Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide

Frontiers in Microbiology

Microbiology

Katy Juarez¹  Alejandro Sanchez-Flores¹  Fernando García-Guevara¹  Alejandra Escobar-Zepeda¹  Liliana Pardo-Lopez¹  Antonio Loza¹  Lorenzo Segovia¹  Maria del Carmen Sanchez-Olmos¹  Enrique Merino¹  Rosa-Maria Gutierrez-Rios² 

[1] Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico;null;

关键词: Gulf of Mexico;    reference metagenomes;    metabolic potential;    metabolic network;    key enzymes;    hydrocarbon degradation;   

DOI  :  10.3389/fmicb.2021.781497

 received in 2021-09-22, accepted in 2021-12-23,  发布年份 2022

来源: Frontiers

【 摘 要 】

Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site.

【 授权许可】

Unknown   
Copyright © 2022 Loza, García-Guevara, Segovia, Escobar-Zepeda, Sanchez-Olmos, Merino, Sanchez-Flores, Pardo-Lopez, Juarez and Gutierrez-Rios.