Ten common issues with reference sequence databases and how to mitigate them

Chorlton, Samuel D.

doi:10.3389/fbinf.2024.1278228

Cited by 9 publications

(1 citation statement)

References 105 publications

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“…Additionally, the accuracy of the bioinformatics tools and databases used can impact the final species identification ( 16 ). (iv) Incompleteness of databases and reference sequences: many microbes have not yet been cultured and sequenced, meaning that even with full-length 16S rRNA sequencing, it might not be possible to accurately identify all species ( 45 ). (v) Ecological and evolutionary factors: gene horizontal transfer and recombination events among microbial species can cause differences in the 16S rRNA gene sequence, which may mislead species identification and analysis ( 46 ).…”

Section: Discussionmentioning

confidence: 99%

Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling

Zhang,

Wang,

Chen

et al. 2024

mSystems

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The skin microbiome plays a pivotal role in human health by providing protective and functional benefits. Furthermore, its inherent stability and individual specificity present novel forensic applications. These aspects have sparked considerable research enthusiasm among scholars across various fields. However, the selection of specific 16S rRNA hypervariable regions for skin microbiome studies is not standardized and should be validated through extensive research tailored to different research objectives and targeted bacterial taxa. Notably, third-generation sequencing (TGS) technology leverages the full discriminatory power of the 16S gene and enables more detailed and accurate microbial community analyses. Here, we conducted full-length 16S sequencing of 141 skin microbiota samples from multiple human anatomical sites using the PacBio platform. Based on this data, we generated derived 16S sub-region data through an in silico experiment. Comparisons between the 16S full-length and the derived variable region data revealed that the former can provide superior taxonomic resolution. However, even with full 16S gene sequencing, limitations arise in achieving 100% taxonomic resolution at the species level for skin samples. Additionally, the capability to resolve high-abundance bacteria (TOP30) at the genus level remains generally consistent across different 16S variable regions. Furthermore, the V1-V3 region offers a resolution comparable with that of full-length 16S sequences, in comparison to other hypervariable regions studied. In summary, while acknowledging the benefits of full-length 16S gene analysis, we propose the targeting of specific sub-regions as a practical choice for skin microbial research, especially when balancing the accuracy of taxonomic classification with limited sequencing resources, such as the availability of only short-read sequencing or insufficient DNA. IMPORTANCE Skin acts as the primary barrier to human health. Considering the different microenvironments, microbial research should be conducted separately for different skin regions. Third-generation sequencing (TGS) technology can make full use of the discriminatory power of the full-length 16S gene. However, 16S sub-regions are widely used, particularly when faced with limited sequencing resources including the availability of only short-read sequencing and insufficient DNA. Comparing the 16S full-length and the derived variable region data from five different human skin sites, we confirmed the superiority of the V1-V3 region in skin microbiota analysis. We propose the targeting of specific sub-regions as a practical choice for microbial research.

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Section: Discussionmentioning

confidence: 99%