CaltechAUTHORS
Published January 23, 2023 | Version Published
Journal Article Open

Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies

Creators

  • 1. ROR icon Albert Einstein College of Medicine
  • 2. ROR icon New York University
  • 3. ROR icon University of California, San Diego
  • 4. ROR icon University of Miami
  • 5. ROR icon San Diego State University
  • 6. ROR icon University of Illinois at Chicago
  • 7. ROR icon University of Minnesota Medical Center
  • 8. ROR icon Fred Hutchinson Cancer Research Center

Abstract

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. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.

Additional Information

Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). The authors gratefully acknowledge the participants of the SOL cohort that chose to provide stool samples that allowed this study to be performed. The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a collaborative study supported by contracts from the National Heart, Lung, and Blood Institute (NHLBI) to the University of North Carolina (HHSN268201300001I/N01-HC-65233), University of Miami (HHSN268201300004I/N01-HC-65234), Albert Einstein College of Medicine (HHSN268201300002I/N01-HC-65235), University of Illinois at Chicago –HHSN268201300003I/N01-HC-65236 Northwestern University), and San Diego State University (HHSN268201300005I/N01-HC-65237). The following institutes/centers/offices have contributed to the HCHS/SOL through a transfer of funds to the NHLBI: National Institute on Minority Health and Health Disparities, National Institute on Deafness and Other Communication Disorders, National Institute of Dental and Craniofacial Research, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, NIH Institution-Office of Dietary Supplements. Additional funding for the "Gut Origins of Latino Diabetes" (GOLD) ancillary study to HCHS/SOL was provided by 1R01MD011389-01 from the National Institute on Minority Health and Health Disparities. In addition, RO1DK126698, P30CA013330, P30AI124414, and U01HL146204 also provided support. None of the funding agencies had a role in the design, conduct, interpretation, or reporting of this study. Author contributions. Conceptualization, M.U. and R.D.B; methodology, M.U., S.K., D.M., Y.V.-B., J.P.S., R.Knight., and R.D.B; software, D.M. and R.Knight; formal analysis, M.U.; resources, C.C.S., M.D.G., G.A.T., M.L.D., B.T., Q.Q., and R.Kaplan.; writing – original draft, M.U. and R.D.B; writing – review & editing, M.U., B.A.P., and R.D.B; supervision, R.D.B. The authors declare no competing interests.

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Additional details

Additional titles

Alternative title
Comprehensive Evaluation of Shotgun Metagenomics and 16S rRNA gene and ITS1 Amplicon Sequencing for Epidemiological Studies Using a Multicenter Large Cohort

Identifiers

PMCID
PMC9939430
Eprint ID
119956
Resolver ID
CaltechAUTHORS:20230313-315432000.1

Funding

NIH
HHSN268201300001I/N01-HC-65233
NIH
HHSN268201300004I/N01-HC-65234
NIH
HHSN268201300002I/N01-HC-65235
NIH
HHSN268201300003I/N01-HC-65236
NIH
HHSN268201300005I/N01-HC-65237
NIH
1R01MD011389-01
NIH
RO1DK126698
NIH
P30CA013330
NIH
P30AI124414
NIH
U01HL146204

Dates

Created
2023-03-14
Created from EPrint's datestamp field
Updated
2023-03-14
Created from EPrint's last_modified field