scholarly journals Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina

2020 ◽  
Author(s):  
Kah-Ooi Chua ◽  
Wah-Seng See-Too ◽  
Jia-Yi Tan ◽  
Sze-Looi Song ◽  
Hoi-Sen Yong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Oecophylla Smaragdina ◽  
Weaver Ant

AbstractIn this study, bacterial strains Ha5T, Ta1 and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were distinguished as different strains based on matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15–37°C (optimum, 28–30°C) and in the presence of 0–1.5 % (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8c cyclo, C14:0 and C16:0 2-OH. Strains Ha5T, Ta1 and Jb2 shared highest 16S rRNA gene sequence similarity (94.56–94.63%) with Neokomagataea tanensis NBRC106556T but were phylogenetically closer to Bombella spp. and Saccharibacterfloricola DSM15669T. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (≤70.7%), in silico DNA-DNA hybridization (≤39.5%) and average amino acid identity (≤66.ü%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1 and Jb2 represent a novel species of a novel genus in family Acetobacteraceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces

2005 ◽  
Vol 55 (4) ◽  
pp. 1675-1680 ◽  
Author(s):  
Marcel Nordhoff ◽  
David Taras ◽  
Moritz Macha ◽  
Karsten Tedin ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genus Treponema indicating that the isolates are members of this genus. Strain 7CPL208T, as well as five further isolates, and 14V28T displayed the highest 16S rRNA gene sequence similarities with Treponema pectinovorum ATCC 33768T (92·3 %) and Treponema parvum OMZ 833T (89·9 %), respectively. Polar lipid profiles distinguished 7CPL208T and 14V28T from each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208T and 14V28T are suggested to represent two novel species of the genus Treponema, for which the names Treponema berlinense sp. nov. and Treponema porcinum sp. nov. are proposed. The type strain for Treponema berlinense is 7CPL208T (=ATCC BAA-909T=CIP 108244T=JCM 12341T) and for Treponema porcinum 14V28T (=ATCC BAA-908T=CIP 108245T=JCM 12342T).

scholarly journals Bacillus crescens sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2531-2536 ◽  
Author(s):  
Y. Shivani ◽  
Y. Subhash ◽  
P. Dave. Bharti ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Two bacterial strains (JC247T and JC248) were isolated from soil samples collected from Rann of Kutch, Gujarat, India. Colonies of both strains were creamy white. Cells were Gram-stain-positive, rods-to-curved rods (crescent-shaped), and produced centrally located oval-shaped endospores. Major (>5 %) fatty acids of both strains were iso-C16  :  0, iso-C14  :  0, iso-C15  :  0, C16  :  1ω11c and C16  :  0, with minor ( < 5 but >1 %) amounts of anteiso-C15  :  0, anteiso-C17  :  0, iso-C16  :  1 H, iso-C17  :  0, iso-C18  :  0, C14  :  0, C17  :  0, C18  :  0, C18  :  1ω9c, iso-C17  :  1ω10c and anteiso-C17  :  0B/isoI. Diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell-wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. The genomic DNA G+C content of strains JC247T and JC248 was 48.2 and 48.1 mol%, respectively. Both strains were closely related with mean DNA–DNA hybridization >90 %. 16S rRNA gene sequence analysis of both strains indicated that they are members of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a 16S rRNA gene sequence similarity of 96.93 % with Bacillus firmus NCIMB 9366T and < 96.92 % with other members of the genus Bacillus. Sequence similarity between strain JC247T and JC248 was 100 %. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strains JC247T and JC248 as representatives of a novel species of the genus Bacillus, for which the name Bacillus crescens sp. nov. is proposed. The type strain is JC247T ( = KCTC 33627T = LMG 28608T).

scholarly journals Paenibacillus humicus sp. nov., isolated from poultry litter compost

2007 ◽  
Vol 57 (10) ◽  
pp. 2267-2271 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Cátia Faria ◽  
M. Fernanda Nobre ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Poultry Litter ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Respiratory Quinone

Two bacterial strains, PC-142 and PC-147T, isolated from poultry litter compost, were characterized with respect to their phenetic and phylogenetic characteristics. The isolates were endospore-forming rods that were reddish in colour after Gram staining. They were catalase- and oxidase-positive, were able to degrade starch and gelatin and grew at 15–40 °C and pH 5.5–10.0. The predominant fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, the major respiratory quinone was menaquinone MK-7, the cell-wall peptidoglycan was of the A1γ type and the G+C content of the DNA was 58 mol%. The 16S rRNA gene sequence analysis and phenetic characterization indicated that these organisms belong to the genus Paenibacillus, with Paenibacillus pasadenensis SAFN-007T as the closest phylogenetic neighbour (97.5 %). Strains PC-142, PC-147T and P. pasadenensis SAFN-007T represent a novel lineage within the genus Paenibacillus, characterized by a high DNA G+C content (58–63 mol%). The low levels of 16S rRNA gene sequence similarity with respect to other taxa with validly published names and the identification of distinctive phenetic features in the two isolates indicate that strains PC-142 and PC-147T represent a novel species of the genus Paenibacillus, for which the name Paenibacillus humicus sp. nov. is proposed. The type strain is PC-147T (=DSM 18784T =NBRC 102415T =LMG 23886T).

