagenome analysis showed that the genomes of the isolates were not found in the available metagenome database. Given their chemotaxonomic, phenotypic and phylogenetic properties, YH-aer221T (= KCTC 25571T=JCM 35699T) and YH-aer222 (=KCTC 25573=JCM 35700) represent a novel taxon. The name Aerococcus kribbianus sp. nov. is proposed.

The novel immunobiotic Clostridium butyricum S-45-5 displays broad-spectrum antiviral activity in vitro and in vivo by inducing immune modulation

Clostridium butyricum is known as a probiotic butyric acid bacterium that can improve the intestinal environment. In this study, we isolated a new strain of C. butyricum from infant feces and evaluated its physiological characteristics and antiviral efficacy by modulating the innate immune responses in vitro and in vivo. The isolated C. butyricum S-45-5 showed typical characteristics of C. butyricum including bile acid resistance, antibacterial ability, and growth promotion of various lactic acid bacteria. As an antiviral effect, C. butyricum S-45-5 markedly reduced the replication of influenza A virus (PR8), Newcastle Disease Virus (NDV), and Herpes Simplex Virus (HSV) in RAW264.7 cells in vitro. This suppression can be explained by the induction of antiviral state in cells by the induction of antiviral, IFN-related genes and secretion of IFNs and pro-inflammatory cytokines. In vivo, oral administration of C. butyricum S-45-5 exhibited prophylactic effects on BALB/c mice against fatal doses of highly pathogenic mouse-adapted influenza A subtypes (H1N1, H3N2, and H9N2). Before challenge with influenza virus, C. butyricum S-45-5-treated BALB/c mice showed increased levels of IFN-β, IFN-γ, IL-6, and IL-12 in serum, the small intestine, and bronchoalveolar lavage fluid (BALF), which correlated with observed prophylactic effects. Interestingly, after challenge with influenza virus, C. butyricum S-45-5-treated BALB/c mice showed reduced levels of pro-inflammatory cytokines and relatively higher levels of anti-inflammatory cytokines at day 7 post-infection. Taken together, these findings suggest that C. butyricum S-45-5 plays an antiviral role in vitro and in vivo by inducing an antiviral state and affects immune modulation to alleviate local and systemic inflammatory responses caused by influenza virus infection. Our study provides the beneficial effects of the new C. butyricum S-45-5 with antiviral effects as a probiotic.

Description and comparative genome analysis of Hallella absiana sp. nov., isolated from pig feces

OBJECTIVE

The genus Hallella was described within Bacteroidaceae, and then reclassified within Prevotellaceae based on its phenotypic and phylogenetic description. It is associated with degradation of carbohydrate. However, some species of Hallella have pathobiotic properties, and are involved in infections and chronic inflammatory disorders.

METHODS

Here, we used a polyphasic taxonomic approach to characterize the two strains: YH-C38^T and YH-C4B9b. A detailed metabolic analysis was conducted to compare the two novel isolates with related strains within the genus Hallella.

RESULT

Analysis of 16S rRNA gene sequences revealed that the isolates were most closely related to Hallella mizrahii JCM 34422^T with 98.5% and 98.6% similarities, respectively. Analysis of the multi-locus species tree based on whole genome sequences of the isolates and related strains revealed that the isolates formed a sub-cluster adjacent to H. mizrahii JCM 34422^T. The average nucleotide identity values for YH-C38^T and YH-C4B9b, and the most closely related strain H. mizrahii JCM 34422^T, were 93.5% and 93.8%, respectively. The main fatty acids were iso C_17:0 3OH and anteiso C_15:0. The predominant menaquinones were MK-12, MK-11, and MK-13. The cell wall contained the peptidoglycan of meso-diaminopimelic acid. Analysis of comparative metabolic analysis revealed that isolates YH-C38^T and YH-C4B9b each contained 155 carbohydrate-active enzymes, and glycoside hydrolase was the largest family.

CONCLUSION

Two rod-shaped, obligately anaerobic, Gram-stain-negative bacteria, isolated from pig feces, were designated as strains YH-C38^T and YH-C4B9b. Based on the chemotaxonomic, phenotypic, and phylogenetic properties, YH-C38^T (=KCTC 25103^T = JCM 35423^T) and YH-C4B9b (=KCTC 25104 = JCM 35609) represent a novel taxon. The name Hallella absiana sp. nov. is proposed.