scholarly journals Description of a new member of the family Erysipelotrichaceae: Clostridium fusiformis sp. nov., isolated from healthy human feces

2019 ◽  
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Joy Scaria
Keyword(s):  
Short Chain Fatty Acid ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Optimal Growth Temperature ◽  
Polyphasic Analysis ◽  
Healthy Human ◽  
Acid Product ◽  
The Family ◽  
Fatty Acid Product ◽  
The 16S Rrna Gene

ABSTRACTA Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from the healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the Clostridium cluster XVI, where, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and Eubacterium tortuosum DSM 3987T were its closest taxa with 95.15%, 94.49%, 93.28%, and 93.20% sequence identities respectively. The optimal growth temperature and pH for the strain SG502T were 37°C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain SG502T when grown in BHI-M medium. The major cellular fatty acids produced by the strain SG502T were C18:1 ω9c, C18:0 and C16:0. The DNA G+C content of the strain was 34.34 mol%. The average nucleotide identity of the genome of the strain SG502T and its closest neighbor C. innocuum ATCC 14501T was 63.48%. Based on the polyphasic analysis, the type strain SG502T (=DSM 107282T), represents a novel species of the genus Clostridium for which the name Clostridium fusiformis sp. nov. is proposed.

scholarly journals Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10071
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Joy Scaria
Keyword(s):  
16S Rrna ◽  
Optimal Growth ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Healthy Human ◽  
Acid Product ◽  
The Family ◽  
Fatty Acid Product ◽  
Rrna Phylogeny ◽  
The 16S Rrna Gene

A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T(=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C18:1ω9c, C18:0and C16:0. Thus, based on the polyphasic analysis, for the type strain SG502T (=DSM 107282T= CCOS 1889T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed.

scholarly journals Description of Pseudobacteriovorax antillogorgiicola gen. nov., sp. nov., a bacterium isolated from the gorgonian octocoral Antillogorgia elisabethae, belonging to the family Pseudobacteriovoracaceae fam. nov., within the order Bdellovibrionales

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 522-530 ◽  
Author(s):  
Erin P. McCauley ◽  
Brad Haltli ◽  
Russell G. Kerr
Keyword(s):  
Optimal Growth ◽  
Rrna Gene ◽  
The Bahamas ◽  
Respiratory Quinone ◽  
Content Type ◽  
San Salvador ◽  
The Family ◽  
Major Respiratory Quinone ◽  
Obligate Aerobe ◽  
The 16S Rrna Gene

A bacterial strain designated RKEM611T was isolated from the octocoral Antillogorgia elisabethae, collected off the coast of San Salvador, The Bahamas. The strain is Gram-stain-negative, an obligate aerobe, and pleomorphic. It requires NaCl for growth and exhibits optimal growth at 1–2 % (w/v) NaCl, 30–37 °C and pH 6.0–8.0. The predominant cellular fatty acids are C16 : 1ω5c and C16 : 0; the major respiratory quinone is menaquinone MK-6, and the DNA G+C content is 46.3 mol%. Based on phylogenetic analysis of the 16S rRNA gene, in addition to phenotypic characteristics, RKEM611T represents a novel species and genus of a novel family within the order Bdellovibrionales . The names Pseudobacteriovoracaceae fam. nov. and Pseudobacteriovorax antillogorgiicola gen., nov., sp., nov. are proposed. Isolate RKEM611T ( = NCCB 100521T = LMG 28452T) is the type strain.

scholarly journals Natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt

2010 ◽  
Vol 60 (11) ◽  
pp. 2529-2534 ◽  
Author(s):  
Yasuhiro Shimane ◽  
Yuji Hatada ◽  
Hiroaki Minegishi ◽  
Toru Mizuki ◽  
Akinobu Echigo ◽  
...  
Keyword(s):  
New Genus ◽  
Lipid Analysis ◽  
Optimal Growth ◽  
Rrna Gene ◽  
New Genus And Species ◽  
Optimal Growth Temperature ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Extremely Halophilic Archaeon ◽  
Type Strains

