Thermosynergistes pyruvativorans gen. nov., sp. nov., an anaerobic, pyruvate-degrading bacterium from Shengli oilfield, and proposal of Thermosynergistaceae fam. nov. in the phylum Synergistetes

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Min Yang ◽  
Jiang Li ◽  
Xiao-meng Lv ◽  
Li-rong Dai ◽  
Ke-jia Wu ◽  
...  
Keyword(s):  
Cellular Fatty Acid ◽  
Amino Acid Identity ◽  
Oily Sludge ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Shengli Oilfield ◽  
Gene Similarity

A strictly anaerobic, thermophilic, Gram-stain-negative bacterium, named as strain S15T, was isolated from oily sludge of Shengli oilfield in PR China. Cells of strain S15T were straight or slightly curved rods with 0.4–0.8 µm width × 1.4–3 µm length and occurred mostly in pairs or short chains. Endospore-formation was not observed. The strain grew optimally at 55 °C (range from 30–65 °C), pH 6.5 (pH 6.0–8.5) and 0–30 g l−1 NaCl (optimum with 10 g l−1 NaCl). Yeast extract was an essential growth factor for strain S15T. The major cellular fatty acid was iso-C15 : 0 (58.2 %), and the main polar lipids were amino phospholipid (APL), glycolipids (GLs) and phosphatidylethanolamine (PE). The G+C content of DNA of strain S15T was 52.2 mol%. Strain S15T shared 89.8 % 16S rRNA gene similarity with the most related organism Acetomicrobium hydrogeniformans DSM 22491T in the phylum Synergistetes . The paired genomic average amino acid identity (AAI) and percentage of conserved proteins (POCP) values showed relatedness of less than 58.0 and 39.7 % with type strains of the species in the phylum Synergistetes . On the basis of phenotypic, phylogenetic and phylogenomic evidences, strain S15T constitutes a novel species in a novel genus, for the name Thermosynergistes pyruvativorans gen. nov., sp. nov. is proposed. The type strain is S15T (=CCAM 583T=JCM 33159T). Thermosynergistaceae fam. nov. is also proposed.

scholarly journals Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse

2021 ◽  
Author(s):  
Torben Sølbeck Rasmussen ◽  
Theresa Streidl ◽  
Thomas C. A. Hitch ◽  
Esther Wortmann ◽  
Paulina Deptula ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Succinate Production ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Average Amino Acid Identity

A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52–74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives ( D. longicatena , Ruminococcus gnavus , C. scindens , Dorea formicigenerans , Ruminococcus lactaris , Clostridium hylemonae , Merdimonas faecis , Faecalicatena contorta and Faecalicatena fissicatena ). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).

scholarly journals Reconstituting the genus Mycobacterium

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Conor J. Meehan ◽  
Roman A. Barco ◽  
Yong-Hwee E. Loh ◽  
Sari Cogneau ◽  
Leen Rigouts
Keyword(s):  
Amino Acid Identity ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
New Genera ◽  
Opportunistic Pathogens ◽  
Content Type ◽  
Link Type ◽  
Genus Mycobacterium ◽  
Definition Of ◽  
Gene Similarity

The definition of a genus has wide-ranging implications both in terms of binomial species names and also evolutionary relationships. In recent years, the definition of the genus Mycobacterium has been debated due to the proposed split of this genus into five new genera ( Mycolicibacterium , Mycolicibacter , Mycolicibacillus , Mycobacteroides and an emended Mycobacterium ). Since this group of species contains many important obligate and opportunistic pathogens, it is important that any renaming of species does not cause confusion in clinical treatment as outlined by the nomen periculosum rule (56a) of the Prokaryotic Code. In this study, we evaluated the proposed and original genus boundaries for the mycobacteria, to determine if the split into five genera was warranted. By combining multiple approaches for defining genus boundaries (16S rRNA gene similarity, amino acid identity index, average nucleotide identity, alignment fraction and percentage of conserved proteins) we show that the original genus Mycobacterium is strongly supported over the proposed five-way split. Thus, we propose that the original genus label be reapplied to all species within this group, with the proposed five genera potentially used as sub-genus complex names.

Desulfotomaculum defluvii sp. nov., a sulfate-reducing bacterium isolated from the subsurface environment of a landfill

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2290-2295 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
Stefan Spring ◽  
Pinnaka Anil Kumar ◽  
Shanmugam Mayilraj ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus Desulfotomaculum . Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus Desulfotomaculum . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to Desulfotomaculum aeronauticum DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus Desulfotomaculum , for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).

Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 800-805 ◽  
Author(s):  
Jun Zhang ◽  
Zhi-Fei Lang ◽  
Jin-Wei Zheng ◽  
Bao-Jian Hang ◽  
Xiao-Qin Duan ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A non-sporulating, non-motile, catalase- and oxidase-positive, Gram-negative, rod-shaped bacterial strain, designated BA-3T, was isolated from activated sludge of a wastewater treatment facility. The strain was able to degrade about 95 % of 100 mg 3-phenoxybenzoic acid l−1 within 2 days of incubation. Growth occurred in the presence of 0–2 % (w/v) NaCl [optimum, 0.5 % (w/v) NaCl], at pH 5.5–9.0 (optimum, pH 7.0) and at 10–37 °C (optimum, 28 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain BA-3T was a member of the genus Sphingobium ; it showed highest gene sequence similarity to Sphingobium qiguonii X23T (98.2 %), and similarities of <97.0 % with strains of other Sphingobium species. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus Sphingobium . Strain BA-3T showed low DNA–DNA relatedness values (21.3±0.8 %) with Sphingobium qiguonii X23T. Based on phenotypic, genotypic and phylogenetic data, strain BA-3T represents a novel species of the genus Sphingobium , for which the name Sphingobium jiangsuense sp. nov. is proposed; the type strain is BA-3T ( = CCTCC AB 2010217T = KCTC 23196T = KACC 16433T).

scholarly journals Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2657-2661 ◽  
Author(s):  
O. A. Podosokorskaya ◽  
E. A. Bonch-Osmolovskaya ◽  
A. V. Beskorovaynyy ◽  
S. V. Toshchakov ◽  
T. V. Kolganova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Hot Water ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3T, was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3T were straight and curved rods, 0.2–0.4 µm in width and 1.5–20 µm in length. Strain P3M-3T grew optimally at 37 °C, pH 7.0–7.5 and in a NaCl concentration of 15 g l−1. Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3T was a member of family Lachnospiraceae , whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12T, the closest relative, was 93.9 %. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3T ( = DSM 26468T = VKM B-2804T).

Paradesulfitobacterium ferrireducens gen. nov., sp. nov., a Fe(III)-reducing bacterium from petroleum-contaminated soil and reclassification of Desulfitobacterium aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Yanling Li ◽  
Guiqin Yang ◽  
Sijie Yao ◽  
Li Zhuang
Keyword(s):  
Contaminated Soil ◽  
Type Species ◽  
Amino Acid Identity ◽  
Gansu Province ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
Petroleum Contaminated Soil

A strictly anaerobic bacterium, strain PLL0T, was isolated from petroleum-contaminated soil sampled in Gansu Province, PR China. Cells were rods, non-motile and Gram-stain-positive. The strain grew at 25–37 °C (optimum, 30 °C) in the presence of 0–3 % (w/v) NaCl (optimum, 2 %). Strain PLL0T was able to reduce ferrihydrite, Fe(III) citrate and thiosulphate. The 16S rRNA gene analysis revealed that this strain clustered with the genus Desulfitobacterium , and showed highest similarity to Desulfitobacterium aromaticivorans UKTLT (95.4 %) followed by Desulfitobacterium chlororespirans Co23T (93.9 %). However, strains PLL0T and UKTLT showed no more than 94.0 % similarity to other species of the genus Desulfitobacterium , and formed an independent group in the phylogenetic tree. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain PLL0T and Desulfitobacterium species (except for D. aromaticivorans ) were 67.4–68.5 % and 12.6–12.7 %, respectively, which are far below the threshold for delineation of a new species. Based on ANI, dDDH, average amino acid identity, phylogenetic analysis and physiologic differences from the previously described taxa, we suggest that strain PLL0T represents a novel species of a novel genus, for which the name Paradesulfitobacterium ferrireducens gen. nov. sp. nov. is proposed. The type strain is PLL0T (=MCCC 1K05549=KCTC 25248). We also propose the reclassification of D. aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.

scholarly journals Capillibacterium thermochitinicola gen. nov., sp. nov., a novel anaerobic thermophilic chitinolytic bacterium from compost

2021 ◽  
Author(s):  
Umbhorn Ungkulpasvich ◽  
Sirilak Baramee ◽  
Ayaka Uke ◽  
Akihiko Kosugi
Keyword(s):  
Type Species ◽  
Carbon Sources ◽  
Dimethyl Acetal ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Phylogenetic Tree Analysis ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Genotypic Analysis

