Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring

Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil

Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity

OBJECTIVE

Faecal microbiota transplantation (FMT) in germ-free (GF) mice is a common approach to study the causal role of the gut microbiota in metabolic diseases. Lack of consideration of housing conditions post-FMT may contribute to study heterogeneity. We compared the impact of two housing strategies on the metabolic outcomes of GF mice colonised by gut microbiota from mice treated with a known gut modulator (cranberry proanthocyanidins (PAC)) or vehicle.

DESIGN

High-fat high-sucrose diet-fed GF mice underwent FMT-PAC colonisation in sterile individual positive flow ventilated cages under rigorous housing conditions and then maintained for 8 weeks either in the gnotobiotic-axenic sector or in the specific pathogen free (SPF) sector of the same animal facility.

RESULTS

Unexpectedly, 8 weeks after colonisation, we observed opposing liver phenotypes dependent on the housing environment of mice. Mice housed in the GF sector receiving the PAC gut microbiota showed a significant decrease in liver weight and hepatic triglyceride accumulation compared with control group. Conversely, exacerbated liver steatosis was observed in the FMT-PAC mice housed in the SPF sector. These phenotypic differences were associated with housing-specific profiles of colonising bacterial in the gut and of faecal metabolites.

CONCLUSION

These results suggest that the housing environment in which gnotobiotic mice are maintained post-FMT strongly influences gut microbiota composition and function and can lead to distinctive phenotypes in recipient mice. Better standardisation of FMT experiments is needed to ensure reproducible and translatable results.

Environmental Selection Shapes Bacterial Community Composition in Traditionally Fermented Maize-Based Foods from Benin, Tanzania and Zambia

Natural (microbial) communities are complex ecosystems with many interactions and cross-dependencies. Among other factors, selection pressures from the environment are thought to drive the composition and functionality of microbial communities. Fermented foods, when processed using non-industrial methods, harbor such natural microbial communities. In non-alcoholic fermented foods the fermenting microbiota is commonly dominated by 4–10 species of bacteria, which make them suitable model systems to study ecosystem assembly and functioning. In this study, we assess the influence of the environment on the composition of microbial communities of traditional fermented products from Africa. We compare differences between microbial communities that are found in similar products but come from different countries, hypothesizing they experience different environmental selection pressures. We analyzed bacterial community composition in 36 samples of various cereal-based fermented foods from Benin, Tanzania and Zambia using 16S rDNA amplicon sequencing. The differential abundance analysis indicates that the bacterial communities of fermented foods from the three countries are dominated by mostly lactic acid bacteria belonging to the genera of Lactobacillus, Weisella and Curvibacter. The samples from Zambia contain the most dissimilar microbial communities in comparison with samples from Benin and Tanzania. We propose this is caused by the relatively low temperature in Zambia, suggesting that indeed environmental selection can shape community composition of fermenting microbes.

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin

Strain SJQ9^T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30-35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9^T fell within the genus Aquabacterium. The closest phylogenetic relatives of strain SJQ9^T were Aquabacterium citratiphilum DSM 11900^T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901^T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9^T were consistent with those of the genus Aquabacterium: the major fatty acid was summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9^T exhibited a DNA-DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900^T and 28±3 % with A. commune DSM 11901^T. Based on the obtained data, strain SJQ9^T represents a novel species of the genus Aquabacterium, for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9^T (=JCM 33106^T=CCTCC AB 2018284^T).

Aquabacterium terrae sp. nov., isolated from soil

A yellow-colored bacterial strain, designated S2^T was isolated from soil in South Korea. Cells of strain S2^T were strictly aerobic, Gram-stain-negative, motile with single polar flagellum, rod-shaped, oxidase and catalase-negative. Growth occurs at 10-37 °C (optimum, 28 °C), pH 5.0-9.0 (optimum, pH 6.5-7.0) and 0-3% NaCl (w/v). Strain S2^T consisted of summed feature 3 (iso-C_15:0 2-OH and/or C_16:1 ω7c), C_16:0 and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) as major fatty acids. The sole respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine and an unidentified lipid. The 16S rRNA gene sequence analysis showed that strain S2^T is phylogenetically closest to Aquabacterium pictum W35^T (98.4% sequence similarity). The genome of strain S2^T was 8,039,486 bp with 56 scaffolds. The genome consisted of 10 putative biosynthetic gene clusters that are responsible for various secondary metabolites. Genomic DNA G + C content of strain S2^T was 69.4%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain S2^T and phylogenetically related taxa were ≤ 77.9 and ≤ 21.4%, and respectively. The results of genotypic and phenotypic data showed that strain S2^T could be distinguished from its phylogenetically related species and represents a novel species in the genus Aquabacterium, for which the name Aquabacterium terrae sp. nov. is proposed. The type strain is S2^T (= KCTC 72741 ^T = NBRC 114609 ^T).

