scholarly journals Proposal for the creation of a new genus Musicola gen. nov., reclassification of Dickeya paradisiaca (Samson et al. 2005) as Musicola paradisiaca comb. nov. and description of a new species Musicola keenii sp. nov.

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Cécile Jacot des-Combes ◽  
Jérôme Briolay ◽  
Leighton Pritchard
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Plant Pathogens ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
A New Species ◽  
Laboratory Collection

The Pectobacteriaceae family of important plant pathogens includes the genus Dickeya . There are currently 12 described species of Dickeya , although some are poorly characterized at the genomic level. Only two genomes of Dickeya paradisiaca , the type strain CFBP 4178T and strain Ech703, have previously been sequenced. Members of this species are mostly of tropical or subtropical origin. During an investigation of strains present in our laboratory collection we sequenced the atypical strain A3967, registered as CFBP 722, isolated from Solanum lycopersicum (tomato) in the South of France in 1965. The genome of strain A3967 shares digital DNA–DNA hybridization and average nucleotide identity (ANI) values of 68 and 96 %, respectively, with the D. paradisiaca type strain CFBP 4178T. However, ANI analysis showed that D. paradisiaca strains are significantly dissimilar to the other Dickeya species, such that less than one third of their genomes align to any other Dickeya genome. On phenotypic, phylogenetic and genomic grounds, we propose a reassignment of D. paradisiaca to the genus level, for which we propose the name Musicola gen. nov., with Musicola paradisiaca as the type species and CFBP 4178T (NCPPB 2511T) as the type strain. Phenotypic analysis showed differences between strain A3967T and CFBP 4178T, such as for the assimilation of melibiose, raffinose and myo-inositol. These results support the description of two novel species, namely Musicola paradisiaca comb. nov. and Musicola keenii sp. nov., with CFBP 4178T (NCPPB 2511T=LMG 2542T) and A3967T (CFBP 8732T=LMG 31880T) as the type strains, respectively.

scholarly journals Vibrio aestuarianus subsp. cardii subsp. nov., pathogenic to the edible cockles Cerastoderma edule in France, and establishment of Vibrio aestuarianus subsp. aestuarianus subsp. nov. and Vibrio aestuarianus subsp. francensis subsp. nov.

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Céline Garcia ◽  
Aurélie Mesnil ◽  
Delphine Tourbiez ◽  
Mirna Moussa ◽  
Christine Dubreuil ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Pacific Oyster ◽  
Phenotypic Traits ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
The Pacific ◽  
Emended Description

Cockle mortality events have been reported in northern France since 2012. In the present study, we describe and investigate the implication of a potential bacterial causative agent in cockle mortality. Bacteria isolated from five different cockle mortality events were characterized and studied. Using phenotypic analysis combined with DNA–DNA hybridization (DDH) and whole genome sequencing, the isolates were shown to belong to Vibrio aestuarianus , a species regularly detected in France during oyster mortality events. Comparison of the strains from cockles with strains from French oysters and the type strain showed that the strains from cockles were genetically different to those from oysters and also different to the V. aestuarianus type strain. Moreover, the cockle and oyster strains were classified into two different, but close, groups both separated from the type strain by: (1) analyses of the ldh gene sequences; (2) DDH assays between 12/122 3T3T (LMG 31436T=DSM 109723T), a representative cockle strain, 02/041T (CIP 109791T=LMG 24517T) representative oyster strain and V. aestuarianus type strain LMG 7909T; (3) average nucleotide identity values calculated on the genomes; and (4) phenotypic traits. Finally, results of MALDI-TOF analyses also revealed specific peaks discriminating the three representative strains. The toxicity of representative strains of these cockle isolates was demonstrated by experimental infection of hatchery-produced cockles. The data therefore allow us to propose two novel subspecies of Vibrio aestuarianus : Vibrio aestuarianus subsp. cardii subsp. nov. for the cockle strains and Vibrio aestuarianus subsp. francensis subsp. nov. for the Pacific oyster strains, in addition to an emended description of the species Vibrio aestuarianus .

scholarly journals Serratia vespertilionis (García-Fraile et al. 2015) is a later heterotypic synonym of Serratia ficaria (Grimont et al. 1981)

