Faculty Opinions recommendation of Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays.

2001 ◽  
Author(s):  
Peter Williams
Keyword(s):  
Dna Hybridization ◽  
Dna Microarrays ◽  
Bacterial Species ◽  
Species Determination

scholarly journals Bacterial Species Determination from DNA-DNA Hybridization by Using Genome Fragments and DNA Microarrays

2001 ◽  
Vol 67 (8) ◽  
pp. 3677-3682 ◽  
Author(s):  
Jae-Chang Cho ◽  
James M. Tiedje
Keyword(s):  
Dna Hybridization ◽  
Genomic Dna ◽  
Dna Microarrays ◽  
Bacterial Species ◽  
Whole Genome ◽  
Microarray Technology ◽  
Bacterial Strains ◽  
Species Determination ◽  
Identification Of Bacteria ◽  
Reference Genomes

ABSTRACT Whole genomic DNA-DNA hybridization has been a cornerstone of bacterial species determination but is not widely used because it is not easily implemented. We have developed a method based on random genome fragments and DNA microarray technology that overcomes the disadvantages of whole-genome DNA-DNA hybridization. Reference genomes of four fluorescent Pseudomonas species were fragmented, and 60 to 96 genome fragments of approximately 1 kb from each strain were spotted on microarrays. Genomes from 12 well-characterized fluorescent Pseudomonas strains were labeled with Cy dyes and hybridized to the arrays. Cluster analysis of the hybridization profiles revealed taxonomic relationships between bacterial strains tested at species to strain level resolution, suggesting that this approach is useful for the identification of bacteria as well as determining the genetic distance among bacteria. Since arrays can contain thousands of DNA spots, a single array has the potential for broad identification capacity. In addition, the method does not require laborious cross-hybridizations and can provide an open database of hybridization profiles, avoiding the limitations of traditional DNA-DNA hybridization.

Peptoniphilus Colimassiliensis sp. nov. and Peptoniphilus Urinimassiliensis sp. nov., Two New Species Isolated From Humans

2021 ◽  
Author(s):  
Babacar Mbaye ◽  
Cheikh Ibrahima LO ◽  
Niokhor Dione ◽  
Sarah Benabdelkader ◽  
Maryam Tidjani Alou ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Kidney Transplant Recipient ◽  
Bacterial Species ◽  
Hexadecanoic Acid ◽  
Anaerobic Conditions ◽  
New Members ◽  
Two New Species ◽  
Type Strains ◽  
Gram Positive Cocci

Abstract Strains Marseille-P3761 and Marseille-P3195 are representatives of two bacterial species isolated from human specimens. Strain Marseille-P3761 was isolated from the stool of a healthy volunteer, while strain Marseille-P3915 was cultivated from the urine of a kidney transplant recipient. Both strains are anaerobic Gram-positive cocci bacteria. Both are catalase-negative and oxidase-negative and grow optimally at 37°C in anaerobic conditions. They also metabolize carbohydrates such as galactose, glucose, fructose, and glycerol. The major fatty acids were hexadecanoic acid for both strains, Marseille-P3761 (38%) and Marseille-P3195 (31%). The highest DNA-DNA hybridization values of Marseille-P3761 and Marseille-P3195 strains when compared to their closest phylogenetic relatives were 52.3% and 56.4%, respectively. The morphological, biochemical, phenotypic and genomic characteristics strongly support that these strains are new members of the Peptoniphilus genus. Thus, we suggest that strains Marseille-P3761 (CSUR P3761 = CCUG71569) and Marseille-P3195 (CSUR P3195 = DSM 103468) are the type strains of two new Peptoniphilus species, for which we propose the names Peptoniphilus colimassiliensis sp. nov. and Peptoniphilus urinimassiliensis sp. nov., respectively.

