Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight
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Published:2023-07-28
Issue:8
Volume:11
Page:2134
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ISSN:2227-9059
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Container-title:Biomedicines
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language:en
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Short-container-title:Biomedicines
Author:
López-García Elio1ORCID, Benítez-Cabello Antonio1ORCID, Arenas-de Larriva Antonio Pablo2, Gutierrez-Mariscal Francisco Miguel23ORCID, Pérez-Martínez Pablo23ORCID, Yubero-Serrano Elena María23ORCID, Arroyo-López Francisco Noé1ORCID, Garrido-Fernández Antonio1ORCID
Affiliation:
1. Food Biotechnology Department, Instituto de la Grasa (CSIC), Carretera Utrera km 1, Campus Universitario Pablo de Olavide, Building 46, 41013 Seville, Spain 2. Unidad de Gestión Clínica Medicina Interna, Lipids and Atherosclerosis Unit, Maimonides Institute for Biomedical Research in Córdoba, Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain 3. CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, 28029 Madrid, Spain
Abstract
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.
Funder
TOBE project Spanish Ministry of Science and Innovation for its FPI contract Junta de Andalucía for its contract Nicolas Monardes Programme from the ‘Servicio Andaluz de Salud, Junta de Andalucia’, Spain
Subject
General Biochemistry, Genetics and Molecular Biology,Medicine (miscellaneous)
Reference42 articles.
1. Introduction to the human gut microbiota;Thursby;Biochem. J.,2017 2. Pawlowsky-Glahn, V., and Egozcue, J.J. (July, January 30). Compositional analysis of microbiome data. Proceedings of the Conference: B-Debates on the Human Microbiome, Barcelona, Spain. 3. How should we measure proportionality on relative gene expression data?;Erb;Theory Biosci.,2016 4. It’s all relative: Analyzing microbiome data as compositions;Gloor;Ann. Epidemiol.,2016 5. Microbiome datasets are compositional: And this is not optional;Gloor;Front. Microbiol.,2017
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