Lactobacillus silagei sp. nov., isolated from orchardgrass silage

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4613-4618 ◽  
Author(s):  
Masanori Tohno ◽  
Maki Kitahara ◽  
Tomohiro Irisawa ◽  
Takaharu Masuda ◽  
Ryuichi Uegaki ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Α Subunit ◽  
Content Type ◽  
Link Type ◽  
Content Classification

A Gram-reaction-positive, facultatively anaerobic, non-spore-forming and catalase-negative rod-shaped bacterial strain, designated IWT126T, was isolated from orchardgrass (Dactylis glomerata L.) silage preserved in Hachimantai, Iwate, Japan. The isolate showed growth at 15–45 °C, pH 3.5–7.5 and with 4.0 % (w/v) NaCl. The cell wall peptidoglycan did not contain meso-diaminopimelic acid, and the DNA G+C content was 45.6 mol%. The major cellular fatty acids were C16 : 0 and C19 : 1 cyclo 9,10. Based on 16S rRNA gene sequence similarity, strain IWT126T was classified as a member of the genus Lactobacillus and was most closely related to Lactobacillus odoratitofui YIT 11304T (98.7 %), Lactobacillus similis JCM 2765T (98.5 %), Lactobacillus collinoides JCM 1123T (97.6 %), Lactobacillus paracollinoides DSM 15502T (97.6 %) and Lactobacillus kimchicus DCY51T (96.9 %). Based on sequence analysis of the phenylalanyl-tRNA synthase α-subunit (pheS) gene, strain IWT126T was well separated from its phylogenetic neighbours in the genus Lactobacillus . Based on physiological, biochemical and genotypic results, as well as low DNA–DNA relatedness to recognized phylogenetic relatives in the genus Lactobacillus , classification of strain IWT126T as a representive of a novel species named Lactobacillus silagei sp. nov. is proposed. The type strain is IWT126T ( = JCM 19001T = DSM 27022T).

scholarly journals Streptomyces catbensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2146-2151 ◽  
Author(s):  
Yayoi Sakiyama ◽  
Nguyen M. Giang ◽  
Shinji Miyadoh ◽  
Dao Thi Luong ◽  
Duong Van Hop ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Traits ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Physiological And Biochemical

Strain VN07A0015T was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015T was near Streptomyces aomiensis M24DS4T (98.5 % 16S rRNA gene sequence similarity) and Streptomyces scabrisporus NBRC 100760T (95.6 %), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus Streptomyces . The aerial mycelia of strain VN07A0015T were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015T were different from those of the type strains of S. aomiensis and S. scabrisporus . The chemotaxonomic characteristics of strain VN07A0015T were typical for all members of the genus Streptomyces , which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C16 : 0 and iso-C15 : 0. DNA–DNA relatedness between strain VN07A0015T and S. aomiensis NBRC 106164T was less than 30 %. In addition, some physiological and biochemical traits differed from those of S. aomiensis . Therefore, we propose that strain VN07A0015T be classified in the genus Streptomyces as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015T = VTCC-A-1889T = NBRC 107860T).

scholarly journals Streptomyces chumphonensis sp. nov., isolated from marine sediments

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2605-2610 ◽  
Author(s):  
Wongsakorn Phongsopitanun ◽  
Chitti Thawai ◽  
Khanit Suwanborirux ◽  
Takuji Kudo ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Two actinomycete strains, KK1-2T and CPB4-7, were isolated from marine sediments collected in Chumphon province, Thailand. Chumphon province, Thailand. Their taxonomic positions were determined using a polyphasic approach. The morphological, cultural and chemotaxonomic characteristics of these isolates were consistent with the classification of the strains as representing a member of the genus Streptomyces . They contained ll-diaminopimelic acid in their cell wall peptidoglycan; the whole-cell sugars were ribose and glucose. The predominant menaquinones were MK9-(H6) and MK9-(H8). The major polar lipids were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. On the basis of 16S rRNA gene sequence similarity studies, these isolates were determined to be closely related to Streptomyces xinghaiensis JCM 16958T (98.2 %), Streptomyces rimosus subsp. paromomycinus JCM 4541T (98.1 %), Streptomyces sclerotialus JCM 4828T (98.1 %) and Streptomyces flocculus JCM 4476T (98.0 %). The G+C contents of the genomic DNA of strains KK1-2T and CPB4-7 were 73.3 and 74.2 mol%, respectively. They could be clearly distinguished from the related type strains by a low DNA–DNA relatedness and phenotypic differences. On the basis of these results, these strains represent a novel species of the genus Streptomyces , for which the name Streptomyces chumphonensis sp. nov. (type strain KK1-2T = JCM 18522T = TISTR 2106T = PCU 330T) is proposed.

