scholarly journals Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Teresa Lucena ◽  
María A. Ruvira ◽  
M. Carmen Macián ◽  
David R. Arahal ◽  
Rosa Aznar ◽  
...  
Keyword(s):  
Drinking Water ◽  
Type Strain ◽  
Water Systems ◽  
Culture Collection ◽  
Species Level ◽  
Human Consumption ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
Drinking Water Systems

A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them revealed that strains CECT 9293T and CECT 9393T could perhaps be related at the species level as they shared 99.5 % similarity. However, whole genome sequencing was performed and the subsequent calculation of relatedness indices, average nucleotide identity and estimated DNA–DNA hybridization, ruled out that possibility and confirmed instead that each of the strains should be considered a separate species in the genus Chryseobacterium . Having clarified their status, we also performed phylogenomic analyses and searched for possible environmental or non-type material sequences that could be related to any of them at the species level. In parallel, the strains were characterized phenotypically and compared to their closest relatives to determine diagnostic traits to support their formal proposal. The proposed species are Chryseobacterium potabilaquae sp. nov. with the type strain CECT 9293T (=LMG 32084T), Chryseobacterium aquaeductus sp. nov. with the type strain CECT 9390T (=LMG 32085T) and Chryseobacterium fistulae sp. nov. with the type strain CECT 9393T (=LMG 32086T).

scholarly journals Reclassification of Ruminococcus obeum as Blautia obeum comb. nov.

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 789-793 ◽  
Author(s):  
Paul A. Lawson ◽  
Sydney M. Finegold
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Strain Number ◽  
Sequence Similarities

During our previous studies we reclassified Clostridium coccoides and a number of misclassified ruminococci into a novel genus Blautia within the family Lachnospiraceae . However, the Rules of the Bacteriological Code currently require that the types of all species and subspecies with new names (including new combinations) be deposited in two different collections in two different countries. The type strain of Ruminococcus obeum was, at that period in time, only deposited in the American Type Culture Collection (ATCC) and a second independent deposit, as required by the Code, was not available. Consequently, the transfer of this species to the genus Blautia could not be made, because the resulting species name would not conform to the Rules governing the valid publication of species names and deposit of type material (Rules 27 and 30) and consequently would not be considered to be validly published. This resulted in a nomenclatural and taxonomic anomaly with R. obeum being phylogenetically placed among members of the genus Blautia with 16S rRNA gene sequence similarities of between 91.8 and 96.6 %. In order to rectify this unsatisfactory situation, through our discussions with the ATCC, the deposit of strain R. obeum ATCC 29174T to the DSMZ as strain number DSM 25238T was completed. Hence, the transfer of R. obeum to the genus Blautia as Blautia obeum comb. nov. is now proposed. The type strain is ATCC 29174T ( = DSM 25238T = KCTC 15206T).

scholarly journals Proposal for transfer of Defluviimonas alba to the genus Frigidibacter as Frigidibacter mobilis nom. nov

2020 ◽  
Vol 70 (5) ◽  
pp. 3553-3558 ◽  
Author(s):  
Yang Liu ◽  
Tao Pei ◽  
Jun Zhang ◽  
Fan Yang ◽  
Honghui Zhu
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Amino Acid Identity ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
Close Relationship ◽  
Exact Position

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42T of the species Defluviimonas alba Pan et al. 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42T shared 99.6 and 99.7 % similarity to that of the type strain SP32T of the species Frigidibacter albus and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42T and SP32T yielded a digital DNA–DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42T and SP32T shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of Defluviimonas alba into the genus Frigidibacter as Frigidibacter mobilis nom. nov. with the type strain cai42T (=CGMCC 1.12518T=LMG 27406T).

scholarly journals Characterizing species interactions that contribute to biofilm formation in a multispecies model of a potable water bacterial community

Microbiology ◽  
2020 ◽  
Vol 166 (1) ◽  
pp. 34-43 ◽  
Author(s):  
Alex F. Thompson ◽  
Erika L. English ◽  
Adam M. Nock ◽  
Graham G. Willsey ◽  
Korin Eckstrom ◽  
...  
Keyword(s):  
Drinking Water ◽  
Bacterial Community ◽  
Species Interactions ◽  
Biofilm Formation ◽  
Type Species ◽  
Potable Water ◽  
Space Station ◽  
Water Systems ◽  
Content Type ◽  
Link Type

Microbial biofilms are ubiquitous in drinking water systems, yet our understanding of drinking water biofilms lags behind our understanding of those in other environments. Here, a six-member model bacterial community was used to identify the interactions and individual contributions of each species to community biofilm formation. These bacteria were isolated from the International Space Station potable water system and include Cupriavidus metallidurans , Chryseobacterium gleum , Ralstonia insidiosa, Ralstonia pickettii, Methylorubrum (Methylobacterium) populi and Sphingomonas paucimobilis , but all six species are common members of terrestrial potable water systems. Using reconstituted assemblages, from pairs to all 6 members, community biofilm formation was observed to be robust to the absence of any single species and only removal of the C. gleum / S. paucimobilis pair, out of all 15 possible 2-species subtractions, led to loss of community biofilm formation. In conjunction with these findings, dual-species biofilm formation assays supported the view that the contribution of C. gleum to community biofilm formation was dependent on synergistic biofilm formation with either R. insidiosa or C. metallidurans . These data support a model of multiple, partially redundant species interactions to generate robustness in biofilm formation. A bacteriophage and multiple predatory bacteria were used to test the resilience of the community to the removal of individual members in situ, but the combination of precise and substantial depletion of a single target species was not achievable. We propose that this assemblage can be used as a tractable model to understand the molecular bases of the interactions described here and to decipher other functions of drinking water biofilms.

