- Volume 58, Issue 1, 2008
Volume 58, Issue 1, 2008
- Validation List No. 119
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 57, part 10, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- List Of Changes In Taxonomic Opinion No. 7
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Notification of changes in taxonomic opinion previously published outside the IJSEM
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429–1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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- New Taxa
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- Actinobacteria
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Micromonospora rifamycinica sp. nov., a novel actinomycete from mangrove sediment
More LessAn actinomycete strain, AM105T, that produces rifamycin, was isolated from mangrove sediment samples collected from the South China Sea. The strain showed closest 16S rRNA gene sequence similarity to Micromonospora matsumotoense (98.0 %). Chemotaxonomic characteristics of the isolate coincided with members of the genus Micromonospora. The value of DNA–DNA relatedness to M. matsumotoense (53.6 %) and phenotypic differences from phylogenetically related Micromonospora species indicated that this isolate belongs to a novel species, for which the name Micromonospora rifamycinica sp. nov. is proposed. The type strain is AM105T (=CGMCC 4.2495T=DSM 44983T).
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Sanguibacter antarcticus sp. nov., isolated from Antarctic sea sand
More LessA Gram-positive, yellow-pigmented bacterium, strain KOPRI 21702T, was isolated from sea sand on King George Island, Antarctica. Cells were irregular rods with peritrichous flagella; their optimum growth temperature was 23–26 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the Antarctic isolate formed a distinct phyletic line in a clade of the genus Sanguibacter and showed highest sequence similarity (97.7 %) to the type strain of Sanguibacter keddieii. The major isoprenoid quinone, predominant cellular fatty acids and DNA G+C content were consistent with placement of the Antarctic isolate in the genus Sanguibacter. Phylogenetic analysis and differences in physiological and biochemical characteristics between strain KOPRI 21702T and the four recognized Sanguibacter species indicate that the isolate represents a novel species of this genus. The name Sanguibacter antarcticus sp. nov. (type strain KOPRI 21702T =KCTC 13143T =JCM 14623T =DSM 18966T) is proposed for this isolate.
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Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov.
More LessTwo novel bacterial strains were isolated from a paddy soil sample collected in Japan using GPM agar plates supplemented with superoxide dismutase and/or catalase. The strains were Gram-positive, catalase-positive and motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The major menaquinone was MK-9(H2). Mycolic acids were not detected. The G+C content of the DNA was 66–68 mol%. On the basis of phenotypic analysis, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, it is proposed that these strains represent two novel species, Arthrobacter oryzae sp. nov. (type strain is KV-651T=NRRL B-24478T=NBRC 102055T) and Arthrobacter humicola sp. nov. (type strain is KV-653T=NRRL B-24479T=NBRC 102056T), respectively.
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Brevibacterium oceani sp. nov., isolated from deep-sea sediment of the Chagos Trench, Indian Ocean
More LessTwo bacterial strains, designated BBH5 and BBH7T, were isolated from a deep-sea sediment sample collected from the Chagos Trench of the Indian Ocean (1 ° 06′ S 7 ° 31′ E). Based on their 16S rRNA gene sequence similarity (99.9 %), level of DNA–DNA relatedness (93 %) and a number of similar phenotypic characteristics, the two strains are identified as representing the same species. Their phylogenetically nearest neighbours, based on 16S rRNA gene sequence similarity values (97.9–98.4 %), were identified as Brevibacterium iodinum, Brevibacterium epidermidis, Brevibacterium linens and Brevibacterium permense. However, strains BBH5 and BBH7T could be distinguished from the above four species by a number of phenotypic characteristics, and levels of DNA–DNA relatedness between the two new isolates and these Brevibacterium species were 35–42 %. Therefore, strains BBH5 and BBH7T are considered to represent a novel species of the genus Brevibacterium, for which the name Brevibacterium oceani sp. nov. is proposed. The type strain is BBH7T (=LMG 23457T =IAM 15353T).
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Dietzia papillomatosis sp. nov., a novel actinomycete isolated from the skin of an immunocompetent patient with confluent and reticulated papillomatosis
More LessAn actinomycete isolated from an immunocompetent patient suffering from confluent and reticulated papillomatosis was characterized using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties that were consistent with its assignment to the genus Dietzia and it formed a distinct phyletic line within the Dietzia 16S rRNA gene tree. It shared a 16S rRNA gene sequence similarity of 98.3 % with its nearest neighbour, the type strain of Dietzia cinnamea, and could be distinguished from the type strains of all Dietzia species using a combination of phenotypic properties. It is apparent from genotypic and phenotypic data that the organism represents a novel species in the genus Dietzia. The name proposed for this taxon is Dietzia papillomatosis; the type strain is N 1280T (=DSM 44961T=NCIMB 14145T).
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Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera)
A Gram-positive, rod-shaped or coccoid, yellow-pigmented bacterial strain, D287T, was isolated from the water flea Daphnia cucullata (Crustacea: Cladocera) collected from Lake Balaton in Hungary. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that the strain represented a distinct lineage within the cluster of the genera Nocardioides and Marmoricola. The following characteristics were consistent with the affiliation of strain D287T to the genus Nocardioides: peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the major menaquinone, iso-C16 : 0 as the predominant cellular fatty acid, the presence of phosphatidylglycerol and diphosphatidylglycerol and a DNA G+C content of 69.9 mol%. Owing to characteristic differences in physiological traits and levels of 16S rRNA gene sequence similarity to its phylogenetically closest neighbours that were below 97 %, strain D287T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daphniae sp. nov. is proposed. The type strain is D287T (=DSM 18664T=CCM 7403T).
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Rothia terrae sp. nov. isolated from soil in Taiwan
A cream-white-coloured, aerobic, Gram-positive, ovoid to spherical-shaped bacterial strain, designated L-143T, was isolated from soil in Taiwan. The highest 16S rRNA gene sequence similarities of strain L-143T (98.3–95.8 %) were with members of the genus Rothia. Chemotaxonomic and phenotypic properties of this organism were consistent with its classification in the genus Rothia. The novel isolate was distinguished from all Rothia species by several phenotypic characteristics. The peptidoglycan type was A3α, containing lysine, glutamic acid and alanine. The isolate contained MK-7 as the major component of the quinone system. The predominant polar lipid consisted of phosphatidylglycerol and diphosphatidylglycerol, with some unknown phospho- and glycolipids as minor components. The major fatty acids were anteiso-15 : 0 (57.3 %), anteiso-17 : 0 (17.0 %) and 16 : 0 (9.3 %). The G+C content of the genomic DNA was 56.1 mol%. Hence, genotypic, chemotaxonomic and phenotypic data demonstrate that strain L-143T should be classified as a novel species in the genus Rothia, for which the name Rothia terrae sp. nov. is proposed. The type strain is L-143T (=BCRC 17588T=LMG 23708T).
