Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.
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ABSTRACT:
SUBMITTER: Usyk M
PROVIDER: S-EPMC9939430 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
Publications
Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.
Usyk Mykhaylo M Peters Brandilyn A BA Karthikeyan Smruthi S McDonald Daniel D Sollecito Christopher C CC Vazquez-Baeza Yoshiki Y Shaffer Justin P JP Gellman Marc D MD Talavera Gregory A GA Daviglus Martha L ML Thyagarajan Bharat B Knight Rob R Qi Qibin Q Kaplan Robert R Burk Robert D RD
Cell reports methods 20230123 1
In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. ...[more]
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