scholarly journals Lactobacillus mixtipabuli sp. nov. isolated from total mixed ration silage

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1981-1985 ◽  
Author(s):  
Masanori Tohno ◽  
Maki Kitahara ◽  
Tomohiro Irisawa ◽  
Hideyuki Ohmori ◽  
Takaharu Masuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Good Growth ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Total Mixed Ration

Using a polyphasic taxonomic approach, we investigated three bacterial strains – IWT30T, IWT8 and IWT75 – isolated from total mixed ration silage prepared in Hachimantai, Iwate, Japan. The isolates comprised Gram-stain positive, non-motile, non-spore-forming, catalase-negative, rod-shaped bacteria. Good growth occurred at 15–45 °C and at pH 4.0–7.5. Their major cellular fatty acids were C18:1ω9c and C19:1 cyclo 9,10.The G+C content of genomic DNA of strain IWT30T was 44.6 mol%. Comparative 16S rRNA gene sequence analysis showed that these novel strains belonged to the genus Lactobacillus. These strains shared 100 % 16S rRNA gene sequence similarity and were most closely related to the type strains of Lactobacillus silagei, Lactobacillus odoratitofui, Lactobacillus similis, Lactobacillus collinoides, Lactobacillus paracollinoides and Lactobacillus kimchicus, with sequence similarity values of 99.5, 98.8, 98.7, 97.8, 97.8 and 96.8 %, respectively. The level of DNA–DNA relatedness between these strains and their closest phylogenetic neighbours was less than 30 %. On the basis of additional phylogenetic analysis of pheS and rpoA gene sequences and phenotypic and chemotaxonomic characteristics, we conclude that these three strains represent a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus mixtipabuli sp. nov. The type strain is IWT30T ( = JCM 19805T = DSM 28580T).

scholarly journals Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India

2019 ◽  
Author(s):  
Kanika Bansal ◽  
Amandeep Kaur ◽  
Samriti Midha ◽  
Sanjeet Kumar ◽  
Suresh Korpole ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Basmati Rice ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Whole Genome ◽  
Rrna Gene Sequence ◽  
Rice Seeds

AbstractThree yellow pigmented, Gram negative, aerobic, rod shaped, motile bacterial strains designated as PPL1, PPL2 and PPL3 were isolated from healthy basmati rice seeds. Phenotypic, biochemical and 16S rRNA gene sequence analysis assigned these strains to the genus Xanthomonas. The 16S rRNA gene sequence was having 99.59% similarity with X. sacchari CFBP4641T. However, whole genome based phylogenomic analysis revealed that these strains formed a distinct monophyletic clade with X. sacchari CFBP4641T as their closest neighbour. Taxonogenomic studies based on average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) values of these strains with type strains (or representative strains) of different Xanthomonas species including X. sacchari showed below recommended threshold values of ANI (<96%) and dDDH (70%) for species delineation. Furthermore, at the whole genome level, PPL1 and PPL2 were found to be clonal, while PPL3 was not a clonal, but belonging to the same species. Our in planta pathogenicity studies revealed that the strains PPL1, PPL2 and PPL3 are non-pathogenic to rice plants. Hence, based on the present study, they form a novel lineage and species associated with rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (CFBP8688T = ICMP23426T = MTCC12491T) and strains PPL2 (CFBP8689 = ICMP23427 = MTCC12492) and PPL3 (CFBP8690 =ICMP23428 = MTCC12492) as other strains of the species.

scholarly journals Salibacterium halotolerans gen. nov., sp. nov., a bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4270-4275 ◽  
Author(s):  
Sultanpuram Vishnuvardhan Reddy ◽  
Mothe Thirumala ◽  
Chintalapati Sasikala ◽  
Chintalapati Venkata Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Biochemical Tests

