Biology subjects

Pardo-De la Hoz, C. J.

Publications and source records attributed to Pardo-De la Hoz, C. J..

3 recordsLinked to original sources

bioRxiv2026

Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection

The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides--a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis. Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patients microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.

microbiology↗

bioRxiv2021

A new approach to integrate phylogenetic structure and partner availability to study biotic specialization in ecological networks

Biotic specialization holds information about the assembly, evolution and stability of biological communities. Phylogenetic diversity metrics have been used to quantify biotic specialization, but their current implementations do not adequately account for the availability of the interacting partners. Also, the overdispersed pattern of phylogenetic specialization has been misinterpreted as an attribute of generalists. We developed an approach that resolves these issues by accounting for partner availability to quantify the phylogenetic structure of specialization (i.e., clustered, overdispersed, or random) in ecological networks. We showed that our approach avoids biases of previous methods. We also implemented it on empirical networks of host-parasite, avian seed-dispersal, lichenized fungi- cyanobacteria and coral-dinoflagellate interactions. We found a large proportion of taxa that interact with phylogenetically random partners, in some cases to a larger extent than detected with an existing method that does not account for partner availability. We also found many taxa that interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much-needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity.

ecology↗

bioRxiv2020

Geographic drivers of diversification in loliginid squids with an emphasis on the western Atlantic species

AimIdentifying the mechanisms driving divergence in marine organisms is challenging as opportunities for allopatric isolation are less conspicuous than in terrestrial ecosystems. Here, we aim to estimate a dated phylogeny of the squid family Loliginidae, and perform ecological niche analyses to explore biogeographic and evolutionary patterns giving rise to extant lineages in this group, with particular focus on cryptic species with population structure along the western Atlantic coast. LocationWorld-wide. TaxonClass Cephalopoda, Family Loliginidae MethodsWe used three loci to infer gene trees and perform species delimitation analysis to detect putative cryptic speciation events. We then estimated a dated species tree under the Bayesian multispecies coalescent and used it to reconstruct ancestral distributions based on the currently known ranges of the species. Also, we tested the hypothesis of niche divergence in three recently diverged species subpopulations of the northwestern and southwestern Atlantic Ocean by ecological niche modeling and niche overlap measurement from occurrence data. ResultsThe phylogenetic analyses confirmed the monophyly for the current twenty-six species of the Loliginidae family. Our ancestral area reconstruction and divergence estimation revealed the origin and geographical dispersal of loliginid lineages. Additionally, the phylogenetic analysis and the species delimitation analysis supported geographic structure within D. pleii, D. pealeii and L. brevis. The ecological niche models revealed unsuitable habitat in the immediately adjacent area of the Amazonian Orinoco Plume, yet suitable habitat characteristics beyond this area. Main conclusionsOur study allowed us to confirm the monophyly of all currently recognized species within the Loliginidae family and we corroborate the biogeographical origin being the Indo-Pacific region in the Cretaceous. We found a possible new cryptic lineage and show evidence of the Amazon-Orinoco Plume as an ecological barrier, which influenced the diversification of this particular group of marine organisms.

evolutionary biology↗