scholarly journals Antimicrobial-Resistant Enteric Bacteria from Dairy Cattle

2006 ◽  
Vol 73 (1) ◽  
pp. 156-163 ◽  
Author(s):  
Ashish A. Sawant ◽  
Narasimha V. Hegde ◽  
Beth A. Straley ◽  
Sarah C. Donaldson ◽  
Brenda C. Love ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Dna Hybridization ◽  
Bacterial Species ◽  
Dairy Herd ◽  
Enteric Bacteria ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
Predominant Species ◽  
Lactating Dairy Cattle

ABSTRACT A study was conducted to understand the descriptive and molecular epidemiology of antimicrobial-resistant gram-negative enteric bacteria in the feces of healthy lactating dairy cattle. Gram-negative enteric bacteria resistant to ampicillin, florfenicol, spectinomycin, and tetracycline were isolated from the feces of 35, 8, 5, and 42% of 213 lactating cattle on 74, 39, 9, 26, and 82% of 23 farms surveyed, respectively. Antimicrobial-resistant gram-negative bacteria accounted for 5 (florfenicol) to 14% (tetracycline) of total gram-negative enteric microflora. Nine bacterial species were isolated, of which Escherichia coli (87%) was the most predominant species. MICs showing reduced susceptibility to ampicillin, ceftiofur, chloramphenicol, florfenicol, spectinomycin, streptomycin, and tetracycline were observed in E. coli isolates. Isolates exhibited resistance to ampicillin (48%), ceftiofur (11%), chloramphenicol (20%), florfenicol (78%), spectinomycin (18%), and tetracycline (93%). Multidrug resistance (≥3 to 6 antimicrobials) was seen in 40% of E. coli isolates from healthy lactating cattle. Of 113 tetracycline-resistant E. coli isolates, tet(B) was the predominant resistance determinant and was detected in 93% of isolates, while the remaining 7% isolates carried the tet(A) determinant. DNA-DNA hybridization assays revealed that tet determinants were located on the chromosome. Pulsed-field gel electrophoresis revealed that tetracycline-resistant E. coli isolates (n = 99 isolates) belonged to 60 subtypes, which is suggestive of a highly diverse population of tetracycline-resistant organisms. On most occasions, E. coli subtypes, although shared between cows within the herd, were confined mostly to a dairy herd. The findings of this study suggest that commensal enteric E. coli from healthy lactating cattle can be an important reservoir for tetracycline and perhaps other antimicrobial resistance determinants.

scholarly journals Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 625-632 ◽  
Author(s):  
Javier Pascual ◽  
Marina García-López ◽  
Gerald F. Bills ◽  
Olga Genilloud
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Bacterial Species ◽  
Phenotypic Traits ◽  
Terminal Electron Acceptor ◽  
Content Type ◽  
Link Type ◽  
Natural Park ◽  
Fatty Acid Compositions

During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770T was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770T belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis , P. koreensis , P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770T in the genus Pseudomonas . DNA–DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas , for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770T ( = DSM 28040T = LMG 27940T).

scholarly journals Mucilaginibacter polysacchareus sp. nov., an exopolysaccharide-producing bacterial species isolated from the rhizoplane of the herb Angelica sinensis

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 632-637 ◽  
Author(s):  
Song-Ih Han ◽  
Hyo-Jin Lee ◽  
Hae-Ran Lee ◽  
Ki-Kwang Kim ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Bacterial Species ◽  
Angelica Sinensis ◽  
Rrna Gene ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three exopolysaccharide-producing bacteria, designated strains DRP28T, DRP29 and DRP31, were isolated from the rhizoplane of Angelica sinensis from the Geumsan, Republic of Korea. Cells were straight rods, Gram reaction-negative, aerobic, non-motile, and catalase- and oxidase- positive. Flexirubin-type pigments were absent. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities to strains of recognized species of the genus Mucilaginibacter were 93.8–97.4 %. The major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The strains contained MK-7 as the major isoprenoid quinone. Strains DRP28T, DRP29 and DRP31 formed a single, distinct genomospecies with DNA G+C contents of 41.9–42.7 mol% and DNA hybridization values of 82.6–86.8 %; the strains exhibited DNA–DNA hybridization values of only 20.4–41.3 % with related species of the genus Mucilaginibacter. On the basis of evidence presented in this study, strains DRP28T, DRP29 and DRP31 were considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter polysacchareus sp. nov. is proposed. The type strain is DRP28T ( = KACC 15075T  = NBRC 107757T).

