Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum.

The novel strain AM35T was isolated from the faeces of C57BL/6 mice. These cells are strictly anaerobic, gram negative, oxidase negative, catalase positive, rod-shaped and non-motile. The strain produced creamy yellowish colonies on brain heart infusion (BHI) agar with hemin. Growth was investigated at 30-41 °C in the presence of 0.5-1.5% (w/v) NaCl at pH 6.5-8.5. Taxonomic analysis based on 16S rRNA gene sequencing revealed that strain AM35T is affiliated with the family Muribaculaceae and closely related to the genus Muribaculum. The genomic DNA G + C content of strain AM35T was 47.8 mol%. We detected the whole-cell sugars ribose and galactose; meso-2,6-diaminopimelic acid was absent. The major fatty acids (> 10%) were anteiso-C15:0 and iso-C15:0; the major polar lipid was phosphatidylethanolamine. The major respiratory quinones were MK-10 and MK-11. Based on our phylogenetic, phenotypic and chemotaxonomic analyses, strain AM35T represents a novel genus within the family Muribaculaceae, for which we propose the name Heminiphilus faecis gen. nov., sp. nov. The type strain of Heminiphilus faecis gen. nov., sp. nov. is AM35T (= KCTC 15907 T = DSM 110151 T).

Dysbiosis-induced IL-33 contributes to impaired antiviral immunity in the genital mucosa.

Commensal microbiota are well known to play an important role in antiviral immunity by providing immune inductive signals; however, the consequence of dysbiosis on antiviral immunity remains unclear. We demonstrate that dysbiosis caused by oral antibiotic treatment directly impairs antiviral immunity following viral infection of the vaginal mucosa. Antibiotic-treated mice succumbed to mucosal herpes simplex virus type 2 infection more rapidly than water-fed mice, and also showed delayed viral clearance at the site of infection. However, innate immune responses, including type I IFN and proinflammatory cytokine production at infection sites, as well as induction of virus-specific CD4 and CD8 T-cell responses in draining lymph nodes, were not impaired in antibiotic-treated mice. By screening the factors controlling antiviral immunity, we found that IL-33, an alarmin released in response to tissue damage, was secreted from vaginal epithelium after the depletion of commensal microbiota. This cytokine suppresses local antiviral immunity by blocking the migration of effector T cells to the vaginal tissue, thereby inhibiting the production of IFN-γ, a critical cytokine for antiviral defense, at local infection sites. These findings provide insight into the mechanisms of homeostasis maintained by commensal bacteria, and reveal a deleterious consequence of dysbiosis in antiviral immune defense.

Dermabacter vaginalis sp. nov., isolated from human vaginal fluid.

A novel actinobacterial strain, AD1-86T, was isolated from the vaginal fluid of a Korean female and was characterized by a polyphasic approach. The strain was a facultatively anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase-positive and oxidase-negative short rod. Colonies were creamy white, of low convexity and 1-2 mm in diameter after growth on DSM 92 agar plates at 37 °C for 2 days. The most closely related strains were Dermabacter hominis DSM 7083T and Helcobacillus massiliensis 6401990T (98.3 and 96.3 % 16S rRNA gene sequence similarity, respectively). The isolate grew optimally at 37 °C and pH 7 in the presence of 0.5% (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the cell-wall hydrolysates contained ribose, galactose and glucose. The DNA G+C content was 62.6 mol% and the mean DNA-DNA relatedness value of the isolate to D. hominis DSM 7083T was 31.1±3.0% (reciprocal: 48.2±5.3%). The major cellular fatty acids (>10%) were anteiso-C17:0, anteiso-C15:0 and iso-C16:0, and the menaquinones were MK-9, MK-8 and MK-7. The polar lipid profile of strain AD1-86T consisted of diphosphatidylglycerol, phosphatidylglycerol, two aminolipids and a glycolipid. Data from this polyphasic study indicate that strain AD1-86T represents a novel species of the genus Dermabacter, for which the name Dermabacter vaginalis sp. nov. is proposed; the type strain is AD1-86T (=KCTC 39585T=DSM 100050T).

Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.