Strain YSM-123T was isolated from commercial salt made from Japanese seawater in Niigata prefecture. Optimal NaCl and Mg2+ concentrations for growth were 4.0–4.5 M and 5 mM, respectively. The isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and pH were 37 °C and pH 8.0–9.0. Phylogenetic analysis based on 16S rRNA gene sequence analysis suggested that strain YSM-123T is a member of the phylogenetic group defined by the family Halobacteriaceae, but there were low similarities to type strains of other genera of this family (≤90 %); for example, Halococcus (similarity <89 %), Halostagnicola (<89 %), Natronolimnobius (<89 %), Halobiforma (<90 %), Haloterrigena (<90 %), Halovivax (<90 %), Natrialba (<90 %), Natronobacterium (<90 %) and Natronococcus (<90 %). The G+C content of the DNA was 63 mol%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylglycerophosphate methyl ester, disulfated diglycosyl diether and an unknown glycolipid. On the basis of the data presented, we propose that strain YSM-123T should be placed in a new genus and species, Natronoarchaeum mannanilyticum gen. nov., sp. nov. The type strain of Natronoarchaeum mannanilyticum is strain YSM-123T (=JCM 16328T =CECT 7565T).

scholarly journals Characterization of Gymnodinialimonas Ceratoperidinii gen. nov.,sp. nov., a New Bacterium Isolated From Rare Marine Dinoflagellate Ceratoperidinium Margalefii

2021 ◽  
Author(s):  
Yue Jiang ◽  
Yuxin Peng ◽  
Hyeon Ho Shin ◽  
Hyun Jung Kim ◽  
Ki-Hyun Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
The Family ◽  
A New Species ◽  
The 16S Rrna Gene ◽  
Core Genes

Abstract A bacterial strain, designated J12C1-MA-4T, was isolated from a liquid culture of dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-stain-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30°C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes sets indicated that the strain J12C1-MA-4T belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represented a separate taxon separated from other genera. 16S rRNA gene sequence of strain J12C1-MA-4T showed high similarities to Loktanella ponticola KCTC 42133T (95.74%), Pseudooctadecabacter jejudonensis KCTC 32525T (95.52%) and Jannaschia helgolandensis KCTC 12191T (95.31%) in the Rhodobacteraceae family. The genome length of strain J12C1-MA-4T was 3621968 bp with a DNA G+C content of 64.48 mol%. The major cellular fatty acids of strain J12C1-MA-4T were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) (>10%). Phosphatidylglycerol (PG), phosphatidylcholine(PC), phospholipids (PL), lipids 1 (L1) and aminolipid (AL) were shown to be the major polar lipids. The sole predominant isoprenoid quinone is Q-10. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, strain J12C1-MA-4T is considered to represent a new species in the new genus of the family Rhodobacteraceae for which the name Gymnodinialimonas ceratoperidinii gen. nov., sp. nov. is proposed. The type strain is J12C1-MA-4T (=KCTC 82770T = GDMCC 1.2729T).

scholarly journals Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3008-3015 ◽  
Author(s):  
Michel Oelschlägel ◽  
Christian Rückert ◽  
Jörn Kalinowski ◽  
Gert Schmidt ◽  
Michael Schlömann ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Phenylacetic Acid ◽  
Optimal Growth ◽  
Soil Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Nearest Neighbours ◽  
The Family ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene

Strain Kp5.2T is an aerobic, Gram-negative soil bacterium that was isolated in Freiberg, Saxony, Germany. The cells were motile and rod-shaped. Optimal growth was observed at 20–30 °C. The fatty acids of strain Kp5.2T comprised mainly C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The major respiratory quinone was Q-10. The major polar lipids of strain Kp5.2T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.7 %. Sequencing of the 16S rRNA gene of strain Kp5.2T allowed its classification into the family Sphingomonadaceae, and the sequence showed the highest similarity to those of members of the genus Sphingopyxis, with Sphingopyxis italica SC13E-S71T (99.15 % similarity), Sphingopyxis panaciterrae Gsoil 124T (98.96 %), Sphingopyxis chilensis S37T (98.90 %) and Sphingopyxis bauzanensis BZ30T (98.51 %) as the nearest neighbours. DNA–DNA hybridization and further characterization revealed that strain Kp5.2T can be considered to represent a novel species of the genus Sphingopyxis. Hence, the name Sphingopyxis fribergensis sp. nov. is proposed, with the type strain Kp5.2T ( = DSM 28731T = LMG 28478T).