2020 ◽  
Vol 70 (3) ◽  
pp. 1961-1962 ◽  
Author(s):  
Paula García-Fraile ◽  
Cathrin Spröer ◽  
Olivier Chesneau ◽  
Alexis Criscuolo ◽  
Elke Lang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Sequence Comparison ◽  
Type Strain ◽  
Type Species ◽  
Whole Genome Sequence ◽  
Species Differentiation ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A previous 16S rRNA gene sequence comparison had demonstrated that the type strains of Serratia vespertilionis and Serratia ficaria shared 99.5 % sequence similarity. Despite the 56.2 % homology by DNA–DNA hybridization previously found between these strains, the results of an in silico whole-genome sequence comparison and a new DNA–DNA hybridization study have clearly demonstrated that the genomes of the type strain of S. vespertilionis deposited in different Culture Collections (52T=CECT 8595T=DSM 28727T) and the type strain of S. ficaria (culture DSM 4569T), cannot support such a species differentiation. Tests for substrate utilization redone on the deposited cultures of these strains has also shown very few differences between the type strains of both species. Based on these results, and since the name S. ficaria was validly published earlier, S. vespertilionis should be considered as a later heterotypic synonym of S. ficaria , in application of the priority rule. The type strain of the species S. ficaria is strain 4024T=DSM 4569T=NCTC 12148T=ATCC 33105T=CIP 79.23T=ICPB 4050T.

scholarly journals Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)

2020 ◽  
Vol 70 (8) ◽  
pp. 4508-4514 ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Céline Brochier-Armanet ◽  
Jean-Pierre Flandrois ◽  
Sylvie Reverchon
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Plant Pathogens ◽  
Genomic Sequence ◽  
Saccharum Officinarum ◽  
Cultivated Plants ◽  
Content Type ◽  
Important Group ◽  
Link Type ◽  
A New Species

The genus Dickeya is an important group of plant pathogens that currently comprises 10 recognized species. Although most Dickeya isolates originated from infected cultivated plants, they are also isolated from water. The genomic sequence of the Australian strain NCPPB 569T clearly established its separation from the previously characterized Dickeya species. The average nucleotide identity and digital DNA–DNA hybridization values obtained by comparing strain NCPPB 569T with strains of characterized Dickeya species were lower than 87 and 32 %, respectively, supporting the delineation of a new species. The name Dickeya poaceiphila sp. nov. is proposed for this taxon with the type strain NCPPB 569T (=CFBP 8731T). Two other strains isolated in Australia, CFBP 1537 and CFBP 2040, also belong to this species. Phenotypic and genomic comparisons enabled the identification of traits distinguishing D. poaceiphila isolates from strains of other Dickeya species.

Diversity within the Dickeya zeae complex, identification of Dickeya zeae and Dickeya oryzae members, proposal of the novel species Dickeya parazeae sp. nov.

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Nicole Hugouvieux-Cotte-Pattat ◽  
Frédérique Van Gijsegem
Keyword(s):  
New Species ◽  
Type Strain ◽  
Type Species ◽  
Plant Pathogens ◽  
Broad Host Range ◽  
The Novel ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Major Pathogens

The genus Dickeya comprises plant pathogens that cause diseases in a large range of economically important crops and ornamentals. Strains previously assigned to the species Dickeya zeae are major pathogens attacking vital crops such as maize and rice. They are also frequently isolated from surface water. The newly described species Dickeya oryzae is closely related to D. zeae members, so that the limit between the two species can be difficult to define. In order to clearly distinguish the two species, globally described by the term ‘ D. zeae complex’, we sequenced the genome of four new water isolates and compared them to 14 genomes available in databases. Calculation of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values confirmed the phylogenomic classification into the two species D. zeae and D. oryzae . It also allowed us to propose a new species, Dickeya parazeae sp. nov., to characterize a clade distinct from those containing the D. zeae type strain NCPPB2538T. Strain S31T (CFBP 8716T=LMG 32070T) isolated from water in France is proposed as the type strain of the new species. Phenotypic analysis of eight publically available strains revealed traits common to the five tested D. oryzae members but apparently not shared by the D. oryzae type strain. Genomic analyses indicated that a simple distinction between the species D. zeae , D. parazeae and D. oryzae can be obtained on the basis of the recA sequence. D. oryzae can be distinguished from the two other species by growth on l-tartaric acid. Based on the recA marker, several strains previously identified as D. zeae were re-assigned to the species D. parazeae or D. oryzae . This study also highlighted the broad host range diversity of these three species.

