scholarly journals Sequences, sequence clusters and bacterial species

2006 ◽  
Vol 361 (1475) ◽  
pp. 1917-1927 ◽  
Author(s):  
William P Hanage ◽  
Christophe Fraser ◽  
Brian G Spratt
Keyword(s):  
Single Gene ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Similar Species ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Microbiological Methods ◽  
Large Populations ◽  
Interspecies Recombination ◽  
Clustering Patterns

Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

Vagococcus entomophilus sp. nov., from the digestive tract of a wasp (Vespula vulgaris)

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 731-737 ◽  
Author(s):  
J. Killer ◽  
P. Švec ◽  
I. Sedláček ◽  
J. Černohlávková ◽  
O. Benada ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Bacterial Species ◽  
Cellular Fatty Acid ◽  
Protein Profiling ◽  
Cell Protein ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Content Type ◽  
Vespula Vulgaris

Three unknown Gram-stain-positive, catalase-negative, facultatively anaerobic and coccus-shaped strains of bacteria were isolated from the digestive tracts of wasps (Vespula vulgaris). Analysis of 16S rRNA gene sequences revealed that these strains had identical sequences and showed that Vagococcus salmoninarum , with 96.2 % sequence similarity, was the closest phylogenetic neighbour. Further analyses based on hsp60 and pheS gene sequences of representatives of the family Enteroccocaceae and genotypic and phenotypic characterization using (GTG)5-PCR fingerprintings, EcoRI ribotyping, DNA G+C content, whole-cell protein profiling, cellular fatty acid profiles analysis and extensive biotyping confirmed that the investigated strains were representatives of a novel bacterial species within the genus Vagoccocus for which the name Vagoccocus entomophilus sp. nov. is proposed. The type strain is VOSTP2T ( = DSM 24756T = CCM 7946T).

scholarly journals Assessment of microbiological and residual antibiotics status in milk sold in Abeokuta, Ogun State. Nigeria

2018 ◽  
Vol 6 (6) ◽  
pp. 642
Author(s):  
Flora Oluwafemi ◽  
Bosede Folashade Oluwabamiwo ◽  
Oluseyi Oluwajubelo Oluwatosin ◽  
Olufunmilayo Ruth Akinrinade ◽  
Adelodun Lawrence Kolapo
Keyword(s):  
Bacterial Species ◽  
Method Comparison ◽  
Antibiotic Sensitivity ◽  
Plate Count ◽  
Diffusion Method ◽  
Rrna Gene ◽  
Antibiotic Residues ◽  
Bacterial Isolates ◽  
Powdered Milk ◽  
Microbiological Methods

This study investigated the prevalence and concentration of antibiotic residues in twenty brands of milk. Determination and quantification of antibiotic residues was done using High Performance Liquid Chromatography. Aerobic plate count was carried out and the associated bacteria isolated. Identification of bacteria was done using standard microbiological methods. Molecular characterization and identification of bacterial isolates was done using 16S rRNA gene sequencing method. Antibiotic sensitivity was carried out on bacterial isolates using disc diffusion method. Plasmid profile of drug resistant isolates was done using alkaline analysis method. Comparison of means was done using Analysis of Variance. Antibiotic residues were detected in 10 (50%) of the 20 milk brands analyzed. The residual levels of tetracycline, oxytetracycline and chlortetracycline ranged between 5ng/kg and 1569ng/kg while none of the samples had doxycycline residues. The prevalence of tetracycline residues in evaporated milk brands and powdered milk samples were 100 and 23 % respectively. The aerobic plate counts ranged from 2.5 × 102 to 6.5 × 102 CFU∕mL for evaporated milk and 2.5 × 101 to 6.0 × 101 CFU∕mL for powdered milk. A total of ten bacterial species were isolated and identified. Susceptibility result showed that 95% of the isolates were sensitive to erythromycin, cefuroxime and gentamycin; 12.5% were resistant to tetracycline and ampicillin, 10% were resistant to ofloxacin and 7.5% to doxycycline and penicillin. Five of the bacterial isolates were resistant to more than one class of antibiotics. Resistant isolates subjected to plasmid profiling had detectable plasmids with estimated sizes between 120bp and 1000bp. The obtained results provide evidence that the presence of antibiotic residues in evaporated and powdered milk is an indication that the public is exposed to the harmful effects of the residues.