scholarly journals Fluviicola taffensis gen. nov., sp. nov., a novel freshwater bacterium of the family Cryomorphaceae in the phylum ‘Bacteroidetes’

2005 ◽  
Vol 55 (5) ◽  
pp. 2189-2194 ◽  
Author(s):  
Louise A. O'Sullivan ◽  
Joachim Rinna ◽  
Gavin Humphreys ◽  
Andrew J. Weightman ◽  
John C. Fry
Keyword(s):  
Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Negative Bacterium ◽  
Polyphasic Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Yellow Orange ◽  
Branched Chain ◽  
The 16S Rrna Gene

A novel, strictly aerobic, Gram-negative, yellow–orange-pigmented, motile, catalase-positive, oxidase-negative bacterium, RW262T, was isolated from water of the River Taff, Cardiff, UK, during January 2000. Phylogenetic analysis of the 16S rRNA gene indicated that strain RW262T was a member of the family Cryomorphaceae within the phylum ‘Bacteroidetes’. The DNA G+C content of strain RW262T was 37·2 mol%. The predominant fatty acid was the branched-chain saturated fatty acid i15 : 0 (44·2 %). On the basis of polyphasic analysis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, it is proposed that this freshwater bacterium represents a novel genus and species within the family Cryomorphaceae, Fluviicola taffensis gen. nov., sp. nov. The type strain is RW262T (=NCIMB 13979T=DSM 16823T).

scholarly journals Actirhodobacter Atrilutea Gen. nov., sp. nov., Isolated from the Surface Water of the Yellow Sea

2021 ◽  
Author(s):  
Hua-Peng Xue ◽  
Dao-Feng Zhang ◽  
Lin Xu ◽  
Ai-Hua Zhang ◽  
Jian-Ke Huang ◽  
...  
Keyword(s):  
Surface Water ◽  
Yellow Sea ◽  
Gene Sequence ◽  
Optimal Growth ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Ubiquinone 10 ◽  
The 16S Rrna Gene

Abstract A gram-stain-negative, aerobic, orange-pigmented bacterial strain, designated as HHU K3-1T, was isolated from the surface water of the Yellow Sea. The strain was observed to grow on 2216E agar medium, and optimal growth occurred at pH 7.0, at 28 ℃ and with 2.0% (w/v) NaCl supplement. The major fatty acids (>10%) were summed feature 3 (C16:1ω6c/C16:1ω7c), C17:1ω6c and summed feature 8 (C18:1ω6c/C18:1ω7c). Strain HHU K3-1T was found to contain ubiquinone-10 as the predominant quinone and the major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and sphingoglycolipid (SGL). The 16S rRNA gene sequence analysis indicated that strain HHU K3-1T shared highest similarities with Pelagerythrobacter marensis KCTC 22370T (97.7%) and Qipengyuania oceanensis MCCC 1A09965T (96.9%). However, a phylogenetic tree based on 288 orthologous clusters (OCs) indicated that HHU K3-1T was close related to Parapontixanthobacter aurantiacus MCCC 1A09962T. The pairwise AAI and evolutionary distance between HHU K3-1T and Parapontixanthobacter aurantiacus MCCC 1A09962T is 67.1% and 0.43, respectively, which meet the recently proposed standard to differentiate genera in the family Erythrobacteraceae. On the basis of the result obtained by the polyphasic taxonomic study, the strain HHU K3-1T can be considered to represent a novel genus in the family Erythrobacteraceae, for which the name Actirhodobacter atrilutea gen. nov., sp. nov. is proposed. The type strain is HHU K3-1T (= MCCC 1K04225T = KCTC 72834T = CGMCC 1.17395T).

