Cargando…

Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease

The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-res...

Descripción completa

Detalles Bibliográficos
Autores principales: Giuffrè, Mauro, Moretti, Rita, Tiribelli, Claudio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10049444/
https://www.ncbi.nlm.nih.gov/pubmed/36982303
http://dx.doi.org/10.3390/ijms24065229
_version_ 1785014460178497536
author Giuffrè, Mauro
Moretti, Rita
Tiribelli, Claudio
author_facet Giuffrè, Mauro
Moretti, Rita
Tiribelli, Claudio
author_sort Giuffrè, Mauro
collection PubMed
description The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe–disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.
format Online
Article
Text
id pubmed-10049444
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-100494442023-03-29 Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease Giuffrè, Mauro Moretti, Rita Tiribelli, Claudio Int J Mol Sci Opinion The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe–disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention. MDPI 2023-03-09 /pmc/articles/PMC10049444/ /pubmed/36982303 http://dx.doi.org/10.3390/ijms24065229 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Opinion
Giuffrè, Mauro
Moretti, Rita
Tiribelli, Claudio
Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title_full Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title_fullStr Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title_full_unstemmed Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title_short Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease
title_sort gut microbes meet machine learning: the next step towards advancing our understanding of the gut microbiome in health and disease
topic Opinion
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10049444/
https://www.ncbi.nlm.nih.gov/pubmed/36982303
http://dx.doi.org/10.3390/ijms24065229
work_keys_str_mv AT giuffremauro gutmicrobesmeetmachinelearningthenextsteptowardsadvancingourunderstandingofthegutmicrobiomeinhealthanddisease
AT morettirita gutmicrobesmeetmachinelearningthenextsteptowardsadvancingourunderstandingofthegutmicrobiomeinhealthanddisease
AT tiribelliclaudio gutmicrobesmeetmachinelearningthenextsteptowardsadvancingourunderstandingofthegutmicrobiomeinhealthanddisease