A novel Gram-negative, spore forming, obligately anaerobic, thermophilic, chitin-degrading bacterium, designated UUS1-1T, was isolated from compost on Ishigaki Island, Japan by enrichment culturing using chitin powder as the carbon source. The strain has unique, long, hair-like rod morphological features and exhibits strong degradation activity toward crystalline chitin under thermophilic conditions. Growth of the novel strain was observed at 45–65 °C (optimum, 55 °C) and pH 6.5–7.5 (optimum, pH 7.0). In addition to chitin, the strain utilized several other carbon sources, including N-acetylglucosamine, glucose, galactose, mannose, maltose, cellobiose, fructose and sucrose. The end products of chitin degradation were acetate, lactate, H2 and CO2. Phylogenetic tree analysis based on 16S rRNA gene sequences revealed a clear affiliation of the proposed bacterium to the phylum Firmicutes ; the most closely related species were Hydrogenispora ethanolica LX-BT and Desulfotomaculum thermobenzoicum DSM6193T with similarities of 90.4 and 87.8 %, respectively. The G+C content of the genomic DNA was 52.1 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of UUS1-1T and H. ethanolica LX-BT were 65.5 and 21.0 %, respectively. The cellular fatty acid composition of the strain was C16 : 0, anteiso-C15 : 0, C14 : 0, C12 : 0 3-OH and dimethyl acetal-C13 : 0. Based on phenotypic, chemotaxonomic and genotypic analysis, strain UUS1-1T represents a novel genus and species, for which the name Capillibacterium thermochitinicola gen. nov., sp. nov. is proposed. The type strain is UUS1-1T (=JCM 33882T=DSM 111537T).

scholarly journals Muribaculum gordoncarteri sp. nov., an anaerobic bacterium from the faeces of C57BL/6J mice

2020 ◽  
Vol 70 (8) ◽  
pp. 4725-4729 ◽  
Author(s):  
Sou Miyake ◽  
Yichen Ding ◽  
Melissa Soh ◽  
Adrian Low ◽  
Henning Seedorf
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Minor Component ◽  
Cellular Fatty Acid ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

An anaerobic bacterial strain, named TLL-A4T, was isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of the 16S rRNA gene indicated that the strain belongs to the phylum Bacteroidetes and, more specifically, to the recently proposed Muribaculaceae (also known as S24-7 clade or Candidatus Homeothermaceae). Strain TLL-A4T’s 16S rRNA gene shared 92.8 % sequence identity with the type strain of the only published species of the genus Muribaculum , Muribaculum intestinale DSM 28989T. Genome-sequencing of TLL-A4T was performed to compare average amino acid identity (AAI) value and percentage of conserved proteins (POCP) between both strains. The AAI analysis revealed that strain TLL-A4T had high identity (69.8 %) with M. intestinale DSM 28989T, while the POCP was 56 %. These values indicate that strain TLL-A4T could be considered a member of the genus Muribaculum but not belonging to the species M. intestinale . Quinone analysis indicated MK10 (63 %) and MK11 (32 %) as major quinones in the membrane, while MK9 was only present as a minor component (5 %). The main cellular fatty acid was anteiso-C15 : 0 (42.8 %); summed feature 11 (17.5 %), C15 : 0 iso (13.4 %), C18 : 1 ω9c (5.6 %), C16.0 3-OH (4.5 %) and C15 : 0 (4.2 %) were detected in minor amounts. Analysis of enzyme activities using the API 32A and API 20A kits indicated major differences between strain TLL-A4T and Muribaculum intestinale DSM 28989T. Based on genotypic, phylogenetic and phenotypic differences, strain TLL-A4T is considered to represent a novel species of the genus Muribaculum , for which the name Muribaculum gordoncarteri sp. nov. is proposed. The type strain is TLL-A4T (=DSM 108194T=KCTC 15770T).

Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yingning Wang ◽  
Fang Ma ◽  
Jixian Yang ◽  
Haijuan Guo ◽  
Delin Su
Keyword(s):  
Type Species ◽  
Treatment Plant ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Pairwise Identity ◽  
Active Sludge ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter , for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

scholarly journals Streptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries (Catagonus wagneri)

2020 ◽  
Vol 70 (11) ◽  
pp. 5734-5739 ◽  
Author(s):  
Kristin Mühldorfer ◽  
Claudia A. Szentiks ◽  
Gudrun Wibbelt ◽  
Mark van der Linden ◽  
Christa Ewers ◽  
...  
Keyword(s):  
Type Species ◽  
Amino Acid Identity ◽  
Physiological Data ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Genome Phylogeny ◽  
Species Boundary ◽  
Gene Similarity

Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested Streptococcus agalactiae with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus Streptococcus , displaying highest similarities to the strains from this study, were S. bovimastitidis NZ1587T (97.5 %), S. iniae ATCC 29178T (97.5 %), S. hongkongensis HKU30T (97.4 %), S. parauberis DSM 6631T (97.1 %), S. penaeicida CAIM 1838T (97.1 %), S. pseudoporcinus DSM 18513T (97.0 %), S. didelphis DSM 15616T (96.6 %), S. ictaluri 707-05T (96.6 %), S. uberis JCM 5709T (96.5 %) and S. porcinus NCTC 10999T (96.4 %). All other Streptococcus species had sequence similarities of below 96.4 %. A sodA gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available Streptococcus genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95–96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA–DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related Streptococcus type strains (23.5–19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name Streptococcus catagoni sp. nov. with the type strain 99-1/2017T (=DSM 110457T=CCUG 74072T) and five reference strains.

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