RT Journal Article
T1 Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.
A1 Casimiro-Soriguer, Carlos S
A1 Loucera, Carlos
A1 Perez Florido, Javier
A1 López-López, Daniel
A1 Dopazo, Joaquin
K1 Antibiotic resistance
K1 Classification
K1 Functional profiling
K1 Machine learning
K1 Metagenomics
K1 Whole genome sequencing
AB The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles. Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification. We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances. Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.
YR 2019
FD 2019-08-20
LK http://hdl.handle.net/10668/14420
UL http://hdl.handle.net/10668/14420
LA en
DS RISalud
RD Apr 12, 2025