scholarly journals A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle

2019 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Jarmo Ritari ◽  
Lars Paulin ◽  
Ger T. Rijkers ◽  
...  
Keyword(s):  
Anaerobic Respiration ◽  
Gene Clusters ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Carbohydrate Utilization ◽  
Soil Isolate ◽  
The Family ◽  
Intestinal Origin ◽  
The Common ◽  
Insight Into

AbstractCultivation-independent surveys have shown that the recently described genus Romboutsia within the family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the human intestinal isolate Romboutsia hominis FRIFIT (DSM 28814) and the soil isolate Romboutsia lituseburensis A25KT (DSM 797) were sequenced. An evaluation of the common traits of this recently defined genus was done based on comparative genome analysis of the two strains together with the previously elucidated genome of the type species Romboutsia ilealis CRIBT. These analyses showed that the genus Romboutsia covers a broad range of metabolic capabilities with respect to carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end products. Main differences between strains were found in their abilities to utilize specific carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. In addition, differences were found with respect to bile metabolism and motility-related gene clusters.

Natural Diversity of Frankia Strains in Actinorhizal Root Nodules from Promiscuous Hosts in the Family Myricaceae

1999 ◽  
Vol 65 (10) ◽  
pp. 4521-4527 ◽  
Author(s):  
Michael L. Clawson ◽  
David R. Benson
Keyword(s):  
Molecular Diversity ◽  
Root Nodule ◽  
Root Nodules ◽  
Reservoir Host ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Myrica Gale ◽  
The Family ◽  
The Common ◽  
Selection Of

ABSTRACT Actinorhizal plants invade nitrogen-poor soils because of their ability to form root nodule symbioses with N2-fixing actinomycetes known as Frankia. Frankia strains are difficult to isolate, so the diversity of strains inhabiting nodules in nature is not known. To address this problem, we have used the variability in bacterial 16S rRNA gene sequences amplified from root nodules as a means to estimate molecular diversity. Nodules were collected from 96 sites primarily in northeastern North America; each site contained one of three species of the family Myricaceae. Plants in this family are considered to be promiscuous hosts because several species are effectively nodulated by most isolated strains ofFrankia in the greenhouse. We found that strain evenness varies greatly between the plant species so that estimating total strain richness of Frankia within myricaceous nodules with the sample size used was problematical. Nevertheless, Myrica pensylvanica, the common bayberry, was found to have sufficient diversity to serve as a reservoir host for Frankia strains that infect plants from other actinorhizal families. Myrica gale, sweet gale, yielded a few dominant sequences, indicating either symbiont specialization or niche selection of particular ecotypes. Strains in Comptonia peregrina nodules had an intermediate level of diversity and were all from a single major group of Frankia.

Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces.

2020 ◽  
Author(s):  
CC Kim ◽  
WJ Kelly ◽  
ML Patchett ◽  
GW Tannock ◽  
Z Jordens ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Middle Lamella ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Citrus Peel ◽  
Human Faeces ◽  
The Family

© 2017 IUMS. A novel anaerobic pectinolytic bacterium (strain 14T) was isolated from human faeces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 14T belonged to the family Ruminococcaceae, but was located separately from known clostridial clusters within the taxon. The closest cultured relative of strain 14T was Acetivibrio cellulolyticus (89.7% sequence similarity). Strain 14T shared ~99% sequence similarity with cloned 16S rRNA gene sequences from uncultured bacteria derived from the human gut. Cells were Gram-stain-positive, non-motile cocci approximately 0.6μm in diameter. Strain 14T fermented pectins from citrus peel, apple, and kiwifruit as well as carbohydrates that are constituents of pectins and hemicellulose, such as galacturonic acid, xylose, and arabinose. TEM images of strain 14T, cultured in association with plant tissues, suggested extracellular fibrolytic activity associated with the bacterial cells, forming zones of degradation in the pectin-rich regions of middle lamella. Phylogenetic and phenotypic analysis supported the differentiation of strain 14T as a novel genus in the family Ruminococcaceae. The name Monoglobus pectinilyticus gen. nov., sp. nov. is proposed; the type strain is 14T (JCM 31914T=DSM 104782T).

scholarly journals Streptohalobacillus salinus gen. nov., sp. nov., a moderately halophilic, Gram-positive, facultative anaerobe isolated from subsurface saline soil

2011 ◽  
Vol 61 (5) ◽  
pp. 1127-1132 ◽  
Author(s):  
Xiaowei Wang ◽  
Yanfen Xue ◽  
Yanhe Ma
Keyword(s):  
Saline Soil ◽  
Qaidam Basin ◽  
Halophilic Bacterium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
The Family ◽  
Diamino Acid

