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  1. Article ; Online: Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly

    Tongyuan Hu / Jianwei Chen / Xiaoqian Lin / Wenxin He / Hewei Liang / Mengmeng Wang / Wenxi Li / Zhinan Wu / Mo Han / Xin Jin / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

    Scientific Reports, Vol 14, Iss 1, Pp 1-

    2024  Volume 9

    Abstract: Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of ... ...

    Abstract Abstract The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572 ; 612
    Language English
    Publishing date 2024-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The genomic landscape of reference genomes of cultivated human gut bacteria

    Xiaoqian Lin / Tongyuan Hu / Jianwei Chen / Hewei Liang / Jianwei Zhou / Zhinan Wu / Chen Ye / Xin Jin / Xun Xu / Wenwei Zhang / Xiaohuan Jing / Tao Yang / Jian Wang / Huanming Yang / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 11

    Abstract: Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, ...

    Abstract Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, including 179 previously unidentified species, and provides information of secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.
    Keywords Science ; Q
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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  3. Article ; Online: A catalog of bacterial reference genomes from cultivated human oral bacteria

    Wenxi Li / Hewei Liang / Xiaoqian Lin / Tongyuan Hu / Zhinan Wu / Wenxin He / Mengmeng Wang / Jiahao Zhang / Zhuye Jie / Xin Jin / Xun Xu / Jian Wang / Huanming Yang / Wenwei Zhang / Karsten Kristiansen / Liang Xiao / Yuanqiang Zou

    npj Biofilms and Microbiomes, Vol 9, Iss 1, Pp 1-

    2023  Volume 13

    Abstract: Abstract The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality ... ...

    Abstract Abstract The oral cavity harbors highly diverse communities of microorganisms. However, the number of isolated species and high-quality genomes is limited. Here we present a Cultivated Oral Bacteria Genome Reference (COGR), comprising 1089 high-quality genomes based on large-scale aerobic and anaerobic cultivation of human oral bacteria isolated from dental plaques, tongue, and saliva. COGR covers five phyla and contains 195 species-level clusters of which 95 include 315 genomes representing species with no taxonomic annotation. The oral microbiota differs markedly between individuals, with 111 clusters being person-specific. Genes encoding CAZymes are abundant in the genomes of COGR. Members of the Streptococcus genus make up the largest proportion of COGR and many of these harbor entire pathways for quorum sensing important for biofilm formation. Several clusters containing unknown bacteria are enriched in individuals with rheumatoid arthritis, emphasizing the importance of culture-based isolation for characterizing and exploiting oral bacteria.
    Keywords Microbial ecology ; QR100-130
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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    Inter-library loan at ZB MED

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