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Ornithinimicrobium pekingense sp. nov., isolated from activated sludge
More LessThe bacterial strain LW6T was isolated from activated sludge of a wastewater treatment bioreactor. Cells of strain LW6T are Gram-positive, irregular, short rods and cocci, 0.5–0.8×1.0–1.6 μm. Colonies are light-yellow, smooth, circular and 0.2–1.0 mm in diameter after 3 days incubation. Strain LW6T is aerobic and heterotrophic. It grows at a temperature range of 26–38 °C and pH range of 6–9, with optimal growth at 33–37 °C and pH 7.8–8.2. The predominant cellular fatty acids of strain LW6T are iso-C15 : 0 (38.9 %) and iso-C17 : 1 ω9c (18.8 %). Strain LW6T has the major respiratory menaquinones MK-8(H4) and MK-8(H2) and polar lipids phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and unknown glycolipid/phospholipids. The cell wall peptidoglycan of strain LW6T contained the amino acids ornithine, lysine, glutamic acid, alanine, glycine and aspartic acid. Its molar DNA G+C content is 69 mol% (T m). Analysis of 16S rRNA gene sequences indicated that strain LW6T was related phylogenetically to members of the genus Ornithinimicrobium, with similarities ranging from 98.3 to 98.7 %. The DNA–DNA relatedness of strain LW6T to Ornithinimicrobium humiphilum DSM 12362T and Ornithinimicrobium kibberense K22-20T was respectively 31.5 and 15.2 %. Based on these results, it is concluded that strain LW6T represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium pekingense sp. nov. is proposed. The type strain is strain LW6T (=CGMCC 1.5362T =JCM 14001T).
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Bifidobacterium tsurumiense sp. nov., from hamster dental plaque
More LessThree novel micro-organisms, designated strains OMB115T, OMB118 and OMB120, were isolated from dental plaque from golden hamsters fed with a high-carbohydrate diet. The three strains were Gram-positive, facultatively anaerobic rods that lacked catalase activity. Analysis of their partial 16S rRNA gene sequences indicated that these isolates belonged to the genus Bifidobacterium. They grew under aerobic conditions and each had a DNA G+C content of 53 mol%. On the basis of phylogenetic analyses involving phenotypic characterization and partial 16S rRNA gene sequencing, strain OMB115T represents a novel species of the genus Bifidobacterium, for which the name Bifidobacterium tsurumiense sp. nov. is proposed. The type strain is OMB115T (=JCM 13495T =DSM 17777T).
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Nocardiopsis ganjiahuensis sp. nov., isolated from a soil from Ganjiahu, China
An actinomycete, strain HBUM 20038T, was isolated from soil from Ganjiahu Natural Reserve in Xinjiang Province, in north-western China, and then characterized using a polyphasic approach. 16S rRNA gene sequence analysis confirmed that strain HBUM 20038T was a member of the genus Nocardiopsis, and the morphological and chemotaxonomic characteristics of the strain were also consistent with those of species of Nocardiopsis. DNA–DNA hybridization between the strain and related type strains gave relatedness values far below 70 %. These results, together with physiological characteristics, showed that strain HBUM 20038T represents a novel species within the genus Nocardiopsis, for which the name Nocardiopsis ganjiahuensis sp. nov. is proposed. The type strain is HBUM 20038T (=DSM 45031T =CGMCC 4.3500T).
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Nocardioides hwasunensis sp. nov.
More LessTwo novel actinomycete strains, designated HFW-18 and HFW-21T, were isolated from a water sample around Hwasun Beach on the coast of Jeju Island, Republic of Korea. The cells of the organisms were aerobic, Gram-positive, non-motile rods. The temperature and initial pH ranges for growth were 4–37 °C and pH 5.1–9.1, respectively. They had ll-diaminopimelic acid in their cell-wall peptidoglycan, MK-8(H4) as the major menaquinone and DNA G+C contents of 71.1–72.2 mol%. The cellular fatty acids consisted of straight-chain saturated, branched, monounsaturated and 10-methyl fatty acids, with a major component of iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The isolates were identical in terms of their 16S rRNA gene sequences and BOX-PCR DNA fingerprints. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates occupied distinct positions within the radiation of the genus Nocardioides. According to 16S rRNA gene sequence similarity, the closest relatives were Nocardioides ganghwensis JC2055T (97.4 %), Nocardioides oleivorans DSM 16090T (97.3 %) and Nocardioides furvisabuli SBS-26T (97.0 %). Levels of 16S rRNA gene sequence similarity between the isolates and other members of the genus Nocardioides were in the range 91.8–95.3 %. On the basis of the phenotypic and molecular genetic data presented here, the isolates represent members of a novel species of the genus Nocardioides. The name Nocardioides hwasunensis sp. nov. is proposed, and the type strain is HFW-21T (=KCTC 19197T=DSM 18584T).
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- Archaea
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Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus
An extremely halophilic archaeon was isolated from a sample of the brine–sediment interface of the Shaban Deep in the northern Red Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed a close proximity to Halorhabdus utahensis (99.3 %), the sole species of the genus Halorhabdus. Strain SARL4BT formed non-pigmented colonies and showed optimum growth at 45 °C, in 27 % (w/v) NaCl and at pH 6.5–7.0. This organism utilized a few complex substrates, such as yeast extract and starch, for growth. Strain SARL4BT grew under anaerobic and microaerophilic conditions but grew extremely poorly under aerobic conditions. The ether lipids were diphytanyl derivatives. The DNA G+C content of the type strain was 61.7 mol%. On the basis of the phylogenetic data and physiological and biochemical characteristics, strain SARL4BT represents a novel species of the genus Halorhabdus, for which the name Halorhabdus tiamatea is proposed. The type strain is SARL4BT (=DSM 18392T=JCM 14471T). An emended description of the genus Halorhabdus is also proposed.
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Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge
A novel methane-producing archaeon, strain NOBI-1T was isolated from an anaerobic, propionate-degradation enrichment culture, which was originally obtained from a mesophilic methanogenic sludge digesting municipal sewage sludge. Cells were non-motile, rod-shaped, 0.7–1.0 μm by 2.0 μm, and formed multicellular filaments longer than 8 μm. Growth was observed between 35 and 55 °C (optimum 50 °C) and pH 6.7 and 8.0 (optimum pH 7.0). The G+C content of the genomic DNA was 56.3 mol%. The strain utilized H2 and formate for growth and methane production. Based on comparative sequence analyses of the 16S rRNA gene and mcrA gene (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-production pathway), strain NOBI-1T was affiliated with the order Methanomicrobiales, but it was significantly distant from any other known species within the order. The most closely related species based on 16S rRNA and mcrA gene sequence similarity were respectively ‘Candidatus Methanoregula boonei’ (93.7 % 16S rRNA gene sequence similarity) and Methanocorpusculum parvum (74.2 % deduced McrA amino acid sequence similarity to the type strain). These phenotypic and genetic properties justified the creation of a novel species of a new genus for the strain, for which we propose the name Methanolinea tarda gen. nov., sp. nov. The type strain of Methanolinea tarda is strain NOBI-1T (=DSM 16494T =JCM 12467T =NBRC 102358T).
