Limosilactobacillus caccae sp. nov., a new bacterial species isolated from the human gut microbiota

2021 ◽  
Vol 368 (18) ◽  
Author(s):  
Cheikh Ibrahima Lo ◽  
Niokhor Dione ◽  
Aminata Mbaye ◽  
Patricia Fernández-Mellado Gómez ◽  
Issa Isaac Ngom ◽  
...  
Keyword(s):  
Anaerobic Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Average Nucleotide Identity ◽  
Fecal Flora ◽  
Rrna Gene Sequence ◽  
Human Gut ◽  
The 16S Rrna Gene

ABSTRACT Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95–96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.

scholarly journals Paenibacillus algorifonticola sp. nov., isolated from a cold spring

2011 ◽  
Vol 61 (9) ◽  
pp. 2167-2172 ◽  
Author(s):  
Qi-Yong Tang ◽  
Na Yang ◽  
Jian Wang ◽  
Yu-Qing Xie ◽  
Biao Ren ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Cold Spring ◽  
Xinjiang Uyghur Autonomous Region ◽  
The 16S Rrna Gene

A Gram-stain-positive, endospore-forming, rod-shaped bacterium, designated XJ259T, was isolated from a cold spring sample from Xinjiang Uyghur Autonomous Region, China. The isolate grew optimally at 20–30 °C and pH 7.3–7.8. Comparative analysis of the 16S rRNA gene sequence showed that isolate XJ259T belonged phylogenetically to the genus Paenibacillus, and was most closely related to Paenibacillus xinjiangensis B538T (with 96.6 % sequence similarity), Paenibacillus glycanilyticus DS-1T (96.3 %) and Paenibacillus castaneae Ch-32T (96.1 %), sharing less than 96.0 % sequence similarity with all other members of the genus Paenibacillus. Chemotaxonomic analysis revealing menaquinone-7 (MK-7) as the major isoprenoid quinone, diphosphatidylglycerol, phosphatidylethanolamine and two unknown phosphoglycolipids as the major cellular polar lipids, a DNA G+C content of 47.0 mol%, and anteiso-C15 : 0 and C16 : 0 as the major fatty acids supported affiliation of the new isolate to the genus Paenibacillus. Based on these data, isolate XJ259T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus algorifonticola sp. nov. is proposed. The type strain is XJ259T ( = CGMCC 1.10223T  = JCM 16598T).

scholarly journals Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

2011 ◽  
Vol 61 (7) ◽  
pp. 1715-1719 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Yingshun Cui ◽  
Sun-Chang Kim ◽  
Chang-Hao Cui ◽  
Chengri Yin ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

A Gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105T, was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5T (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105T had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105T represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105T ( = KCTC 13942T  = DSM 18389T).

scholarly journals Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1929-1934 ◽  
Author(s):  
Morgane Rossi-Tamisier ◽  
Samia Benamar ◽  
Didier Raoult ◽  
Pierre-Edouard Fournier
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Taxonomy ◽  
Associated Species

Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.

scholarly journals Tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3′-dithiodipropionic acid

2006 ◽  
Vol 56 (6) ◽  
pp. 1305-1310 ◽  
Author(s):  
Jan Hendrik Wübbeler ◽  
Tina Lütke-Eversloh ◽  
Stefanie Van Trappen ◽  
Peter Vandamme ◽  
Alexander Steinbüchel
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Rrna Gene Sequence ◽  
Nearest Neighbours ◽  
The 16S Rrna Gene

In this study, a novel betaproteobacterium, strain DPN7T, was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3′-dithiodipropionic acid. Analysis of the 16S rRNA gene sequence of strain DPN7T revealed 98.5 % similarity to that of Tetrathiobacter kashmirensis LMG 22695T. Values for sequence similarity to members of the genera Alcaligenes, Castellaniella and Taylorella, the nearest neighbours of the genus Tetrathiobacter, were about 95 % or less. The DNA G+C content of strain DPN7T was 55.1 mol%. The level of DNA–DNA hybridization between strain DPN7T and T. kashmirensis LMG 22695T was 41 %, whereas it was much lower between strain DPN7T and Alcaligenes faecalis LMG 1229T (7 %) or Castellaniella defragrans LMG 18538T (5 %). This genotypic divergence was supported by differences in biochemical and chemotaxonomic characteristics. For this reason, and because of the differences in the protein and fatty acid profiles, strain DPN7T should be classified within a novel species of Tetrathiobacter, for which the name Tetrathiobacter mimigardefordensis sp. nov. is proposed. The type strain is strain DPN7T (=DSM 17166T=LMG 22922T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Salinisphaera dokdonensis sp. nov., isolated from surface seawater