Micromonospora kangleipakensis sp. nov., isolated from a sample of limestone quarry

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4546-4551 ◽  
Author(s):  
Salam Nimaichand ◽  
Yong-Guang Zhang ◽  
Juan Cheng ◽  
Li Li ◽  
Dao-Feng Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Limestone Quarry ◽  
Link Type ◽  
Unknown Lipid

Strain MBRL 34T, isolated from a sample of limestone quarry located at Hundung, Manipur, India, was characterized by polyphasic taxonomy. The strain showed the highest 16S rRNA gene sequence similarity with Micromonospora echinaurantica DSM 43904T (98.4 %), but formed a monophyletic clade with Micromonospora coerulea DSM 43143T (98.3 %) in the neighbour-joining tree. DNA–DNA hybridization experiments gave a DNA–DNA relatedness value of 53.1 % between MBRL 34T and M. coerulea DSM 43143T. Strain MBRL 34T contained meso-diaminopimelic acid, galactose and glucose in the whole-cell hydrolysates along with small amounts of mannose, xylose, rhamnose and ribose. The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside, along with an unknown lipid. MK-10(H6), MK-10(H2) MK-11(H4) and MK-10(H4) were the predominant menaquinones detected. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA was 73.5 %. Based on the taxonomic characteristics from a polyphasic study, strain MBRL 34T merits recognition as a representative of a novel species of the genus Micromonospora for which the name Micromonospora kangleipakensis sp. nov. is proposed; the type strain is MBRL 34T ( = DSM 45612T = JCM 17696T).

Prosthecobacter algae sp. nov., isolated from activated sludge using algal metabolites

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 663-667 ◽  
Author(s):  
Jangho Lee ◽  
Banghyo Park ◽  
Sung-Geun Woo ◽  
Juyoun Lee ◽  
Joonhong Park
Keyword(s):  
Activated Sludge ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

A Gram-stain-negative, fusiform-shaped, facultatively anaerobic bacterial strain, designated EBTL04T, was isolated from activated sludge using algal metabolites and taxonomically characterized through polyphasic investigation. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain EBTL04T belongs to the family Verrucomicrobiaceae , class Verrucomicrobiae , and is closely related to Prosthecobacter dejongeii DSM 12251T (98.6 % sequence similarity), Prosthecobacter fusiformis ATCC 25309T (97.9 %), Prosthecobacter debontii DSM 14044T (97.5 %), Prosthecobacter vanneervenii DSM 12252T (94.7 %) and Prosthecobacter fluviatilis KCTC 22182T (93.7 %). The G+C content of the genomic DNA of strain EBTL04T was 62.7 mol%. The menaquinone MK-6 was detected as the predominant quinone. Strain EBTL04T contained phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine as major polar lipids. A fatty acid profile with C16 : 1ω5c, iso-C14 : 0, C16 : 0, anteiso-C15 : 0 and C14 : 0 as the major components supported the classification of strain EBTL04T in the genus Prosthecobacter . Based on several phenotypic, genotypic and chemotaxonomic features, strain EBTL04T was clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL04T should be considered to represent a novel species of the genus Prosthecobacter , for which the name Prosthecobacter algae sp. nov. is proposed. The type strain is EBTL04T ( = KCTC 23681T = JCM 18053T).

scholarly journals Streptomyces lasalocidi sp. nov. (formerly ‘Streptomyces lasaliensis’), an actinomycete isolated from soil which produces the polyether antibiotic lasalocid

2020 ◽  
Vol 70 (5) ◽  
pp. 3076-3083 ◽  
Author(s):  
Gary S. Erwin ◽  
Jouni Heikkinen ◽  
Pauliina Halimaa ◽  
Christopher L. Haber
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Description

Strain ATCC 31180T was isolated from soil collected in Hyde Park, Massachusetts (USA), and found to produce the polyether antibiotic lasalocid. The name ‘Streptomyces lasaliensis’ has been in common use since 1974, without a recognized taxonomic description. The most closely related type cultures determined by rRNA gene sequence similarity were Streptomyces longwoodensis DSM 41677T (100 %) and Streptomyces galbus DSM 40089T (100 %). OrthoANI values with S. longwoodensis and S. galbus were 95.50 and 94.41 %, respectively. Chemotaxonomic characteristics supported inclusion within the genus Streptomyces . The cell wall peptidoglycan contained ll-diaminopimelic acid, and the major whole-cell sugars were glucose and ribose. Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, one unidentified lipid and one unidentified glycolipid. The major menaquinones detected were MK9(H4), MK9(H6) and MK9(H8). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 1. Its DNA had a G+C content of 72.6 %. Differentiation of ATCC 31180T from the closely related species was evident from digital DNA–DNA hybridization values of 61.80 and 56.90 % for S. longwoodensis and S. galbus respectively. Significant differences were seen in the polyphasic phenotypic analyses. ATCC 31180T produced lasalocid, grew from 10 to 45 °C, pH4-8 and in the presence of 0–10 % NaCl, 0.01 % NaN3 and 1 % phenol. Melanin was produced; H2S and indole were not. Nitrate was not reduced. Spore chains were retinaculum-apertum and spore surfaces were smooth. Spore colour, mycelia colour and soluble pigment production were medium-dependent. The proposed name is Streptomyces lasalocidi sp. nov.; the type strain being ATCC 31180T (=NRRL 3382T=DSM 46487T).