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- Bacteroidetes
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Tenacibaculum discolor sp. nov. and Tenacibaculum gallaicum sp. nov., isolated from sole (Solea senegalensis) and turbot (Psetta maxima) culture systems
More LessTwo Gram-negative, rod-shaped, gliding bacterial strains, designated strain LL04 11.1.1T and strain A37.1T, were isolated from a diseased sole (Solea senegalensis) and from seawater from a holding tank for turbot (Psetta maxima), respectively. The strains grew on solid media as bright yellow colonies with uneven edges; the colonies did not adhere to the agar. The bacteria were able to grow at temperatures in the range 14 to 38 °C and from pH 6.0 to pH 8.0. The DNA G+C contents of strains LL04 11.1.1T and A37.1T were 32.1 and 32.7 mol%, respectively. Analysis of the 16S rRNA gene sequences indicated that strains LL04 11.1.1T and A37.1T were members of the genus Tenacibaculum in the family Flavobacteriaceae. The sequence similarities of the two isolates with respect to the type strains of recognized members of the genus ranged from 94.2 to 99.4 %. DNA–DNA hybridization studies revealed that the strains studied represent two distinct novel species of the genus Tenacibaculum, for which the names Tenacibaculum discolor sp. nov. [type strain LL04 11.1.1T (=NCIMB 14278T=DSM 18842T)] and Tenacibaculum gallaicum sp. nov. [type strain A37.1T (=NCIMB 14147T=DSM 18841T)] are proposed.
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Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants
More LessFour Gram-negative, rod-shaped, non-spore-forming and non-motile bacterial strains were isolated from surfaces and biofilms associated with beer-bottling plants. Based on their 16S rRNA gene sequences these isolates were allocated to the genus Chryseobacterium. The sequence similarities of the isolates to the next most closely related type strains of this genus ranged from 96.4 to 98.3 %. The presence of menaquinone MK-6 and predominant fatty acids 15 : 0 iso, 17 : 1 iso cis9, 15 : 0 iso 2-OH and 17 : 0 iso 3-OH supported the affiliation of these strains to the genus. The results of DNA–DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from the next most closely related Chryseobacterium species with validly published names. Therefore, the isolates represent four novel species for which the names Chryseobacterium ureilyticum (type strain F-Fue-04IIIaaaaT=DSM 18017T=CCUG 52546T), Chryseobacterium gambrini (type strain 5-1St1aT=DSM 18014T=CCUG 52549T), Chryseobacterium pallidum (type strain 26-3St2bT=DSM 18015T=CCUG 52548T) and Chryseobacterium molle (type strain DW3T=DSM 18016T=CCUG 52547T) are proposed.
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Prevotella amnii sp. nov., isolated from human amniotic fluid
More LessTwo Gram-negative, anaerobic, non-spore-forming, rod-shaped organisms were isolated from human amniotic fluid. Based on morphological and biochemical criteria, the strains were tentatively identified as Bacteroidaceae but they did not appear to correspond to any recognized species of this family. Comparative 16S rRNA gene sequencing studies showed the strains were highly related to each other and confirmed their placement in the genus Prevotella, but sequence divergence values of >4 % with reference Prevotella species demonstrated that the organisms from human clinical sources represent a novel species. Phylogenetic analysis revealed the novel organism to be most closely related to Prevotella bivia, an organism frequently associated with pelvic inflammatory diseases. The major long-chain cellular fatty acids of the novel species consist of iso-C14 : 0, anteiso-C15 : 0, iso-C15 : 0, C16 : 0, iso-C16 : 0 and iso-3-OH-C17 : 0. Based on biochemical criteria and phylogenetic considerations, it is proposed that the unknown isolates from human amniotic fluid be assigned to a new species of the genus Prevotella, as Prevotella amnii sp. nov. The type strain of Prevotella amnii is CCUG 53648T (=JCM 14753T).
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Transfer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients
Numerous novel anaerobic bacteria were isolated from the crevicular spaces of dogs with periodontitis. The phenotypic characteristics of these bacterial isolates indicated that they were similar to members of the genus Porphyromonas. However, comparison of the 16S rRNA gene sequences of the isolates indicated that they were related to members of the Bacteroides splanchnicus subgroup. A representative of the novel isolates, strain B106T, induced alveolar bone loss in a mouse model of experimental periodontal disease. Based on biochemical, morphological, molecular phylogenetic, and pathogenic evidence, it is proposed that the taxonomic subgroup containing these novel isolates and B. splanchnicus should be classified in a new genus, Odoribacter gen. nov., within the family ‘Porphyromonadaceae’. In addition, it is proposed that B. splanchnicus should be reclassified as Odoribacter splanchnicus comb. nov., and that the newly identified isolates should be classified as representing Odoribacter denticanis sp. nov., the type strain of which is B106T (=ATCC PTA-3625T=CNCM I-3225T).
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Actibacter sediminis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment
More LessA yellow-pigmented, Gram-negative, aerobic bacterial strain comprising rod-shaped cells devoid of flagellar and gliding motility, designated strain JC2129T, was isolated from tidal flat sediment of Dongmak on Ganghwa Island, South Korea. Results from a 16S rRNA gene sequence analysis indicated that the isolate belonged to the family Flavobacteriaceae; the highest level of nucleotide sequence similarity (91.9 %) occurred with Polaribacter dokdonensis DSW-5T. The predominant cellular fatty acids were iso-C15 : 0 (19.8 %), iso-C15 : 1 G (14.0 %), iso-C17 : 0 3-OH (13.7 %) and iso-C13 : 0 (6.4 %). Flexirubin-type pigments were absent. The major isoprenoid quinone was MK-6. The DNA G+C content was 43–45 mol%. Data from a polyphasic taxonomy study suggested that the isolate represents a novel genus and species in the family Flavobacteriaceae, for which the name Actibacter sediminis gen. nov., sp. nov. is proposed. The type strain of Actibacter sediminis is JC2129T (=KCTC 12704T =JCM 14002T).
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Chryseobacterium arothri sp. nov., isolated from the kidneys of a pufferfish
More LessA Gram-negative, non-flagellated, rod-shaped bacterium, designated strain P2K6T, was isolated from the kidneys of a pufferfish (Arothron hispidus) caught off the coast of Kaneohe Bay, O‘ahu, Hawai‘i. The strain formed yellowish colonies when grown on marine agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P2K6T was related most closely to members of the genus Chryseobacterium. Levels of 16S rRNA gene sequence similarity between strain P2K6T and the type strains of recognized species of the genus Chryseobacterium were 94–96.6 %, suggesting that the strain represents a novel species within this genus. The DNA G+C content of strain P2K6T was 36.5 mol%, the dominant fatty acids were iso-C15 : 0 (35.3 %) and iso-C17 : 0 3-OH (14.9 %), and the most abundant quinone was menaquinone MK6. On the basis of the data from this polyphasic study, it is suggested that strain P2K6T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium arothri sp. nov. is proposed. The type strain is P2K6T (=CIP 109575T=DSM 19326T).
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- Other Bacteria
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Physiological and phylogenetic characterization of a novel lithoautotrophic nitrite-oxidizing bacterium, ‘Candidatus Nitrospira bockiana’
More LessA new isolate of a lithoautotrophic nitrite-oxidizing bacterium was obtained from internal corrosion deposits from a steel pipeline of the Moscow heating system. The organism oxidized nitrite as the sole energy source and fixed carbon dioxide as the only carbon source. The cells were extremely pleomorphic: loosely wound spirals, slightly curved and even straight rods were detected, as well as coccoid cells. The highest rate of nitrite consumption (1.5 mM nitrite as substrate) was measured at 42 °C, with a temperature range of 28–44 °C. In enrichment cultures with Nocardioides sp. as an accompanying organism, optimal oxidation of 5.8 mM nitrite occurred at 45 °C, with a range of 28–48 °C. Neither pyruvate nor yeast extract stimulated nitrification. Organotrophic growth was not observed. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel isolate represents a new sublineage of the genus Nitrospira. On the basis of physiological, chemotaxonomic and molecular characteristics, the name ‘Candidatus Nitrospira bockiana’ is proposed.
