Biology subjects

Bustamante, M.

Publications and source records attributed to Bustamante, M..

13 recordsLinked to original sources

bioRxiv2026

Bacterial Mercury Resistance Reveals a Robust Species-Structured Human Antimicrobial Mobilome

Antimicrobial resistance (AMR) is increasingly recognized as an ecological and evolutionary phenomenon that extends beyond clinical environments. Despite the predominant focus on antibiotics, bacterial metal resistance genes are among the oldest and most widespread adaptive antimicrobial systems, yet their distribution within human-associated microbial communities remains poorly characterized. Here, we investigated the ecology of mercury (Hg) resistance in children from a birth cohort with relatively high Hg exposure. Fecal samples from 234 children aged 4-8 years were analyzed using culture-based screening, whole-genome sequencing, and comparative analyses of metal- and antibiotic-resistance determinants and associated mobile genetic elements (MGEs). Hg-resistance was detected in 79.7% of samples, with HgR Enterobacterales isolated from 57% of children. Hair mercury concentrations were not associated with carriage. Sequencing revealed a phylogenetically diverse collection dominated by Escherichia spp. (61%). Hg resistance was mediated by 79 mer operons primarily associated with Tn21, Tn1696, and Tn5053 families circulating on chromosomes and a highly diverse plasmidome. Both rare and globally distributed plasmids related to foodborne, animal, and clinical Enterobacterales were identified. Metal resistance determinants exhibited strong taxonomic structuring, with Escherichia enriched in iron-uptake systems and siderophores whereas non-Escherichia taxa carried multimetal resistance operons. These findings indicate that Hg-resistance is shaped by ecological interactions and MGEs, becoming partially decoupled from contemporary Hg-exposure and bacterial community composition. The human gut therefore serves as an important reservoir linking environmental metal resistance to the broader evolution of AMR and provides insight into the baseline resistome and plasmidome of human populations.

microbiology↗

bioRxiv2026

Nerve Injury-Induced Protein 2 Is Necessary for the Lysosome Membrane Integrity and Protects Cells from Ferroptosis

Nerve injury-induced protein 1 (NINJ1), a cell adhesion molecule, is oligomerized during lytic cell death and mediates plasma membrane rupture to release large intracellular molecules that propagate the inflammatory response. We and others previously showed that NINJ2, a close relative of NINJ1, does not promote plasma membrane rupture to spread inflammation. Here, we identify that NINJ2 is necessary for the lysosome membrane integrity to protect cells from ferroptosis. Specifically, we found that NINJ2 localizes to lysosomes and interacts with LAMP1, an anchor glycoprotein of the lysosome membranes and a sensor of stressed lysosomes. We also found that loss of NINJ2 exacerbates lysosomal membrane permeabilization (LMP), which allows for selective leakage of lysosomal contents, such as labile iron, into the cytosol. Accordingly, loss of NINJ2 elevates cellular labile iron accumulation and decreases expression of ferritins, the primary intracellular iron storage protein complexes. Mechanistically, we found that loss of NINJ2 promotes ferritin FTH degradation in lysosomes, which can be reversed by knockdown of LAMP1. Moreover, we found that loss of NINJ2 sensitizes cells to ferroptosis induced by RSL3 and Erastin, consistent with a recent study that loss of Ninj2 predisposes mice to chronic inflammation. Together, these findings uncover a previously unrecognized activity of NINJ2 from lysosome homeostasis to ferroptosis, which can be explored as a cancer therapeutic strategy especially considering that NINJ2 and ferritins are found to be overexpressed and positively associated with iron-addicted cancers.

cancer biology↗

bioRxiv2026

Maximum entropy networks predict fluctuations and stability of food web energetics

