scholarly journals Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum

2004 ◽  
Vol 54 (2) ◽  
pp. 401-406 ◽  
Author(s):  
Paul J. Simpson ◽  
R. Paul Ross ◽  
Gerald F. Fitzgerald ◽  
Catherine Stanton
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Growth Parameters ◽  
Novel Species ◽  
Growth Conditions ◽  
Heat Shock Protein 60 ◽  
Gene Sequences ◽  
Phenotypic Data ◽  
Hsp60 Gene ◽  
Rdna Sequencing

In a previous study that was based primarily on 16S rDNA sequencing, two groups of bifidobacteria that had been recovered from a pig caecum were proposed to belong to two novel species, termed ‘Bifidobacterium pyschroaerophilum’ and ‘Bifidobacterium aerophilum’. In this study, based on DNA G+C content and partial heat-shock protein 60 (HSP60) gene sequences, the assignment of ‘B. pyschroaerophilum’, corrected to Bifidobacterium pyschraerophilum, to the genus Bifidobacterium was confirmed. The DNA G+C content of ‘B. aerophilum’ was relatively low, which was consistent with its segregation into subcluster II of the 16S rDNA phylogenetic tree. Based on partial 16S rDNA and HSP60 gene sequences, the species was transferred to a novel genus and reclassified as Aeriscardovia aeriphila gen. nov., sp. nov. Biochemical profiles and growth parameters were established for both novel species. Interestingly, each had a high tolerance to oxygen and grew on agar media under aerobic conditions, a trait that may relate to their caecal habitat. Under aerobic growth conditions, the short-rod morphology of A. aeriphila lengthened considerably. This appeared to arise from incomplete cell division. In addition, B. pyschraerophilum was unusual in that it grew at temperatures as low as 4 °C. On the basis of genetic, phylogenetic and phenotypic data, the identities of Bifidobacterium pyschraerophilum sp. nov. (type strain, T16T=LMG 21775T=NCIMB 13940T) and Aeriscardovia aeriphila gen. nov., sp. nov. (type strain, T6T=LMG 21773T=NCIMB 13939T) are confirmed.

scholarly journals Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract

2011 ◽  
Vol 61 (6) ◽  
pp. 1315-1321 ◽  
Author(s):  
J. Killer ◽  
J. Kopečný ◽  
J. Mrázek ◽  
I. Koppová ◽  
J. Havlík ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Digestive Tract ◽  
Type Strain ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Heat Shock Protein 60 ◽  
Gene Sequences

Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA and heat-shock protein 60 (hsp60) gene sequences. Analysis of 16S rRNA gene sequence similarities revealed that the isolates of the first group were affiliated to Bifidobacterium asteroides YIT 11866T, B. indicum JCM 1302T and B. coryneforme ATCC 25911T (96.2, 96.0 and 95.9 % sequence similarity, respectively), together with other bifidobacteria showing lower sequence similarity. Additional representatives of the second group were found to be affiliated to Bifidobacterium minimum YIT 4097T and B. coryneforme ATCC 25911T (96.0 and 96.3 % sequence similarity) and also to other bifidobacteria with lower sequence similarity. These results indicate that the isolates of the two groups belong to novel species within the genus Bifidobacterium. This observation was further substantiated by the results of partial sequencing of hsp60. On the basis of phylogenetic and phenotypic analyses and analysis of 16S rRNA and partial hsp60 gene sequences, we propose two novel species, Bifidobacterium actinocoloniiforme sp. nov. (type strain LISLUCIII-P2T  = DSM 22766T  = CCM 7728T) and Bifidobacterium bohemicum sp. nov. (type strain JEMLUCVIII-4T  = DSM 22767T  = CCM 7729T).

scholarly journals Ancylobacter rudongensis sp. nov., isolated from roots of Spartina anglica

2004 ◽  
Vol 54 (2) ◽  
pp. 385-388 ◽  
Author(s):  
Yu Hua Xin ◽  
Yu Guang Zhou ◽  
Hui Ling Zhou ◽  
Wen Xin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Binding ◽  
16S Rdna ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Spartina Anglica ◽  
Phenotypic Data ◽  
16S Rdna Sequence ◽  
Bacterium Strain

