Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]

doi:10.3390/nu15112451

. 2023 May 24;15(11):2451.

doi: 10.3390/nu15112451.

Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]

Riley L Hughes¹, Cara L Frankenfeld², Daryl M Gohl^{3

4}, Curtis Huttenhower^{5

6

7}, Scott A Jackson⁸, Doris Vandeputte⁹, Emily Vogtmann¹⁰, Sarah S Comstock¹¹, Mary E Kable¹²

Affiliations

¹ Independent Researcher, Seattle, WA 98115, USA.
² Public Health Program, University of Puget Sound, Tacoma, WA 98416, USA.
³ University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.
⁴ Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA.
⁵ Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁷ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
⁸ Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
⁹ Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA.
¹⁰ Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
¹¹ Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA.
¹² USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA.

PMID: 37299414
PMCID: PMC10255073
DOI: 10.3390/nu15112451

Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]

Riley L Hughes et al. Nutrients. 2023.

. 2023 May 24;15(11):2451.

doi: 10.3390/nu15112451.

Authors

Riley L Hughes¹, Cara L Frankenfeld², Daryl M Gohl^{3

4}, Curtis Huttenhower^{5

6

7}, Scott A Jackson⁸, Doris Vandeputte⁹, Emily Vogtmann¹⁰, Sarah S Comstock¹¹, Mary E Kable¹²

Affiliations

¹ Independent Researcher, Seattle, WA 98115, USA.
² Public Health Program, University of Puget Sound, Tacoma, WA 98416, USA.
³ University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.
⁴ Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA.
⁵ Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁷ Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
⁸ Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
⁹ Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA.
¹⁰ Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
¹¹ Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA.
¹² USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA.

PMID: 37299414
PMCID: PMC10255073
DOI: 10.3390/nu15112451

Abstract

The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.

Keywords: bioinformatics; methods; microbiota; nutrition; sample collection; sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Diet–Microbiome–Health Interactions. Direct effect arrows are black, indirect effect arrow is red. Diet has direct effects on both health and the gut microbiome. The gut microbiome also has a direct effect on health as a result of changes in the community composition and/or function due to diet. However, the gut microbiome can also modulate (indirect effect) the effects of diet on health independent of diet-related changes in composition or function.

See this image and copyright information in PMC

References

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[1] Thaiss C.A., Elinav E. The remedy within: Will the microbiome fulfill its therapeutic promise? J. Mol. Med. 2017;95:1021–1027. doi: 10.1007/s00109-017-1563-z. - DOI - PubMed

[2] Thaiss C.A., Elinav E. The remedy within: Will the microbiome fulfill its therapeutic promise? J. Mol. Med. 2017;95:1021–1027. doi: 10.1007/s00109-017-1563-z. - DOI - PubMed

[3] Gilbert J.A., Blaser M.J., Caporaso J.G., Jansson J.K., Lynch S.V., Knight R. Current understanding of the human microbiome. Nat. Med. 2018;24:392–400. doi: 10.1038/nm.4517. - DOI - PMC - PubMed

[4] Gilbert J.A., Blaser M.J., Caporaso J.G., Jansson J.K., Lynch S.V., Knight R. Current understanding of the human microbiome. Nat. Med. 2018;24:392–400. doi: 10.1038/nm.4517. - DOI - PMC - PubMed

[5] Yatsunenko T., Rey F.E., Manary M.J., Trehan I., Dominguez-Bello M.G., Contreras M., Magris M., Hidalgo G., Baldassano R.N., Anokhin A.P., et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–227. doi: 10.1038/nature11053. - DOI - PMC - PubMed

[6] Yatsunenko T., Rey F.E., Manary M.J., Trehan I., Dominguez-Bello M.G., Contreras M., Magris M., Hidalgo G., Baldassano R.N., Anokhin A.P., et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–227. doi: 10.1038/nature11053. - DOI - PMC - PubMed

[7] Cho I., Blaser M.J. The human microbiome: At the interface of health and disease. Nat. Rev. Genet. 2012;13:260–270. doi: 10.1038/nrg3182. - DOI - PMC - PubMed

[8] Cho I., Blaser M.J. The human microbiome: At the interface of health and disease. Nat. Rev. Genet. 2012;13:260–270. doi: 10.1038/nrg3182. - DOI - PMC - PubMed

[9] Zeevi D., Korem T., Zmora N., Israeli D., Rothschild D., Weinberger A., Ben-Yacov O., Lador D., Avnit-Sagi T., Lotan-Pompan M. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163:1079–1094. doi: 10.1016/j.cell.2015.11.001. - DOI - PubMed

[10] Zeevi D., Korem T., Zmora N., Israeli D., Rothschild D., Weinberger A., Ben-Yacov O., Lador D., Avnit-Sagi T., Lotan-Pompan M. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163:1079–1094. doi: 10.1016/j.cell.2015.11.001. - DOI - PubMed

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Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]

Affiliations

Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]

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Abstract

Conflict of interest statement

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Abstract

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