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- Proteobacteria
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Description of Roseateles aquatilis sp. nov. and Roseateles terrae sp. nov., in the class Betaproteobacteria, and emended description of the genus Roseateles
More LessThree strains of aerobic Gram-negative bacilli, two isolated from industrial water and freshwater (strains CCUG 48205T and CCUG 52220) and the third from soil (strain CCUG 52222T), were analysed phenotypically and genotypically to clarify their taxonomic classification. 16S rRNA gene sequence analysis revealed that the three strains were located on the same phylogenetic branch, closely related to Roseateles depolymerans, the only recognized species in the genus. DNA–DNA hybridization studies, analyses of fatty acid contents, and physiological and biochemical tests supported the proposal of two novel species, Roseateles aquatilis sp. nov. (type strain, CCUG 48205T=CECT 7248T) and Roseateles terrae sp. nov. (type strain, CCUG 52222T=CECT 7247T).
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Amphritea atlantica gen. nov., sp. nov., a gammaproteobacterium from the Logatchev hydrothermal vent field
More LessA novel Gram-negative, motile, aerobic rod-shaped bacterium was isolated from a Bathymodiolus sp. specimen collected from the Logatchev hydrothermal vent field at the Mid-Atlantic Ridge. The novel strain, M41T, was catalase- and oxidase-positive and metabolised various carbohydrates and amino acids. It grew well in marine broth with an optimal growth temperature of 31 °C to 34 °C (range 4–40 °C) and salinity requirement of 3 % (range 0.3–9 %). The pH range for growth was pH 4.6 to 9.5, with an optimum at pH 8.0. The predominant fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The DNA G+C content of strain M41T was 52.2 mol%. The 16S rRNA gene sequence was 94 % similar to that of the type strain of Oceanospirillum beijerinckii, the closest cultivated relative. Other related type strains were Oceanospirillum multiglobuliferum (93 % gene sequence similarity), Neptunomonas naphthovorans (92%) and Marinobacterium jannaschii (92 %). According to phylogenetic analysis and physiological characteristics, it is suggested that strain M41T represents a new genus and novel species for which the name Amphritea atlantica gen. nov., sp. nov. is proposed. The type strain is M41T (=DSM 18887T=LMG 24143T).
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Halomonas sabkhae sp. nov., a moderately halophilic bacterium isolated from an Algerian sabkha
A novel moderately halophilic bacterium belonging to the genus Halomonas was isolated from brine samples collected from Ezzemoul sabkha in north-eastern Algeria. The cells of strain 5-3T were Gram-negative, rod-shaped and non-motile. The strain was catalase- and oxidase-positive and produced an exopolysaccharide. Growth occurred at NaCl concentrations of 5–25 % (optimum at 7.5 %), at 30–50 °C (optimum at 37–40 °C) and at pH 6.0–9.0 (optimum at pH 7.5). The major fatty acids were C12 : 0 3-OH, C16 : 1 ω7c/iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c and C19 : 0 ω8c cyclo. The G+C content of the genomic DNA was 57.0 mol% (T m). The affiliation of strain 5-3T with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas halmophila, which showed a 16S rRNA gene sequence similarity of 99.7 %. However, the level of DNA–DNA relatedness between the novel isolate and the related Halomonas species was less than 31.4 %. On the basis of the data from this polyphasic study, strain 5-3T represents a novel species of the genus Halomonas, for which the name Halomonas sabkhae sp. nov. is proposed. The type strain is 5-3T (=CECT 7246T=DSM 19122T=LMG 24084T).
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Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge
More LessFour Gram-negative, rod-shaped, non-spore-forming, denitrifying isolates were obtained from the activated sludge of an aerobic–anaerobic wastewater treatment plant in Belgium. Analysis of repetitive sequence-based PCR showed that the four isolates were genetically different from each other. Results of 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments indicated that these four isolates were affiliated to the genus Acidovorax and could be differentiated from all recognized species of the genus. Analysis of whole-cell proteins and results of physiological and biochemical tests allowed differentiation of the new isolates from their closest phylogenetic neighbours. These new isolates therefore represent a novel species of the genus Acidovorax, for which the name Acidovorax caeni sp. nov. is proposed. The type strain is R-24608T (=LMG 24103T =DSM 19327T).
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Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea
Two bacterial strains isolated from air samples, 5317S-33T and 5413S-11T, were characterized by determining their phenotypic characteristics, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that these isolates belonged to the genus Methylobacterium. Strain 5317S-33T was most closely related to Methylobacterium adhaesivum AR27T (97.9 % sequence similarity). Strain 5413S-11T was most closely related to Methylobacterium fujisawaense DSM 5686T (97.3 % sequence similarity), Methylobacterium oryzae CBMB20T (97.1 % similarity) and Methylobacterium radiotolerans JCM 2831T (97.0 % similarity). Cells of both strains were strictly aerobic, Gram-negative, motile and rod-shaped. The major fatty acid was C18 : 1 ω7c. The G+C contents of the genomic DNA were 68.0 mol% for strain 5317S-33T and 73.2 mol% for strain 5413S-11T. According to DNA–DNA hybridization data, strain 5317S-33T showed a level of DNA–DNA relatedness of 33 % with M. adhaesivum DSM 17169T, and strain 5413S-11T showed low levels of DNA–DNA relatedness (<35 %) with M. fujisawaense DSM 5686T, M. oryzae CBMB20T and M. radiotolerans DSM 1819T. On the basis of this polyphasic analysis, it was concluded that strains 5317S-33T and 5413S-11T represent two novel species within the genus Methylobacterium, for which the names Methylobacterium iners sp. nov. (type strain 5317S-33T =KACC 11765T =DSM 19015T) and Methylobacterium aerolatum sp. nov. (type strain 5413S-11T =KACC 11766T =DSM 19013T) are proposed.
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Perlucidibaca piscinae gen. nov., sp. nov., a freshwater bacterium belonging to the family Moraxellaceae
More LessA freshwater bacterium, designated IMCC1704T, was isolated from a eutrophic pond. The strain was Gram-negative, oxidase-positive, catalase-negative, chemoheterotrophic and facultatively aerobic with cells that were motile rods with a single polar flagellum. Based on 16S rRNA gene sequence similarity analyses, the novel strain was most closely related to the genera Alkanindiges (91.7 %), Acinetobacter (89.0–91.2 %), Moraxella (87.9–90.1 %), Psychrobacter (87.2–89.5 %) and Enhydrobacter (87.8 %). Phylogenetic trees generated using 16S rRNA gene sequences showed that the novel isolate belonged to the family Moraxellaceae of the class Gammaproteobacteria and formed a distinct phyletic lineage within the family. The DNA G+C content of the strain was 63.1 mol% and the predominant constituents of the cellular fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH (21.2 %), C18 : 1 ω7c (12.8 %) and C12 : 0 3-OH (12.3 %). These chemotaxonomic properties, together with several phenotypic characteristics, differentiated the novel strain from other members of the family Moraxellaceae. From the taxonomic data, which revealed the distant relationship of the new strain to the related genera, the strain should be classified as a novel genus and species in the family Moraxellaceae, for which the name Perlucidibaca piscinae gen. nov., sp. nov. is proposed. The type strain of Perlucidibaca piscinae sp. nov. is IMCC1704T (=KCCM 42363T=NBRC 102354T).