A curved, ring-like bacterium, strain AS 1.1761T, isolated from the roots of Spartina anglica, was studied by a polyphasic approach. According to phylogenetic analysis, strain AS 1.1761T belongs to the genus Ancylobacter, with 99·21 % 16S rDNA sequence similarity to Ancylobacter aquaticus, the only species described so far in this genus. However, strain AS 1.1761T had no significant DNA–DNA binding with the type strain of A. aquaticus. In addition, strain AS 1.1761T differed from A. aquaticus in many phenotypic features. Based on molecular and phenotypic data, a novel species, Ancylobacter rudongensis sp. nov., is proposed. The type strain is AS 1.1761T (=JCM 11671T).

scholarly journals Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

2011 ◽  
Vol 61 (7) ◽  
pp. 1606-1611 ◽  
Author(s):  
Enrico Tortoli ◽  
Erik C. Böttger ◽  
Anna Fabio ◽  
Enevold Falsen ◽  
Zoe Gitti ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polyphasic Analysis ◽  
Mycobacterium Simiae

Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228T ( = DSM 45397T  = CCUG 58464T) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the ‘Mycobacterium simiae complex’ for this group.

scholarly journals Isoptericola chiayiensis sp. nov., isolated from mangrove soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1667-1670 ◽  
Author(s):  
M. Tseng ◽  
H. C. Liao ◽  
W. P. Chiang ◽  
G. F. Yuan
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Dna Relatedness ◽  
Mangrove Soil ◽  
Low Levels ◽  
Type Strains

A novel actinomycete, designated strain 06182M-1T, was isolated from a mangrove soil sample collected from Chiayi County in Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences revealed levels of similarity of 97.0–98.8 % to the type strains of recognized species of the genus Isoptericola. Chemotaxonomic data also supported the placement of strain 06182M-1T within the genus Isoptericola. However, the low levels of DNA–DNA relatedness between the novel strain and the type strains of recognized species of the genus Isoptericola, in combination with differential phenotypic data, demonstrate that strain 06182M-1T represents a novel species of the genus Isoptericola, for which the name Isoptericola chiayiensis sp. nov. is proposed. The type strain is 06182M-1T ( = BCRC 16888T  = KCTC 19740T).

scholarly journals Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments

2011 ◽  
Vol 61 (9) ◽  
pp. 2320-2327 ◽  
Author(s):  
Carolina H. Pohl ◽  
Martha S. Smit ◽  
Jacobus Albertyn
Keyword(s):  
Internal Transcribed Spacer ◽  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Carbon Sources ◽  
The Other ◽  
26S Rdna ◽  
Rdna Sequencing ◽  
Physiological Tests

Recent rDNA sequencing of 25 isolates from a previous study, during which limonene-utilizing yeasts were isolated from monoterpene-rich environments by using 1,4-disubstituted cyclohexanes as sole carbon sources, led to the identification of four hitherto unknown Rhodotorula species. Analyses of the 26S rDNA D1/D2 region as well as the internal transcribed spacer (ITS) domain indicated that two isolates (CBS 8499T and CBS 10736) were identical and were closely related to Rhodotorula cycloclastica, a previously described limonene-utilizing yeast. These novel isolates differed from known yeast species and could be distinguished from R. cycloclastica by standard physiological tests. The other three isolates represent three novel Rhodotorula species, closely related to Sporobolomyces magnisporus. These three species could also be distinguished from other Rhodotorula species by standard physiological tests. Based on these results, we suggest that the new isolates represent novel species, for which the names Rhodotorula eucalyptica sp. nov. (type strain CBS 8499T  = NRRL Y-48408T), Rhodotorula pini sp. nov. (type strain CBS 10735T  = NRRL Y-48410T), Rhodotorula bloemfonteinensis sp. nov. (type strain CBS 8598T  = NRRL Y-48407T) and Rhodotorula orientis sp. nov. (type strain CBS 8594T  = NRRL Y-48719T) are proposed. R. eucalyptica and R. pini can also utilize limonene.

scholarly journals Williamsia marianensis sp. nov., a novel actinomycete isolated from the Mariana Trench

