Mannheimia pernigra sp. nov., isolated from bovine respiratory tract

2021 ◽  
Author(s):  
Peter Kuhnert ◽  
Isabelle Brodard ◽  
Lutz Schönecker ◽  
Hatice Akarsu ◽  
Henrik Christensen ◽  
...  
Keyword(s):  
Type Species ◽  
Reference Strain ◽  
New Taxon ◽  
Species Status ◽  
Content Type ◽  
Identification Schemes ◽  
Link Type ◽  
Distinct Cluster ◽  
Veal Calf ◽  
Phenotypic Methods

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia . As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena . Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena . Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.

Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2463-2471 ◽  
Author(s):  
Parag Vaishampayan ◽  
Christine Moissl-Eichinger ◽  
Rüdiger Pukall ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
New Taxon ◽  
The Novel ◽  
Clean Room ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Unique Cell ◽  
Spacecraft Assembly

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MAT and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with Arthrobacter crystallopoietes ATCC 15481T, Arthrobacter luteolus ATCC BAA-272T, Arthrobacter tumbae DSM 16406T and Arthrobacter subterraneus DSM 17585T. In contrast with previously described Arthrobacter species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod–coccus life cycle typically observed in nearly all Arthrobacter species, except A. agilis . The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related Arthrobacter species. Based on these observations, the authors propose that strains 1P05MAT and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MAT and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MAT ( = NRRL B-59547T = DSM 30849T).

Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2598-2601 ◽  
Author(s):  
Georges Wauters ◽  
Michèle Janssens ◽  
Thierry De Baere ◽  
Mario Vaneechoutte ◽  
Pieter Deschaght
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Reference Strain ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Group Ii ◽  
Indole Production ◽  
The 16S Rrna Gene

Two clinical strains, NF 296 and NF 931, present in our collection, were identified biochemically as members of CDC group II-i. Determination of the 16S rRNA gene sequence revealed highest similarity with strains of Sphingobacterium mizutaii . Because these strains produced indole, whereas S. mizutaii has been described as indole-negative, we also investigated the type strain and a reference strain of S. mizutaii , LMG 8340T ( = CCUG 15907T) and LMG 8341 ( = CCUG 15908), and found both strains also to be positive for indole production. These data warrant inclusion of some of the CDC group II-i strains into S. mizutaii and emended descriptions of Sphingobacterium mizutaii as indole-production-positive and of the genus Sphingobacterium as variable for indole production.

scholarly journals Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance

2021 ◽  
Author(s):  
Kara K. Tsang ◽  
Finlay Maguire ◽  
Haley L. Zubyk ◽  
Sommer Chou ◽  
Arman Edalatmand ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Type Species ◽  
Multidrug Resistant ◽  
Content Type ◽  
Logistic Regression Models ◽  
Link Type ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Targeted Gene Expression ◽  
Phenotypic Methods

Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia coli and Pseudomonas aeruginosa multidrug-resistant clinical isolate genomes. By inspecting and evaluating these models, we identified previously unknown β-lactamase substrate activities. In total, 22 unknown β-lactamase substrate activities were experimentally validated using targeted gene expression studies. Our results demonstrate that generating and analysing predictive models can help guide researchers to the mechanisms driving resistance and improve annotation of AMR genes and phenotypic prediction, and suggest that we cannot solely rely on curated knowledge to predict resistance phenotypes.

scholarly journals Domestication of Campylobacter jejuni NCTC 11168

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Ben Pascoe ◽  
Lisa K. Williams ◽  
Jessica K. Calland ◽  
Guillaume Meric ◽  
Matthew D. Hitchings ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Campylobacter Jejuni ◽  
Type Species ◽  
Reference Strain ◽  
Careful Consideration ◽  
Trait Variation ◽  
Content Type ◽  
Link Type ◽  
The Uk ◽  
Reference Strains

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status

2021 ◽  
Author(s):  
Scott Van Nguyen ◽  
Scott A. Cunningham ◽  
Patricio Jeraldo ◽  
Anthony Tran ◽  
Robin Patel
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Average Nucleotide Identity ◽  
Species Status ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Genomic Relatedness

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA–DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.

Arsenicicoccus dermatophilus sp. nov., a hypha-forming bacterium isolated from the skin of greater flamingos (Phoenicopterus roseus) with pododermatitis

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4046-4051 ◽  
Author(s):  
Stefanie Gobeli ◽  
Andreas Thomann ◽  
Fabia Wyss ◽  
Kathrin Kuehni-Boghenbor ◽  
Isabelle Brodard ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Reference Strain ◽  
Polymyxin B ◽  
Wall Structure ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Greater Flamingos