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Desulfatirhabdium butyrativorans gen. nov., sp. nov., a butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic bioreactor
More LessA novel sulfate-reducing bacterium, strain HB1T, was isolated from an upflow anaerobic sludge blanket (UASB) reactor treating paper-mill wastewater operated at 37 °C. Cells of strain HB1T were oval to rod-shaped, 1–1.3 μm wide and 2.6–3.5 μm long and Gram-negative. The optimum temperature for growth was 28–30 °C. In the presence of sulfate, the isolate was able to grow on H2/acetate, formate, ethanol, propionate, fumarate, succinate, butyrate, crotonate, catechol, benzoate, 4-hydroxybenzoate, palmitate and stearate. The isolate only grew on H2 when acetate was added as a carbon source; when grown on formate, acetate was not required. Growth was also possible on pyruvate and crotonate without an electron acceptor. The isolate showed very poor growth on acetate. Thiosulfate and sulfate were used as electron acceptors. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain HB1T represents a novel lineage within the Deltaproteobacteria; sequence similarities between strain HB1T and members of other related genera were less than 91 %. Strain HB1T was also distinguished from members of related genera based on differences in several phenotypic characteristics. It is a member of the family Desulfobacteraceae. The major cellular fatty acids of strain HB1T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C14 : 0. β-Hydroxy fatty acids were also present in the range of C14 : 0 to C18 : 0, of which C16 : 0 was the most abundant. The G+C content of the DNA was 55.1 mol%. Based on physiological, biochemical and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain HB1T is considered to represent a novel species in a new genus, for which the name Desulfatirhabdium butyrativorans gen. nov., sp. nov. is proposed. The type strain of Desulfatirhabdium butyrativorans is HB1T (=DSM 18734T =JCM 14470T).
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Uliginosibacterium gangwonense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea
More LessA yellow-pigmented, Gram-negative, aerobic bacterial strain, designated 5YN10-9T, was isolated from a wetland, Yongneup, of the Inje region, Korea. Cells were motile by means of one polar flagellum. Based on 16S rRNA gene sequence analyses, strain 5YN10-9T was shown to be related to the genera Azoarcus, Azovibrio, Thauera and Zoogloea, showing moderate sequence similarities of 90.2–93.3, 92.7, 90.9–93.3 and 92.4–92.6 % to members of these genera, respectively. Its distinct phylogenetic position and the low 16S rRNA gene sequence similarity values toward the closest related genera support the inclusion of this novel isolate in a new genus. The major isoprenoid quinone was ubiquinone 8 (Q-8). The predominant cellular fatty acids were C16 : 0 and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content was 59.3 mol%. The results of phenotypic, chemotaxonomic and phylogenetic analyses indicate that strain 5YN10-9T represents a novel species of a new genus within the family Rhodocyclaceae, class Betaproteobacteria, for which the name Uliginosibacterium gangwonense gen. nov., sp. nov. is proposed. The type strain is 5YN10-9T (=KACC 11603T=DSM 18521T).
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Reclassification of Pseudomonas mephitica Claydon and Hammer 1939 as a later heterotypic synonym of Janthinobacterium lividum (Eisenberg 1891) De Ley et al. 1978
More LessPseudomonas mephitica CCUG 2513T has been reinvestigated to clarify its taxonomic position. 16S rRNA gene sequence comparisons demonstrated that this strain clusters phylogenetically closely with Janthinobacterium lividum (99.8 % sequence similarity to the type strain). Investigation of fatty acid patterns, polar lipid profiles, polyamine patterns and quinone systems supported this delineation. Substrate utilization profiles and biochemical characteristics displayed no differences from the type strain of J. lividum, CCUG 2344T. Therefore, the reclassification of Pseudomonas mephitica as a later heterotypic synonym of Janthinobacterium lividum is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data and chemotaxonomic and biochemical data.
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Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica
More LessA Gram-negative, strictly aerobic, marine bacterium, designated strain CL-YJ9T, was isolated from sediment closely associated with the roots of a plant (Suaeda japonica) inhabiting a coastal tidal flat. Cells of the novel strain were straight and rod-shaped and were motile by means of monopolar flagella. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CL-YJ9T belongs to the genus Marinobacterium and was most closely related to Marinobacterium halophilum mano11T (94.1 % sequence similarity) and to other members of the genus Marinobacterium (92.5–93.7 % sequence similarity). The strain grew with 1–5 % NaCl (optimum, 3 %) and at 5–30 °C (optimum, approx. 25 °C) and pH 6.0–9.0 (optimum, pH 7.0). The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 40.3 %), C18 : 1 ω7c (26.6 %), C16 : 0 (16.6 %) and C10 : 0 3-OH (7.1 %). The major isoprenoid quinone was Q-8. The G+C content of the genomic DNA was 61 mol%. On the basis of the data from this polyphasic study, strain CL-YJ9T belongs to the genus Marinobacterium but is distinguishable from the recognized species. Strain CL-YJ9T therefore represents a novel species, for which the name Marinobacterium rhizophilum sp. nov. is proposed. The type strain is CL-YJ9T (=KCCM 42386T =DSM 18822T).
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Daeguia caeni gen. nov., sp. nov., isolated from sludge of a textile dye works
More LessA Gram-negative, non-spore-forming, rod-shaped bacterial strain, K107T, was isolated from sludge collected from a textile dye works in Korea and its taxonomic position was investigated by means of a polyphasic analysis. Strain K107T contained Q-10 as the predominant ubiquinone. The major fatty acids (>10 % of total fatty acids) were C18 : 1 ω7c and C18 : 1 2-OH. The DNA G+C content was 57.0 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain K107T was closely related to the genera Mycoplana, Brucella and Ochrobactrum. Strain K107T exhibited 16S rRNA gene sequence similarity values of 96.3–97.1 % with respect to the type strains of two Mycoplana species and 94.8–96.8 % with respect to members of the genera Brucella and Ochrobactrum. A phylogenetic analysis based on recA gene sequences showed that strain K107T forms a distinct phylogenetic lineage within the Alphaproteobacteria. The recA gene sequence of strain K107T showed similarity values of 84.5 % with respect to type strains of Brucella species and values of 77.6–83.1 % with respect to members of the genera Pseudochrobactrum, Ochrobactrum and Mycoplana. Strain K107T could be differentiated from phylogenetically related genera by differences in phenotypic properties and fatty acid profiles. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain K107T represents a novel genus and species, for which the name Daeguia caeni gen. nov., sp. nov. is proposed. The type strain of Daeguia caeni is strain K107T (=KCTC 12981T =CCUG 54520T).
