Biology subjects

Aizpurua, O.

Publications and source records attributed to Aizpurua, O..

8 recordsLinked to original sources

bioRxiv2026

Interspecific faecal microbiota transplantation tests microbial contributions to thermal physiology in lizards

While the influence of microorganisms in the thermal physiology of animals is increasingly recognised, the role of the gut microbiome in enhancing phenotypic plasticity remains underexplored, particularly in ectotherms. Here, we tested the effect of gut microbiomes in modulating the physiological response of lizards to sudden temperature fluctuations. In captivity, we conducted an experiment with wild-caught Podarcis lizards: Mediterranean Podarcis liolepis (n=9) adapted to warm and dry environments, and Atlantic P. muralis (n=18) adapted to cooler and wetter conditions. Animals were assigned to three groups (intervention, control-cold and control-warm) and subjected to microbiota manipulations using antibiotics and faecal microbiota transplants (FMT). In the intervention group, cold-adapted P. muralis received faecal suspension from warm-adapted P. liolepis, while control-cold and control-warm groups received intraspecific transplants. Microbiome variation was analysed through genome-resolved metagenomics of 162 faecal samples, yielding 313 MAGs across 15 phyla, containing almost 1M annotated genes. One week after transplantation, microbiomes of control animals differed from their original state, whereas those of the intervention group (P. muralis), transitioned to a state resembling P. liolepis. After two weeks, both control groups showed trends of reversing their microbiomes to their original states. However, the intervention group displayed a distinct trajectory, resembling the microbial donors'. Although potentially relevant trends were observed, these microbiome alterations did not translate into detectable significant differences in their thermal physiology. Nevertheless, our results provide proof of concept for microbial transplants in lizards, and opportunities to further explore the link between gut microbes and host physiological responses in ectotherms.

zoology↗

bioRxiv2026

Impact of sequencing approach on ecological inference from highly variable bat gut microbiomes

Understanding the functional potential of animal gut microbiomes requires analytical approaches that can accurately capture both taxonomic and functional diversity, particularly in hosts with samples with low and variable microbial DNA fractions, such as bats. Here, we compared 16S amplicon sequencing and genome-resolved metagenomics for characterising the gut microbiomes of three sympatric insectivorous bats (Pipistrellus kuhlii, Hypsugo ariel, and Cnephaeus bottae). Amplicon sequencing recovered 3,536 amplicon sequence variants (ASVs) spanning 29 microbial phyla, including five archaeal groups, while metagenomics yielded 135 metagenome-assembled genomes (MAGs) across 15 bacterial phyla. Alpha and beta diversity patterns differed significantly between approaches. Applying prevalence- and abundance-based filtering to amplicon data improved alpha diversity congruence with metagenomic profiles, indicating that low-abundance and rare ASVs inflate diversity estimates, while the low microbial DNA fractions in bat faeces challenge genome reconstruction of such taxa. Functional reconstructions diverged notably, with metagenomics-based functional profiles yielding consistently lower metabolic capacities than those indirectly inferred from 16S amplicon sequencing, both before and after prevalence- and abundance-based filtering, due to incompleteness of many reconstructed genomes. However, metagenome-assembled genomes harboured metabolic capacities missed by the indirect functional inference of metabarcoding, which largely rely on genomes of strains characterised in model organisms. Together, these findings highlight the influence of chosen methodology, host species, and data filtering on microbiome profiling in taxa with low microbial biomass. We propose practical guidelines to improve analytical consistency and reliability when studying gut microbiomes of bats and other hosts with similarly variable microbial communities.

microbiology↗

bioRxiv2025

Beyond the core: endemic microbiota drive functional and microdiversity differences across salamander populations

Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments (Pyrenean subalpine brooks and Atlantic montane streams). From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes (MAGs), respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. While alpha diversity remained consistent, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community--shared across environments and accounting for over 85% of reads--that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not explained by dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.

microbiology↗

bioRxiv2025

Characterization and description of Clostridium filamentum ETTB, a novel gut bacterium with TLR5 modulating properties

