Gynurincola endophyticus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

Paraflavitalea devenefica sp. nov., isolated from urban soil

A Gram-stain-negative, rod-shaped, mesophilic, milky white-pigmented, aerobic, non-spore-forming and non-flagellated bacterium, designated strain X16^T, was isolated from urban soil of Zibo, Shandong, China. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Paraflavitalea soli 5GH32-13^T (97.6 %), Pseudoflavitalea soli KIS20-3^T (96.2 %), Pseudobacter ginsenosidimutans Gsoil 221^T (96.0 %) and Pseudoflavitalea rhizosphaerae T16R-265^T (95.8 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain X16^T formed a subcluster with Paraflavitalea soli 5GH32-13^T, and the subcluster was closely related to Pseudoflavitalea soli KIS20-3^T, Pseudobacter ginsenosidimutans Gsoil 221^T and Pseudoflavitalea rhizosphaerae T16R-265^T. Strain X16^T also formed a subcluster with Paraflavitalea soli 5GH32-13^T in phylogenetic tree based on genomic sequences. The polar lipids are phosphatidylethanolamine, two unknown aminolipids, two unknown aminophospholipids, two unknown lipids and two unknown phospholipids. The major quinone of strain X16^T is menaquinone-7 and the main fatty acids (>10 % of total fatty acids) of strain X16^T are iso-C_15 : 0, iso-C_17 : 0 3-OH and iso-C_15 : 1 G. The genome length of strain X16^T is 8.7 Mb with a DNA G+C content of 47.4 %. ANI values among strain X16^T and strain Paraflavitalea soli 5GH32-13^T, Pseudobacter ginsenosidimutans Gsoil 221^T, and Pseudoflavitalea rhizosphaerae T16R-265^T are 78.1, 70.7, 70.6 %, respectively. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain X16^T represents a novel species. Besides, strain X16^T can detoxify high toxicity selenite [Se(IV)] to low toxicity elemental selenium [Se(0)], for which the name Paraflavitale devenefica sp. nov. is proposed. The type strain is X16^T (=KACC 21698^T=GDMCC1.1757^T).

Agriterribacter humi gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from soil of a farming field

A Gram-stain-negative bacterium, designated strain YJ03^T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ03^T was found to be an aerobic, non-motile and non-spore-forming bacterium which can grow at 10-33 °C (optimum, 25-28 °C), at pH 6.6-9.5 (optimum, pH 7.0-7.5) and at salinities of 0-1.0 % (w/v) NaCl (optimum, 0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ03^T with the closely related relatives were in the range 93.9-92.2 %, and the results of phylogenomic analysis indicated that strain YJ03^T was clearly separated from species of the genera in the family Chitinophagaceae, showing average nucleotide identity values of 68.8-64.3 %. The predominant isoprenoid quinone was identified as MK-7 and the major fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and an unidentified fatty acid with an equivalent chain-length of 13.565. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, four unidentified aminolipids and six unidentified lipids. The G+C content of the genome was determined to be 41.8 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences in this study, strain YJ03^T is considered to represent a novel species of a new genus in the family Chitinophagaceae, for which the name Agriterribacter humi gen. nov., sp. nov., is proposed. The type strain of Agriterribacter humi is YJ03^T (=KACC 19548^T=NBRC 113195^T).

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov

A Gram-stain-negative, microaerophilic, non-motile, rod-shaped bacterium strain designated PMP191F^T, was isolated from a human peritoneal tumour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism formed a lineage within the family Chitinophagaceae that was distinct from members of the genus Pseudoflavitalea (95.1-95.2 % sequence similarity) and Pseudobacter ginsenosidimutans (94.4 % sequence similarity). The average nucleotide identity values between strain PMP191F^T and Pseudoflavitalea rhizosphaerae T16R-265^T and Pseudobacter ginsenosidimutans Gsoil 221^T was 68.9 and 62.3% respectively. The only respiratory quinone of strain PMP191F^T was MK-7 and the major fatty acids were iso-C_15 : 0, iso-C_15 : 1 G and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine and some unidentified amino and glycolipids. The G+C content of strain PMP191F^T calculated from the genome sequence was 43.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strain PMP191F^T represents a novel species and genus for which the name Parapseudoflavitalea muciniphila gen. nov., sp. nov. is proposed. The type strain is PMP191F^T (=DSM 104999^T=ATCC BAA-2857^T = CCUG 72691^T). The phylogenetic analyses also revealed that Pseudobacter ginsenosidimutans shared over 98 % sequence similarly to members of the genus Pseudoflavitalea. However, the average nucleotide identity value between Pseudoflavitalea rhizosphaerae T16R-265^T, the type species of the genus and Pseudobacter ginsenosidimutans Gsoil 221^T was 86.8 %. Therefore, we also propose that Pseudobacter ginsenosidimutans be reclassified as Pseudoflavitalea ginsenosidimutans comb. nov.