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Sphingosinicella soli sp. nov., isolated from an alkaline soil in Korea
More LessA Gram-negative, motile, rod-shaped bacterial strain, KSL-125T, was isolated from an alkaline soil from Kwangchun, Korea, and its taxonomic position was investigated in a polyphasic study. Strain KSL-125T grew optimally at 30 °C, at pH 7.5–8.0 and in the presence of 0.5 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain KSL-125T joins the cluster comprising the two Sphingosinicella species at a bootstrap resampling value of 100 %. The values for similarity between the 16S rRNA gene sequence of strain KSL-125T and those of the type strains of the two Sphingosinicella species were 98.9–99.0 %. Strain KSL-125T contained Q-10 as the predominant ubiquinone and C17 : 1 ω6c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and an unidentified phospholipid. The DNA G+C content was 65.1 mol%. Strain KSL-125T was distinguishable from the two recognized Sphingosinicella species on the basis of differential phenotypic properties, DNA–DNA relatedness data and repetitive-sequence-based PCR genomic fingerprinting patterns. The phenotypic, phylogenetic and genetic data showed that strain KSL-125T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella soli sp. nov. is proposed. The type strain is KSL-125T (=KCTC 12482T =DSM 17328T).
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Description of Sinobacter flavus gen. nov., sp. nov., and proposal of Sinobacteraceae fam. nov.
More LessA novel Gram-negative, non-motile, rod-shaped bacterium, designated CW-KD 4T, was isolated from a polluted soil sample collected from Jiangsu Province, China, by using a classic enrichment method. Based on 16S rRNA gene sequence analysis, the novel strain represented a deep-rooting lineage within the class Gammaproteobacteria that was clustered with the genera Hydrocarboniphaga and Nevskia and some other unidentified bacteria. Polyphasic taxonomic studies revealed that strain CW-KD 4T showed rather distant relationships to its phylogenetically closest neighbours, including the two recognized genera Hydrocarboniphaga and Nevskia. Strain CW-KD 4T showed only 89.9 % and 89.7 % 16S rRNA gene sequence similarities to the type species of the genera Hydrocarboniphaga and Nevskia, respectively. The predominant isoprenoid quinone of strain CW-KD 4T was Q-8 with minor components including Q-9, MK-7 and MK-6. The major fatty acids were C16 : 0, C18 : 1 ω7c and summed feature 3. The G+C content of the DNA was 65.1 mol%. On the basis of its distinctive phenotypic and genotypic characteristics, strain CW-KD 4T represents a new genus and a novel species in the class Gammaproteobacteria, for which the name Sinobacter flavus gen. nov., sp. nov. is proposed. The type strain is CW-KD 4T (=DSM 18980T=KCTC 12881T=CCTCC AB 206145T). In addition, a new family, Sinobacteraceae fam. nov., is proposed to house the genus Sinobacter gen. nov.
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Paludibacterium yongneupense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea
A cream-coloured bacterial strain, 5YN8-15T, was isolated from a wetland, Yongneup, in the Inje region of the Republic of Korea. The bacterium was facultatively anaerobic, Gram-negative, motile with a single polar flagellum and curved-rod-shaped. Based on 16S rRNA gene sequence analysis, strain 5YN8-15T is a member of the Betaproteobacteria. Closely related taxa were Gulbenkiania mobilis E4FC31T (94.9 % sequence similarity), Chromobacterium species (94.1–94.4 %), Aquitalea magnusonii TRO-001DR8T (93.2 %) and Aquaspirillum serpens IAM 13944T (92.5 %). All other species with validly published names analysed showed sequence similarities of below 92 %. Strain 5YN8-15T had ubiquinone 8 as the major isoprenoid quinone. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 63.0 mol%. Based on the data from the polyphasic study, strain 5YN8-15T represents a novel genus and species of the family Neisseriaceae, for which the name Paludibacterium yongneupense gen. nov., sp. nov. is proposed. The type strain is 5YN8-15T (=KACC 11601T=DSM 18731T).
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Sphingomonas insulae sp. nov., isolated from soil
More LessA Gram-negative, motile and rod-shaped Sphingomonas-like bacterial strain, DS-28T, was isolated from the soil of Dokdo, Korea, and was subjected to a polyphasic taxonomic study. It grew optimally at around pH 6.5 and 25 °C in the presence of 0–0.5 % NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c, C14 : 0 2-OH and C16 : 0 as the major fatty acids. Major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-28T belonged to the genus Sphingomonas. Levels of 16S rRNA gene sequence similarity between strain DS-28T and the type strains of Sphingomonas species were in the range 93.3–98.3 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain DS-28T is distinguishable from recognized Sphingomonas species. On the basis of phenotypic, phylogenetic and genetic data, strain DS-28T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas insulae sp. nov. is proposed. The type strain is DS-28T (=KCTC 12872T=JCM 14603T).
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Enterobacter pulveris sp. nov., isolated from fruit powder, infant formula and an infant formula production environment
Six Gram-negative, facultatively anaerobic, non-spore-forming, coccoid rod-shaped isolates were obtained from fruit powder (n=3), infant formula (n=2) and an infant formula production environment (n=1) and investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated the isolates to the family Enterobacteriaceae. The highest rpoB gene sequence similarities (91.2–95.8 %) were obtained with Enterobacter helveticus, Enterobacter radicincitans, Enterobacter turicensis and Enterobacter sakazakii and the phylogenetic branch formed by these species was supported by a high bootstrap value. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by their ability to utilize melibiose, sucrose, d-arabitol, mucate and 1-O-methyl-α-galactopyranoside and their negative reactions for d-sorbitol utilization and the Voges–Proskauer test. On the basis of the phylogenetic analyses, DNA–DNA hybridization data, and unique physiological and biochemical characteristics, it is proposed that the isolates represent a novel species of the genus Enterobacter, Enterobacter pulveris sp. nov. The type strain is 601/05T (=LMG 24057T=DSM 19144T).
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Comamonas composti sp. nov., isolated from food waste compost
A bacterial strain designated YY287T, isolated from food waste compost, was investigated by polyphasic taxonomic approach. The cells were rod-shaped, Gram-negative, non-pigmented, non-spore-forming and non-fermentative. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas; its closest neighbours were the type strains Comamonas testosteroni DSM 50244T (96.5 %), Comamonas terrigena DSM 7099T (95.4 %), Comamonas odontotermitis Dant 3-8T (95.2 %) and Comamonas koreensis KCTC 12005T (94.6 %). Strain YY287T was clearly distinguished from all of these strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. The major fatty acids were 16 : 0 (33 %), 18 : 1ω7c (13 %) and summed feature 3 (16 : 1ω7c and/or 15 : 0 iso 2-OH; 41 %). The DNA G+C content of the genomic DNA was 62.8 mol%. It is evident from the genotypic and phenotypic data that strain YY287T represents a novel species in the genus Comamonas, for which the name Comamonas composti sp. nov. is proposed. The type strain is YY287T (=BCRC 17659T=LMG 24008T).