The Clostridium genus is highly heterogeneous, encompassing numerous species and strains, many of which remain to be isolated and characterized to better understand their relationship to host physiology. This study aimed to isolate and characterize novel bacterial species within the Clostridium genus and explore their potential links to host health. Under microaerophilic conditions, we isolated and characterized three bacterial isolates belonging to a new anaerobic Clostridium species, designating Clostridium sp. DSM 115107 (Clostridium filamentum ETTB3) as the type strain. C. filamentum ETTB isolates are rod- to filament-shaped, Gram-positive bacteria and exhibit poor growth when cultured on rich media such as LYBHI. Genome sequencing and phylogenetic analysis revealed that C. filamentum ETTB belongs to the Clostridium genus and clusters closely with Clostridium saudiense JCC. Interestingly, C. filamentum ETTB has a significantly smaller genome compared to C. saudiense JCC containing a reduced repertoire of genes involved in carbohydrate degradation and amino acid synthesis and a larger number of genes related to cell motility, including an additional copy of the fliC gene. Unlike C. saudiense, C. filamentum ETTB adopted a filamentous morphology when in contact with Caco-2 cells and stimulate the TLR5 pathway in Caco-2 cells. Metagenomics analysis revealed that C. filamentum ETTB is present in both industrialized and non-industrialized populations, although the relative abundance varying considerably between and within individuals. Our study identifies a novel bacterial strain adapted for the human gut that has the potential to influence host immune response by activating TLR5 pathway.

microbiology↗

bioRxiv2024

Dietary intervention in captive-bred hares fails to enrich gut microbiomes with wild-like functions

Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyse the taxonomic and functional differences in the gut microbiota of wild and captive European hares (Lepus europaeus), as well as to assess the impact of a dietary switch to grass aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While the dietary switch to grass induced some minor changes in the gut microbiota, it did not result in a shift towards a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggest that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions. ImportanceThis study sheds light on the critical role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the gut microbiota of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Dietary interventions, such as switching to grass, showed limited success in restoring a wild-like microbiota, highlighting the need for tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasise that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.

ecology↗

bioRxiv2024

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide

Feralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 draft genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed distinct taxonomic and functional profiles between the two groups. While taxonomic enrichment was balanced, microbial functional capacities were significantly enriched in feral cats. These functional enhancements, particularly in amino acid and lipid degradation, correspond to feral cats dietary reliance on crude protein and fat. Additionally, functional differences were consistent with behavioural contrasts, such as the more aggressive and elusive behaviour measured in feral cats compared to the docile behaviour of domestic cats. Finally, the observed enrichment in short-chain fatty acid, neurotransmitter, and vitamin B12 production in feral cats aligns with improved cognitive function and potentially contributes to their heightened aggression and elusiveness. Our findings suggest that microbiome shifts may play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, supporting the adaptive success of feral cats in the wild.

evolutionary biology↗

bioRxiv2023

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 faecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: i) 20 Gbp of Illumina short-read data, ii) 40 Gbp of short-read data, iii) 20 Gbp of PacBio HiFi long-read data, and iv) 40 Gbp of hybrid (20 Gbp of short-read + 20 Gbp of long-read) data. No strategy was best for all metrics, but instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies, and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific, and depends on how researchers assess the tradeoff between the quantity and quality of recovered genomes. ImportanceOur understanding of microbial communities is limited by the technologies we employ. Here, we test several different DNA sequencing techniques to better understand the pros and cons of each. Long read DNA sequencing allowed for the reconstruction of higher quality and even complete microbial genomes, however, the cost was greater than commonly used short-read DNA sequencing. We suggest researchers consider the trade-offs between each method and decide based on the goals of their research question/s.

microbiology↗

bioRxiv2019

Diet diversification shapes broad-scale distribution patterns in European bats

Large-scale species distributions have been traditionally attributed to physiological traits related to abiotic factors, while behavioural features linked to biotic interactions have received little attention. We tested the relationship between trophic and spatial niche breadths through combining species distribution modelling with dietary DNA metabarcoding of over 400 bats sampled across Europe belonging to seven species. Our results point to a causality cascade between hunting plasticity, trophic niche breadth and spatial niche breadth, and thus indicate that behavioral plasticity and dietary diversification can contribute to shaping broad-scale species distributions.

ecology↗