A Gram-stain-positive, rod-shaped, non-sporulating, motile and moderately halophilic bacterium, designated strain H96B60T, was isolated from a saline soil sample of the Qaidam basin, China. The strain was facultatively anaerobic. Major end products formed from glucose fermentation were acetate, ethanol and lactic acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone component was menaquinone-6 (MK-6). The predominant cellular fatty acids were C16 : 0, anteiso-C13 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of strain H96B60T was 36.2 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequences indicated that strain H96B60T represented a novel phyletic lineage within the family Bacillaceae and was related most closely to Halolactibacillus species (96.1–96.4 % similarity). Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain H96B60T is considered to represent a novel species of a new genus, for which the name Streptohalobacillus salinus gen. nov., sp. nov. is proposed. The type strain of Streptohalobacillus salinus is H96B60T ( = DSM 22440T  = CGMCC 1.7733T).

Muriicola soli sp. nov., isolated from soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph ◽  
Genomic Characterization

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

scholarly journals Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2289-2295 ◽  
Author(s):  
Madalin Enache ◽  
Takashi Itoh ◽  
Tadamasa Fukushima ◽  
Ron Usami ◽  
Lucia Dumitru ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Marker ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Rpob Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.

scholarly journals Mesoflavibacter aestuarii sp. nov., a zeaxanthin-producing marine bacterium isolated from seawater

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1932-1937 ◽  
Author(s):  
Ji Hee Lee ◽  
Yeoung Min Hwang ◽  
Keun Sik Baik ◽  
Kap Seong Choi ◽  
Jong-Ok Ka ◽  
...  
Keyword(s):  
Marine Bacterium ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Carotenoid Pigment ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Gwangyang Bay

An orange, rod-shaped, Gram-reaction-negative, aerobic and gliding bacterial strain devoid of flagella, designated strain KYW614T, was isolated from seawater collected from Gwangyang Bay, Republic of Korea. Zeaxanthin was the major carotenoid pigment produced and flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW614T belonged to the family Flavobacteriaceae and it was most closely related to Mesoflavibacter zeaxanthinifaciens TD-ZX30T (96.5 %, sequence similarity). The predominant cellular fatty acids of strain KYW614T were iso-C15 : 1 G (10.5 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 10.0 %), iso-C15 : 0 (9.5 %), C15 : 0 (7.5 %) and iso-C17 : 0 3-OH (7.4 %). MK-6 was the only isoprenoid quinone and the DNA G+C content was 32.6 mol%. Data from a polyphasic taxonomic study suggested that the isolate represents a novel species in the genus Mesoflavibacter , for which the name Mesoflavibacter aestuarii sp. nov. is proposed. The type strain is KYW614T ( = KCTC 32269T = JCM 19524T).

scholarly journals Emticicia aquatica sp. nov., a species of the family Cytophagaceae isolated from fresh water

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4358-4362 ◽  
Author(s):  
Yochan Joung ◽  
Mi-ae Seo ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Tae-seok Ahn ◽  
...  
Keyword(s):  
Fresh Water ◽  
Type Strain ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Gram Staining ◽  
The Family ◽  
Distinct Lineage ◽  
Unidentified Glycolipid

A Gram-staining-negative, non-gliding, orange-pigmented bacterial strain, designated HMF2925T, was isolated from fresh water in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HMF2925T formed a distinct lineage within the genus Emticicia. Strain HMF2925T was closely related to Emticicia oligotrophica DSM 17448T (95.5 %) and Emticicia ginsengisoli Gsoil 085T (94.1 %). The major fatty acids of strain HMF2925T were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0, C16 : 1ω5c and C16 : 0.The major polar lipids of strain HMF2925T were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, two unidentified amino lipids and three unidentified polar lipids. The DNA G+C content of strain HMF2925T was 36.5 mol%. On the basis of the evidence presented in this study, strain HMF2925T represents a novel species of the genus Emticicia, for which the name Emticicia aquatica sp. nov. is proposed. The type strain is HMF2925T ( = KCTC 42574T = CECT 8858T).

scholarly journals Niabella tibetensis sp. nov., isolated from soil, and emended description of the genus Niabella

2011 ◽  
Vol 61 (5) ◽  
pp. 1201-1205 ◽  
Author(s):  
Jun Dai ◽  
Fan Jiang ◽  
Yang Wang ◽  
Bo Yu ◽  
Huan Qi ◽  
...  
Keyword(s):  
Novel Species ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Emended Description ◽  
Taxonomic Approach ◽  
Physiological And Biochemical ◽  
Sequence Similarities ◽  
Biochemical Features

