Biology subjects

Parras-Molto, M.

Publications and source records attributed to Parras-Molto, M..

3 recordsLinked to original sources

bioRxiv2020

Detection of phylogenetic core groups in diverse microbial ecosystems

The detection and subsequent analysis of phylogenetic core groups (PCGs) in a microbial ecosystem has been recently proposed as a potentially important analytical framework with which to increase our understanding of its structure and function. However, it was still unclear whether PCGs represented an infrequent phenomenon in nature. Here we provide evidence of PCGs in a large and diverse array of environments, which seems to indicate that their existence is indeed a predominant feature of microbial ecosystems. Moreover, we offer dedicated scripts to examine the presence and characteristics of PCGs in other microbial community datasets.

microbiology↗

bioRxiv2019

A comprehensive human minimal gut metagenome extends the host’s metabolic potential

Accumulating evidence suggests that humans should be considered as holobionts in which the gut microbiota plays essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis, and present in all healthy individuals. Despite its interest, this concept has received little attention following its initial description in terms of various ubiquitous pathways in Western cohorts. This study analyzes the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3,412 gene clusters, mapping to 1,856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.

microbiology↗

bioRxiv2019

Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy

In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxa and taxonomic rank. Subsequently, we employ the same data to delimit the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. IMPORTANCEWhile bacterial taxonomy and phylogeny resources as well as related bioinformatic tools continue to improve, the question remains as to how they should best be employed in studies using 16S rRNA gene surveys to assess bacteria-ecosystem relationships, a widespread approach. The results contained herein lead to the recommendation that all ranks from genus to class/phylum be employed if using taxonomic binning in the analysis of 16S rRNA gene surveys. With regards to the use of phylogeny or clustering-based approaches, single or arbitrary tree topology or sequence distance thresholds should not be employed. Instead, the results presented here can be used to obtain more meaningful results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data.

microbiology↗