scholarly journals Paenibacillus Piscarius Sp. Nov., a Novel Nitrogen-Fixing Species Isolated from the Gut of the Armored Catfish Parotocinclus Maculicauda

2021 ◽  
Author(s):  
Mariana Barbalho Farias da silva ◽  
Ericka Arregue Lemos ◽  
Renata E. Vollú ◽  
Fernanda Abreu ◽  
Alexandre S. Rosado ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Distinct Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Nitrogen Fixing ◽  
Closely Related Species ◽  
A Genome ◽  
Encoding Gene ◽  
Encoding Genes

Abstract A gram-positive, nitrogen-fixing and endospore-forming strain, designated P121T, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA encoding gene, rpoB, gyrB and nifH genes and phenotypic analyses. The most closely related species to strain P121T were Paenibacillus rhizoplanae DSM 103993T, Paenibacillus silagei DSM 101953T and Paenibacillus borealis DSM 13188T, with similarity values of 98.9%, 98.3% and 97.6%, respectively, based on 16S rRNA gene sequences. Genome sequencing revealed a genome size of 7,513,698 bp, DNA G + C content of 53.9 mol% and the presence of the structural nitrogenase encoding genes (nifK, nifD and nifH) necessary for nitrogen fixation. Digital DNA-DNA hybridization (dDDH) experiments and average nucleotide identity (ANI) analyses between strain P121T and the type strains of the closest species demonstrated that the highest values were below the thresholds of 70% dDDH (42.3% with P. borealis) and 95% ANI (84.28% with P. silagei) for bacterial species delineation, indicating that strain P121T represents a distinct species. Its major cellular fatty acid was anteiso-C15:0 (42.4%), and the major isoprenoid quinone was MK-7. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain P121T represents a novel species for which the name Paenibacillus piscarius sp. nov. is proposed (type strain = DSM 25072 = LFB-Fiocruz 1636).

scholarly journals Vagococcus silagei sp. nov., isolated from brewer’s grain used to make silage in Taiwan

2020 ◽  
Vol 70 (3) ◽  
pp. 1953-1960 ◽  
Author(s):  
Yen-Chi Wu ◽  
Shih-Ting Lin ◽  
Jia-Rong Guu ◽  
Tomohiko Tamura ◽  
Koji Mori ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2T, was isolated from a brewer’s grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, hsp60 and pheS gene sequences demonstrated that strain 2B-2T was a member of the genus Vagococcus . On the basis of 16S rRNA gene sequence similarity, the type strains of Vagococcus teuberi (98.4 % similarity), Vagococcus carniphilus (98.4 %), Vagococcus martis (98.2 %), Vagococcus penaei (98.2 %) and Vagococcus fluvialis (98.0 %) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences (hsp60 and pheS) between strain 2B-2T and these closely related species ranged from 84.5 to 88.0 %. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 2B-2T and its closest relatives were lower than 72.9 and 21.6 %, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2T represents a novel species of the genus Vagococcus , for which the name Vagococcus silagei sp. nov. is proposed. The type strain is 2B-2T (=BCRC 81132T=NBRC 113536T).

scholarly journals Halomonas almeriensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium from Cabo de Gata, Almería, south-east Spain

2005 ◽  
Vol 55 (5) ◽  
pp. 2007-2011 ◽  
Author(s):  
Fernando Martínez-Checa ◽  
Victoria Béjar ◽  
M. José Martínez-Cánovas ◽  
Inmaculada Llamas ◽  
Emilia Quesada
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrolytic Enzymes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Closely Related Species ◽  
Moderately Halophilic ◽  
Wildlife Reserve

Halomonas almeriensis sp. nov. is a Gram-negative non-motile rod that was isolated from a saltern in the Cabo de Gata-Níjar wildlife reserve in Almería, south-east Spain. It is moderately halophilic, capable of growth at concentrations of 5–25 % w/v sea-salt mixture, the optimum being 7·5 % w/v. It is chemo-organotrophic and strictly aerobic, produces catalase but not oxidase, does not produce acid from any sugar and does not synthesize hydrolytic enzymes. The most notable difference between this micro-organism and other Halomonas species is that it is very fastidious in its use of a carbon source. It forms mucoid colonies due to the production of an exopolysaccharide. Its G+C content is 63·5 mol%. A comparison of 16S rRNA gene sequences confirmed its relationship to Halomonas species. The most closely related species is Halomonas halmophila with 95·8 % similarity between their 16S rRNA gene sequences. DNA–DNA hybridization with H. halmophila is 10·1 %. Its major fatty acids are 18 : 1ω7c, 16 : 0, 16 : 1ω7c/15 : 0 iso 2-OH, 12 : 0 3-OH, 12 : 0, 11-methyl 18 : 1ω7c and 10 : 0. The proposed name is Halomonas almeriensis sp. nov., with strain M8T (=CECT 7050T=LMG 22904T) as the type strain.