Flavobacterium chungbukense sp. nov., isolated from soil

2011 ◽  
Vol 61 (11) ◽  
pp. 2734-2739 ◽  
Author(s):  
Chae-Sung Lim ◽  
Yong-Sik Oh ◽  
Jae-Kwan Lee ◽  
A-Rum Park ◽  
Jae-Soo Yoo ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Gram Staining ◽  
Flavobacterium Johnsoniae ◽  
The Family ◽  
Major Respiratory Quinone ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A yellow-pigmented, Gram-staining-negative, non-motile, strictly aerobic and rod-shaped bacterium, designated CS100T, was isolated from soil in Chungbuk, Korea. Phylogenetic analysis and comparative studies based on the 16S rRNA gene sequence showed that strain CS100T belonged to the genus Flavobacterium in the family Flavobacteriaceae. Strain CS100T showed the highest sequence similarities to Flavobacterium glaciei JCM 13953T (97.6 %) and Flavobacterium johnsoniae KACC 11410T (97.1 %). Sequence similarity to other members of the genus Flavobacterium was 91.5–97.0 %. Growth occurred at 4–30 °C, at pH 5.0–9.0 and in the presence of 0–2 % (w/v) NaCl. Flexirubin-type pigments were produced. Menaquinone-6 (MK-6) was the major respiratory quinone and the major fatty acids were iso-C15 : 0 (17.3 %), summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, 15.5 %) and C16 : 0 (11.8 %). The DNA G+C content was 36.4 mol%. Strain CS100T hydrolysed skimmed milk and gelatin, but not chitin or pectin, and showed oxidase and catalase activities. DNA–DNA relatedness was 3.0 % with F. glaciei JCM 13953T and 11.5 % with F. johnsoniae KACC 11410T. On the basis of the evidence from this study, strain CS100T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium chungbukense sp. nov. is proposed. The type strain is CS100T ( = KACC 15048T = JCM 17386T).

scholarly journals Paenibacillus physcomitrellae sp. nov., isolated from the moss Physcomitrella patens

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3400-3406 ◽  
Author(s):  
Xun Zhou ◽  
Guan Nan Guo ◽  
Le Qi Wang ◽  
Su Lan Bai ◽  
Chun Li Li ◽  
...  
Keyword(s):  
Physcomitrella Patens ◽  
Optimal Growth ◽  
Major Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Beijing China ◽  
The 16S Rrna Gene

A Gram-stain-positive, facultatively anaerobic and rod-shaped bacterium, designated strain XBT, was isolated from Physcomitrella patens growing in Beijing, China. The isolate was identified as a member of the genus Paenibacillus based on phenotypic characteristics and phylogenetic inferences. The novel strain was spore-forming, motile, catalase-negative and weakly oxidase-positive. Optimal growth of strain XBT occurred at 28°C and pH 7.0–7.5. The major polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unidentified components, including one phospholipid, two aminophospholipids, three glycolipids, one aminolipid and one lipid. The predominant isoprenoid quinone was MK-7. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major fatty acid components (>5 %) were anteiso-C15 : 0 (51.2 %), anteiso-C17 : 0 (20.6 %), iso-C16 : 0 (8.3 %) and C16 : 0 (6.7 %). The G+C content of the genomic DNA was 53.3 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that strain XBT fell within the evolutionary distances encompassed by the genus Paenibacillus; its closest phylogenetic neighbour was Paenibacillus yonginensis DCY84T (96.6 %). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain XBT is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus physcomitrellae sp. nov., is proposed. The type strain is XBT ( = CGMCC 1.15044T = DSM 29851T).

scholarly journals Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3333-3338 ◽  
Author(s):  
Wei Fang ◽  
Yong Li ◽  
Han Xue ◽  
Guozhong Tian ◽  
Laifa Wang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Populus Euramericana ◽  
The Family ◽  
Distinct Branch ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

Sign in / Sign up

Export Citation Format

Share Document