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. 2024 Aug 21;90(8):e0103324.
doi: 10.1128/aem.01033-24. Epub 2024 Jul 31.

A host of issues: pseudoreplication in host-microbiota studies

Hannah McKinnon Reish  1 , Lindsey Dewey  1   2 , Lucas J Kirschman  1
Affiliations

A host of issues: pseudoreplication in host-microbiota studies

Hannah McKinnon Reish et al. Appl Environ Microbiol. .

Abstract

Pseudoreplication compromises the validity of research by treating non-independent samples as independent replicates. This review examines the prevalence of pseudoreplication in host-microbiota studies, highlighting the critical need for rigorous experimental design and appropriate statistical analysis. We systematically reviewed 115 manuscripts on host-microbiota interactions. Our analysis revealed that 22% of the papers contained pseudoreplication, primarily due to co-housed organisms, whereas 52% lacked sufficient methodological details. The remaining 26% adequately addressed pseudoreplication through proper experimental design or statistical analysis. The high incidence of pseudoreplication and insufficient information underscores the importance of methodological reporting and statistical rigor to ensure reproducibility of host-microbiota research.

Keywords: experimental unit; host–microbiota; individual replicate; mixed models; pseudoreplication.

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Conflict of interest statement

The authors declare no conflict of interest.

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