scholarly journals Gottfriedia Endophyticus sp. nov., a Novel Indole-Acetic Acid Producing Bacterium Isolated From The Roots of Rice Plant

2022 ◽  
Author(s):  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Taegun Seo
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rice Plant ◽  
Indole Acetic Acid ◽  
Bacterial Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

Abstract A Gram-stain-positive, aerobic, motile and rod-shaped bacterium, designated RG28T, was isolated from the roots of rice plant collected from paddy fields in Goyang, South Korea. Cells of the strain were oxidase-negative but catalase-positive. Strain RG28T was found to grow at 10–50°C (optimum, 25–30°C), pH 5.0–10.0 (optimum, pH 7.0) and in 1.0–5.0 % (w/v) NaCl (optimum, 0%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and the predominant menaquinones were MK-7 and MK-6.The predominant cellular fatty acids were C16:0, iso-C15:0 and anteiso-C15:0. The major polar lipids included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, four unidentified aminophosphoglycolipids, four unidentified aminophospholipids, two unidentified glycolipids, one unidentified aminoglycolipid and four unidentified lipids. The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was closely related to Gottfriedia acidiceleris CBD 119T (98.6%), Gottfriedia solisilvae LMG 18422T (98.5 %) and Gottfriedia luciferensis LMG 18422T (98.4 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between strain RG28T and type strains of Gottfriedia species were lower than the cut-offs (≥95–96 % for ANI and ≥70 % for isDDH) required to define a bacterial species. Meanwhile, the strain has the ability to produce indole-acetic acid (40.5 µg/mL). Phylogenetic, physiological and chemotaxonomic data suggested that strain RG28T represented a novel species of the genus Gottfriedia, for which the name Gottfriedia endophyticus sp. nov. is proposed, with the type strain RG28T (=KCTC 43327T=TBRC 15151T).Repositories: The draft genome and 16S rRNA gene sequences of strain RG28T have been deposited in GenBank/EMBL/DDBJ under accession numbers JAGIYQ000000000 and MW386408 respectively.

scholarly journals Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus)

2010 ◽  
Vol 60 (4) ◽  
pp. 892-895 ◽  
Author(s):  
José Luis Balcázar ◽  
José Pintado ◽  
Miquel Planas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Positive Staining ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
North West ◽  
Hippocampus Guttulatus

A Gram-positive-staining, motile, rod-shaped, endospore-forming bacterium (BFLP-1T) was isolated from faeces of wild long-snouted seahorses (Hippocampus guttulatus) captured in north-west Spain (Toralla, Galicia). Strain BFLP-1T grew at 10–30 °C and pH 5.5–9 (optimally at 20 °C and pH 7.2) and with 0–7 % (w/v) NaCl (optimally with 2 % NaCl). The G+C content of the DNA was 48.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BFLP-1T was a member of the genus Bacillus and was most closely related to Bacillus herbersteinensis D-1,5aT (96.6 %), B. shackletonii LMG 18435T (96.0 %) and B. isabeliae CVS-8T (95.9 %). Chemotaxonomic data (peptidoglycan type, meso-diaminopimelic acid; major menaquinone, MK-7; predominant fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1 ω11c; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown aminoglycophospholipid) supported the affiliation of strain BFLP-1T to the genus Bacillus. Comparative analysis of 16S rRNA gene sequences and chemotaxonomic and phenotypic features indicated that strain BFLP-1T represents a novel species within the genus Bacillus, for which the name Bacillus galliciensis sp. nov. is proposed. The type strain is BFLP-1T (=DSM 21539T =LMG 24668T).

scholarly journals Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4061-4065 ◽  
Author(s):  
Kouta Hatayama ◽  
Teruaki Kuno
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Soil ◽  
Rice Paddy ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Rice Paddy Soil