A novel bacterial strain, SR79T, was isolated from a Korean faecal sample and characterized using a polyphasic approach. SR79T was found to be a strictly anaerobic, Gram-stain-positive, non-spore-forming, non-motile, catalase- and oxidase-negative short rod with no flagella. SR79T grew optimally at 37 °C in the presence of 0.5 % (w/v) NaCl at pH 7. The NaCl range for growth was 0-1 % (w/v). The isolate produced butyric acid (>18 mM) as a major end product. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the most closely related type strains were Eubacteriumdesmolans ATCC 43058T and Butyricicoccus pullicaecorum 25-3T (96.4 and 96.0 % similarity, respectively). The DNA G+C content was determined to be 52.9 mol%. The major cellular fatty acids (>10 %) were C16 : 0, C18 : 1cis-9, C19 : 1 cyc 9,10 and C14 : 0. Meso-diaminopimelic acid was present in the cell wall peptidoglycan and the cell wall hydrolysates contained ribose, glucose and galactose. The 16S rRNA gene sequence similarity, phylogenetic analysis, chemotaxonomic and phenotypic characteristics allowed differentiation of SR79T, which represents a novel species of a new genus within the family Ruminococcaceae, for which the name Agathobaculum butyriciproducens gen. nov. sp. nov. is proposed. The type strain is SR79T (=KCTC 15532T=DSM 100391T). Based on the results of this study, it is also proposed to transfer Eubacteriumdesmolans to this new genus, as Agathobaculum desmolans comb. nov. The type strain of Agathobaculum desmolans is ATCC 43058T (=CCUG 27818T).

Pseudomonas kribbensis sp. nov., isolated from garden soils in Daejeon, Korea.

Two bacterial strains, 46-1 and 46-2T, were isolated from garden soil. These strains were observed to be aerobic, Gram-stain negative, rod-shaped, non-spore-forming, motile and catalase and oxidase positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains shared 100 % sequence similarity with each other and belong to the genus Pseudomonas in the class Gammaproteobacteria. The concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences further confirmed that the isolates belong to the Pseudomonas koreensis subgroup (SG), with P. koreensis Ps 9-14T, Pseudomonas moraviensis 1B4T and Pseudomonas granadensis F-278,770T as their close relatives (>96 % pairwise similarity). DNA-DNA hybridization with the closely related type strain P. koreensis SG revealed a low level of relatedness (<50 %). A cladogram constructed using whole-cell matrix-assisted laser desorption/ionization time-of-flight (WC-MALDI-TOF) MS analysis showed the isolates formed a completely separate monophyletic group. The isolates were negative for utilization of glycogen, D-psicose, α-keto butyric acid, α-keto valeric acid, succinamic acid and D, L-α-glycerol phosphate. In contrast, all these reactions were positive in P. koreensis JCM 14769T and P. moraviensis DSM 16007T. The fatty acid C17:0 cyclo was detected as one of the major cellular fatty acids (>15 %) in the isolates but it was a minor component (<4 %) in both reference type strains. In contrast, the fatty acid, C12:0 was not observed in the isolates but was present in both reference strains. Based on differences such as phylogenetic position, low-level DNA-DNA hybridization, WC-MALDI-TOF MS analysis, fluorescence pigmentation, fatty acid profiles, and substrate utilization, we propose that the isolates 46-1 and 46-2T represent a novel species of the genus Pseudomonas, for which the name Pseudomonas kribbensis sp. nov. is proposed; the type strain is 46-2T (=KCTC 32541T = DSM 100278T).

Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae).

A novel, Gram-stain positive, facultative anaerobic, non-motile and straight to curve rod shaped bacterium, strain LV19(T) was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus, which was collected from Yeong-dong, Chuncheongbuk-do, South Korea. The colonies of the new isolate were convex, circular, cream white in color and 1-2 mm in diameter after 3 days incubation on Tryptic Soy Agar at 37 °C. Based on the 16S rRNA gene sequence similarity, the new isolate was most closely related to Erysipelothrix inopinata MF-EP02(T), E. rhusiopathiae ATCC 19414 (T) and E. tonsillarum T-305(T) (94.8, 93.8 and 93.7 % similarity, respectively). Strain LV19(T) grew optimally at 37 °C, at pH 8.0 and in the presence of 0.5 % (w/v) NaCl. Oxidase activity and catalase activity were negative. The major cellular fatty acids (>10 %) were C18:2 cis-9,12 (28.9 %), C18:1 cis-9 (22.3 %), C16:0 (22.2 %) and C18:0 (18.5 %). The cell-wall hydrolysates contained ribose as a major sugar. Major polar lipids were phosphatidylglycerol and three unidentified glycolipids. No quinone was detected. The G+C content of the genomic DNA was 36.3 mol%. The levels of DNA-DNA relatedness between strain LV19(T) and all the reference strains were less than 20 %. On the basis of polyphasic evidence from this study, the isolate is considered to represent a novel species of the genus Erysipelothrix, for which the name Erysipelothrix larvae sp. nov. is proposed; the type strain is LV19(T) (=KCTC 33523(T) = DSM 28480(T)).

Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse.