A central goal of ecology is understanding how the architecture of food webs, which represent the structural backbone of ecosystems, affects their stability. The analysis of stability in the classical sense of population dynamics (i.e. return to equilibrium) can be successful for a single instance of an empirical food web but ignores the multiplicity of alternative states in which the system could be found as a result of intrinsic variability and fluctuations. Here we propose and test a new methodology to reconstruct, from single empirical observations of a food web, the viable ensemble of alternative realizations respecting the observed resource-consumer linkages and empirical ener-getics. The reconstruction can be handled analytically within a maximum-entropy framework which predicts how empirical food webs access a multitude of alternative states with comparable stability and reactivity. The (measurable) entropy of the reconstructed ensemble directly quantifies this multiplicity and serves as a novel proxy of system resilience, that is the rate of return to equilibrium in response to an external perturbation. We show that the associated ensemble fluctuations provide explicit predictions for the expected response of food webs to external perturbations, such as anthropogenic or climate-induced stresses. We do that by validating the proposed fluctuation-response relation on empirical soil food webs subjected to experimentally controlled perturbations, confirming that intrinsic fluctuations in the unperturbed state predict responses to subsequent stresses. The perturbed states are associated with higher entropy, indicating less likely spontaneous recovery.

ecology↗

bioRxiv2025

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution

Background and objectivesAntimicrobial resistance is a major global health threat, driven in part by the rapid evolution of resistance in pathogens, which undermines the effectiveness of antimicrobial treatment. In infections, pathogens rarely live in a well-mixed, single species environment. It is an open question how microbial interactions in contrasting environmental structures affect plasmid mediated antibiotic resistance evolution. MethodologyThis study investigates how a spatially structured versus a well-mixed liquid environment, together with microbial interactions, affect antibiotic resistance evolution in uropathogenic Escherichia coli. We conducted a serial transfer experiment under increasing concentrations of trimethoprim-sulfamethoxazole comparing resistance evolution in the well-mixed and spatially structured environments, both in the presence and absence of a polymicrobial community. ResultsOur results revealed that E. coli in community context displayed parallel evolutionary trajectories, leading to higher final antibiotic tolerance, while the spatial structure allowed for prolonged resistance evolution. Copy number variation of the plasmid-borne resistance locus varied significantly across conditions; E. coli evolved in the well-mixed, monoculture conditions, exhibited the greatest increases in copy number, whereas lineages evolved in the presence of the community showed minimal changes relative to the ancestor. Conclusions and implicationsThese findings underscore the complex interplay between the genetic basis of resistance, the environmental structure and microbial ecology in shaping plasmid-mediated antimicrobial resistance evolution. Lay summaryAntibiotic resistance depends on environmental context, microbial interactions, and genetics. This study shows that E. coli evolved resistance differently in mixed versus structured environments, with changes in plasmid-borne resistance gene copy number. Community interactions led to similar evolutionary paths and higher tolerance, while well-mixed, single-species conditions drove larger genetic changes.

microbiology↗

bioRxiv2025

Museums and Zoos: Rapid genetic identification of rare species and practical applications for conservation and systematics in a biodiverse country

AbstractObtaining genetic information from rare species is challenging for scientists, but it is crucial for understanding animal evolutionary history and informing conservation management initiatives. We present the first example of a collaborative local network that includes zoos and natural history collections to investigate the evolution, systematics, and conservation concerns of olingos (genus Bassaricyon, Procyonidae, Carnivora, Mammalia). We sequenced the entire (1,146 base pairs) cytochrome b gene to phylogenetically identify individuals that have been victims of wildlife trafficking. Unexpectedly, we detected an individual specimen belonging to Bassaricyon medius orinomus (western lowland olingo), which may represent a new geographical record for this taxon in Ecuador. Through our practical experiences, we describe how local collaboration is possible and crucial for promoting wildlife genetic research in the Global South and contributing to protecting the last populations of rare mammals. We also discuss the significance of wild animals under human care as a valuable genetic resource for scientific research, conservation strategies, and informed wildlife management decisions.

genetics↗

bioRxiv2024

Community context influences the conjugation efficiency of E. coli

In urinary tract infections different bacteria can live in a polymicrobial community, it is unknown how such community members affect the conjugation rate of uropathogenic Escherichia coli. We investigated the influence of the polymicrobial urinary tract infection (UTI) community context on the conjugation rate of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing pOXA-48 and six uropathogenic E. coli isolates in the presence and absence of five community members to elucidate their effect on the rate of conjugation. We found that the basal conjugation rates in the absence of community members are genotype dependent. Interestingly, bacterial interactions have an overall positive effect on E. coli conjugation rates. Particularly Gram-positive enterococcal species were found to enhance the conjugation rates of most uropathogenic E. coli isolates. We hypothesize that the nature and co-culture of the interactions is important for these increased conjugation rates in AUM.