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Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969
More LessAn aerobic bacterial isolate, strain HN-182T, was isolated from sediments of the South China Sea. Cells of strain HN-182T are coccoid to short rods, Gram-negative, non-spore-forming and non-motile. Strain HN-182T is heterotrophic and grows well on marine broth (Difco 2216), and is not capable of growing autotrophically on reduced sulfur. Grows at temperatures ranging from 7 to 42 °C (optimum at 25 °C), but not at 4 or 45 °C, and at pH 5.0–9.0 (optimum at pH 7.0), but not at pH 4.5 or 9.5. NaCl is required for growth [0.5–8.5 % (w/v)] with an optimum of 4.5 %. Cells are positive for catalase, oxidase and urease activities. Nitrate is not reduced. Strain HN-182T contains ubiquinone-10 as sole respiratory quinone. The major polar lipids are phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. Major cellular fatty acids are C18 : 1ω7c (60.7 %), C16 : 0 (12.5 %) and C18 : 0 (8.1 %). DNA G+C content is 67.2 mol% (by T m). The analysis of 16S rRNA gene sequences indicated that strain HN-182T was related to members of the genus Paracoccus, with similarities ranging from 91.2 to 96.7 % (highest to Paracoccus versutus) and a close relationship with Paracoccus sulfuroxidans, indicating that strain HN-182T is a member of Paracoccus. Based on these results, it is concluded that strain HN-182T represents a novel species of the genus Paracoccus, for which the name Paracoccus halophilus sp. nov. is proposed. The type strain is HN-182T (=CGMCC 1.6117T=JCM 14014T).
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Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov.
More LessTwo novel Gram-negative bacterial strains, designated CL-GR15T and CL-GR35, were isolated from coastal seawater of the east coast of Korea. Identical 16S rRNA gene sequences were found in the two strains, and it was found that the strains represented a distinct and deep evolutionary lineage of descent in the order Rhizobiales, and clustered with yet-uncultured marine bacteria. This lineage could not be associated with any of 12 known families in the order Rhizobiales. The most closely related established genus was Ochrobactrum (90.7–92.5 % sequence similarity) in the family Brucellaceae. Cells of the strains were facultatively anaerobic, weakly motile rods which occasionally exhibited cohesion with each other. The strains were catalase-, oxidase- and gelatinase-positive, and accumulated intracellular poly-β-hydroxybutyrate granules. Ubiquinone 10 was the major quinone. The major polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminolipid and an unidentified glycolipid. The cellular fatty acids mainly consisted of C18 : 1 ω7c, summed feature 3 (C15 : 0 iso 2-OH and/or C16 : 1 ω7c) and C20 : 1 ω7c. The DNA G+C content was 52.8–53.0 mol%. DNA–DNA hybridization experiments revealed high values (>97 %) for relatedness between strains CL-GR15T and CL-GR35 and suggested that these two strains constituted a single species. The distinct phylogenetic position and combinations of genotypic, phenotypic and chemotaxonomic characteristics support the proposal of Cohaesibacter gen. nov., with the type species Cohaesibacter gelatinilyticus sp. nov. (type strain, CL-GR15T=KCCM 42319T=DSM 18289T). Cohaesibacteraceae fam. nov. is also proposed.
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Albimonas donghaensis gen. nov., sp. nov., a non-photosynthetic member of the class Alphaproteobacteria isolated from seawater
A moderately halophilic Gram-negative bacterium, strain DS2T, was isolated from seawater from the East Sea in Korea. Strain DS2T grew at salinities of 0–14 % (w/v) NaCl and at temperatures in the range 10–38 °C. The cells were non-motile short rods (1.0–1.4 μm in width and 1.6–2.6 μm in length) and the major fatty acids were C18 : 1 ω7c and 11-methyl C18 : 1 ω7c. The genomic DNA G+C content was 72.0 mol% and the predominant lipoquinone was Q-10. The major cellular phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS2T formed a distinct phyletic line from the genus Rubrimonas within the Alphaproteobacteria. The levels of 16S rRNA gene sequence similarity with respect to the type strains of related genera were below 94 %. On the basis of physiological and phylogenetic properties, strain DS2T represents a novel genus and species of the Alphaproteobacteria, for which the name Albimonas donghaensis gen. nov., sp. nov. is proposed. The type strain is DS2T (=KCTC 12586T=DSM 17890T).
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Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil
More LessA non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48T, was positive for catalase and oxidase activities and grew at 4–37 °C, 0–1 % NaCl and pH 5–9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48T was closely related to Variovorax paradoxus IAM 12373T (99.3 % sequence similarity), Variovorax soli GH9-3T (98.3 %) and Variovorax dokdonensis DS-43T (97.0 %). DNA–DNA hybridization values between strain BAM-48T and V. paradoxus NBRC 15149T, V. soli KACC 11579T and V. dokdonensis KCTC 12544T were only 49.1, 25.4 and 24.6 %, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48T contained C16 : 0 (36.1 %), C16 : 1 ω7c (21.4 %) and C17 : 0 cyclo (19.0 %) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48T should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48T (=NBRC 103145T =KCTC 22010T).
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- Eukaryotic Micro-Organisms
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Ogataea chonburiensis sp. nov. and Ogataea nakhonphanomensis sp. nov., thermotolerant, methylotrophic yeast species isolated in Thailand, and transfer of Pichia siamensis and Pichia thermomethanolica to the genus Ogataea
More LessTwo thermotolerant, methylotrophic yeast strains, PT44T and S051T, were respectively isolated from a tree exudate and soil collected in Thailand. They were categorized as thermotolerant strains on the basis of their good growth below 20 °C and up to a relatively high temperature (37 °C). The major characteristics of the two strains that place them in the genus Ogataea are the formation of four helmet- or hat-shaped ascospores in a deliquescent ascus that may be produced parthenogenetically or by conjugation between a cell and its bud or between independent cells; multilateral budding; assimilation of nitrate; the presence of ubiquinone Q7; negative for Diazonium blue B colour and urease reactions; and the absence of arthroconidia and ballistoconidia. Analysis of the D1/D2 domains of the large-subunit rDNA sequence revealed that strain PT44T was differentiated from the strain S051T by 25 nucleotide substitutions and 1 gap in 554 nt, which was sufficient to justify the description of two separate species. The closest recognized species in terms of pairwise sequences similarity to PT44T was Pichia (Ogataea) dorogensis, with 13 nucleotide substitutions and 1 gap in 554 nt. Strain S051T was closest to Pichia thermomethanolica, with 7 nucleotide substitutions in 566 nt. Phenotypic characteristics of strains PT44T and S051T allowed them to be differentiated from each other and from the closest related species. On the basis of the above finding, the two strains represent two novel species of the genus Ogataea, for which the names Ogataea chonburiensis sp. nov. (type strain PT44T =BCC 21227T =NBRC 101965T =CBS 10363T) and Ogataea nakhonphanomensis sp. nov. (type strain S051T =BCC 21228T =NBRC 101966T =CBS 10362T) are proposed. We also propose the transfer of two thermotolerant methylotrophic members of the genus Pichia described previously to the genus Ogataea: Pichia siamensis is renamed Ogataea siamensis (Limtong, Srisuk, Yongmanitchai, Kawasaki, Yurimoto, Nakase & Kato) Limtong, Srisuk, Yongmanitchai, Yurimoto & Nakase comb. nov. (type strain JCM 12264T =TISTR 5818T) and Pichia thermomethanolica is renamed Ogataea thermomethanolica (Limtong, Srisuk, Yongmanitchai, Yurimoto, Nakase & Kato) Limtong, Srisuk, Yongmanitchai, Yurimoto & Nakase comb. nov. (type strain CBS 10098T =JCM 12984T =BCC 16875T).