Dermatophilus -like bacteria were observed in histological examinations of samples of diseased foot skin from greater flamingos (Phoenicopterus roseus) living in zoological gardens in Switzerland. When grown on TSA-SB containing polymyxin B, the bacteria isolated from these skin samples formed hyphae, as is typical for Dermatophilus congolensis , but these bacteria were non-haemolytic. The closest relatives based on 16S rRNA gene sequences were the two members of the genus Arsenicicoccus , Arsenicicoccus bolidensis and Arsenicicoccus piscis . A representative of the isolated strains shared 34.3 % DNA–DNA relatedness with the type strain of A. bolidensis , 32.3 % with the type strain of A. piscis and 34.5 % with the type strain of D. congolensis , demonstrating that these strains do not belong to any of these species. The phenotypic characteristics differed from those of members of the genus Arsenicicoccus as well as from those of D. congolensis . The G+C content of strain KM 894/11T was 71.6 mol%. The most abundant fatty acids were iso-C15 : 0, summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω9c. MK-8(H4) was the predominant menaquinone. Cell-wall structure analysis revealed that the peptidoglycan type was A3γ ll-Dpm–Gly (type A41.1). Based on genotypic and chemotaxonomic characteristics, the isolated strains represent a novel species within the genus Arsenicicoccus , for which the name Arsenicicoccus dermatophilus sp. nov. is proposed. The type strain is KM 894/11T ( = DSM 25571T = CCUG 62181T = CCOS 690T), and strain KM 1/12 ( = DSM 25572 = CCUG 62182 = CCOS 691) is a reference strain.

scholarly journals Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Damien Farrell ◽  
Joseph Crispell ◽  
Stephen V. Gordon
Keyword(s):  
Mycobacterium Bovis ◽  
Bovine Tuberculosis ◽  
Type Species ◽  
Reference Strain ◽  
Reference Genome ◽  
Coding Sequences ◽  
Content Type ◽  
Link Type ◽  
New Gene ◽  
New Protein

Mycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. Here we report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications that replace many of the old hypothetical coding sequences and proteins of unknown function in the genome. These changes integrate information from functional assignments of orthologous coding sequences in the Mycobacterium tuberculosis H37Rv genome. We have also added 69 additional new gene names.

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.

2021 ◽  
Author(s):  
Undine Behrendt ◽  
Sonja Wende ◽  
Steffen Kolb ◽  
Andreas Ulrich
Keyword(s):  
Type Species ◽  
Taxonomic Status ◽  
Amino Acid Identity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Status ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
A Genome

The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae . The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA–DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae . Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.

Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1506-1511 ◽  
Author(s):  
Verena S. J. Schmidt ◽  
Mareike Wenning ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Reference Strain ◽  
Sequence Similarity ◽  
Raw Milk ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Four non-fermenting, rod-shaped, Gram-staining-negative bacterial strains, designated WCC 4512T, WS 4555, WCC 4521T and WS 4556, were isolated from raw milk and the dairy environment. Phylogenetic analyses based on 16S rRNA and groEL gene sequences demonstrated the affiliation of the four strains to two distinct clusters within the class Sphingobacteriia , phylum ‘ Bacteroidetes ’. Strains WCC 4512T and WS 4555 showed the highest 16S rRNA gene sequence similarity to the type strain of S. daejeonense (97.3 and 97.2 %, respectively), whereas strains WCC 4521T and WS 4556 were most closely related to S. composti LMG 23401T (97.6 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains WCC 4512T and WCC 4521T were 44.2 and 39.3 mol%, respectively. The major cellular fatty acids and the presence of menaquinone MK-7 as the predominant quinone for both strains WCC 4512T and WCC 4521T supported their affiliation to the genus Sphingobacterium . DNA–DNA hybridization experiments between strain WCC 4512T and S. daejeonense LMG 23402T and between strain WCC 4521T and S. composti LMG 23401T revealed DNA relatedness values of 2 % (repetition, 3 %) and 8 % (repetition, 17 %), respectively. On the basis of phenotypic and genetic properties, as well as phylogenetic distinctiveness, it is suggested that the four strains represent two novel Sphingobacterium species with strain WCC 4512T ( = DSM 22361T = LMG 25272T) as the type strain of Sphingobacterium lactis sp. nov. (WS 4555 is a reference strain of S. lactis) and strain WCC 4521T ( = DSM 22362T = LMG 25273T) as the type strain of Sphingobacterium alimentarium sp. nov. (WS 4556 is a reference strain of S. alimentarium).

Classification of Pasteurella species B as Pasteurella oralis sp. nov.

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1396-1401 ◽  
Author(s):  
Henrik Christensen ◽  
Mads F. Bertelsen ◽  
Anders Miki Bojesen ◽  
Magne Bisgaard
Keyword(s):  
Related Species ◽  
Sequence Comparison ◽  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Species Status ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
A Genome

Pasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794T), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794T, respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76–100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae . 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species ( Pasteurella canis ), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species ( P. canis ). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683T ( = CCUG 19794T = CCM 7950T = strain 23193T = MCCM 00102T), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C16 : 0, C16 : 1ω7c and C14 : 0, with minor amounts of C18 : 0 and C18 : 1ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%.

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