Amycolatopsis dendrobii sp. nov., an endophytic actinomycete isolated from Dendrobium heterocarpum Lindl.

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nisachon Tedsree ◽  
Somboon Tanasupawat ◽  
Boonchoo Sritularak ◽  
Nattakorn Kuncharoen ◽  
Kittisak Likhitwitayawuid
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Genotypic Characteristics

Three novel actinomycete strains, designated as DR6-1T, DR6-2 and DR6-4, isolated from the roots of Dendrobium heterocarpum Lindl in Thailand were studied using a polyphasic taxonomic approach. The strains grew at 20–37 °C, at pH 5–10 and with 5 % (w/v) NaCl. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and MK-9(H4) was a major menaquinone. Arabinose and galactose were the major sugars in the cell wall. The predominant cellular fatty acids were iso-C16 : 0 and iso-C15 : 0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1T, DR6-2 and DR6-4 shared 99.9–100 % 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831T (98.7-98.8%). The approximate genome size of strain DR6-1T was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1T and Amycolatopsis echigonensis JCM21831T, Amycolatopsis rubida JCM 10871T and Amycolatopsis nivea KCTC 39515T were 90.55, 92.25, 92.60%, and 47.20, 52.10 and 52.50%, respectively. Based on the phenotypic, chemotaxonomic and genotypic characteristics, it has been concluded that strains DR6-1T, DR6-2 and DR6-4 represent a novel species of the genus Amycolatopsis for which the name Amycolatopsis dendrobii sp. nov. is proposed. The type strain is DR6-1T (=JCM 33742T=KCTC 49546T=TISTR 2840T).

scholarly journals Paenibacillus relictisesami sp. nov., isolated from sesame oil cake

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1534-1539 ◽  
Author(s):  
Takefumi Shimoyama ◽  
Nurziha Binti Johari ◽  
Atsuki Tsuruya ◽  
Arun Nair ◽  
Toru Nakayama
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Sesame Oil ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid

A facultatively anaerobic, Gram-stain-positive, rod-shaped bacterium, designated strain KB0549T, was isolated from sesame oil cake. Cells were motile, round-ended rods, and produced central or terminal spores. The cell wall peptidoglycan contained meso-diaminopimelic acid as the diamino acid. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain KB0549T was 51.9 mol%. On the basis of 16S rRNA gene sequence phylogeny, strain KB0549T was affiliated with the genus Paenibacillus in the phylum Firmicutes and was most closely related to Paenibacillus cookii with 97.4 % sequence similarity. Strain KB0549T was physiologically differentiated from P. cookii by the high content of anteiso-C17 : 0, inability to grow at 50 °C, spore position, and negative Voges–Proskauer reaction. Based on these unique physiological and phylogenetic characteristics, it is proposed that the isolate represents a novel species, Paenibacillus relictisesami sp. nov.; the type strain is KB0549T ( = JCM 18068T = DSM 25385T).

scholarly journals Streptomyces pharmamarensis sp. nov. isolated from a marine sediment

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1165-1170 ◽  
Author(s):  
Lorena Carro ◽  
Paz Zúñiga ◽  
Fernando de la Calle ◽  
Martha E. Trujillo
Keyword(s):  
Fatty Acids ◽  
Marine Sediment ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Physiological Data ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-positive actinobacterium, strain PM267T, was isolated from a marine sediment sample in the Mediterranean Sea. The novel strain produced extensively branched substrate and aerial hyphae that carried spiral spore chains. Substrate and aerial mycelia were cream–white and white, respectively. Diffusible pigments were not observed. 16S rRNA gene sequence analysis revealed that strain PM267T belonged to the genus Streptomyces and shared a gene sequence similarity of 97.1 % with Streptomyces artemisiae YIM 63135T and Streptomyces armeniacus JCM 3070T. Values <97 % were obtained with other sequences representing members of the genus Streptomyces . The cell wall peptidoglycan contained ll -diaminopimelic acid. MK-9(H8) was the major menaquinone. The phospholipid pattern included phosphatidylethanolamine as diagnostic lipid (type II). Major fatty acids found were iso- and anteiso- fatty acids. The G+C content of the DNA was 71.2 mol%. The strain was halotolerant and was able to grow in the presence of 9 % (w/v) NaCl (with an optimum of 2 %). On the basis of these results and additional physiological data obtained in the present study, strain PM267T represents a novel species within the genus Streptomyces for which the name Streptomyces pharmamarensis sp. nov. is proposed (type strain PM267T  = CECT 7841T  = DSM 42032T).

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

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