scholarly journals Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

2021 ◽  
Vol 12 ◽  
Author(s):  
Kuleshwar Prasad Sahu ◽  
Asharani Patel ◽  
Mukesh Kumar ◽  
Neelam Sheoran ◽  
Sahil Mehta ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rice Blast ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Rice Cultivar ◽  
Disease Suppression ◽  
Blast Disease ◽  
Rrna Gene ◽  
Isolation And Identification ◽  
Microbiological Methods

Phyllosphere—the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members Pantoea, Enterobacter, Pseudomonas, and Erwinia on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.

scholarly journals 16SpeB: Towards defining bacterial species boundaries by intra-species gene sequence identity

2016 ◽  
Author(s):  
Adam Chun-Nin Wong ◽  
Patrick Ng ◽  
Angela E. Douglas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
Region Of Interest ◽  
Supplementary Information ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Link Type ◽  
V Region ◽  
The Relationship

ABSTRACTSummary16SpeB (16S rRNA-based Species Boundary) is a package of Perl programs that evaluates total sequence variation of a bacterial species at the levels of the whole 16S rRNA sequences or single hypervariable (V) regions, using publicly-available sequences. The 16SpeB pipelines filter sequences from duplicated strains and of low quality, extracts a V region of interest using general primer sequences, and calculates sequence percentage identity (%ID) through all possible pairwise alignments.ResultsThe minimum %ID of 16S rRNA gene sequences for 15 clinically-important bacterial species, as determined by 16SpeB, ranged from 82.6% to 99.8%. The relationship between minimum %ID of V2/V6 regions and full-gene sequences varied among species, indicating that %ID species limits should be resolved independently for each region of the 16S rRNA gene and bacterial species.Availability16SpeB and user manual are freely available for download from: https://github.com/pnpnpn/16SpeB. A video tutorial is available at: https://youtu.be/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Updated phylogeny of the genus Aeromonas

2006 ◽  
Vol 56 (10) ◽  
pp. 2481-2487 ◽  
Author(s):  
M. J. Saavedra ◽  
M. J. Figueras ◽  
A. J. Martínez-Murcia
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
16S Rrna Gene Sequencing ◽  
Original Description ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Single Strain ◽  
Phylogenetic Affiliation

Recent phylogenetic studies of the genus Aeromonas based on gyrB and rpoD gene sequences have improved the phylogeny based on 16S rRNA gene sequences first published in 1992, particularly in the ability to split closely related species. These studies did not include the recently described species Aeromonas simiae and Aeromonas molluscorum and only a single strain of Aeromonas culicicola was available for analysis at that time. In the present work, these Aeromonas species and newly isolated strains of A. culicicola were examined. Sequence analysis indicates that A. simiae and A. molluscorum belong to non-described phylogenetic lines of descent within this genus, which supports the original description of both species. The most closely related species are Aeromonas schubertii and Aeromonas encheleia, respectively, which is consistent with 16S rRNA gene sequencing results. However, while the five strains of A. molluscorum showed nucleotide differences in their gyrB and rpoD gene sequences, the only two known A. simiae strains exhibited identical gene sequences, suggesting that they are isolates of the same strain. On the basis of the rpoD gene sequence phylogeny, A. culicicola strains from the original description and new isolates from drinking water and ornamental fish clustered within the species Aeromonas veronii, suggesting inconsistencies with previous results. Other strains with previously controversial taxonomy and new isolates from other studies were included in this study in order to clarify their phylogenetic affiliation at the species level.

scholarly journals Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

2019 ◽  
Vol 60 (1) ◽  
pp. 54-61
Author(s):  
Princy Hira ◽  
Priya Singh ◽  
Anil Kumar Pinnaka ◽  
Suresh Korpole ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hiroyuki Sawada ◽  
Takashi Fujikawa ◽  
Mamoru Satou
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Bacterial Rot ◽  
Phylogenomic Analyses ◽  
The 16S Rrna Gene

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c), C16 : 0 and summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA–DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

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