scholarly journals The status of the species Hyphomonas rosenbergii Weiner et al. 2000. Request for an Opinion

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 321-321 ◽  
Author(s):  
Qiliang Lai ◽  
Chongping Li ◽  
Zongze Shao
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Status ◽  
Rejected Names

On the basis of 16S rRNA gene sequence analysis and several key phenotypic features, it was ascertained that the culture cited as the type strain of the species Hyphomonas rosenbergii , ATCC 43869T, does not conform to the description of the species, [Weiner, R. M., Melick, M., O’Neill, K. & Quintero, E. (2000). Int J Syst Evol Microbiol 50, 459–469]. The type strain does not exist in any other established culture collection or with the authors who described this species. Therefore, it cannot be included in any scientific study. It is proposed that the Judicial Commission place the name Hyphomonas rosenbergii on the list of rejected names if a suitable replacement type strain is not found or a neotype is not proposed within two years following the publication of this Request for an Opinion.

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%.

scholarly journals Reclassification of Francisella noatunensis subsp. orientalis Ottem et al. 2009 as Francisella orientalis sp. nov., Francisella noatunensis subsp. chilensis subsp. nov. and emended description of Francisella noatunensis

2020 ◽  
Vol 70 (3) ◽  
pp. 2034-2048 ◽  
Author(s):  
Jose Gustavo Ramirez-Paredes ◽  
Pär Larsson ◽  
Kim D. Thompson ◽  
David J. Penman ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Atlantic Cod ◽  
Bacterial Pathogen ◽  
Whole Genome ◽  
Separate Species ◽  
Content Type ◽  
Link Type ◽  
Serious Disease ◽  
Farmed Atlantic Salmon

Francisella noatunensis is a fastidious facultative intracellular bacterial pathogen that causes ‘piscine francisellosis’, a serious disease affecting both marine and fresh water farmed and wild fish worldwide. Currently two F. noatunensis subspecies are recognized, i.e. F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis . In the present study, the taxonomy of F. noatunensis was revisited using a polyphasic approach, including whole genome derived parameters such as digital DNA–DNA hybridization, whole genome average nucleotide identity (wg-ANIm), whole genome phylogenetic analysis, whole genome G+C content, metabolic fingerprinting and chemotaxonomic analyses. The results indicated that isolates belonging to F. noatunensis subsp. orientalis represent a phenotypically and genetically homogenous taxon, clearly distinguishable from F. noatunensis subsp. noatunensis that fulfils requirements for separate species status. We propose, therefore, elevation of F. noatunensis subsp. orientalis to the species rank as Francisella orientalis sp. nov. with the type strain remaining as Ehime-1T (DSM 21254T=LMG 24544T). Furthermore, we identified sufficient phenotypic and genetic differences between F. noatunensis subsp. noatunensis recovered from diseased farmed Atlantic salmon in Chile and those isolated from wild and farmed Atlantic cod in Northern Europe to warrant proposal of the Chilean as a novel F. noatunensis subspecies, i.e. Francisella noatunensis subsp. chilensis subsp. nov. with strain PQ1106T (CECT 9798T=NCTC14375T) as the type strain. Finally, we emend the description of F. noatunensis by including further metabolic information and the description of atypical strains.

scholarly journals The status of the species Lactobacillus fornicalis Dicks et al. 2000. Request for an opinion

2020 ◽  
Vol 70 (6) ◽  
pp. 3953-3954 ◽  
Author(s):  
Teresa Gonçalves Ribeiro ◽  
Joana Rocha ◽  
Magdalena Ksiezarek ◽  
Svetlana Ugarcina Perovic ◽  
Filipa Grosso ◽  
...  
Keyword(s):  
Comparative Study ◽  
Lactobacillus Plantarum ◽  
Cell Cultures ◽  
Type Strain ◽  
Type Species ◽  
Culture Collection ◽  
Content Type ◽  
Link Type ◽  
The Status ◽  
Online Catalogue

During a recent study on members of the genus Lactobacillus we realized that cultures of Lactobacillus fornicalis TV 1018T (=DSM 13171T=ATCC 700934T) are no longer available from the online catalogue of the German Collection of Microorganisms and Cell Cultures GmbH, being displayed as Lactobacillus plantarum at the American Type Culture Collection. Based on data currently available, the organism deposited as ATCC 700934T is a member of the species Lactobacillus plantarum subs. plantarum. Therefore, the type strain of Lactobacillus fornicalis cannot be included in any further scientific comparative study. This matter is referred to the Judicial Commission, asking for an opinion on the status of the species.

scholarly journals Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1457-1464 ◽  
Author(s):  
Carrie L. Brady ◽  
Ilse Cleenwerck ◽  
Lorinda van der Westhuizen ◽  
Stephanus N. Venter ◽  
Teresa A. Coutinho ◽  
...  
Keyword(s):  
South Africa ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Gene Sequencing ◽  
Culture Collection ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Rrna Gene Sequencing

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa , Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

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