A mesophilic, aerobic, Gram-stain-positive, filamentous bacterial strain, designated ZYf1a3T, was isolated from rice paddy soil in Japan. This strain grew on a solid medium with formation of substrate mycelium; endospores were produced singly along the mycelium. Formation of aerial mycelium was not observed on any of the media tested. This strain produced a characteristic saffron yellow soluble pigment. Cloned 16S rRNA gene sequences of strain ZYf1a3T yielded three different copies (similarity between the three sequences: 99.8–99.9 %). One of these sequences had one base deletion. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain ZYf1a3T belongs to an independent phylogenetic lineage of the family Thermoactinomycetaceae. The cell wall of strain ZYf1a3T contained meso-diaminopimelic acid, alanine and glutamic acid, but no characteristic sugars. It contained menaquinone 7 as the sole menaquinone. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0.The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-N-methylethanolamine and unidentified aminophospholipids. The DNA G+C content was 42.5 mol%. From phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, this strain is considered to represent a novel species in a new genus, for which the name Croceifilum oryzae gen. nov., sp. nov. is proposed. The type strain of Croceifilum oryzae is ZYf1a3T ( = JCM 30426T = CCUG 66446T = DSM 46876T).

Novel mycolic acid-containing bacteria in the family Segniliparaceae fam. nov., including the genus Segniliparus gen. nov., with descriptions of Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov.

2005 ◽  
Vol 55 (4) ◽  
pp. 1615-1624 ◽  
Author(s):  
W. Ray Butler ◽  
Margaret M. Floyd ◽  
June M. Brown ◽  
Sean R. Toney ◽  
Maryam I. Daneshvar ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Health Department ◽  
Mycolic Acid ◽  
Diaminopimelic Acid ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Mycolic Acids

Four strains of novel, rapidly growing, acid–alcohol-fast-staining bacteria were characterized with a polyphasic approach. Isolates were received by the Centers for Disease Control and Prevention from domestic health department laboratories for reference testing as unidentifiable, clinical mycobacteria. Bacteria were rod-shaped and produced non-pigmented (white to beige), non-photochromogenic, smooth or wrinkled-rough colonies on Middlebrook 7H10 and 7H11 media at 33 °C. The smooth and wrinkled colony forms were representative of two species with 68·0 and 72·0 mol% DNA G+C content. The cell wall contained meso-diaminopimelic acid and mycolic acids. Species were characterized by cellular fatty acids of C10 : 0, C14 : 0, C16 : 1ω9t, C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). HPLC analysis of mycolic acids produced a novel late-emerging, genus-specific mycolate pattern. TLC analysis demonstrated a novel α +-mycolate. Species were 98·9 % similar by comparison of 16S rRNA gene sequences; however, the DNA–DNA association was <28 %. Phylogenetic analysis of 16S rRNA gene sequences demonstrated an association with Rhodococcus equi, although a DNA–DNA relatedness value of 2 % did not support a close relationship. PCR analysis of a proposed, selected actinomycete-specific 439 bp fragment of the 65 kDa heat-shock protein was negative for three of the four isolates. The creation of Segniliparaceae fam. nov. is proposed to encompass the genus Segniliparus gen. nov., including two novel species, the type species Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov., with the respective type strains CDC 1076T (=ATCC BAA-972T=CIP 108378T) and CDC 945T (=ATCC BAA-974T=CIP 108380T).

scholarly journals Nocardioides kribbensis sp. nov., isolated from an alkaline soil

2005 ◽  
Vol 55 (4) ◽  
pp. 1611-1614 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Alkaline Soil ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Three Gram-positive, rod- or coccoid-shaped bacterial strains, KSL-2T, KSL-5 and KSL-6, were isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomical analysis. These isolates grew optimally at pH 9·0 and 30 °C. They were characterized chemotaxonomically as having cell wall peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. The DNA G+C content of the isolates was 73–74 mol%. Strains KSL-2T, KSL-5 and KSL-6 were identical in their 16S rRNA gene sequences and exhibited DNA–DNA relatedness values of 88–93 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the three isolates fell within the evolutionary radiation encompassed by the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species ranged from 93·6 % (with Nocardioides albus) to 97·2 % (with Nocardioides aquiterrae). DNA–DNA relatedness levels between the three isolates and N. aquiterrae CJ-14T were 8–15 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-2T, KSL-5 and KSL-6 were classified in the genus Nocardioides as members of a novel species for which the name Nocardioides kribbensis sp. nov. is proposed, with KSL-2T (=KCTC 19038T=DSM 16314T) as the type strain.

