High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease.

The clinical spectra of irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) intersect to form a scantily defined overlap syndrome, termed pre-IBD. We show that increased Enterobacteriaceae and reduced Clostridia abundance distinguish the fecal microbiota of pre-IBD patients from IBS patients. A history of antibiotics in individuals consuming a high-fat diet was associated with the greatest risk for pre-IBD. Exposing mice to these risk factors resulted in conditions resembling pre-IBD and impaired mitochondrial bioenergetics in the colonic epithelium, which triggered dysbiosis. Restoring mitochondrial bioenergetics in the colonic epithelium with 5-amino salicylic acid, a PPAR-γ (peroxisome proliferator-activated receptor gamma) agonist that stimulates mitochondrial activity, ameliorated pre-IBD symptoms. As with patients, mice with pre-IBD exhibited notable expansions of Enterobacteriaceae that exacerbated low-grade mucosal inflammation, suggesting that remediating dysbiosis can alleviate inflammation. Thus, environmental risk factors cooperate to impair epithelial mitochondrial bioenergetics, thereby triggering microbiota disruptions that exacerbate inflammation and distinguish pre-IBD from IBS.

Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings.

A strictly anaerobic bacterium, strain B5(T), was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5(T) were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5-7.5 and 25-45°C, respectively. Growth of strain B5(T) was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0-4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5(T) grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5(T) did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5(T) is most closely related to the genus Tepidibacillus (T. fermentans STGH(T); 96.3%) and Vulcanibacillus (V. modesticaldus BR(T); 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5(T) was higher than those of T. fermentans STGH(T) (34.8 mol%) and V. modesticaldus BR(T) (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5(T) (=KCTC 15397(T) =JCM 19989(T)), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater.

A novel strain (designated sjH1T), characterized as aerobic, Gram-stain-negative, oxidase-positive, catalase-negative, motile and rod-shaped, was isolated from mine wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain sjH1T belonged to the genus Rhodanobacter. Strain sjH1T was closely related to Rhodanobacter thiooxydans LCS2T (98.0% 16S rRNA gene sequence similarity), Rhodanobacter denitrificans 2APBS1T (97.7%), Rhodanobacter soli DCY45T (97.2%) and Rhodanobacter caeni MJ01T (97.0%). The DNA G+C content of strain sjH1T was 69.2 mol%. DNA-DNA relatedness ( < 60%) indicated that strain sjH1T represents a distinct species that is separate from R. thiooxydans, R. denitrificans, R. soli and R. caeni. The major ubiquinone was Q-8, and major fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. Based on data from this polyphasic study, it is proposed that sjH1T ( = KCTC 42660T = JCM 30774T) is the type strain of a novel species, Rhodanobacter aciditrophus sp. nov.

Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated from an oil-contaminated site.

In this study, an alkaliphilic and heterotrophic iron-reducing bacterial strain, IRF9(T), was isolated from an oil-contaminated soil in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IRF9(T) belongs to the genus Geosporobacter in the family Clostridiaceae and is most closely related to Geosporobacter subterraneus VNs68(T) (96.9 % sequence similarity). Cells of strain IRF9(T) were observed to be straight or curved rod-shaped, motile and Gram-negative. Optimal growth of strain IRF9(T) was observed at pH 9.0-9.5 and 40 °C. The strain was found to grow within pH and temperature ranges of 6.5-10.0 and 25-45 °C, respectively. NaCl was not required for growth. Fe(III), but not sulfate, thiosulfate or elemental sulfur can be used by strain IRF9(T) as an electron acceptor. A limited number of carbohydrates and amino acids, including D-glucose, D-fructose, D-mannitol, D-ribose and L-arginine, support growth of strain IRF9(T). The main fatty acids (>10 %) of strain IRF9(T) were identified as C14:0 (18.4 %), C16:1 cis9 (13.6 %), C16:0 (12.4 %) and C16:0 dimethyl acetal (17.7 %). Major respiratory quinone was identified as menaquinone MK-5 (V-H2). The main polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content of strain IRF9(T) was determined to be 37.2 mol%, which is lower than that of G. subterraneus VNs68(T) (42.2 mol%). Based on phenotypic, chemotaxonomic, and phylogenetic studies, we conclude that strain IRF9(T) (=JCM 19987(T) = KCTC 15395(T)) represents a new species of the genus Geosporobacter, for which we propose the name Geosporobacter ferrireducens sp. nov.