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.

scholarly journals Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively

2020 ◽  
Vol 70 (5) ◽  
pp. 3547-3552 ◽  
Author(s):  
Mari Tohya ◽  
Shin Watanabe ◽  
Tatsuya Tada ◽  
Htay Htay Tin ◽  
Teruo Kirikae
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Bacterial Species ◽  
Taxonomic Status ◽  
Species Delineation ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Group Species

This study was conducted to clarify the taxonomic status of the species Pseudomonas fuscovaginae and Pseudomonas shirazica . Whole genome sequences for the type strains of P. fuscovaginae and P. shirazica were compared against the closely related type strains of the Pseudomonas putida group and the Pseudomonas fluorescens group species. Average nucleotide identity and digital DNA–DNA hybridization values between P. fuscovaginae LMG 2158T and Pseudomonas asplenii ATCC 23835T were 98.4 and 85.5 %, and between P. shirazica VM14T and Pseudomonas asiatica RYU5T were 99.3 and 95.3 %. These values were greater than recognized thresholds for bacterial species delineation, indicating that they belong to the same genomospecies, respectively. Therefore, P. fuscovaginae and P. shirazica should be reclassified as later heterotypic synonyms of P. asplenii and P. asiatica , respectively.

scholarly journals 16S rRNA Gene-Based Identification of Midgut Bacteria from Field-Caught Anopheles gambiae Sensu Lato and A. funestus Mosquitoes Reveals New Species Related to Known Insect Symbionts

2005 ◽  
Vol 71 (11) ◽  
pp. 7217-7223 ◽  
Author(s):  
Jenny M. Lindh ◽  
Olle Terenius ◽  
Ingrid Faye
Keyword(s):  
16S Rrna ◽  
Anopheles Gambiae ◽  
Bacterial Species ◽  
Anopheles Funestus ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Malaria Vectors ◽  
Rrna Gene ◽  
Species Determination ◽  
Insect Symbionts

ABSTRACT Field-collected mosquitoes of the two main malaria vectors in Africa, Anopheles gambiae sensu lato and Anopheles funestus, were screened for their midgut bacterial contents. The midgut from each blood-fed mosquito was screened with two different detection pathways, one culture independent and one culture dependent. Bacterial species determination was achieved by sequence analysis of 16S rRNA genes. Altogether, 16 species from 14 genera were identified, 8 by each method. Interestingly, several of the bacteria identified are related to bacteria known to be symbionts in other insects. One isolate, Nocardia corynebacterioides, is a relative of the symbiont found in the vector for Chagas' disease that has been proven useful as a paratransgenic bacterium. Another isolate is a novel species within the γ-proteobacteria that could not be phylogenetically placed within any of the known orders in the class but is close to a group of insect symbionts. Bacteria representing three intracellular genera were identified, among them the first identifications of Anaplasma species from mosquitoes and a new mosquito-Spiroplasma association. The isolates will be further investigated for their suitability for a paratransgenic Anopheles mosquito.

scholarly journals The bacterial species dilemma and the genomic–phylogenetic species concept

2006 ◽  
Vol 361 (1475) ◽  
pp. 1899-1909 ◽  
Author(s):  
James T Staley
Keyword(s):  
New Species ◽  
Dna Hybridization ◽  
Species Concept ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Phylogenetic Species ◽  
Bacterial Taxonomy ◽  
Species Definition ◽  
Phylogenetic Species Concept

The number of species of Bacteria and Archaea ( ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA–DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic–phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.

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