scholarly journals Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

2019 ◽  
Vol 60 (1) ◽  
pp. 54-61
Author(s):  
Princy Hira ◽  
Priya Singh ◽  
Anil Kumar Pinnaka ◽  
Suresh Korpole ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

scholarly journals Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales

2006 ◽  
Vol 56 (8) ◽  
pp. 1747-1753 ◽  
Author(s):  
Linda Cavaletti ◽  
Paolo Monciardini ◽  
Peter Schumann ◽  
Manfred Rohde ◽  
Ruggiero Bamonte ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Whole Cell ◽  
Distinct Cluster

Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C15 : 0, i-C16 : 0 and ai-C15 : 0 and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766T and galactose in strain GE134769T). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769T (=DSM 44927T=NRRL B-24432T) and GE134766T (=DSM 44926T=NRRL B-24431T), respectively. The DNA G+C contents of strains GE134769T and GE134766T are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.

scholarly journals Bacillus rigui sp. nov., isolated from wetland fresh water

2010 ◽  
Vol 60 (9) ◽  
pp. 2204-2209 ◽  
Author(s):  
Keun Sik Baik ◽  
Chae Hong Lim ◽  
Seong Chan Park ◽  
Eun Mi Kim ◽  
Moon Soo Rhee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fresh Water ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties

Two Gram-stain-positive strains, WPCB074T and WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074T and WPCB165 belonged to the genus Bacillus and that strain WPCB074T was most closely related to Bacillus solisalsi YC1T (98.4 % sequence similarity), B. barbaricus V2-BIII-A2T (97.7 %), B. macauensis ZFHKF-1T (96.9 %), B. arsenicus Con a/3T (96.4 %) and B. gelatini LMG 21880T (95.1 %). The 16S rRNA gene sequences of strains WPCB074T and WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA–DNA relatedness between strain WPCB074T and the type strains of B. solisalsi, B. barbaricus, B. macauensis, B. arsenicus and B. gelatini were 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074T was characterized by having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The DNA G+C content of strain WPCB074T was 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074T represents a novel species of the genus Bacillus for which the name Bacillus rigui sp. nov. is proposed. The type strain is WPCB074T (=KCTC 13278T =JCM 16348T).

scholarly journals Blautia faecicola sp. nov., isolated from faeces from a healthy human

2020 ◽  
Vol 70 (3) ◽  
pp. 2059-2065 ◽  
Author(s):  
Ji-Sun Kim ◽  
Jam-Eon Park ◽  
Keun Chul Lee ◽  
Seung-Hyeon Choi ◽  
Byeong Seob Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Separate Branch

An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111T, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111T was closely related to Ruminococcus gauveauii CCRI-16110T (93.9 %) and Blautia stercoris GAM6-1T (93.7 %), followed by Clostridium nexile DSM 1787T (93.5 %), Blautia producta ATCC 27340T (93.4 %), Blautia hydrogenotrophica DSM 10507T (93.1 %) and Blautia coccoides ATCC 29236T (93.1 %) within the family Lachnospiraceae ( Clostridium rRNA cluster XIVa). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that KGMB01111T formed a separate branch with species in the genus Blautia . The major cellular fatty acids (>10.0 %) were C16 : 0 and C18 : 1 cis 9 dimethyl acetal (DMA), and the major polar lipids were aminophospholipids and lipids. KGMB01111T contained meso-diaminopimelic acid in cell-wall peptidoglycan. The predominant end product of fermentation produced by KGMB01111T was acetic acid. Based on the whole-genome sequence, the DNA G+C content of the isolate was 44.7 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, KGMB01111T represents a novel species within the genus Blautia for which the name Blautia faecicola sp. nov. is proposed. The type strain is KGMB01111T (=KCTC 15706T=DSM 107827T).

scholarly journals Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov.

