Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Yajun Ge ◽  
Gui Zhang ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Dong Jin ◽  
...  
Keyword(s):  
Type Species ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Anaerobic ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Healthy Humans ◽  
Type Strains

Four unknown strains, characterized as Gram-stain-negative, strictly anaerobic, non-motile and rod-shaped, were isolated from fresh faeces of healthy humans in PR China. Pairwise sequence comparisons of the 16S rRNA genes showed that these isolates were separated into two clusters. Cluster I (strains HF-5141T and HF-106) was most closely related to Bacteroides xylanisolvens XB1AT (98.0–98.3 % similarity) and Bacteroides ovatus ATCC 8483T (97.3–97.5 %), whereas cluster II (strains HF-5287T and HF-5300) exhibited a similarity range of 96.8–97.0 % to Bacteroides finegoldii JCM 13345T, 96.7–96.9 % to Bacteroides faecis MAJ27T and 96.4–96.5 % to Bacteroides xylanisolvens XB1AT. The DNA G+C contents of type strains HF-5141T and HF-5287T were 41.5 and 42.6 mol%, respectively. These strains had anteiso-C15 : 0 as the major cellular fatty acid, MK-9 and MK-11 as the predominant respiratory quinones, and phosphatidylethanolamine, aminophospholipids and phospholipids as major polar lipids, which is typical for members of the genus Bacteroides . However, the average nucleotide identity and digital DNA–DNA hybridization values, accompanied by different phenotypic and biochemical characteristics, distinguished them from their corresponding closest relatives as well as from other recognized members of the genus Bacteroides . Therefore, strains HF-5141T and HF-5287T represent two novel species in the genus Bacteroides , for which the names Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov. are proposed, with HF-5141T (=CGMCC 1.16787T=GDMCC 1.1591T=JCM 33480T) and HF-5287T (=CGMCC 1.16724T=GDMCC 1.1590T=JCM 33481T) as type strains.

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

scholarly journals Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov

2020 ◽  
Vol 70 (3) ◽  
pp. 1993-2002 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Nevzat Sahin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Three isolates, 5K138T, 8K307T and KC603T, with typical morphological characteristics of members of the genus Jiangella were obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliations of the strains. The strains showed chemotaxonomic properties consistent with their classification as representing members of the genus Jiangella such as ll-diaminopimelic acid in the cell wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as major polar lipids as well as MK-9(H4) as a major menaquinone. Pairwise sequence comparisons of the 16S rRNA genes showed that the strains were closely related to Jiangella alba DSM 45237T, Jiangella rhizosphaerae NEAU-YY265T and Jiangella mangrovi 3SM4-07T with higher than 99 % sequence identities. However, a combination of phenotypic and phylogenetic approaches as well as genome-based comparative analyses confirmed the taxonomic positions of these strains as representing distinct species within the genus Jiangella . Therefore, strains 5K138T, 8K307T and KC603T should each be classified as representing a novel species within the genus Jiangella , for which the names Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. are proposed, respectively. The type strains of the proposed novel species are as follows: Jiangella asiatica 5K138T (=JCM 33518T=CGMCC 4.7672T), Jiangella aurantiaca 8K307T (=JCM 33519T=CGMCC 4.7621T) and Jiangella ureilytica KC603T (=JCM 33520T=CGMCC 4.7618T).

scholarly journals Capnocytophaga felis sp. nov. isolated from the feline oral cavity

2020 ◽  
Vol 70 (5) ◽  
pp. 3355-3360 ◽  
Author(s):  
Michio Suzuki ◽  
Kaoru Umeda ◽  
Masanobu Kimura ◽  
Koichi Imaoka ◽  
Shigeru Morikawa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Oral Cavity ◽  
Type Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Type Strains