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- Other Gram-Positive Bacteria
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Proteiniborus ethanoligenes gen. nov., sp. nov., an anaerobic protein-utilizing bacterium
Lili Niu, Lei Song and Xiuzhu DongA novel anaerobic, mesophilic, protein-utilizing bacterial strain, GWT, was isolated from the mesophilic hydrogen-producing granular sludge used to treat food industry wastewater. The strain was a Gram-positive, non-spore-forming and non-motile rod. Growth of the strain was observed at 20–48 °C and at pH 6.4–10.0. The strain used yeast extract and peptone as carbon and energy sources. Weak growth was also observed with tryptone and Casamino acids as carbon and energy sources. The strain used none of the tested carbohydrates, alcohols or fatty acids. The fermentation products in peptone-yeast broth included ethanol, acetic acid, hydrogen and carbon dioxide. Gelatin was not hydrolysed. Nitrate was reduced. Indole was produced. NH3 and H2S were not produced. The DNA G+C content of strain GWT was 38.0 mol%. The predominant cellular fatty acids were the saturated fatty acids C14 : 0 (15.58 %), C16 : 0 (25.40 %) and C18 : 0 (12.03 %). Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain GWT represented a new branch within cluster XII of the Clostridium subphylum, with <89.6 % 16S rRNA gene sequence similarities to all described species. On the basis of polyphasic evidence from this study, strain GWT represents a new genus and novel species, for which the name Proteiniborus ethanoligenes gen. nov., sp. nov. is proposed. The type strain is GWT (=CGMCC 1.5055T=JCM 14574T).
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Lentibacillus salinarum sp. nov., isolated from a marine solar saltern in Korea
More LessA Gram-positive, motile, moderately halophilic and rod-shaped bacterium, strain AHS-1T, was isolated from a marine solar saltern in Korea, and its exact taxonomic position was investigated by use of a polyphasic study. Strain AHS-1T grew optimally at pH 6.5–7.0 and 37–40 °C in the presence of 10–12 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain AHS-1T belonged to the genus Lentibacillus. Strain AHS-1T exhibited a 16S rRNA gene sequence similarity value of 97.0 % to the type strain of Lentibacillus salarius and values of 95.0–96.7 % to the type strains of other recognized Lentibacillus species. Strain AHS-1T had cell-wall peptidoglycan based on meso-diaminopimelic acid. It contained MK-7 as the predominant menaquinone. The major fatty acids (>10 % of total fatty acids) were anteiso-C15 : 0 and anteiso-C17 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids. The DNA G+C content was 49.0 mol%. Strain AHS-1T shared a mean level of DNA–DNA relatedness of 8.5 % with L. salarius KCTC 3911T. Strain AHS-1T could also be distinguished from recognized Lentibacillus species based on several phenotypic properties. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain AHS-1T is considered to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus salinarum sp. nov. is proposed. The type strain is AHS-1T (=KCTC 13162T=CCUG 54822T).
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Clostridiisalibacter paucivorans gen. nov., sp. nov., a novel moderately halophilic bacterium isolated from olive mill wastewater
A moderately halophilic, strictly anaerobic bacterium, designated 37HS60T, was isolated from an olive mill wastewater in southern Morocco (Marrakesh). The cells were straight, motile and stained Gram-positive, forming spherical and terminal spores and with an atypical thick and stratified multilayered cell wall. Major fatty acid components were iso-C17 : 1ω10c or anteiso-C17 : 1ω3c (19.3 %), C14 : 0 (14.3 %), C16 : 1ω7c (9.9 %), C16 : 1ω7c DMA (8.5 %) and C16 : 0 (7.6 %). Strain 37HS60T grew from 20 to 50 °C with an optimum at 40–45 °C, and growth was observed from pH 5.5 to 8.5 with an optimum of 6.8. The salinity range for growth was 10–100 g NaCl l−1 with an optimum at 50 g NaCl l−1. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 37HS60T fell within the evolutionary radiation enclosed by cluster XII of the Clostridium subphylum. Strain 37HS60T exhibited highest 16S rRNA gene sequence similarity of 92.0 % with Caloranaerobacter azorensis and 90.6 % with Clostridium purinilyticum. Moreover, 37HS60T did not grow on basal medium with hexose or pentose sugars as carbon and energy sources. Pyruvate, fumarate and succinate were the best substrates for 37HS60T growth with 1.0 g yeast extract l−1. The DNA G+C content was 33.0 mol%. Due to its phenotypic and genotypic characteristics, isolate 37HS60T is proposed as a novel species of a new genus, Clostridiisalibacter paucivorans gen. nov., sp. nov. The type strain is 37HS60T (=JCM 14354T=CCUG 53849T).
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Bacillus polygoni sp. nov., a moderately halophilic, non-motile obligate alkaliphile isolated from indigo balls
A moderately halophilic, obligate alkaliphile (growth range pH 8–12), designated strain YN-1T, was isolated from indigo balls obtained from Ibaraki, Japan. The cells of the isolate stained Gram-positive, and were aerobic, non-motile, sporulating rods which grew optimally at pH 9. The strain grew in 3–14 % NaCl with optimum growth in 5 % NaCl. It hydrolysed casein and Tweens 20, 40 and 60, but not gelatin, starch, DNA or pullulan. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15 : 0, anteiso-C17 : 0 and anteiso-C17 : 1. 16S rRNA phylogeny suggested that strain YN-1T was a member of group 7 (alkaliphiles) of the genus Bacillus, with the closest relative being Bacillus clarkii DSM 8720T (similarity 99.5 %). However, DNA–DNA hybridization showed a low DNA–DNA relatedness (7 %) of strain YN-1T with B. clarkii DSM 8720T. Owing to the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic and DNA–DNA relatedness data, the isolate merits classification as a new species, for which the name Bacillus polygoni is proposed. The type strain of this species is YN-1T (=JCM 14604T=NCIMB 14282T).
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Halobacillus mangrovi sp. nov., a moderately halophilic bacterium isolated from the black mangrove Avicennia germinans
A moderately halophilic, spore-forming, Gram-positive, short-rod-shaped bacterium, designated strain MS10T, was isolated from the surface of leaves of the black mangrove Avicennia germinans and was subjected to a polyphasic taxonomic study. Strain MS10T was able to grow at NaCl concentrations in the range 5–20 % (w/v) with optimum growth at 10 % (w/v) NaCl. Growth occurred at temperatures of 10–50 °C (optimal growth at 33–35 °C) and pH 6.0–9.0 (optimal growth at pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MS10T fell within the branch encompassing members of the genus Halobacillus and was most closely related to Halobacillus dabanensis JCM 12772T (99.2 % 16S rRNA gene sequence similarity). The DNA G+C content of strain MS10T was 45.7 mol%, the major respiratory isoprenoid quinone was MK-7 and the cell-wall peptidoglycan was of the l-Orn–d-Asp type, characteristics consistent with its affiliation to the genus Halobacillus. Strain MS10T showed a level of DNA–DNA hybridization with H. dabanensis JCM 12772T of 29 % and levels below 70 % were also obtained with respect to other recognized members of the genus Halobacillus. The major fatty acids of strain MS10T were iso-C16 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C15 : 0. Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MS10T represents a novel species of the genus Halobacillus, for which the name Halobacillus mangrovi sp. nov. is proposed. The type strain is MS10T (=CECT 7206T=CCM 7397T).
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