Biology subjects

Valdivia, C.

Publications and source records attributed to Valdivia, C..

8 recordsLinked to original sources

bioRxiv2026

Insect COI barcoding data as an untapped resource for surveying Wolbachia symbioses

O_LIDNA barcoding of the mitochondrial cytochrome c oxidase I (COI) gene is widely used to characterise insect diversity and distributions; however, its potential to reveal information on species interactions, including host-symbiont associations, remains largely unexplored. Here, we assess whether COI amplicon data can be used to identify Wolbachia - one of the most widely distributed bacterial symbionts known to profoundly affect their hosts biology. C_LIO_LIWe demonstrate that several commonly used invertebrate COI primer sets perfectly match many reference Wolbachia genomes, leading to frequent co-amplification. C_LIO_LIBy screening 7,901 individual-insect COI amplicon libraries obtained with the popular BF3-BR2 primer set, we detected Wolbachia sequences in over 35% of samples, revealing that co-amplification is indeed widespread. After removing low-abundance reads, Wolbachia detection based on COI amplicons showed over 90% agreement with simultaneously generated 16S-V4 rRNA amplicon data from the same specimens. The degree of agreement, however, varied depending on the thresholds used, among datasets and insect clades. C_LIO_LIFurther, we show that Wolbachia abundance inferred from COI amplicons correlated with their abundance in metagenomic datasets for 152 specimens, supporting the quantitative relevance of the signal. C_LIO_LIFinally, we find that Wolbachia COI sequences provide greater phylogenetic resolution than 16S-V4 rRNA data (mean pairwise genetic distance of COI sequences - 9.6%, 16S-V4 rRNA - 2.8%), and the reconstructed Wolbachia COI-based genotype network largely agrees with genome-based phylogenies. C_LIO_LICollectively, our results demonstrate that off-target Wolbachia sequences recovered from standard insect COI barcoding data may reliably detect symbiont presence, provide phylogenetic insight, and guide sample selection for metagenomics. Given the rapid expansion of global insect barcoding initiatives, these findings highlight an opportunity for cost-effective monitoring of their most prevalent bacterial symbionts, offering new perspectives on how host-microbe interactions may shape insect communities. C_LI

ecology↗

bioRxiv2026

Accuracy of occurrence and abundance estimates from insect metabarcoding

1. DNA metabarcoding--high-throughput sequencing of barcode regions from bulk samples--has become a key tool for insect biodiversity assessment. Yet, how methodological choices affect the accuracy of metabarcoding data remains insufficiently explored. In this paper, we ask: (1) How does the lysis method (non-destructive lysis vs. destructive homogenization) affect community recovery? (2) How comprehensively does metabarcoding capture species richness? (3) To what extent can spike-ins improve abundance estimates? (4) How accurately can species abundances be estimated? 2. We evaluated the accuracy of insect metabarcoding using 4,749 bulk samples from a large-scale biodiversity survey subjected to mild lysis. Of these samples, 856 were also homogenized, allowing a systematic comparison of the effect of alternative treatments. To potentially improve abundance estimates, we added six biological spike-ins (i.e., foreign insects) to all samples, and two synthetic spike-ins (artificial DNA fragments) to the homogenization treatment. In addition, we established the contents of 15 samples by individually barcoding all specimens, enabling direct assessment of occurrence and abundance estimates. 3. Our results revealed consistent differences between destructive and non-destructive treatments. While both methods reliably detected the majority of species, small and soft-bodied taxa were more often recovered after mild lysis than after homogenization, while the reverse was true for heavily sclerotized, hairy, and large taxa. Using biological spike-ins for calibration reduced the variance in read numbers per specimen considerably, especially in homogenized samples, while synthetic spike-ins were less effective. In a Bayesian analysis, where species data were matched to the best-fitting spike-in calibration curve, accurate abundance estimates (+/-1 individual) were obtained for 72.9% of species occurrences. 4. Our results show that it is possible to obtain reasonably accurate abundance estimates from metabarcoding data, and that mild lysis and homogenization result in different taxon-specific biases in terms of occurrence data, with neither method outperforming the other. Accuracy is improved by homogenization rather than mild lysis of samples, and by the use of biological rather than synthetic spike-ins. Together, these findings provide a major step towards robust, quantitative biodiversity monitoring using DNA-metabarcoding.

zoology↗

bioRxiv2025

Multilayered human activities shape the microbial communities of groundwater-dependent ecosystems in an arid oceanic island

Island coastal aquifers, though physically small compared to continental groundwater systems, are of huge ecological and societal importance, sustaining functions that connect to locally crucial provision, maintenance and culture ecosystem services. Those functions are largely dependent on the presence of highly adapted biological communities, for which, their microbial communities remain understudied. Our goal is to describe the bacterial communities across the groundwater-dependent ecosystems on Lanzarote, spanning a gradient of anthropogenic pollution using 16SrRNA amplicon sequencing. We sampled coastal caves and pools, wells and water galleries, springs, saltworks and marine bays affected by submarine groundwater discharge. Ecological analyses highlight that richness and composition of bacterial communities strongly depend on the type of habitats. Pathogens and human-derived species were ubiquitous in our samples, but, strikingly, caves and wells were strongly enriched with them compared to other habitats. We propose that our results highlight the susceptibility of groundwater environments to pollution and indicate that aquifers act as reservoirs of biological contamination in addition to natural diversity--regardless of their salinity. Since this enrichment might compromise some of the functions and services that groundwater-dependent ecosystems provide in oceanic islands, we call for integrative conservation strategies that include hydrological and biological perspectives into the decision making.

