scholarly journals Phylogenetic position ofRickettsia tsutsugamushiand the relationship among its antigenic variants by analyses of 16S rRNA gene sequences

1995 ◽  
Vol 125 (2-3) ◽  
pp. 299-304 ◽  
Author(s):  
Norio Ohashi ◽  
Masahiro Fukuhara ◽  
Masahiko Shimada ◽  
Akira Tamura
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Relationship

scholarly journals Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes

2018 ◽  
Author(s):  
Mingwei Cai ◽  
Yang Liu ◽  
Zhichao Zhou ◽  
Yuchun Yang ◽  
Jie Pan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Analysis ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Group D ◽  
Origin Of Eukaryotes

AbstractAsgard is a newly proposed archaeal superphylum. Phylogenetic position of Asgard archaea and its relationships to the origin of eukaryotes is attracting increasingly research interest. However, in-depth knowledge of their diversity, distribution, and activity of Asgard archaea remains limited. Here, we used phylogenetic analysis to cluster the publicly available Asgard archaeal 16S rRNA gene sequences into 13 subgroups, including five previously unknown subgroups. These lineages were widely distributed in anaerobic environments, with the majority of 16S rRNA gene sequences (92%) originating from sediment habitats. Co-occurrence analysis revealed potential relationships between Asgard, Bathyarchaeota, and Marine Benthic Group D archaea. Genomic analysis suggested that Asgard archaea are potentially mixotrophic microbes with divergent metabolic capabilities. Importantly, metatranscriptomics confirmed the versatile lifestyles of Lokiarchaeota and Thorarchaeota, which can fix CO2using the tetrahydromethanopterin Wood-Ljungdahl pathway, perform acetogenesis, and degrade organic matters. Overall, this study broadens the understandings of Asgard archaea ecology, and also provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.

scholarly journals Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2204-2209 ◽  
Author(s):  
Qian-Qian Liu ◽  
Ying Wang ◽  
Juan Li ◽  
Zong-Jun Du ◽  
Guan-Jun Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Position ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, facultatively anaerobic, gliding, yellow-pigmented bacterium, designated SS12T, was isolated from shark gill homogenate and characterized using a polyphasic approach. The strain was catalase-positive and oxidase-negative. Optimal growth occurred at 28–30 °C, pH 7.0–7.5 and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The strain contained MK-7 as the prevailing menaquinone; iso-C15 : 0 and anteiso-C15 : 0 as the major cellular fatty acids; and phosphatidylethanolamine and an unknown lipid as the predominant polar lipids. Comparative analysis of 16S rRNA gene sequences demonstrated that the novel isolate showed the highest sequence similarity (94.68 %) to Saccharicrinis fermentans DSM 9555T and the sequence similarities among the type strains of all other species studied were less than 92 %. A phylogenetic tree, based on 16S rRNA gene sequences, showed that strain SS12T and Saccharicrinis fermentans DSM 9555T formed a distinct cluster within the family Marinilabiliaceae . On the basis of its phylogenetic position and phenotypic traits, strain SS12T represents a novel species of genus Saccharicrinis , for which the name Saccharicrinis carchari sp. nov. is proposed. The type strain is SS12T ( = CICC 10590T = DSM 27040T). Emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans are also provided.

scholarly journals Phylogenetic Position of Riemerella anatipestifer Based on 16S rRNA Gene Sequences

1997 ◽  
Vol 47 (2) ◽  
pp. 562-565 ◽  
Author(s):  
S. SUBRAMANIAM ◽  
K.-L. CHUA ◽  
H.-M. TAN ◽  
H. LOH ◽  
P. KUHNERT ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Riemerella Anatipestifer

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 Phytoplasma: Ecology and Genomic Diversity

1998 ◽  
Vol 88 (12) ◽  
pp. 1359-1366 ◽  
Author(s):  
Ing-Ming Lee ◽  
Dawn E. Gundersen-Rindal ◽  
Assunta Bertaccini
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genomic Diversity ◽  
Phylogenetic Position ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Insect Vectors ◽  
Plant Interactions ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

The recent development of molecular-based probes such as mono- and polyclonal antibodies, cloned phytoplasma DNA fragments, and phytoplasma-specific primers for polymerase chain reaction (PCR) has allowed for advances in detection and identification of uncultured phytoplasmas (formerly called mycoplasma-like organisms). Comprehensive phylogenetic studies based on analysis of 16S ribosomal RNA (rRNA) or both 16S rRNA and ribosomal protein gene operon sequences established the phylogenetic position of phytoplasmas as members of the class Mollicutes, and the revealed phylogenetic interrelationships among phytoplasmas formed a basis for their classification. Based on restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rRNA gene sequences, phytoplasmas are currently classified into 14 groups and 38 subgroups that are consistent with groups delineated based on phylogenetic analysis using parsimony of 16S rRNA gene sequences. In the past decades, numerous phyto-plasma strains associated with plants and insect vectors have been identified using molecular-based tools. Genomic diversity of phytoplasma groups appears to be correlated with their sharing common insect vectors, host plants, or both in nature. The level of exchange of genetic information among phytoplasma strains in a given group is determined by three-way, vector-phytoplasma-plant interactions. A putative mechanism for the creation of new ecological niches and the evolution of new ecospecies is proposed.

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 The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

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