2012 ◽  
Vol 62 (1) ◽  
pp. 144-149 ◽  
Author(s):  
Masami Morotomi ◽  
Fumiko Nagai ◽  
Yohei Watanabe
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Human Faeces

A novel, strictly anaerobic, non-motile, non-spore-forming, Gram-negative, short, straight rod with tapered ends, designated YIT 12065T, was isolated from human faeces. Strain YIT 12065T was saccharolytic and negative for catalase, oxidase and urease, hydrolysis of aesculin and gelatin, nitrate reduction and indole production. The end products of glucose fermentation were acetic acid and a small amount of butyric acid. The DNA G+C content was 51.3 mol%. The predominant fatty acids were iso-C15 : 0, C16 : 0 and C14 : 0. Respiratory quinones were not detected. The cell wall contained glutamic acid, serine, alanine and ll-diaminopimelic acid. The whole-cell sugars were ribose, rhamnose, galactose and glucose. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel family-level lineage within the phylum Firmicutes, class Clostridia, order Clostridiales. Caldicoprobacter oshimai JW/HY-331T was shown to be the closest named relative on the basis of 16S rRNA gene sequence similarity (86.9 %), followed by Tindallia californiensis DSM 14871T (86.3 %) and Clostridium ganghwense JCM 13193T (86.1 %). Similar 16S rRNA gene sequences (98.6–96.7 %) were found amongst faecal uncultured clones of human and dugong (Dugong dugon). They clustered with strain YIT 12065T in a distinct and deep evolutionary lineage of descent in the order Clostridiales. The distinct phylogenetic position supports the proposal of Christensenella gen. nov., with the type species Christensenella minuta sp. nov. (type strain YIT 12065T  = DSM 22607T  = JCM 16072T). A new family Christensenellaceae fam. nov. is also proposed.

scholarly journals Tenggerimyces mesophilus gen. nov., sp. nov., a member of the family Nocardioidaceae

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3359-3364 ◽  
Author(s):  
Hong-Min Sun ◽  
Tao Zhang ◽  
Yu-Zhen Wei ◽  
Hong-Yu Liu ◽  
Li-Yan Yu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
North West ◽  
The Family ◽  
Combined Data

A novel aerobic actinomycete, designated strain I12A-02601T, was isolated from a desert soil crusts sample collected from the Shapotou region of Tengger Desert, north-west China. The substrate mycelia of this isolate were well-developed and branched, but not fragmented. The maturity aerial mycelia formed short chains of small, rod-shaped spores. The strain contained ll-diaminopimelic acid, dd-diaminopimelic acid, galactose, glucose, ribose and xylose in its whole-cell hydrolysates. The polar lipids consisted of diphosphatidylglycerol, N-acetylglucosamine-containing phospholipids, phosphatidylinositolmannoside and glycolipids. The predominant menaquinones were MK-10(H6) and MK-10(H8). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of the genomic DNA was 72.2 mol%. The 16S rRNA gene sequences comparison showed that strain I12A-02601T was most closely related to members of the family Nocardioidaceae, such as Actinopolymorpha alba YIM 48868T (93.3 % sequence similarity), Actinopolymorpha pittospori PIP 143T (93.2 %), and Flindersiella endophytica EUM 378T (93.2 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain I12A-02601T formed a clade with the members of the genera Flindersiella, Thermasporomyces, and Actinopolymorpha in the family Nocardioidaceae. Combined data from this taxonomic study using a polyphasic approach, led to the conclusion that strain I12A-02601T represents a novel species of a new genus in the family Nocardioidaceae, for which the name Tenggerimyces mesophilus gen. nov., sp. nov. is proposed. The type strain of the type species is I12A-02601T ( = CPCC 203544T = DSM 45829T = NBRC 109454T).

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