microbiology↗

bioRxiv2025

Isolation and characterization of broad-range Staphylococcus epidermidis sepunaviruses

Staphylococcus epidermidis is a major contributor to biofilm-associated infections, bacteraemia, and sepsis in humans. Additionally, it is an important veterinary pathogen. The spread of multi-drug resistant S. epidermidis (MRSE) poses an even greater challenge, requiring the development of antibiotic-alternative approaches. Here, we isolated four new broad-range phages capable of infecting a large panel of 65 clinical and veterinary isolates of S. epidermidis. Phages with the broadest host range produced plaques on 37% of the hosts tested and halos on an additional 40%. These phages belonged to the Sepunavirus genus, as supported by their morphology and genome analysis. A genome-wide association study identified a significant correlation between resistance to phage lysis and the presence of the sbcCD complex and the ica operon, highlighting the protective role of biofilms against the phages isolated in this study. Furthermore, distinct phage-encoded methyltransferases identified in the phage genomes may contribute to differences in host ranges. This study advances our knowledge on the diversity and characteristics of S. epidermidis phages, which could be considered as interesting tools for phage therapeutics. RepositoriesPhage genomes are available under Genbank accession numbers PV426907-PV426910. Bacterial genome sequences determined as part of this study, and all Bakta annotations, are available via Figshare (doi:10.6084/m9.figshare.29066417 and doi:10.6084/m9.figshare.29079968 respectively).

microbiology↗

bioRxiv2025

Identification of a novel papillary renal cell carcinoma molecular subtype characterized by HIF-pathway over-activation

PurposePapillary renal cell carcinoma (pRCC), the second most common subtype of renal cancer, exhibits heterogeneity in molecular features and response to targeted therapies, including antiangiogenic drugs. Discovering molecular biomarkers able to stratify pRCC patients into clinically relevant subgroups and understanding the underlying mechanisms are urgently needed to advance precision medicine. Here, we molecularly dissect a large pRCC series through the expression of the targets of hypoxia inducible factors (HIF), master regulators of angiogenesis, metabolic reprogramming and immune microenvironment. Experimental DesignWe merged and analyzed multi-omic and clinical data of 346 patients derived from two pRCC series (TCGA-KIRP and a Spanish metastatic series). Altered pathways and differences in tumor microenvironment were identified through tumor transcriptomic analyses. Tumor metabolome analysis was performed in selected cases. ResultsMolecular revision of driver mutations classified 302 patients as pRCC, while uncovering misclassified cases. Analysis of HIF targets gene expression identified a subset of pRCC tumors with increased HIF activity (31%; "HIF-active"). These tumors were characterized by high hypoxia scores, increased angiogenesis, low expression of Krebs cycle genes and mitochondrial activity, high immune infiltration and increased epithelial-mesenchymal transition (P<0.0001; each feature) and they were associated with increased metastasis risk and worse overall survival (P<0.005). Metabolome analyses revealed that HIF-active tumors accumulated L-2-hydroxyglutarate (L-2-HG), an oncometabolite that leads to pseudohypoxia by inhibiting HIF prolyl hydroxylases and preventing HIF degradation. L-2-HG-accumulation agreed with diminished L2HGDH expression, associated with losing one copy of the gene and low expression of PPARGC1A, which regulates its transcription. ConclusionsHIF-pathway overactivation defines a pseudohypoxic pRCC molecular subgroup characterized by high angiogenesis, immune infiltration and aggressive features. These findings advance our understanding of pRCC diversity, revealing potential clues for the variable response of patients to targeted therapies and paving the way to more personalized pRCC treatments.