Aquabacterium lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated KMB7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed cream colonies. Optimal growth occurred at 25 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain KMB7^T is affiliated with species in the genus Aquabacterium. The 16S rRNA gene sequence similarity indicated that strain KMB7^T is closely related to species within the genus Aquabacterium (95.2-97.6 % sequence similarity) and is most similar to A. fontiphilum CS-6^T (97.6 %), followed by A. parvum B6^T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization identity between strain KMB7^T and the closely related strains were 74.6-78.0 % and 19.0-21.2 %, respectively. The major fatty acids of strain KMB7^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_18 : 1  ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unidentified phospholipids. The sole isoprenoid quinone was ubiquinone-8 (Q-8). Genomic DNA G+C content of strain KMB7^T was 65.4 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KMB7^T should be classified in a novel species of the genus Aquabacterium, for which the name Aquabacterium lacunae sp. nov. is proposed. The type strain is KMB7^T (=BCRC 81156^T=LMG 30924^T=KCTC 62867^T).

Geomonas soli gen. nov., sp. nov., a New Member of the Family Comamonadaceae, Isolated from Soil

A Gram-stain negative, facultative aerobic bacterial strain, designated strain S-16^T, was isolated from soil in South Korea. Colonies were white-milkish and cells were non-motile rods with oxidase- and catalase-positive activities. The growth of strain S-16^T was observed at 20-40 °C (optimum, 25-30 °C) and pH 5.5-7.0 (optimum, pH 6.5). Ubiquinone-8 was identified as the sole respiratory quinone and C_12:0, C_16:0, C_18:0, C_15:1ω5c and summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c) were identified as the major fatty acids (>5%). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and an unidentified polar lipid. The G + C content of the genomic DNA calculated from the whole genome sequence was 66.8 mol%. Strain S-16^T was most closely related to Piscinibacter aquaticus IMCC1728^T, Rhizobacter gummiphilus NS21^T and Rhizobacter dauci H6^T with 16S rRNA gene sequence similarities of 97.93%, 97.93% and 97.44%, respectively. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences suggested that strain S-16^T could form a distinct phyletic lineage as a new genus within the family Comamonadaceae. Based on the phenotypic, chemotaxonomic and molecular features, strain S-16^T represents the type strain of a novel species of a novel genus within the family Comamonadaceae, for which the name Geomonas soli gen. nov., sp. nov. is proposed. The type strain is S-16^T (= KACC 19792^T = JCM 32971^T).

Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria

A strictly aerobic, bacteriochlorophyll a-containing betaproteobacterium, designated strain W35^T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35^T was closely related to species in the genus Aquabacterium. The closest phylogenetic relatives of strain W35^T were Aquabacterium commune B8^T (97.9 % sequence similarity), Aquabacterium citratiphilum B4^T (97.2 %) and Aquabacterium limnoticum ABP-4^T (97.0 %). The major cellular fatty acids were C_{16  :  1}ω7c (50.4 %), C_{16  :  0} (22.7 %), summed feature 8 (C_{18  :  1}ω7c/C_{18  :  1}ω6c; 9.7 %), C_{18  :  3}ω6c (5.5 %), C_{12  :  0} (5.3 %) and C_{10  :  0} 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35^T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35^T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35^T was clearly distinguishable from other members of the genus Aquabacterium. Therefore, we propose a new species in the genus Aquabacterium, namely, Aquabacterium pictum sp. nov. The type strain is W35^T (=DSM 106757^T=NBRC 111963^T). The description of the genus Aquabacterium is also emended.

Pseudaminobacter arsenicus sp. nov., an arsenic-resistant bacterium isolated from arsenic-rich aquifers

An arsenic-resistant strain, CB3^T, was isolated from arsenic-rich aquifers at the Jianghan Plain in Hubei, China. Phylogenetic and biochemical analysis suggested that it should represent a new species of the genus Pseudaminobacter in the family Phyllobacteriaceae. The 16S rRNA gene of CB3^T shared the highest sequence similarities to those of the type strains Pseudaminobacter defluvii THI 051^T (97.8 % identity) and Pseudaminobacter salicylatoxidans BN12^T (97.4 %). The DNA-DNA relatedness values of CB3^T with respect to strains belonging to the genus Pseudaminobacter were less than 70 %. The fatty acid profile of CB3^T consisted of C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as major components. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and diphosphatidylglycerol. The DNA G+C content was 61.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CB3^T was distinct from previously described Pseudaminobacter species. Therefore, we propose that strain CB3^T represents a novel species of the genus Pseudaminobacter, Pseudaminobacterarsenicus sp. nov., strain CB3^T (=CCTCC AB2016116^T=KCTC 52625^T) is designated as the type strain.