Four strains, KC07070T, KC07105, 11 025B-8C and 11 026B-8-C, were isolated from the oral cavity of cats in 2007 or 2011 in Japan. These strains were Gram-stain-negative rods, exhibited gliding motility, grew in air with 5 % CO2 and showed catalase and oxidase activity. The sequences of 16S rRNA genes of the four strains were 100 % identical. Additionally, the sequences of 16S rRNA genes of KC07070T had identity to those of the type strains of Capnocytophaga canimorsus (97.7 %), Capnocytophaga cynodegmi (97.8 %) and Capnocytophaga canis (97.4 %) and 91.2–93.8% identity to those of other species of the genus Capnocytophaga . The major cellular fatty acids of KC07070T were iso-C15 : 0 (56.2 %) and summed feature 11 (14.9 %). The G+C content of the DNA from KC07070T was 35.6 mol%, and the genome size was 2.88 Mbp. KC07070T had digital DNA–DNA hybridization (dDDH) values of 26.2–27.6% and average nucleotide identity (ANI) values of 75.4–83.3 % to the type strains of the closest relatives, C. canimorsus , C. cynodegmi and C. canis . These results of phylogenetic analysis of 16S rRNA gene sequence, cellular fatty acids compositions and dDDH and ANI values indicate that strain KC07070T represents a novel species, for which we propose the name Capnocytophaga felis sp. nov., with type strain KC07070T (=JCM 32681T=DSM 107251T).

scholarly journals Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Xiaoying Liu ◽  
Jessica L. Sutter ◽  
Jacobo de la Cuesta-Zuluaga ◽  
Jillian L. Waters ◽  
Nicholas D. Youngblut ◽  
...  
Keyword(s):  
Type Species ◽  
Evolutionary Relationship ◽  
Single Copy ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Anaerobic ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Link Type

The genera Catabacter (family ‘Catabacteraceae’) and Christensenella (family Christensenellaceae ) are close relatives within the phylum Firmicutes . Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis . A concatenated alignment of 135 shared protein sequences of single-copy core genes present in the included strains indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the genus Christensenella as Christensenella hongkongensis comb. nov.

Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4606-4612 ◽  
Author(s):  
Karoline Kläring ◽  
Laura Hanske ◽  
Nam Bui ◽  
Cédric Charrier ◽  
Michael Blaut ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Methyl Ester ◽  
Type Species ◽  
Rumen Fluid ◽  
Acid Methyl Ester ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type

A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNFdeltaARE mouse. The isolate, referred to as strain SRB-521-5-IT, was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-IT were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus , strain SRB-521-5-IT contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-IT differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-IT produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii , the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-IT ( = DSM 26588T = CCUG 63529T) as the type strain.

scholarly journals Cultivation and description of Duncaniella dubosii sp. nov., Duncaniella freteri sp. nov. and emended description of the species Duncaniella muris

2020 ◽  
Vol 70 (5) ◽  
pp. 3105-3110 ◽  
Author(s):  
Sou Miyake ◽  
Yichen Ding ◽  
Melissa Soh ◽  
Adrian Low ◽  
Henning Seedorf
Keyword(s):  
Type Species ◽  
16S Rrna Genes ◽  
Morphological Properties ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Respective Type ◽  
Type Strains

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae , and shared 91.6–99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA–DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae ( Muribaculum intestinale DSM 28989T , Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella , for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).

Description of Acidovorax wautersii sp. nov. to accommodate clinical isolates and an environmental isolate, most closely related to Acidovorax avenae

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2203-2206 ◽  
Author(s):  
Mario Vaneechoutte ◽  
Michèle Janssens ◽  
Véronique Avesani ◽  
Michel Delmée ◽  
Pieter Deschaght
Keyword(s):  
Nitrate Reduction ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenol Red ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three Gram-negative strains, NF 1078T, NF 1598 and NF 1715, were isolated from clinical (two) and environmental (one) samples, respectively. Sequence analysis of the 16S rRNA genes revealed similarity of 100 % among the three strains and next highest similarity to the type strain of Acidovorax avenae (98.16 %). The three strains were able to acidify lactose and rhamnose on low peptone phenol red agar and to alkalinize citrate on Simmons’ agar and were negative for nitrate reduction. The DNA G+C content of strain NF 1078T was 67.1 mol%. The level of DNA–DNA relatedness between this strain and the type strains of A. avenae (ATCC 19860T, LMG 2117T) was 29 %. Based on these phylogenetic, phenotypic and genotypic analyses, the three strains could be distinguished clearly from all other recognized Acidovorax species and should be classified as representatives of a novel species of the genus Acidovorax , for which the name Acidovorax wautersii sp. nov. is proposed. The type strain is NF 1078T ( = LMG 26971T = CCUG 62584T).