2006 ◽  
Vol 56 (5) ◽  
pp. 1123-1126 ◽  
Author(s):  
Wasu Pathom-aree ◽  
Yuichi Nogi ◽  
Iain C. Sutcliffe ◽  
Alan C. Ward ◽  
Koki Horikoshi ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Gene Tree ◽  
Taxonomic Status ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Hexadecenoic Acid ◽  
Phenotypic Data ◽  
Mariana Trench ◽  
Phyletic Line

The taxonomic status of an actinomycete isolated from sediment collected from the Mariana Trench was established using a combination of genotypic and phenotypic data. Isolate MT8T had chemotaxonomic and morphological properties consistent with its classification in the genus Williamsia, and formed a distinct phyletic line in the 16S rRNA gene tree together with the type strain of Williamsia muralis. The isolate was readily distinguished from the latter, and from representatives of other Williamsia species, using DNA–DNA relatedness and phenotypic criteria. Predominant cellular fatty acids were oleic, palmitic and tuberculostearic acids and a hexadecenoic acid. The DNA G+C content was 65.2 mol%. It is apparent that the isolate belongs to a novel species of Williamsia. Strain MT8T (=DSM 44944T=NCIMB 14085T) was thus considered to be the type strain of a novel species in the genus Williamsia, for which the name Williamsia marianensis sp. nov. is proposed.

scholarly journals Corynebacterium pyruviciproducens sp. nov., a pyruvic acid producer

2010 ◽  
Vol 60 (5) ◽  
pp. 1135-1140 ◽  
Author(s):  
Jia Tong ◽  
Chengxu Liu ◽  
Paula H. Summanen ◽  
Huaxi Xu ◽  
Sydney M. Finegold
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Corynebacterium Glucuronolyticum ◽  
Taxonomic Methods ◽  
Groin Abscess

A coryneform strain, 06-1773OT (=WAL 19168T), derived from a groin abscess sample was characterized using phenotypic and molecular taxonomic methods. Comparative analyses revealed more than 3 % divergence of the 16S rRNA gene sequence and about 10 % divergence of the partial rpoB gene sequence from the type strain of Corynebacterium glucuronolyticum. The strain could also be differentiated from C. glucuronolyticum by a set of phenotypic properties. A DNA–DNA relatedness study between strain WAL 19168T and C. glucuronolyticum CCUG 35055T showed a relatedness value of 13.3 % (13.7 % on repeat analysis). The genotypic and phenotypic data show that the strain merits classification within a novel species of Corynebacterium. We propose the name Corynebacterium pyruviciproducens sp. nov. for the novel species. The type strain is 06-1773OT (=WAL 19168T =CCUG 57046T =ATCC BAA-1742T).

scholarly journals Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea

2006 ◽  
Vol 56 (7) ◽  
pp. 1645-1649 ◽  
Author(s):  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Sylvie Cousin ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils ◽  
Sequence Similarities

Two yellow-pigmented, Gram-negative, rod-shaped bacterial strains, GH1-10T and GH29-5T, were isolated from greenhouse soils in Korea. 16S rRNA gene sequence analysis indicated that these strains were related to members of the genus Flavobacterium. Strain GH1-10T was most closely related to Flavobacterium psychrolimnae and Flavobacterium denitrificans, with sequence similarities of 95.9 and 95.2 %, respectively. Strain GH29-5T was most closely related to ‘Flavobacterium saliodium’, F. denitrificans and Flavobacterium frigoris, with sequence similarities of 94.3, 92.5 and 92.5 %, respectively. The major cellular fatty acids of GH1-10T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH, and those of GH29-5T were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. Both strains contained menaquinone with six isoprene units (MK-6) as the sole quinone. The DNA G+C contents of GH1-10T and GH29-5T were 35 and 39 mol%, respectively. Based on the phylogenetic and phenotypic data presented, it is concluded that the two bacteria represent two separate novel species of the genus Flavobacterium. The names proposed to accommodate these organisms are Flavobacterium daejeonense sp. nov., with type strain GH1-10T (=KACC 11422T=DSM 17708T), and Flavobacterium suncheonense sp. nov., with type strain GH29-5T (=KACC 11423T=DSM 17707T).

