Ultrafast clustering algorithms for metagenomic sequence analysis

Li, Weizhong; Fu, Li‐Chen; Niu, Beifang; Wu, Sitao; Wooley, John

doi:10.1093/bib/bbs035

Cited by 428 publications

(276 citation statements)

References 81 publications

(106 reference statements)

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“…Sequencing data were denoised, low quality sequences were removed and the sequences were clustered into operational taxonomic units (OTUs) at 97% identity using the CD-HIT-OTU pipeline (12). Subsequently, taxonomy classification was analyzed using the Quantitative Insights into Microbial Ecology pipeline, as previously reported (13).…”

Section: Introductionmentioning

confidence: 99%

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study

et al. 2017

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Abstract. In a previous study, the present research group reported that males had a significantly higher prevalence of human papillomavirus (HPV)16 than females in oral rinse samples. The objective of the present study was to examine the relationship between HPV16 viral load and clinical factors, including remaining teeth, denture use and numbers of oral bacteria. A total of 124 patients (48 males and 76 females; mean age, 61.6 years; age range, 20-97 years) who visited the Department of Oral and Maxillofacial Reconstructive Surgery of Hiroshima University Hospital (Hiroshima, Japan) between November 2016 and August 2017 were analyzed. None of the patients had evidence of oral cancer or pre-malignant lesions, including epithelial dysplasia and leukoplakia. Quantitative polymerase chain reaction (qPCR) analysis was employed to examine the number of HPV16 viral copies. Furthermore, the number of oral bacteria was determined using the dielectrophoretic impedance measurement method. HPV16 was below the limit of detection in qPCR findings for samples obtained from 30 of the 124 subjects, thus the association of HPV16 viral copy number with clinical parameters was examined in the remaining 94 patients. The average number of HPV16 E6 DNA copies was 1.65±3.47 copies/cell (range, 0.07-25.3 copies/cell) and was significantly higher in subjects with a high oral bacteria count [≥10 6.5 colony forming unit (CFU)/ml] than in those with a low count (<10 6.5 CFU/ml) (0.79±0.98 vs. 2.06±4.11 copies/cell; P=0.030). The present results indicated that HPV16 viral load may be related to an increased bacterial number in the oral cavity. Further investigations are required to clarify the correlation between oral HPV load and oral hygiene status. IntroductionHuman papillomavirus (HPV) infection is a major cause of cervical cancer and is also associated with the development of oropharyngeal cancer and prognosis in affected patients (1-3). To date, >170 HPV genotypes have been reported, of which ~50 are known to infect the anogenital and oral mucosa regions (4-6). As for oral cancer, a previous study conducted by the present research group indicated that ~80% of patients with HPV16-positive moderate epithelial dysplasia progressed to oral squamous cell carcinoma (OSCC), indicating that oral HPV16 infection may also be associated with the development of oral cancer (7). However, few epidemiologic studies have focused on oral HPV prevalence in non-OSCC cases and the risk factors for oral HPV infection have not been fully elucidated. Hence, we previously performed a meta-analysis, which demonstrated that sexual behavior and smoking are significant risk factors for oral HPV infection in cancer-free individuals (8). In addition, other factors, such as poor oral hygiene related to periodontitis and gingivitis, have been indicated to be associated with oral HPV infection (8).In order to examine the correlation between HPV16 prevalence in the oral cavity and clinical factors, we also investigated HPV16 prevalence using oral rinse samples obtaine...

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Section: Introductionmentioning

confidence: 99%

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study

et al. 2017

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“…The filtered reads were denoised and clustered at 100% identity using the CD-HIT-OTU clustering program [20] . The remaining representative reads after removing the identified chimeric reads were clustered into operational taxonomic units (OTUs) using a greedy algorithm with a cutoff of >97% identity at the species level.…”

Section: Sequence Process and Analysismentioning

confidence: 99%

Köpek ve Kedi Diş Taşı Mikrobiyomunun İleri Jenerasyon Sekanslama Kullanarak Araştırılması

Radeerom¹,

Thongkorn²,

Buddhachat³

et al. 2018

Kafkas Univ Vet Fak Derg

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“…PANDA (Masella et al, 2012), which allows zero mismatches in the overlapping region, served to pair raw Illumina reads; thereafter, we removed any chimeric reads and assigned operational taxonomic units (OTUs) by pairwise similarity at a threshold of 97% using cd-hit-otu (Li et al, 2012). We used SINA 1.2 (Pruesse et al, 2012) against the SILVA database (v. 115) to classify unique OTUs and estimated the abundance of each OTU using in-house Python script.…”

Section: Dna Extraction Sequencing and Classification Of Otusmentioning

confidence: 99%

Autochthonous Dissolved Organic Matter Drives Bacterial Community Composition during a Bloom of Filamentous Cyanobacteria

et al. 2016

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The dynamics of dissolved organic matter (DOM) and the succession of bacterial community composition (BCC) were investigated during bloom of filamentous cyanobacteria in a mesocosm experiment conducted in the western Gulf of Finland, the Baltic Sea. The effects of labile dissolved organic carbon (glucose), inorganic nutrients (N and P) and large zooplankton (> 100 µm) on the DOM pool, bacterial production and the composition of bacterial communities were analyzed over a period of 10 days. In addition, the bioavailability of dissolved organic carbon (DOC) and its turnover by heterotrophic bacteria (biomass and respiration) were investigated in three 1-week bacterial bioassays. Heterotrophic bacteria rapidly utilized about 25-55% of the DOC released from the plankton community, thus assuming it to be highly labile DOC. More than half of the accumulating net DOC pool was degraded over 7 days, thus assuming it to be labile. In average, labile autochthonous DOC was degraded with bacterial growth efficiency of 25%. A distinct succession of bacterial communities accompanied the supply of autochthonous DOM, with the most prominent responses occurring in a few single phylotypes of the Delta-and Gammaproteobacterial classes. About 40% of the variation in the relative shares of dominant bacterial classes could be explained by changes in the functional groups of autotrophs. Inorganic nutrient treatment proved beneficial to Deltaproteobacteria and increased bacterial production over that of other mesocosms.

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Ultrafast clustering algorithms for metagenomic sequence analysis

Cited by 428 publications

References 81 publications

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study

Köpek ve Kedi Diş Taşı Mikrobiyomunun İleri Jenerasyon Sekanslama Kullanarak Araştırılması

Autochthonous Dissolved Organic Matter Drives Bacterial Community Composition during a Bloom of Filamentous Cyanobacteria

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