Biology subjects

Parras-Molto, M.

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

5 recordsLinked to original sources

bioRxiv2024

The transfer of antibiotic resistance genes between evolutionary distant bacteria

Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionary distant bacteria, here defined based on their phylum. We implemented an algorithm that identified inter-phyla transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million resistance genes identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3) while the levels for beta-lactamases were, generally, lower. ARGs involved in IPTs also differed between phyla where, for example, tetracycline resistance genes were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or under-represented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline resistance genes involved in ITPs almost always were +95% identical between phyla, corresponding {beta}-lactamases showed a median identity of < 60%. We conclude that inter-phyla transfer is recurrent and our results offer new insights into how resistance genes are disseminated between evolutionary distant bacteria.

microbiology↗

bioRxiv2024

Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes

The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aimed to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. From the analysis of [~]1 million bacterial genomes and >20,000 metagenomes, we developed random forest models that could reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increased the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns were observed. This study provides new ways to predict the spread of ARGs and provides new insights into the mechanisms governing this evolutionary process.

microbiology↗

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↗