scholarly journals Rhodanobacter glycinis sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2023-2028 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Selvaraj Poonguzhali ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Soon-Wo Kwon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Analysis ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel, yellow-pigmented bacterium, designated strain MO64T, was isolated from the rhizoplane of field-grown soybean, collected from an experimental plot at Coimbatore, India. Cells were Gram-reaction-negative, motile, non-spore-forming rods that produced yellow-pigmented colonies on R2A agar. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain MO64T belonged to the genus Rhodanobacter . Strain MO64T was related most closely to Rhodanobacter ginsengisoli GR17-7T (98.0 % 16S rRNA gene sequence similarity), Rhodanobacter spathiphylli B39T (97.9 %), Rhodanobacter panaciterrae LnR5-47T (97.7 %), Rhodanobacter terrae GP18-1T (97.6 %), Rhodanobacter soli DCY45T (97.3 %) and Rhodanobacter caeni MJ01T (97.2 %); levels of similarity to the type strains of all other recognized species of the genus Rhodanobacter were less than 97.0 %. Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C16 : 0, iso-C15 : 0, C17 : 0 cyclo, iso-C17 : 1ω9c, iso-C17 : 0 and iso-C11 : 0 as the major fatty acids) also supported the affiliation of strain MO64T with the genus Rhodanobacter . The G+C content of the genomic DNA was 64 mol%. The results of DNA–DNA hybridization and phenotypic analysis showed that strain MO64T can be distinguished from all known species of the genus Rhodanobacter and therefore represents a novel species of the genus, for which the name Rhodanobacter glycinis sp. nov. is proposed. The type strain is MO64T ( = ICMP 17626T = NBRC 105007T).

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

2020 ◽  
Vol 70 (12) ◽  
pp. 6301-6306
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1  ω7c and/or C16 : 1  ω6c, C16 : 0 and C18 : 1  ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).

scholarly journals Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris

2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1790-1798 ◽  
Author(s):  
V. Venkata Ramana ◽  
S. Kalyana Chakravarthy ◽  
P. Shalem Raj ◽  
B. Vinay Kumar ◽  
E. Shobha ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Rhodopseudomonas Palustris ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Geographical Regions ◽  
Emended Description ◽  
Type Strains

Four strains (JA310T, JA531T, JA447 and JA490) of red to reddish brown pigmented, rod-shaped, motile and budding phototrophic bacteria were isolated from soil and freshwater sediment samples from different geographical regions of India. All strains contained bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The major cellular fatty acid of strains JA310T and JA531T was C18 : 1ω7c, the quinone was Q-10 and polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminohopanoid and an unidentified aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that all strains clustered with species of the genus Rhodopseudomonas in the class Alphaproteobacteria . Strains JA531T, JA447 and JA490 were genotypically (>80 % related based on DNA–DNA hybridization) and phenotypically closely related to each other and the three strains were distinct from strain JA310T (33 % related). Furthermore, all four strains had less than 48 % relatedness (DNA–DNA hybridization) with type strains of members of the genus Rhodopseudomonas , i.e. Rhodopseudomonas palustris ATCC 17001T, Rhodopseudomonas faecalis JCM 11668T and Rhodopseudomonas rhenobacensis DSM 12706T. The genomic DNA G+C contents of strains JA310T and JA531T were 63.8 and 62.4 mol%, respectively. On the basis of phenotypic, chemotaxonomic and molecular genetic evidence, it is proposed that strains JA310T ( = NBRC 106083T = KCTC 5839T) and JA531T ( = NBRC 107575T = KCTC 5841T) be classified as the type strains of two novel species of the genus Rhodopseudomonas , Rhodopseudomonas parapalustris sp. nov. and Rhodopseudomonas harwoodiae sp. nov., respectively. In addition, we propose that strain DSM 123T ( = NBRC 100419T) represents a novel species, Rhodopseudomonas pseudopalustris sp. nov., since this strain differs genotypically and phenotypically from R. palustris ATCC 17001T and other members of the genus Rhodopseudomonas . An emended description of R. palustris is also provided.

