Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)

Göker, Markus; Held, Brittany; Lucas, Susan; Nolan, Matt; Yasawong, Montri; Rio, Tijana Glavina del; Tice, Hope; Cheng, Jan‐Fang; Bruce, David; Detter, John C.; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun Juan; Jeffries, Cynthia D.; Rohde, Manfred; Sikorski, Johannes; Pukall, Rüdiger; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Lapidus, Alla

doi:10.4056/sigs.1082860

Cited by 43 publications

(30 citation statements)

References 33 publications

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“…P. piscolens has been found in odontogenic abscesses, inflamed gingival crevices and infected canals 21 22 . Olsenella uli and Porphyromonas endodontalis are associated with human endodontic infections 23 24 . C. cellulans (strain LMG 16121), identified in A1 with a coverage of 10.32%, is an inhabitant of soil, water, decaying plant material and brewery sewage 25 .…”

Section: Resultsmentioning

confidence: 99%

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

Shen

Xie

et al. 2015

Sci Rep

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Despite the high worldwide prevalence of gallstone disease, the role of the biliary microbiota in gallstone pathogenesis remains obscure. Next-generation sequencing offers advantages for systematically understanding the human microbiota; however, there have been few such investigations of the biliary microbiome. Here, we performed whole-metagenome shotgun (WMS) sequencing and 16S rRNA sequencing on bile samples from 15 Chinese patients with gallstone disease. Microbial communities of most individuals were clustered into two types, according to the relative enrichment of different intestinal bacterial species. In the bile samples, oral cavity/respiratory tract inhabitants were more prevalent than intestinal inhabitants and existed in both community types. Unexpectedly, the two types were not associated with fever status or surgical history, and many bacteria were patient-specific. We identified 13 novel biliary bacteria based on WMS sequencing, as well as genes encoding putative proteins related to gallstone formation and bile resistance (e.g., β-glucuronidase and multidrug efflux pumps). Bile samples from gallstone patients had reduced microbial diversity compared to healthy faecal samples. Patient samples were enriched in pathways related to oxidative stress and flagellar assembly, whereas carbohydrate metabolic pathways showed varying behaviours. As the first biliary WMS survey, our study reveals the complexity and specificity of biliary microecology.

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Section: Resultsmentioning

confidence: 99%

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

Shen

Xie

et al. 2015

Sci Rep

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“…Based upon the two CSPs that are uniquely found in the class Actinobacteria and members of the classes Acidimicrobiia, Rubrobacteria, and Thermoleophilia, a case can also be made that these bacterial groups are specifically related to the class Actinobacteria and that they should thus be part of the phylum Actinobacteria. However, detailed analyses of the genomes of Actinobacteria have not identified any CSP or CSI that is commonly shared by the above-mentioned classes Actinobacteria and Coriobacteriia, which is now represented by five sequenced genomes (Table 1) (108,195,251). This observation in conjunc- …”

Section: Figmentioning

confidence: 97%

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Gao

Gupta

2012

Microbiol Mol Biol Rev

243

237

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SUMMARY The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades ( viz ., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia ) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria . The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria -specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria .

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“…Profiles reported by Dewhirst et al (2001) were 2012033705 for O. uli and 4516053705 for O. profusa . ‡ Data from Göker et al (2010). § Data from Dewhirst et al (2001). …”

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confidence: 99%

Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces

Jensen

Højberg

et al. 2015

International Journal of Systematic and Evolutionary Microbiology

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Strain SK9K4T , which is a strictly anaerobic, non-motile, non-sporulating, Gram-stain-positive, saccharolytic coccobacillus, was isolated from pig faeces. SK9K4T metabolized indol-3-acetic acid to 3-methylindole (skatole), which is the main contributor to boar taint; it also produced 4-methylphenol (p-cresol) from p-hydroxyphenylacetic acid. umbonata were 28.3 %, 69.1 % and 27.2 %, respectively. The genomic DNA G+C content was 62.1 mol% and the major cellular fatty acids (constituting .10 % of the total) were C 14 : 0 and C 18 : 1 v9c. The major end product of glucose fermentation was lactic acid, with minor amounts of acetic acid and formic acid; no H 2 was produced. Discrepancies in the fatty acid profiles, the MALDI-TOF mass spectra of cell extracts and the physiological and biochemical characteristics differentiated strain SK9K4 T from other species of the genus Olsenella and indicate that the isolate represents a novel species within this genus. The name Olsenella scatoligenes sp. nov., is proposed and the type strain is SK9K4 T (5JCM 19907 T 5DSM 28304 T ).

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Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)

Cited by 43 publications

References 33 publications

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria

Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces

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