scholarly journals Antioxidant Potential of Pediococcus Pentosaceus Strains from the Sow Milk Bacterial Collection in Weaned Piglets

2021 ◽  
Author(s):  
Leli Wang ◽  
Qihang Liu ◽  
Yuwei Chen ◽  
Xinlei Zheng ◽  
Chuni Wang ◽  
...  
Keyword(s):  
16S Rdna ◽  
Signaling Pathway ◽  
Commensal Bacteria ◽  
Functional Evaluation ◽  
Gene Sequences ◽  
16S Rdna Gene ◽  
Maternal Milk ◽  
Pediococcus Pentosaceus ◽  
Rdna Gene ◽  
Rdna Sequencing

Abstract Background: In modern animal husbandry, breeders pay increasing attention to improving sow nutrition during pregnancy and lactation to favor the health of neonates. Sow milk is a main food for piglets during their first three weeks of life, which is not only a rich repository of essential nutrients and a broad range of bioactive compounds, but also an indispensable source of commensal bacteria. Maternal milk microorganisms are important sources of commensal bacteria for neonatal gut. Bacteria from maternal milk may serve as an additive to confer a health benefit on the composition of the indigenous microbiota of piglets. Methods: The sow milk microbiota was collected using the culturomics methods of Continuous Culture and Interval Sampling, following by the identification of 16S rDNA gene sequences. To screen potential probiotics, the functional evaluation was conducted to assess their antagonistic activity against pathogens in vitro and evaluate their resistance against oxidative stress in damaged Drosophila induced by paraquat. In piglet feeding trial, a total of 54 newborn suckling piglets were chosen from nine sows and randomly assigned to three treatments with different concentration of a candidate strain. Multiple approaches were carried out to verify its antioxidant function including western blotting, enzyme activity analysis, metabolomics and 16S rDNA sequencing. Results: The 1240 isolates were screened out from the sow milk microbiota and grouped into 271 bacterial taxa based on a nonredundant set of 16S rDNA gene sequences. Among 80 Pediococcus isolates, a new Pediococcus pentosaceus strain (SMM914) showed best performance in inhibition ability against swine pathogens and in Drosophila model challenged by paraquat. Pretreatment of piglets with SMM914 induces the Nrf2-Keap1 antioxidant signaling pathway and greatly affected the pathways of amino acid metabolism and lipid metabolism in plasma. In colon, Lactobacillus was significantly increased in the high dose of SMM914 group compared with the control group. Conclusion: SMM914 functions as a promising probiotic conferring antioxidant capacity by activating the Nrf2-Keap1 antioxidant signaling pathway in piglets. Our study provided useful resources for deeply understanding the relationships between the maternal microbiota and offspring.

scholarly journals Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov.

2006 ◽  
Vol 56 (9) ◽  
pp. 2223-2228 ◽  
Author(s):  
Peter Kämpfer ◽  
Chiu-Chung Young ◽  
K. R. Sridhar ◽  
A. B. Arun ◽  
Wei An Lai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Phenotypic Differences ◽  
The 16S Rrna Gene

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Flexibacter has shown extensive intrageneric phylogenetic heterogeneity. It has been shown in previous studies that the species [Flexibacter] sancti, [Flexibacter] filiformis and [Flexibacter] japonensis were most closely related to Chitinophaga pinensis. In addition, [Cytophaga] arvensicola and species of the genus Terrimonas also clustered into this phylogenetic group. Although the similarities of 16S rRNA gene sequences were low (88.5–96.4 %), there is no evidence for clear phenotypic differences between these organisms that justify assignment to different genera. A proposal is made to transfer these species to the genus Chitinophaga as Chitinophaga sancti comb. nov., Chitinophaga filiformis comb. nov., Chitinophaga japonenis comb. nov. and Chitinophaga arvensicola comb. nov. on the basis of phylogenetic and phenotypic data. Furthermore, a novel species is described within this genus, Chitinophaga skermanii sp. nov., with strain CC-SG1BT (=CCUG 52510T=CIP 109140T) as the type strain.

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