cancer biology↗

bioRxiv2023

Co-habiting ants and silverfish display a converging feeding ecology

O_LISpecies from a great number of animal taxa have specialized to living with social hosts. Depending on their level of specialization, these symbiotic animals are characterized by distinct behavioural, chemical, and morphological traits that enable close heterospecific interactions. Despite its functional importance, our understanding of the feeding ecology of specialized animals living with social hosts remains limited. C_LIO_LIIn this study, we examined how host specialization of silverfish co-habiting with ants affects several components of their feeding ecology. We combined stable isotope profiling, feeding assays, phylogenetic reconstruction, and microbial community characterization of the Neoasterolepisma silverfish genus and a wider nicoletiid and lepismatid silverfish panel where divergent myrmecophilous lifestyles are observed. C_LIO_LIStable isotope profiling ({delta}13C and {delta}15N) showed that the isotopic niches (proxy for trophic niches) of granivorous Messor ants and Messor-specialized Neoasterolepisma exhibit a remarkable overlap within an ant nest. Trophic experiments and gut dissections further supported that these specialized Neoasterolepisma silverfish transitioned to a diet that includes plant seeds. In contrast, the isotopic niches of generalist Neoasterolepisma silverfish and generalist nicoletiid silverfish were clearly different from their ant hosts within the shared nest environment. C_LIO_LIThe impact of the myrmecophilous lifestyle on feeding ecology was also evident in the internal silverfish microbiome. Compared to generalists, Messor-specialists exhibited a higher bacterial density and a higher proportion of heterofermentative lactic acid bacteria. Moreover, the nest environment explained the infection profile (or the 16S rRNA genotypes) of Weissella bacteria in Messor-specialized silverfish and the ant hosts. C_LIO_LITogether, we show that social hosts are important determinants for the feeding ecology of symbiotic animals, and can induce diet convergence. C_LI

ecology↗

bioRxiv2022

Microbial symbionts are shared between ants and their associated beetles

The transmission of microbial symbionts across individuals and generations can be critical for animal development and survival. Likewise, the transmission of microbes across closely interacting species could also affect host biology. Army ants (Formicidae: Dorylinae) and their hundreds of closely associated insect species (myrmecophiles) can provide a unique insight into interspecific symbiont sharing. Here, we compared the microbiota of workers and larvae of the army ant Eciton burchellii with those of 13 myrmecophile beetle species using 16S rRNA amplicon sequencing. We found that the previously characterized symbionts of army ant workers (Unclassified Firmicutes and Unclassified Entomoplasmatales) were largely absent from ant larvae and from myrmecophiles, whose microbial communities were usually dominated by Rickettsia, Wolbachia, Rickettsiella, and/or Weissella. Strikingly, different species of myrmecophiles and ant larvae often shared identical 16S rRNA genotypes of common bacteria. In particular, army ant larvae, some workers, and several myrmecophile species often hosted identical Weissella (Lactobacillales), based on 16S rRNA and also protein-coding gene sequences. Also, we found high relatedness between some newly characterized Weissella and animal-associated strains from aquatic and marine habitats. Looking more broadly, we found Weissella OTUs in 11.6% of samples from nearly all habitats and environments characterized by the Earth Microbiome Project. Together, our data show that unrelated but closely interacting species can share much of their microbiota. The high relatedness of strains found across such disparate hosts as ants, beetles, trout, and whales suggests that some versatile microbes move between hosts and habitats despite few opportunities for direct interaction.

ecology↗

bioRxiv2020

Convergence of Heteromodal Lexical Retrieval in the Lateral Prefrontal Cortex

Lexical retrieval requires selecting and retrieving the most appropriate word from the lexicon to express a desired concept. Prior studies investigating the neuroanatomic underpinnings of lexical retrieval used lesion models that rely on stereotyped vascular distributions, functional neuroimaging methods that lack causal certainty, or awake brain mapping that is typically limited to narrow cortical exposures. Further, few studies have probed lexical retrieval with tasks other than picture naming and when non-picture naming lexical retrieval tasks have been applied, both convergent and divergent models emerged. Because of this existing controversy, we set out to test the hypothesis that cortical and subcortical brain regions specifically involved in lexical retrieval in response to visual and auditory stimuli represent overlapping neural systems. Fifty-three patients with dysnomic aphasia due to dominant-hemisphere brain tumors performed four language tasks: picture naming, auditory naming, text reading, and describing line drawings with correct syntax. A subset of participants also underwent the Quick Aphasia Battery which provides a validated measure of lexical retrieval via the word finding subtest. Generalized linear modeling and principal components analysis revealed multicollinearity between picture naming, auditory naming, and word finding, implying redundancies between the linguistic measures. Support vector regression lesion-symptom mapping across participants was used to model accuracies on each of the four language tasks. Picture naming and auditory naming survived cluster-level corrections. Specifically, lesions within overlapping clusters of 8,333 voxels and 21,512 voxels in the left lateral PFC were predictive of impaired picture naming and auditory naming, respectively. These data indicate a convergence of heteromodal lexical retrieval within the PFC. Importance of the StudyLexical retrieval (i.e., selecting and retrieving words to convey desired concepts) is a crucial component of language processing. However, existing studies of the neuroanatomic underpinnings of lexical retrieval lack causal relationships and have provided conflicting evidence, suggesting both convergent and divergent models. In order to resolve these conflicting models, we used lesion-symptom mapping to investigate lexical retrieval in 53 patients with dominant-hemisphere brain tumors. We observed significant associations between performance on visual and auditory naming tasks. Further, performance on these tasks predicted performance on a validated neuropsychological measure of lexical retrieval. Critically, multivariate, nonparametric lesion-symptom mapping within a brain tumor framework revealed that lesions in overlapping regions of the left lateral prefrontal cortex (PFC) predict impaired visual and auditory naming. In a clinical context, this approach to identifying causal brain-behavior relationships could help to guide brain tumor therapies such as cytoreductive surgery and supportive rehabilitation services.

neuroscience↗