Publications by authors named "Yong-Wei Yan"

Background: Amplification of small subunit (SSU) rRNA genes with universal primers is a common method used to assess microbial populations in various environmental samples. However, owing to limitations in coverage of these universal primers, some microorganisms remain unidentified. The present study aimed to establish a method for amplifying nearly full-length SSU rRNA gene sequences of previously unidentified prokaryotes, using newly designed targeted primers via primer evaluation in meta-transcriptomic datasets.

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is commercially the most important edible red alga in China, and red rot disease is viewed as one of the major constraints for its cultivation. Microbes within the oomycetic genus have been reported as the causative agents for this disease; however, little is known about the interactions between the disease and the epiphytic and planktonic bacterial communities. In the present study, bacterial communities associated with uninfected, locally infected, and seriously infected thalli collected from cultivation farms, and within seawater adjacent to the thalli, were investigated using in-depth 16S ribosomal RNA (rRNA) gene sequencing in conjunction with assessing multiple environmental factors.

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Here, we report the draft whole-genome sequence of a bacterial strain, sp. strain BS1, isolated from black soil during ethane oxidation culture. Medium- or long-chain alkane oxidation-related genes were identified; however, the short-chain alkane monooxygenase was not detected.

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We propose a modified RNA-Seq method for small subunit ribosomal RNA (SSU rRNA)-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step. Using this method, we could obtain more 16S rRNA sequences of the same regions (variable regions V1-V2) without the interference of DNA in order to analyze OTU (operational taxonomic unit)-based microbial communities and diversity.

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Intertidal mudflats are land-sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected.

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RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription.

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