Strain 15-4T, a Gram-stain-negative, rod-shaped, non-motile bacterial strain that produced flexirubin-type pigments, was isolated from Tibet Province, China, and characterized by using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the family Chitinophagaceae, phylum ‘Bacteroidetes’, and was related to members of the genus Niabella, with sequence similarities ranging from 94.1 to 96.4 %. Strain 15-4T contained MK-7 as the predominant menaquinone and its DNA G+C content was 46.9 mol%. The major fatty acids of strain 15-4T were iso-C15 : 0 (41.3 %), iso-C15 : 1 G (14.9 %), iso-C17 : 0 3-OH (13.2 %) and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH, 16.0 %). These chemotaxonomic data supported the affiliation of strain 15-4T to the genus Niabella. However, a number of physiological and biochemical features enabled the isolate to be differentiated phenotypically from recognized species of the genus Niabella. On the basis of the evidence presented, it is proposed that strain 15-4T represents a novel species, Niabella tibetensis sp. nov.; the type strain is 15-4T ( = CCTCC AB 209167T = NRRL B-59394T). On the basis of these data, an emended description of the genus Niabella is also proposed.

Herbiconiux moechotypicola sp. nov., a xylanolytic bacterium isolated from the gut of hairy long-horned toad beetles, Moechotypa diphysis (Pascoe)

2012 ◽  
Vol 62 (1) ◽  
pp. 90-95 ◽  
Author(s):  
Byung-Chun Kim ◽  
Doo-Sang Park ◽  
Hyangmi Kim ◽  
Hyun-Woo Oh ◽  
Kang Hyun Lee ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
16S Rrna Gene Sequences ◽  
Cellular Fatty Acids ◽  
The Family ◽  
Diamino Acid ◽  
Isoprenoid Quinones

A novel Gram-positive, non-motile, rod-shaped bacterium, designated strain RB-62T, was isolated during a study of culturable bacteria from the gut of Moechotypa diphysis (Pascoe) and its taxonomic position was investigated. Strain RB-62T grew at 15–30 °C and pH 5.0–8.5. The isoprenoid quinones were menaquinones MK-11 (77.1 %), MK-10 (11.7 %) and MK-12 (11.2 %). The major cellular fatty acids were anteiso-C15 : 0 (34.6 %), anteiso-C17 : 0 (29.8 %), iso-C16 : 0 (17.0 %) and cyclohexyl-C17 : 0 (11.4 %). The diagnostic diamino acid of the cell-wall peptidoglycan was 2,4-diaminobutyric acid. The G+C content of the genomic DNA of strain RB-62T was 70.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RB-62T was affiliated with the genus Herbiconiux cluster within the family Microbacteriaceae, and was related most closely to Herbiconiux ginsengi wged11T (98.08 % similarity). The level of DNA–DNA relatedness between strain RB-62T and H. ginsengi wged11T was 43.2 % (reciprocal 66.7 %). Phenotypic and phylogenetic characteristics clearly distinguished strain RB-62T from recognized species of the genus Herbiconiux. Based on data from the present polyphasic study, strain RB-62T is considered to represent a novel species of the genus Herbiconiux, for which the name Herbiconiux moechotypicola sp. nov. is proposed. The type strain is RB-62T ( = KCTC 19653T = JCM 16117T).

scholarly journals Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea

2006 ◽  
Vol 56 (11) ◽  
pp. 2677-2681 ◽  
Author(s):  
Leonid N. Ten ◽  
Sang-Hoon Baek ◽  
Wan-Taek Im ◽  
Myungjin Lee ◽  
Hyun Woo Oh ◽  
...  
Keyword(s):  
South Korea ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
The Family ◽  
Paenibacillus Illinoisensis ◽  
Signature Sequences ◽  
Type Strains

A Gram-positive, facultatively anaerobic, motile, spore-forming bacterium, designated Gsoil 1411T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 1411T belongs to the family Paenibacillaceae, with closest sequence similarity to the type strains of Paenibacillus xylanilyticus (95.7 %), Paenibacillus illinoisensis (95.2 %) and Paenibacillus pabuli (94.8 %). Strain Gsoil 1411T showed less than 94 % sequence similarity to the type strains of other recognized members of the genus Paenibacillus. In addition, the presence of MK-7 as the major menaquinone, anteiso-C15 : 0 as a major fatty acid (44.8 %) and the presence of PAEN513F and PAEN862F signature sequences suggest that it is affiliated to the genus Paenibacillus. The G+C content of the genomic DNA was 53.9 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 1411T is suggested to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus panacisoli sp. nov. is proposed. The type strain is Gsoil 1411T (=KCTC 13020T=LMG 23405T).

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