2010 ◽  
Vol 60 (3) ◽  
pp. 680-685 ◽  
Author(s):  
Gi Duk Bae ◽  
Chung Yeon Hwang ◽  
Hye Min Kim ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).

scholarly journals Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

2010 ◽  
Vol 60 (2) ◽  
pp. 429-433 ◽  
Author(s):  
Kiran Bala ◽  
Pooja Sharma ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Physiological Tests ◽  
The 16S Rrna Gene

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25T, was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006T (97.7 %). The 16S rRNA gene sequence similarity between strain P25T and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA–DNA relatedness between strain P25T and Sphingobium amiense IAM 15006T and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25T was 65 mol%. The polyamine profile showed the presence of spermidine. The predominant cellular fatty acids were summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25T also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished strain P25T from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25T (=MTCC 9472T =CCM 7543T).

scholarly journals Chryseobacterium shandongense sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1860-1865 ◽  
Author(s):  
Fan Yang ◽  
Hong-ming Liu ◽  
Rong Zhang ◽  
Ding-bin Chen ◽  
Xiang Wang ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Rrna Gene Sequence ◽  
Yellow Orange ◽  
The 16S Rrna Gene

YF-3T is a Gram-stain-negative, non-motile, non-spore-forming, yellow–orange, rod-shaped bacterium. Optimal growth conditions were at 30 °C, pH 7.0 and 1 % (w/v) NaCl. Phylogenetic analysis, on the basis of the 16S rRNA gene sequence, showed that strain YF-3T was closely related to the strains Chryseobacterium hispalense AG13T and Chryseobacterium taiwanense Soil-3-27T with 98.71 % and 96.93 % sequence similarity, respectively. Strain YF-3T contained MK-6 as the main menaquinone and had a polyamine pattern with sym-homospermidine as the major component. Its major polar lipid was phosphatidylethanolamine. The dominant fatty acids of strain YF-3T were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain YF-3T was 37 mol%. The DNA–DNA relatedness levels between strain YF-3T and the most closely related strains, C. hispalense AG13T and C. taiwanense Soil-3-27T, were 31.7 ± 2.1 % and 28.4 ± 5.4 %, respectively. Based on these results, a novel species named Chryseobacterium shandongense sp. nov. is proposed. The type strain is YF-3T ( = CCTCC AB 2014060T = JCM 30154T).

scholarly journals Proposal of Lentzea deserti (Okoro et al. 2010) Nouioui et al. 2018 as a later heterotypic synonym of Lentzea atacamensis (Okoro et al. 2010) Nouioui et al. 2018 and an emended description of Lentzea atacamensis

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246533
Author(s):  
Mo Ping ◽  
Zhao Yun-Lin ◽  
Liu Jun ◽  
Gao Jian ◽  
Xu Zheng-Gang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Relationship Of ◽  
Type Strains ◽  
The 16S Rrna Gene

The taxonomic relationship of Lentzea atacamensis and Lentzea deserti were re-evaluated using comparative genome analysis. The 16S rRNA gene sequence analysis indicated that the type strains of L. atacamensis and L. deserti shared 99.7% sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the genomes of two type strains were 88.6% and 98.8%, respectively, greater than the two recognized thresholds values of 70% dDDH and 95–96% ANI for bacterial species delineation. These results suggested that L. atacamensis and L. deserti should share the same taxonomic position. And this conclusion was further supported by similar phenotypic and chemotaxonomic features between them. Therefore, we propose that L. deserti is a later heterotypic synonym of L. atacamensis.

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