scholarly journals Melghirimyces algeriensis gen. nov., sp. nov., a member of the family Thermoactinomycetaceae , isolated from a salt lake

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1491-1498 ◽  
Author(s):  
Ammara Nariman Addou ◽  
Peter Schumann ◽  
Cathrin Spröer ◽  
Hocine Hacene ◽  
Jean-Luc Cayol ◽  
...  
Keyword(s):  
Type Species ◽  
Salt Lake ◽  
Rrna Gene ◽  
Phenotypic Analysis ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A novel filamentous bacterium, designated NariEXT, was isolated from soil collected from Chott Melghir salt lake, which is located in the south-east of Algeria. The strain was an aerobic, halotolerant, thermotolerant, Gram-positive bacterium that was able to grow in NaCl concentrations up to 21 % (w/v), at 37–60 °C and at pH 5.0–9.5. The major fatty acids were iso- and anteiso-C15 : 0. The DNA G+C content was 47.3 mol%. The major menaquinone was MK-7, but MK-6 and MK-8 were also present. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine (methyl-PE). Results of molecular and phenotypic analysis led to the description of the strain as a new member of the family Thermoactinomycetaceae . The isolate was distinct from members of recognized genera of this family by morphological, biochemical and chemotaxonomic characteristics. Strain NariEXT showed 16S rRNA gene sequence similarities of 95.38 and 94.28 % with the type strains of Desmospora activa and Kroppenstedtia eburnea , respectively, but differed from both type strains in its sugars, polar lipids and in the presence of methyl-PE. On the basis of physiological and phylogenetic data, strain NariEXT represents a novel species of a new genus of the family Thermoactinomycetaceae for which the name Melghirimyces algeriensis gen. nov., sp. nov. is proposed. The type strain of Melghirimyces algeriensis, the type species of the genus, is NariEXT ( = DSM 45474T = CCUG 59620T).

Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4081-4086 ◽  
Author(s):  
Dao-Feng Zhang ◽  
Xiu Chen ◽  
Xiao-Mei Zhang ◽  
Xiao-Yang Zhi ◽  
Ji-Cheng Yao ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Cell Protein ◽  
Rrna Gene ◽  
Good Growth ◽  
Sand Sample ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Two novel isolates of rapidly growing, Gram-stain-positive, non-chromogenic species of the genus Mycobacterium , strain YIM M13028T from a sediment sample collected from the South China Sea (19° 30.261′ N 111° 0.247′ E) at a depth of 42 m and strain YIM 121001T from a coastal zone sand sample collected in Dubai, United Arab Emirates, were obtained in our laboratory. Their taxonomic positions were determined by a polyphasic approach. Good growth of the two strains was observed at 28 °C and pH 7.0 with 0–2 % NaCl on tryptic soy agar medium. Both strains formed round orange–red colonies, strain YIM M13028T had a rough surface, while YIM 121001T was smooth. Cellular fatty acids, whole-cell protein profiles and TLC analysis of their mycolic acids show significant differences from reference stains. Phenotypic characteristics and multilocus sequence analysis (MLSA) of 16S rRNA gene, hsp65, rpoB and 16S–23S internal transcribed spacer (ITS) sequences indicated that both strains YIM M13028T and YIM 121001T belong to the genus Mycobacterium . DNA–DNA hybridization values revealed a low relatedness (<70 %) of the two isolates with the type strains Mycobacterium neoaurum DSM 44074T and Mycobacterium hodleri DSM 44183T. The low DNA–DNA hybridization values (40.4±3.5 %) between strains YIM M13028T and YIM 121001T and phenotypic distinctiveness indicated that the two strains were representatives of different novel species of the genus Mycobacterium . The names proposed for these novel species are Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., and the type strains are YIM M13028T ( = DSM 45643T = KCTC 19999T) and YIM 121001T ( = DSM 45768T = JCM 18538T), respectively.

scholarly journals Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2060-2065 ◽  
Author(s):  
Wei-Chun Hung ◽  
Hsiao-Jan Chen ◽  
Jui-Chang Tsai ◽  
Sung-Pin Tseng ◽  
Tai-Fen Lee ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.

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