Two novel Gram-stain-positive, rod-shaped, non-motile, non-endospore-forming bacterial strains, S7T and IB5, were isolated from Khavda, India. Based on 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae, and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strains S7T and IB5 might not be members of the genus Bacillus. The DNA–DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 ± 0.8. The cell-wall peptidoglycan of strains S7T and IB5 contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. anteiso-C15 : 0 was the predominant fatty acid. The results of the phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, suggesting that they represent a novel member of the family Bacillaceae, for which the name Salibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of Salibacterium halotolerans is S7T ( = KCTC 33658T = CGMCC 1.15324T). Based on the results of the present study, it is also suggested that B. qingdaonensis and B. halochares should be transferred to this novel genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.

scholarly journals Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

2006 ◽  
Vol 56 (4) ◽  
pp. 889-893 ◽  
Author(s):  
Cheng-Hui Xie ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99·9 % 16S rRNA gene sequence similarity and greater than 70 % DNA–DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99·5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68·0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA–DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T=IAM 15283T=CCTCC AB205007T).

Labrys wisconsinensis sp. nov., a budding bacterium isolated from Lake Michigan water, and emended description of the genus Labrys

2010 ◽  
Vol 60 (7) ◽  
pp. 1570-1576 ◽  
Author(s):  
Richard A. Albert ◽  
Nancy E. Waas ◽  
Stefan Langer ◽  
Shawn C. Pavlons ◽  
Jamie L. Feldner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Lake Michigan ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains

Two facultatively anaerobic, budding bacterial strains, designated W1215-PCA4T and SRNK-1, were isolated from water from Lake Michigan, USA. The two strains showed identical ERIC-PCR-generated genomic fingerprints and shared 99.9 % 16S rRNA gene sequence similarity. Strain W1215-PCA4T showed highest 16S rRNA gene sequence similarities to Labrys monachus VKM B-1479T (95.8 %), Labrys methylaminiphilus DSM 16812T (95.1 %), Labrys okinawensis MAFF 210191T (96.0 %), Labrys miyagiensis G24103T (95.4 %), Labrys neptuniae BCRC 17578T (95.7 %) and Labrys portucalensis DSM 17916T (95.8 %). Data suggested that the two strains were members of a single novel species of the genus Labrys. The major cellular fatty acids of the two isolates were C18 : 1 ω7c, C19 : 0 cyclo ω8c and C16 : 0. Their polar lipid profiles were highly similar to that of Labrys monachus DSM 5896T. The primary quinone was ubiquinone Q-10, with minor amounts of Q-9 and Q-11. sym-Homospermidine was the predominant polyamine, with putrescine present in moderate amounts. The two strains were identical in terms of their biochemical and physiological traits, but were distinguishable from other species of the genus Labrys. Hence, the description of a novel species in this genus appears to be justified. The name Labrys wisconsinensis sp. nov. is proposed; the type strain is W1215-PCA4T (=DSM 19619T=NRRL B-51088T).

scholarly journals Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (9) ◽  
pp. 2259-2265 ◽  
Author(s):  
Lei Zhang ◽  
Juan Bai ◽  
Yang Wang ◽  
Gao-Lin Wu ◽  
Jun Dai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Sequence Similarities

Two Gram-reaction-negative, rod-shaped, gliding, yellow-pigmented bacterial strains, designated ZLD-17T and ZLD-29T, were isolated from arid soil samples collected from Xinjiang Province, north-west China, and subjected to analysis using a polyphasic taxonomic approach. Both novel strains required 1.0–2.0 % (w/v) sea salts for optimal growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belong to the genus Lysobacter within the class Gammaproteobacteria. Strain ZLD-17T showed highest 16S rRNA gene sequence similarities to Lysobacter capsici KCTC 22007T (96.9 %), Lysobacter spongiicola DSM 21749T (96.8 %) and Lysobacter koreensis KCTC 12204T (96.8 %), whereas strain ZLD-29T showed highest sequence similarities to Lysobacter niastensis DSM 18481T (96.0 %) and Lysobacter enzymogenes DSM 2043T (95.9 %). 16S rRNA gene sequence similarity between ZLD-17T and ZLD-29T was 96.1 %. The DNA G+C contents of strains ZLD-17T and ZLD-29T were 67.9 and 68.2 mol%, respectively. The major cellular fatty acids of both strains were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c, iso-C16 : 0, C16 : 0 and iso-C11 : 0 3-OH; their predominant isoprenoid quinone was Q-8 and their major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on their phenotypic characteristics, phylogenetic position as determined by 16S rRNA gene sequence analysis and chemotaxonomic data, strains ZLD-17T ( = CCTCC AB 207174T  = KCTC 23076T) and ZLD-29T ( = CCTCC AB 207175T = KCTC 23077T) represent two novel species of the genus Lysobacter, for which the names Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov. are proposed, respectively.

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