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Microbiome Evaluation

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Basic Protocols in Foods and Nutrition

Part of the book series: Methods and Protocols in Food Science ((MPFS))

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Abstract

Various studies suggest that the intestinal microbiome may modulate the risk of developing different chronic diseases, including type 2 diabetes, allergy, cardiovascular disease, and colorectal cancer (CRC). Next-generation sequencing techniques have allowed a better understanding of the metabolic, physiological, and ecological roles of the microbiome. However, different conditions can affect the microbiome analysis, including experimental model, sample processing, sequencing, assembly, binning, annotation, and visualization. Besides, in order to translate microbiome research into clinical application, it is necessary to address host–microbe and microbe–microbe interactions. In this sense, animal models in association with “omics” approaches are indispensable for investigating host–microbiome interactions. Therefore, this chapter reviews the optimal approach to study the gut microbiome in experimental models highlighting their benefits, drawbacks, and limitations, as well as it provides an efficient protocol to determine the gut microbial community diversity and composition from animal stool samples.

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Acknowledgments

This work received financial support from Junta de Andalucía (CTS 164), and by Instituto de Salud Carlos III (PI19/1058) with funds from the European Union. CIBER-EHD is funded by Instituto de Salud Carlos III. A. Rodriguez-Nogales is a postdoctoral fellow of Instituto de Salud Carlos III (Miguel Servet Program); A.J. Ruiz-Malagon is a predoctoral fellow from University of Granada (Programa de Doctorado: Medicina Clínica y Salud Pública); J.A Molina-Tijeras is a predoctoral fellow from Instituto de Salud Carlos III (PFIS program) (Programa de Doctorado: Nutrición y Ciencias de los Alimentos).

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Authors and Affiliations

  1. CIBER-EHD, Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, Granada, Spain

    Alba Rodríguez-Nogales, Antonio Jesús Ruiz-Malagón, Jose Alberto Molina-Tijeras, Maria Elena Rodríguez-Cabezas & Julio Gálvez

  2. Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain

    Alba Rodríguez-Nogales, Antonio Jesús Ruiz-Malagón, Jose Alberto Molina-Tijeras, Maria Elena Rodríguez-Cabezas & Julio Gálvez

  3. Servicio de Digestivo, Hospital Universitario Virgen de las Nieves, Granada, Spain

    Alba Rodríguez-Nogales

Authors
  1. Alba Rodríguez-Nogales
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  2. Antonio Jesús Ruiz-Malagón
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  3. Jose Alberto Molina-Tijeras
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  4. Maria Elena Rodríguez-Cabezas
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  5. Julio Gálvez
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Corresponding author

Correspondence to Julio Gálvez .

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Editors and Affiliations

  1. Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil

    Cinthia Baú Betim Cazarin

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Rodríguez-Nogales, A., Ruiz-Malagón, A.J., Molina-Tijeras, J.A., Rodríguez-Cabezas, M.E., Gálvez, J. (2022). Microbiome Evaluation. In: Betim Cazarin, C.B. (eds) Basic Protocols in Foods and Nutrition. Methods and Protocols in Food Science . Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2345-9_11

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  • DOI: https://doi.org/10.1007/978-1-0716-2345-9_11

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2344-2

  • Online ISBN: 978-1-0716-2345-9

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