scholarly journals Use of recA as an alternative phylogenetic marker in the family Vibrionaceae

2004 ◽  
Vol 54 (3) ◽  
pp. 919-924 ◽  
Author(s):  
C. C. Thompson ◽  
F. L. Thompson ◽  
K. Vandemeulebroecke ◽  
B. Hoste ◽  
P. Dawyndt ◽  
...  
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
The Other ◽  
Vibrio Splendidus ◽  
Gene Sequences ◽  
Vibrio Tubiashii ◽  
Wide Range ◽  
The Family ◽  
Vibrio Mimicus ◽  
Taxonomic Studies

This study analysed the usefulness of recA gene sequences as an alternative phylogenetic and/or identification marker for vibrios. The recA sequences suggest that the genus Vibrio is polyphyletic. The high heterogeneity observed within vibrios was congruent with former polyphasic taxonomic studies on this group. Photobacterium species clustered together and apparently nested within vibrios, while Grimontia hollisae was apart from other vibrios. Within the vibrios, Vibrio cholerae and Vibrio mimicus clustered apart from the other genus members. Vibrio harveyi- and Vibrio splendidus-related species formed compact separated groups. On the other hand, species related to Vibrio tubiashii appeared scattered in the phylogenetic tree. The pairs Vibrio coralliilyticus and Vibrio neptunius, Vibrio nereis and Vibrio xuii and V. tubiashii and Vibrio brasiliensis clustered completely apart from each other. There was a correlation of 0·58 between recA and 16S rDNA pairwise similarities. Strains of the same species have at least 94 % recA sequence similarity. recA gene sequences are much more discriminatory than 16S rDNA. For 16S rDNA similarity values above 98 % there was a wide range of recA similarities, from 83 to 99 %.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Chlamydiales – Taxonomy, Pathogenicity, and Zoonotic Potential

2012 ◽  
Vol 56 (3) ◽  
pp. 267-270
Author(s):  
Krzysztof Niemczuk ◽  
Marian Truszczyńsk ◽  
Monika Szymańska-Czerwińska
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Genes ◽  
23S Rrna ◽  
Zoonotic Potential ◽  
16S Rdna Gene ◽  
The Family ◽  
23S Rrna Genes

Abstract Changes in the taxonomy of the order Chlamydiales, after its separation from the order Rickettsiales, were presented. These changes resulted in the recognition of the following families: Chlamydiaceae, Chlavichlamydiaceae, Criblamydiaceae, Parachlamydiaceae, Piscichlamydiaceae, Rhabdochlamydiaceae, Simkaniaceae, and Waddliaceae. Other described changes concerned particularly the family Chlamydiaceae. Its genus Chlamydia was divided into Chlamydia and Chlamydophila. However, in the following years, a revision to the single original genus was made, based upon phylogenetic analysis of 16S and 23S rRNA genes of the strains belonging to these two taxonomic units. The review also discusses other families outside the family Chlamydiaceae, which contain so-called Chlamydia-related or Chlamydia-like organisms. Members of each family share a 16S rDNA gene sequence similarity >90%. Furthermore, characterisation of the pathogenecity is presented, focusing especially on the representatives of the family Chlamydiaceae, which cause animal infections, and describing their zoonotic potential. Available data on this topic, connected with the representatives of other families, were mentioned.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Photobacterium aphoticum sp. nov., isolated from coastal water

2011 ◽  
Vol 61 (7) ◽  
pp. 1579-1584 ◽  
Author(s):  
Teresa Lucena ◽  
María A. Ruvira ◽  
Javier Pascual ◽  
Esperanza Garay ◽  
M. Carmen Macián ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Brown Pigment ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
The Family ◽  
Biolog Gn

A facultatively anaerobic marine gammaproteobacterium, designated strain M46T, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized by using a polyphasic approach and was found to be situated within the genus Photobacterium in the family Vibrionaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46T was closely related to P. rosenbergii CECT 7644T, P. halotolerans CECT 5860T and P. ganghwense CECT 7641T, showing sequence similarities of 96.8, 96.4 and 96.2 %, respectively. According to the results of phylogenetic analyses based on recA and gyrB gene sequences, the most closely related taxon was P. ganghwense CECT 7641T with 87.4 and 85.0 % sequence similarity, respectively. Regardless of the gene used in phylogenetic analysis, strain M46T always formed a separate and stable clade containing these three species of the genus Photobacterium. Strain M46T was not luminescent and produced a diffusible brown pigment. It required NaCl to grow, reduced nitrate to nitrite and oxidized a small number of substrates in Biolog GN plates. Strain M46T was positive for arginine dihydrolase (ADH), β-galactosidase, aesculin hydrolysis and DNase activity. In API ZYM tests, the novel strain was positive for alkaline phosphatase, leucine arylamidase and acidic phosphatase activities. The major cellular fatty acids were unsaturated C18 and C16, as in other members of the genus Photobacterium, but their relative amounts and the presence or absence of other fatty acids differentiated strain M46T from its closest relatives. Based on the results of this polyphasic taxonomic study, strain M46T represents a novel species of the genus Photobacterium, for which the name Photobacterium aphoticum is proposed. The type strain is M46T ( = CECT 7614T  = KCTC 23057T).