Anaerosolibacter carboniphilus gen. nov., sp. nov., a strictly anaerobic iron-reducing bacterium isolated from coal-contaminated soil.

A strictly anaerobic, mesophilic, iron-reducing bacterial strain, IRF19(T), was isolated from coal-contaminated soil in the Republic of Korea. IRF19(T) cells were straight, rod-shaped, Gram-staining-negative and motile by means of flagella. The optimum pH and temperature for their growth were determined to be pH 7.5-8.0 and 40 °C, while the optimum range was pH 6.5-10.0 and 20-45 °C, respectively. Strain IRF19(T) did not require NaCl for growth but it tolerated up to 2% (w/v). Growth was observed with yeast extract, D-glucose, D-fructose, D-ribose, D-mannitol, D-mannose, L-serine, L-alanine and L-isoleucine. Fe(III), elemental sulfur, thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain IRF19(T) is affiliated to the family Clostridiaceae and is most closely related to Salimesophilobacter vulgaris Zn2(T) (93.5% similarity), Geosporobacter subterraneus VNs68(T) (93.2%) and Thermotalea metallivorans B2-1(T) (92.3%). The major cellular fatty acids of strain IRF19(T) were C14 : 0, iso-C15 : 0 and C16 : 0, and the profile was distinct from those of the closely related species. The major respiratory quinone of strain IRF19(T) was menaquinone MK-5 (V-H2). The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and two unknown polar lipids. The G+C content of the genomic DNA of strain IRF19(T) was determined to be 37.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic results, strain IRF19(T) is considered to represent a novel species of a novel genus of the family Clostridiaceae , for which we propose the name Anaerosolibacter carboniphilus gen. nov., sp. nov., with the type strain IRF19(T) ( =KCTC 15396(T) =JCM 19988(T)).

Draft genome sequence of an aromatic compound-degrading bacterium, Desulfobacula sp. TS, belonging to the Deltaproteobacteria.

Herein, we report a high-quality draft genome sequence of an uncultivated aromatic compound-degrading bacterium, obtained by the stable isotope probing method from a sulfate-reducing microcosm from an oil-contaminated tidal flat. The obtained genome was closely related with that of Desulfobacula toluolica Tol2. Abundant genes for various anaerobic aromatic degradation pathways and putative mobile elements were detected in the genome.

Methanomethylovorans uponensis sp. nov., a methylotrophic methanogen isolated from wetland sediment.

A novel mesophilic, methylotrophic, methanogenic archaeon, designated strain EK1(T), was enriched and isolated from wetland sediment. Phylogenetic analysis showed that strain EK1(T) was affiliated with the genus Methanomethylovorans within the family Methanosarcinaceae, and shared the highest 16S rRNA and methyl-coenzyme M reductase alpha-subunit gene sequence similarity with the type strain of Methanomethylovorans hollandica (98.8 and 92.6 %, respectively). The cells of strain EK1(T) were observed to be Gram-negative, non-motile and irregular cocci that did not lyse in 0.1 % (w/v) sodium dodecyl sulfate. Methanol, mono-, di- and trimethylamine, dimethyl sulfide and methanethiol were found to be used as catabolic and methanogenic substrates, whereas H2/CO2, formate, 2-propanol and acetate were not. Growth was observed at 25-40 °C (optimum, 37 °C), at pH 5.5-7.5 (optimum, pH 6.0-6.5) and in the presence of 0-0.1 M NaCl (optimum, 0 M). Growth and methane production rates were stimulated in the presence of H2/CO2 although methane production and growth yields were not significantly affected; acetate, formate, 2-propanol and CO/CO2/N2 did not affect methane production. CoCl2 (0.6-2.0 µM) and FeCl2 (25 mg/l) stimulated growth, while yeast extract and peptone did not. The DNA-DNA hybridization experiment revealed a relatedness of <20 % between EK1(T) and the type strains of the genus Methanomethylovorans. The DNA G+C content of strain EK1(T) was determined to be 39.2 mol%. Based on the polyphasic taxonomic study, strain EK1(T) represents a novel species belonging to the genus Methanomethylovorans, for which the name Methanomethylovorans uponensis sp. nov. is proposed. The type strain is strain EK1(T)(=NBRC 109636(T) = KCTC 4119(T) = JCM 19217(T)).