Usearch: A Meta Search Engine based on a New Result Merging Strategy

Alloui, Tarek; Boussebough, Imane; Chaoui, Allaoua; Nouar, Ahmed Zakaria; Chettah, Mohamed Chaouki

doi:10.5220/0005642905310536

Cited by 22 publications

(15 citation statements)

References 3 publications

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“…The main software used for sequence analysis were Vsearch v2.8.1 ( 21 ) and Usearch v10 (bit 32) ( 22 ). The original data were merged by double-ended sequences by Vsearch, followed by data quality control, excision of primers and barcode, and the 164,772 sequence was removed, leaving 20,594,067 sequences.…”

Section: Methodsmentioning

confidence: 99%

Bacterial Alterations in Post-Cholecystectomy Patients Are Associated With Colorectal Cancer

Ren

Zhang

et al. 2020

Front. Oncol.

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Background: Although increasing evidences showed a correlation between cholecystectomy and the prevalence rate of colorectal cancer (CRC), and shed light on gut microbiota in colorectal pathogenesis, only a few studies focused on microbial alterations after cholecystectomy, and its sequent role in carcinogenesis and progression of CRC has not been reported. Thus, we aimed to investigate the bacterial alterations and tried to clarify their clinical significance. Methods: 104 subjects were enrolled and divided into post-cholecystectomy patients (PC, n = 52) and healthy controls (HC, n = 52). To investigate the bacterial role in carcinogenesis, PC patients were further separated into preCA_CRC (patients with precancerous lesions and/or CRC, n = 9) and non-CA (patients without precancerous lesions and CRC, n = 43) based on the histopathology. Qualified stool samples were collected for 16S rRNA gene sequencing to analyze the bacterial profile. Results: Our data showed noteworthy compositional and abundant alterations of bacterial microbiota in PC patients, characterized as Bacteroides ovatus, Prevotella copri , and Fusobacterium varium remarkably increased; Faecalibacterium prausnitzii, Roseburia faecis , and Bifidobacterium adolescentis significantly decreased. Additionally, the duration after cholecystectomy was the critical factor that affected bacterial composition. Machine learning-based analysis showed a pivotal role of Megamonas funiformis in discriminating PC from HC subjects and involving in the progression of CRC. Conclusions: The bacterial dysbiosis may associate with CRC in PC patients, and the duration after cholecystectomy was highlighted as an important factor. Altered bacterial microbiota was likely to play a pivotal role in related-disease in the long-term follow-up of PC patients.

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Section: Methodsmentioning

confidence: 99%

Bacterial Alterations in Post-Cholecystectomy Patients Are Associated With Colorectal Cancer

Ren

Zhang

et al. 2020

Front. Oncol.

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“…Clean tags were searched against the reference database ( http://drive5.com/uchime/uchime_download.html ) to perform reference-based chimera checking using the UCHIME algorithm (Edgar et al 2011 ). This analysis was performed on USEARCH ( http://www.drive5.com/usearch/manual/uchime_algo.html ) (Alloui et al 2015 ). All chimeric tags were removed and effective tags were obtained for further analysis (Haas et al 2011 ).…”

Section: Methodsmentioning

confidence: 99%

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

et al. 2020

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Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.

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“…Raw Data were trimmed using Trimmomatic (version 0.36) 42 with default parameters. Then the clean paired-end reads were assembled into raw tags using Usearch (version 9.2.64) 43 . The primer sequences in the raw tags were trimmed, and effective tags were obtained.…”

Section: Methodsmentioning

confidence: 99%

Dominant egg surface bacteria of Holotrichia oblita (Coleoptera: Scarabaeidae) inhibit the multiplication of Bacillus thuringiensis and Beauveria bassiana

Wang

Liu

et al. 2021

Sci Rep

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Holotrichia oblita (Coleoptera: Scarabaeidae) and some other scarab beetles are the main soil-dwelling pests in China. Bacillus thuringiensis (Bt) and Beauveria bassiana (Bb) are entomopathogens that have been used as biocontrol agents of various pests. However, scarab larvae especially H. oblita exhibited strong adaptability to these pathogens. Compared to other scarabs, H. oblita could form a specific soil egg case (SEC) structure surrounding its eggs, and young larvae complete the initial development process inside this structure. In this study, we investigated the role of SEC structure and microorganisms from SEC and egg surface in pathogen adaptability. 16S rRNA gene analysis revealed low bacterial richness and high community unevenness in egg surface, with Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria dominating. In terms of OTUs composition analysis, the data show that the egg surface contains a large number of unique bacteria, indicating that the egg bacterial community may be derived from maternal transmission. Furthermore, we found that all culturable bacteria isolated from egg surface possessed antimicrobial activity against both Bt and Bb. The Pseudomonas bacteria with a significantly higher abundance in egg surface showed strong Bt- and Bb antagonistic ability. In conclusion, this study demonstrated a unique and antimicrobial bacterial community of H. oblita egg surface, which may contribute to its adaptability. Furthermore, the specific SEC structure surrounding the H. oblita eggs will provide a stable microenvironment for the eggs and egg surface bacteria, which probably provides more advantages for H. oblita adaptation ability.

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Usearch: A Meta Search Engine based on a New Result Merging Strategy

Cited by 22 publications

References 3 publications

Bacterial Alterations in Post-Cholecystectomy Patients Are Associated With Colorectal Cancer

Bacterial Alterations in Post-Cholecystectomy Patients Are Associated With Colorectal Cancer

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

Dominant egg surface bacteria of Holotrichia oblita (Coleoptera: Scarabaeidae) inhibit the multiplication of Bacillus thuringiensis and Beauveria bassiana

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