Novosphingobium decolorationis sp. nov., an aniline blue-decolourizing bacterium isolated from East Pacific sediment

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Xiunuan Chen ◽  
Bingxia Dong ◽  
Ting Chen ◽  
Na Ren ◽  
Jing Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Aniline Blue ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
East Pacific ◽  
Type Strains

Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).

scholarly journals Genome-based classification of Calidifontibacillus erzurumensis gen. nov., sp. nov., isolated from a hot spring in Turkey, with reclassification of Bacillus azotoformans as Calidifontibacillus azotoformans comb. nov. and Bacillus oryziterrae as Calidifontibacillus oryziterrae comb. nov.

2020 ◽  
Vol 70 (12) ◽  
pp. 6418-6427
Author(s):  
Ahmet Adiguzel ◽  
Hilal Ay ◽  
Mustafa Ozkan Baltaci ◽  
Sumeyya Akbulut ◽  
Seyda Albayrak ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Hot Spring ◽  
Rrna Genes ◽  
Sequence Comparisons ◽  
Novel Genus ◽  
Content Type ◽  
Sequence Identity ◽  
Link Type ◽  
Bacillus Azotoformans

A novel Gram-stain-positive, rod-shaped, endospore-forming, motile, aerobic bacterium, designated as P2T, was isolated from a hot spring water sample collected from Ilica-Erzurum, Turkey. Phylogenetic analyses based on 16S rRNA gene sequence comparisons affiliated strain P2T with the genus Bacillus , and the strain showed the highest sequence identity to Bacillus azotoformans NBRC 15712T (96.7 %). However, the pairwise sequence comparisons of the 16S rRNA genes revealed that strain P2T shared only 94.7 % sequence identity with Bacillus subtilis subsp. subtilis NCIB 3610T, indicating that strain P2T might not be a member of the genus Bacillus . The digital DNA–DNA hybridization and average nucleotide identity values between strain P2T and B. azotoformans NBRC 15712T were 19.8 and 74.2 %, respectively. The cell-wall peptidoglycan of strain P2T contained meso-diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid, five unidentified phospholipids and two unidentified lipids while the predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0 and iso-C16 : 0. The draft genome of strain P2T was composed of 82 contigs and found to be 3.5 Mb with 36.1 mol% G+C content. The results of phylogenomic and phenotypic analyses revealed that strain P2T represents a novel genus in the family Bacillaceae , for which the name Calidifontibacillus erzurumensis gen. nov., sp. nov. is proposed. The type strain of Calidifontibacillus erzurumensis is P2T (=CECT 9886T=DSM 107530T=NCCB 100675T). Based on the results of the present study, it is also suggested that Bacillus azotoformans and Bacillus oryziterrae should be transferred to this novel genus as Calidifontibacillus azotoformans comb. nov. and Calidifontibacillus oryziterrae comb. nov., respectively.

Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Yan Gao ◽  
Guangyu Li ◽  
Chen Fang ◽  
Zongze Shao ◽  
Yue-Hong Wu ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Overlying Water ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, rod-shaped and aerobic bacterial strain, named Ery12T, was isolated from the overlying water of the Lau Basin in the Southwest Pacific Ocean. Strain Ery12T showed high 16S rRNA gene sequences similarity to Tsuneonella flava MS1-4T (99.9 %), T. mangrovi MCCC 1K03311T (98.1 %), Altererythrobacter ishigakiensis NBRC 107699T (97.3 %) and exhibited ≤97.0 % sequence similarity with other type strains of species with validly published names. Growth was observed in media with 0–10.0 % NaCl (optimum 0–1.0 %, w/v), pH 5.0–9.5 (optimum 6.0–7.0) and 10–42 °C (optimum 30–37 °C). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acid was summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The major polar lipids were sphingoglycolipid, phosphatidyglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified glycolipids, one unidentified aminoglycolipid and one unidentified lipid. The DNA G+C content was 60.8 %. The ANI and in silico DDH values between strain Ery12T and the type strains of its closely related species were 71.0- 91.8 % and 19.5- 44.6 %, respectively. According to the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain Ery12T represents a novel species of the genus Tsuneonella , for which the name Tsuneonella suprasediminis is proposed. The type strain is Ery12T (=CGMCC 1.16500 T=MCCC 1A04421T=KCTC 62388T). We further propose to reclassify Altererythrobacter rhizovicinus and Altererythrobacter spongiae as Pelagerythrobacter rhizovicinus comb. nov. and Altericroceibacterium spongiae comb. nov., respectively.

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