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Review
. 2024 Sep;10(5):e70002.
doi: 10.1002/2056-4538.70002.

Challenges for pathologists in implementing clinical microbiome diagnostic testing

Yulia Gerasimova  1 , Haroon Ali  2 , Urooba Nadeem  3
Affiliations
Review

Challenges for pathologists in implementing clinical microbiome diagnostic testing

Yulia Gerasimova et al. J Pathol Clin Res. 2024 Sep.

Abstract

Recent research has established that the microbiome plays potential roles in the pathogenesis of numerous chronic diseases, including carcinomas. This discovery has led to significant interest in clinical microbiome testing among physicians, translational investigators, and the lay public. As novel, inexpensive methodologies to interrogate the microbiota become available, research labs and commercial vendors have offered microbial assays. However, these tests still have not infiltrated the clinical laboratory space. Here, we provide an overview of the challenges of implementing microbiome testing in clinical pathology. We discuss challenges associated with preanalytical and analytic sample handling and collection that can influence results, choosing the appropriate testing methodology for the clinical context, establishing reference ranges, interpreting the data generated by testing and its value in making patient care decisions, regulation, and cost considerations of testing. Additionally, we suggest potential solutions for these problems to expedite the establishment of microbiome testing in the clinical laboratory.

Keywords: microbiome; microbiome testing; pathologist; pathologist and microbiome.

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Figures

Figure 1
Figure 1
Challenges of implementing microbiome testing in clinical pathology laboratories and proposed solutions. Created with BioRender.com.
Figure 2
Figure 2
Currently available methods for studying microbiome‐host interactions in the context of health and disease states. Created with BioRender.com.
See this image and copyright information in PMC

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References

    1. Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet 2018; 20: 341–355. - PMC - PubMed
    1. Gilbert JA, Blaser MJ, Caporaso JG, et al. Current understanding of the human microbiome. Nat Med 2018; 24: 392–400. - PMC - PubMed
    1. Integrative HMP (iHMP) Research Network Consortium . The integrative human microbiome project: dynamic analysis of microbiome‐host omics profiles during periods of human health and disease. Cell Host Microbe 2014; 16: 276–289. - PMC - PubMed
    1. Manor O, Levy R, Borenstein E. Mapping the inner workings of the microbiome: genomic‐ and metagenomic‐based study of metabolism and metabolic interactions in the human microbiome. Cell Metab 2014; 20: 742–752. - PMC - PubMed
    1. Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012; 489: 242–249. - PubMed

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