ecology↗

bioRxiv2020

Identification of blood autosomal cis-expression quantitative trait methylation (cis-eQTMs) in children

BackgroundThe identification of expression quantitative trait methylation (eQTMs), defined as associations between DNA methylation levels and gene expression, might help the biological interpretation of epigenome-wide association studies (EWAS). We aimed to identify autosomal cis eQTMs in childrens blood, using data from 832 children of the Human Early Life Exposome (HELIX) project. MethodsBlood DNA methylation and gene expression were measured with the Illumina 450K and the Affymetrix HTA v2 arrays, respectively. The relationship between methylation levels and expression of nearby genes (1 Mb window centered at the transcription start site, TSS) was assessed by fitting 13.6 M linear regressions adjusting for sex, age, cohort, and blood cell composition. ResultsWe identified 39,749 blood autosomal cis eQTMs, representing 21,966 unique CpGs (eCpGs, 5.7% of total CpGs) and 8,886 unique transcript clusters (eGenes, 15.3% of total transcript clusters, equivalent to genes). In 87.9% of these cis eQTMs, the eCpG was located at <250 kb from eGenes TSS; and 58.8% of all eQTMs showed an inverse relationship between the methylation and expression levels. Only around half of the autosomal cis-eQTMs eGenes could be captured through annotation of the eCpG to the closest gene. eCpGs had less measurement error and were enriched for active blood regulatory regions and for CpGs reported to be associated with environmental exposures or phenotypic traits. 40.4% of eQTMs had at least one genetic variant associated with methylation and expression levels. The overlap of autosomal cis eQTMs in childrens blood with those described in adults was small (13.8%), and age-shared cis eQTMs tended to be proximal to the TSS and enriched for genetic variants. ConclusionsThis catalogue of autosomal cis eQTMs in childrens blood can help the biological interpretation of EWAS findings and is publicly available at https://helixomics.isglobal.org/. Funding: The study has received funding from the European Communitys Seventh Framework Programme (FP7/2007-206) under grant agreement no 308333 (HELIX project); the H2020-EU.3.1.2. - Preventing Disease Programme under grant agreement no 874583 (ATHLETE project); from the European Unions Horizon 2020 research and innovation programme under grant agreement no 733206 (LIFECYCLE project), and from the European Joint Programming Initiative "A Healthy Diet for a Healthy Life" (JPI HDHL and Instituto de Salud Carlos III) under the grant agreement no AC18/00006 (NutriPROGRAM project). The genotyping was supported by the project PI17/01225, funded by the Instituto de Salud Carlos III and co-funded by European Union (ERDF, "A way to make Europe") and the Centro Nacional de Genotipado-CEGEN (PRB2-ISCIII).

genomics↗

bioRxiv2020

A toolkit to generate inducible and interconvertible Drosophila transgenes

The existence of three independent binary systems for conditional gene expression (Gal4/UAS; LexA/LexAop; QF/QUAST) has greatly expanded versatile genetic analyses in the fruit fly Drosophila melanogaster; however, the experimental application of these tools is limited by the need to generate multiple collections of non-interchangeable transgenic fly strains for each inducible gene expression system. To address this practical limitation, we developed a modular vector that contains the regulatory elements from all three binary systems, enabling Gal4-, LexA- or QF-dependent expression of transgenes. Our methods also incorporate DNA elements that facilitate independent site-specific recombination and elimination of regulatory UAS, LexAop or QUAST modules with spatial and temporal control, thus offering unprecedented possibilities and logistical advantages for in vivo genetic modulation and efficient interconversion of overexpression transgenic fly lines.

genetics↗

bioRxiv2019

Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas.