scholarly journals Tree inhabiting gnomoniaceous species from China, with Cryphogonomonia gen. nov. proposed

MycoKeys ◽  
2020 ◽  
Vol 69 ◽  
pp. 71-89
Author(s):  
Qin Yang ◽  
Ning Jiang ◽  
Cheng-Ming Tian
Keyword(s):  
Leaf Spot ◽  
Woody Plants ◽  
Phylogenetic Analyses ◽  
Polyphasic Approach ◽  
Forest Trees ◽  
Gene Sequences ◽  
Tree Diseases ◽  
Wide Range ◽  
The Family ◽  
Cultural Data

Species of Gnomoniaceae are commonly associated with leaf spot diseases of a wide range of plant hosts worldwide. During our investigation of fungi associated with tree diseases in China, several gnomoniaceous isolates were recovered from symptomatic branches and leaves on different woody plants in the Fagaceae, Pinaceae, and Salicaceae families. These isolates were studied by applying a polyphasic approach including morphological, cultural data, and phylogenetic analyses of partial ITS, LSU, tef1, rpb2 and tub2 gene sequences. As a result, three species were identified with characters fitting into the family Gnomoniaceae. One of these species is described herein as Cryphognomonia pinigen. et sp. nov., characterized by developed pseudostromata and ascospores with obvious hyaline sheath; Gnomoniopsis xunwuensissp. nov. is illustrated showing sympodially branched conidiophore, oval or fusiform conidia; and one known species, Plagiostoma populinum. The current study improves the understanding of gnomoniaceous species causing diebacks and leaf spot on ecological and economic forest trees.

scholarly journals Salinibacillus aidingensis gen. nov., sp. nov. and Salinibacillus kushneri sp. nov., moderately halophilic bacteria isolated from a neutral saline lake in Xin-Jiang, China

2005 ◽  
Vol 55 (2) ◽  
pp. 949-953 ◽  
Author(s):  
Pei-Gen Ren ◽  
Pei-Jin Zhou
Keyword(s):  
Type Strain ◽  
Saline Lake ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Moderately Halophilic ◽  
The Family ◽  
Taxonomic Studies

Three Gram-positive, moderately halophilic, heterotrophic bacterial strains were isolated from a neutral saline lake in the Xin-Jiang area of China. The strains, designated 8-2T, W11-1 and 25-7T, were motile, spore-forming, aerobic rods and contained meso-diaminopimelic acid in their cell walls. Their DNA G+C contents were 37·4, 37·2 and 39·9 mol%, respectively. The main fatty acids in the cellular membranes of these novel strains were C15 and C17 methyl-branched. No species with validly published names showed 16S rRNA gene sequence similarity of more than 95 % with respect to these novel isolates; the most closely related species was a halophilic denitrifier, Bacillus halodenitrificans (94·6 %). Polyphasic taxonomic studies revealed that these strains belong to the Bacillaceae and are distantly related to other genera of the family. It is proposed that a new genus, Salinibacillus, should be created, with Salinibacillus aidingensis (type strain, 25-7T=AS 1.3565T=JCM 12389T) as the type species. Another species, Salinibacillus kushneri, is also proposed, with 8-2T (=AS 1.3566T=JCM 12390T) as the type strain.

scholarly journals Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2424-2430 ◽  
Author(s):  
Kristin Mühldorfer ◽  
Stephanie Speck ◽  
Gudrun Wibbelt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae . Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3–99.9 %) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96 % sequence similarity to known members of the Pasteurellaceae . The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6–100 % sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8–96 % similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08T is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08T ( = CCUG 64585T = DSM 27238T). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.

Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4259-4265 ◽  
Author(s):  
Malka Halpern ◽  
Svetlana Fridman ◽  
Nof Atamna-Ismaeel ◽  
Ido Izhaki
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Floral Nectar ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family

Gram-negative, rod-shaped, oxidase-negative, facultatively anaerobic, yellow–orange-pigmented and motile bacterial strains, designated 8N4T, 9N2 and 10N3, were isolated from flower nectar of Amygdalus communis (almond) and Citrus paradisi (grapefruit). The 16S rRNA gene sequences of the strains shared highest sequence similarity of 97.0 % with that of Phaseolibacter flectens ATCC 12775T and lower similarity with sequences from other type strains of genera of the Enterobacteriaceae . A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, gyrB, rpoB and atpD gene sequences supported the classification of strains 8N4T, 9N2 and 10N3 within a novel species in a novel genus in the family Enterobacteriaceae . Strain 8N4T, and the reference strains of the novel species, grew at 4–35 °C (optimum, 28–30 °C), with 0–5.0 % NaCl (optimum, 3 % NaCl) and with 0–60 % sucrose (optimum, 10–25 % sucrose). Their major cellular fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain 8N4T was 46.8 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the floral nectar isolates are classified within a novel species in a new genus in the family Enterobacteriaceae , for which the name Rosenbergiella nectarea gen. nov., sp. nov. is proposed. The type strain of Rosenbergiella nectarea is 8N4T ( = LMG 26121T = DSM 24150T).

scholarly journals Receptor selectivity from minimal backbone modification of a polypeptide agonist

2018 ◽  
Vol 115 (49) ◽  
pp. 12383-12388 ◽  
Author(s):  
Shi Liu ◽  
Ross W. Cheloha ◽  
Tomoyuki Watanabe ◽  
Thomas J. Gardella ◽  
Samuel H. Gellman
Keyword(s):  
Sequence Similarity ◽  
The Other ◽  
Side Chain ◽  
General Strategy ◽  
Human Parathyroid Hormone ◽  
Receptor Selectivity ◽  
Wide Range ◽  
Methylene Unit ◽  
Backbone Modification ◽  
Selective Agonists

Human parathyroid hormone (PTH) and N-terminal fragments thereof activate two receptors, hPTHR1 and hPTHR2, which share ∼51% sequence similarity. A peptide comprising the first 34 residues of PTH is fully active at both receptors and is used to treat osteoporosis. We have used this system to explore the hypothesis that backbone modification of a promiscuous peptidic agonist can provide novel receptor-selective agonists. We tested this hypothesis by preparing a set of variants of PTH(1–34)-NH2 that contained a single β-amino-acid residue replacement at each of the first eight positions. These homologs, each containing one additional backbone methylene unit relative to PTH(1–34)-NH2 itself, displayed a wide range of potencies in cell-based assays for PTHR1 or PTHR2 activation. The β-scan series allowed us to identify two homologs, each containing two α→β replacements, that were highly selective, one for PTHR1 and the other for PTHR2. These findings suggest that backbone modification of peptides may provide a general strategy for achieving activation selectivity among polypeptide-modulated receptors, and that success requires consideration of both β2- and β3-residues, which differ in terms of side-chain location.

Aeromonas

1984 ◽  
Vol 5 (11) ◽  
pp. 542-544 ◽  
Author(s):  
Paul E. Schoch ◽  
Burke A. Cunha
Keyword(s):  
Diarrheal Disease ◽  
Clinical Manifestations ◽  
Neonatal Meningitis ◽  
True Incidence ◽  
Wide Range ◽  
The Family ◽  
Eighth Edition ◽  
Tract Infections ◽  
Human Infections ◽  
Taxonomic Studies

The genera Aeromonas and Plesiomonas are gram-negative, cytochrome oxidase-positive, asporogenous, facultatively anaerobic rods that ferment carbohydrates with the production of acid or acid and gas. They are members of the family Vibrionaceae. Members of these genera are motile by means of polar flagella but in many other ways, resemble organisms belonging to the Enterobacteriaceae. Three species of Aeromonas are currently recognized in the eighth edition of Bergey's Manual, based on the studies of Schubert. A. salmonicida, a pathogen in fish which is non-motile and incapable of growing at 37°C, A. punctata, an aquatic environmental isolate possessing two subspecies and A. hydrophila, an organism associated with a wide range of clinical manifestations including wound cellulitis, septicemia, acute diarrheal disease, urinary tract infections and rarely, endocarditis, neonatal meningitis, otitis, peritonitis and osteomyelitis. In 1976, Popoff and Vern described a new species of Aeromonas A. sobria, which while motile, differed from A. hydrophila by a lack or significant decrease in the presence of several enzymes such as elastase, lipase and B-glucosidase. This organism represented a minority of environmental strains in a survey conducted by Seidler but seemed to predominate in a series of clinical isolates reviewed by Daily and colleagues in which the majority of Aeromonas isolates studied were A. sobria, characteristically cytotoxic, enterotoxigenic and lethal for mice. Unfortunately, since many clinical laboratories have not differentiated A. sobria from A. hydrophila in the past, the true incidence of this organism in human infections is largely unknown. Taxonomic studies performed by Maclnnes and Trust suggested that A. sobria should be included as a biotype of A. hydrophila.

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