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Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight

This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSe...

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Autores principales: López-García, Elio, Benítez-Cabello, Antonio, Arenas-de Larriva, Antonio Pablo, Gutierrez-Mariscal, Francisco Miguel, Pérez-Martínez, Pablo, Yubero-Serrano, Elena María, Arroyo-López, Francisco Noé, Garrido-Fernández, Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10452682/
https://www.ncbi.nlm.nih.gov/pubmed/37626632
http://dx.doi.org/10.3390/biomedicines11082134
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author López-García, Elio
Benítez-Cabello, Antonio
Arenas-de Larriva, Antonio Pablo
Gutierrez-Mariscal, Francisco Miguel
Pérez-Martínez, Pablo
Yubero-Serrano, Elena María
Arroyo-López, Francisco Noé
Garrido-Fernández, Antonio
author_facet López-García, Elio
Benítez-Cabello, Antonio
Arenas-de Larriva, Antonio Pablo
Gutierrez-Mariscal, Francisco Miguel
Pérez-Martínez, Pablo
Yubero-Serrano, Elena María
Arroyo-López, Francisco Noé
Garrido-Fernández, Antonio
author_sort López-García, Elio
collection PubMed
description This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer’s sex (male or female), age (19–46 years), and weight (48.6–99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers’ age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota.
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spelling pubmed-104526822023-08-26 Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight López-García, Elio Benítez-Cabello, Antonio Arenas-de Larriva, Antonio Pablo Gutierrez-Mariscal, Francisco Miguel Pérez-Martínez, Pablo Yubero-Serrano, Elena María Arroyo-López, Francisco Noé Garrido-Fernández, Antonio Biomedicines Article This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer’s sex (male or female), age (19–46 years), and weight (48.6–99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers’ age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota. MDPI 2023-07-28 /pmc/articles/PMC10452682/ /pubmed/37626632 http://dx.doi.org/10.3390/biomedicines11082134 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 Article
López-García, Elio
Benítez-Cabello, Antonio
Arenas-de Larriva, Antonio Pablo
Gutierrez-Mariscal, Francisco Miguel
Pérez-Martínez, Pablo
Yubero-Serrano, Elena María
Arroyo-López, Francisco Noé
Garrido-Fernández, Antonio
Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title_full Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title_fullStr Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title_full_unstemmed Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title_short Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
title_sort application of compositional data analysis to study the relationship between bacterial diversity in human faeces and sex, age, and weight
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10452682/
https://www.ncbi.nlm.nih.gov/pubmed/37626632
http://dx.doi.org/10.3390/biomedicines11082134
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