Transcriptional profiling of hematopoietic cell subpopulations has helped characterize the developmental stages of the hematopoietic system and the molecular basis of malignant and non-malignant blood diseases for the past three decades. The introduction of high-throughput RNA sequencing has increased knowledge of the full repertoire of RNA molecules in hematopoietic cells of different types, without relying on prior gene annotation. Here, we introduce the analysis of the BLUEPRINT consortium gene expression data for mature hematopoietic cells, comprising 90 total RNA and 32 small RNA sequencing experiments, from 27 different cell types. We used these data to describe the transcriptional profile of each we used guided transcriptome assembly to extend the annotation of the transcribed genome, which led to the identification of hundreds of novel non-coding RNA genes, which display a high degree of cell type specificity. We also characterized the expression of circular RNAs and found that these are also highly cell type specific. This resource refines the active transcriptional landscape of mature hematopoietic cells, highlights abundant genes and transcriptional isoforms for each cell type, and provides valuable data and visualisation tools for the scientific community working on hematological development and diseases.

genomics↗

bioRxiv2019

Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth

Maternal smoking during pregnancy (MSDP) contributes to poor birth outcomes, in part through disrupted placental functions, which may be reflected in the placental epigenome. We meta-analyzed the associations between MSDP and placental DNA methylation (DNAm) and between DNAm and birth outcomes within the Pregnancy And Childhood Epigenetics (PACE) consortium (7 studies, N=1700, 344 with any MSDP). We identified 1224 CpGs that were associated with MSDP, of which 341 associated with birth outcomes and 141 associated with gene expression. Only 6 of these CpGs were consistent with the findings from a prior meta-analysis of cord blood DNAm, demonstrating substantial tissue-specific responses to MSDP. The placental MSDP associated CpGs were enriched for growth-factor signaling, hormone activity, inflammation, and vascularization, which play important roles in placental function. We demonstrate links between placental DNAm, MSDP and poor birth outcomes, which may better inform the mechanisms through which MSDP impacts placental function and fetal growth.

genomics↗

bioRxiv2018

Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 are associated with gestational duration

The duration of pregnancy is influenced by fetal and maternal genetic and non-genetic factors. We conducted a fetal genome-wide association meta-analysis of gestational duration, and early preterm, preterm, and postterm birth in 84,689 infants. One locus on chromosome 2q13 was associated with gestational duration; the association was replicated in 9,291 additional infants (combined P = 3.96 x 10-14). Analysis of 15,536 mother-child pairs showed that the association was driven by fetal rather than maternal genotype. Functional experiments showed that the lead SNP, rs7594852, alters the binding of the HIC1 transcriptional repressor. Genes at the locus include several interleukin 1 family members with roles in pro-inflammatory pathways that are central to the process of parturition. Further understanding of the underlying mechanisms will be of great public health importance, since giving birth either before or after the window of term gestation is associated with increased morbidity and mortality.

genetics↗

bioRxiv2018

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs) that are ancient components of immune defence. Despite important medical relevance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here we show that AMP- and antibiotic-resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics revealed that AMP resistance genes originating from phylogenetically distant bacteria only have a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Third, the phenotypic impact of acquired AMP resistance genes heavily depends on the genetic background of the recipient bacteria. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota with implications for disease risks.

microbiology↗

bioRxiv2018

Vascular brassinosteroid receptors confer drought resistance without penalizing plant growth

Drought represents a major threat to food security. Mechanistic data describing plant responses to drought have been studied extensively and genes conferring drought resistance have been introduced into crop plants. However, plants with enhanced drought resistance usually display lower growth, highlighting the need for strategies to uncouple drought resistance from growth. Here, we show that overexpression of BRL3, a vascular-enriched member of the brassinosteroid receptor family, can confer drought stress tolerance in Arabidopsis. Whereas loss-of-function mutations in the ubiquitously expressed BRI1 receptor leads to drought resistance at the expense of growth, overexpression of BRL3 receptor confers drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress, increased BRL3 triggers the accumulation of osmoprotectant metabolites including proline and sugars. Transcriptomic analysis suggests that this results from differential expression of genes in the vascular tissues. Altogether, this data suggests that manipulating BRL3 expression could be used to engineer drought tolerant crops.

plant biology↗