A novel strictly anaerobic strain, ALO17(T), was isolated from mouse faeces and found to produce lactic acid as a major metabolic end product. The isolate was observed to be Gram-stain positive, non-motile, non-spore forming small rods, oxidase and catalase negative, and to form cream-coloured colonies on DSM 104 agar plates. The NaCl range for growth was determined to be 0-2 % (w/v). The isolate was found to grow optimally at 37 °C, with 0.5 % (w/v) NaCl and at pH 7. The cell wall hydrolysates were found to contain ribose as a major sugar. The genomic DNA G+C content was determined to be 52.3 mol%. A phylogenetic analysis of the 16S rRNA gene sequence revealed that Holdemanella biformis DSM 3989(T), Faecalicoccus pleomorphus ATCC 29734(T), Faecalitalea cylindroides ATCC 27803(T), and Allobaculum stercoricanis DSM 13633(T) are closely related to the isolate (87.4, 87.3, 86.9 and 86.9 % sequence similarity), respectively. The major cellular fatty acids (>10 %) of the isolate were identified as C18:1 cis 9 FAME (36.9 %), C16:0 FAME (33.7 %) and C18:0 FAME (13.2 %). In contrast to the tested reference strains, C20:0 FAME (4.0 %) was detected only in strain ALO17(T) whilst C16:0 DMA was absent. The isolate also differed in its substrate oxidation profiles from the reference strains by being positive for D-melibiose and stachyose but negative for N-acetyl-D-galactosamine and 3-methyl-D-glucose. On the basis of polyphasic taxonomic evidence from this study, the isolate is concluded to belong to a novel genus within the family Erysipelothricaceae. We propose the name Faecalibaculum rodentium gen. nov., sp. nov. to accommodate strain ALO17(T) (=KCTC 15484(T) = JCM 30274(T)) as the type strain.

Bacillus solimangrovi sp. nov., isolated from mangrove soil.

Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2% similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85% similarity to those of the most closely related strains. The isolates grew at pH 5-12 (optimal growth at pH 9), at 10-40 °C (optimum 30-35 °C) and at 0-9% (w/v) NaCl (optimum 1-3% NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA-DNA relatedness between the isolates and five related reference strains was 20-24%. Strain GH2-4T exhibited 81% DNA-DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15:0, iso-C16:0, iso-C14:0 and anteiso-C15:0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 (=KCTC 33143=JCM 18995=DSM 27084) represent a novel species of the genus Bacillus, for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T (=KCTC 33142T=JCM 18994T=DSM 27083T).

Agathobaculum butyriciproducens improves ageing-associated cognitive impairment in mice.

AIMS: The gut microbiota is increasingly recognised as a pivotal regulator of immune system homeostasis and brain health. Recent research has implicated the gut microbiota in age-related cognitive impairment and dementia. Agathobaculum butyriciproducens SR79 T (SR79), which was identified in the human gut, has been reported to be beneficial in addressing cognitive deficits and pathophysiologies in a mouse model of Alzheimer's disease. However, it remains unknown whether SR79 affects age-dependent cognitive impairment. MAIN METHOD: To explore the effects of SR79 on cognitive function during ageing, we administered SR79 to aged mice. Ageing-associated behavioural alterations were examined using the open field test (OFT), tail suspension test (TST), novel object recognition test (NORT), Y-maze alternation test (Y-maze), and Morris water maze test (MWM). We investigated the mechanisms of action in the gut and brain using molecular and histological analyses. KEY FINDINGS: Administration of SR79 improved age-related cognitive impairment without altering general locomotor activity or depressive behaviour in aged mice. Furthermore, SR79 increased mature dendritic spines in the pyramidal cells of layer III and phosphorylation of CaMKIIα in the cortex of aged mice. Age-related activation of astrocytes in the cortex of layers III-V of the aged brain was reduced following SR79 administration. Additionally, SR79 markedly increased IL-10 production and Foxp3 and Muc2 mRNA expression in the colons of aged mice. SIGNIFICANCE: These findings suggest that treatment with SR79 may be a beneficial microbial-based approach for enhancing cognitive function during ageing.

The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation.

Akkermansia muciniphila has received great attention because of its beneficial roles in gut health by regulating gut immunity, promoting intestinal epithelial development, and improving barrier integrity. However, A. muciniphila-derived functional molecules regulating gut health are not well understood. Microbiome-secreted proteins act as key arbitrators of host-microbiome crosstalk through interactions with host cells in the gut and are important for understanding host-microbiome relationships. Herein, we report the biological function of Amuc_1409, a previously uncharacterised A. muciniphila-secreted protein. Amuc_1409 increased intestinal stem cell (ISC) proliferation and regeneration in ex vivo intestinal organoids and in vivo models of radiation- or chemotherapeutic drug-induced intestinal injury and natural aging with male mice. Mechanistically, Amuc_1409 promoted E-cadherin/ß-catenin complex dissociation via interaction with E-cadherin, resulting in the activation of Wnt/ß-catenin signaling. Our results demonstrate that Amuc_1409 plays a crucial role in intestinal homeostasis by regulating ISC activity in an E-cadherin-dependent manner and is a promising biomolecule for improving and maintaining gut health.