Antton Alberdi

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Verified

Antton verified their affiliation via an institutional email.

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• PhD
• Professor (Associate) at University of Copenhagen

During times of rapid environmental change, survival of most vertebrate populations depends on their phenomic plasticity. Although differential gene-expression and post-transcriptional processes of the host genome receive focus as the main molecular mechanisms, growing evidence points to the gut microbiota as a key driver defining hosts’ phenotypes...

With the advent of DNA sequencing‐based techniques, the way we detect and measure biodiversity is undergoing a radical shift. There is also an increasing awareness of the need to employ intuitively meaningful diversity measures based on unified statistical frameworks, so that different results can be easily interpreted and compared. This article ai...

Inferences of the interactions between species’ ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary nic...

Research on animal–microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study...

Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between ge...

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...

Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise...

Successfully adapting to a feral lifestyle 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 microb...

The HoloFood project used a hologenomic approach to understand the impact of host–microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project’s raw data, derived analyses, and metadata are deposited in public, open archives (BioSamp...

Despite increasing evidence for the contribution of microbiomes to host fitness and evolution, their role in the adaptation and successful establishment of invasive animal species remains underexplored. Animal microbiomes can mediate key host phenotypic traits such as energy metabolism, detoxification and disease resistance. Therefore, harbouring a...

Bats provide important ecosystem services, particularly in agriculture, yet integrating bat management into conservation plans remains challenging. Some landscape features considerably influence bat presence, diversity, and ecosystem service provision. Understanding the relationship between landscape structure, composition, pest suppression, and ec...

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 diff...

Hologenomics, the joint analysis of host genomes and microbial metagenomes, has the potential to address fundamental biological questions from a systemic host‐microbiota perspective. However, multiple fieldwork, laboratory and bioinformatic steps challenge quality, representativeness and comparability of hologenomic data. Leveraging the first 2025...

Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated microbiomes, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across va...

Microorganisms associated with animals harbour a unique set of functional traits pivotal for the normal functioning of their hosts. This realisation has led researchers to hypothesise that animal‐associated microbial communities may boost the capacity of their hosts to acclimatise and adapt to environmental changes, two eco‐evolutionary processes w...

Minimizing the utilization of antibiotics in animal production is crucial to prevent the emergence of antimicrobial resistances. Thus, research on alternatives is needed to maintain productivity, sustainability, and animal health. To gain a comprehensive understanding of probiotics’ modes of action on performance, intestinal microbiota, and gut hea...

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 pla...

Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One f...

The fast-growing expansion of urban areas pose severe pressures on wildlife. However, some generalist native mammals thrive in urbanized landscapes, while invasive alien species (IAS) are often more abundant in cities than in rural habitats. Variation in phenotypes—such as differences in personality traits—can influence the probability to colonize...

Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main diff...

In a recent Matters Arising article, Osburn et al. ¹ raised concerns about the estimation of bacterial life history traits Piton et al. discerned from soil metagenomes ² . The criticism focused on the possible overestimation of the bacterial Average Genome Size (AGS) due to the presence of eukaryotes in the soil samples. Here, we apply a newly deve...

The animal gut microbiota is strongly influenced by environmental factors that shape their temporal dynamics. Although diet is recognized as a major driver of gut micro-biota variation, dietary patterns have seldom been linked to gut microbiota dynamics in wild animals. Here, we analysed the gut microbiota variation between dry and rainy seasons ac...

The Earth Hologenome Initiative (EHI) is a global collaboration to generate and analyse hologenomic data from wild animals and associated microorganisms using standardised methodologies underpinned by open and inclusive research principles. Initially focused on vertebrates, it aims to re-examine ecological and evolutionary questions by studying hos...

Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assumption that all reads are microbial. For instance, the success of metagenome-assembled genome (MAG) recovery ef...

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 fecal DNA extracts collected weekly for 11 weeks fr...

Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many o...

Unravelling the colonisation dynamics and physiological effects of zoonotic bacteria such as Campylobacter is imperative to prevent foodborne diseases. We employed a hologenomic approach to jointly analyse metabolic networks and gene expression of the caecal microbiota, with the intestinal gene expression of 613 broiler chickens that did and did no...

We conducted a quantitative systematic review to evaluate the scientific evidence for the contribution of gut microorganisms to the acclimation and adaptation capacity of wild vertebrate hosts. After screening 1974 publications, we scrutinised the 109 studies that met the inclusion criteria based on 10 metrics encompassing study design, methodology...

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 f...

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinfor...

The ability of the gut microbiome has been posited as an additional axis of animals’ phenotypic plasticity. However, whether and how such plasticity varies across hosts with different biological features remains unclear. We performed a captivity experiment to compare how the taxonomic, phylogenetic, and functional microbial dynamics varied across a...

Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicu...

Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, man...

Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive co...

Understanding the development of functional attributes of host-associated microbial communities is essential for developing novel microbe-based solutions for sustainable animal production. We applied multi-omics to 388 broiler chicken caecal samples to characterise and model the functional dynamics of 822 bacterial strains. Although microbial commu...

Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. G...

Freshwater habitats are under increasing pressure from numerous anthropogenic forces, including the introduction of alien species capable of altering ecosystems and threatening native species. Although alien species themself are likely to experience loss of genetic diversity when colonising novel environments, some manage to become invasive, sugges...

The gut microbiomes that associate with animals can represent labile units of cooperating and competing microbes. This lability, sometimes referred to as metagenomic plasticity, has been posited to have an important role as an additional axis of hosts’ phenotypic plasticity. However, whether and how metagenomic plasticity varies across hosts with d...

Background Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and...

As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences...

Over 40% of the Earth’s surface has been converted to agricultural use and agroecosystems have become important habitats for wildlife. In arid regions, intensive agriculture creates artificial oasis-like habitats due to their high irrigation inputs. Date production is one of the primary agricultural practices in the deserts of the Middle East and N...

Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between ge...

As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild‐like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild‐c...

Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doi...

Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of MAGs has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genom...

Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between ge...

Metagenomic datasets of host‐associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two‐step strategy is tested...

The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food...

The gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic...

Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet. Results We first c...

Metagenomic data sets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, if a reference panel is available, genotype imputation can be employed to reconstruct host genotypes and maximise the use of such a priori useless data. We...

Aim The need to forecast range shifts under future climate change has motivated an increasing interest in better understanding the role of biotic interactions in driving diversity patterns. The contribution of biotic interactions to shaping broad-scale species distributions is, however, still debated, partly due to the difficulty of detecting their...

In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity wi...

Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.ResultsWe first comp...

There is an open debate on whether and how captivity alters the gut microbiota of vertebrates, due to the contrasting results reported in different taxa and the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species, including fish, repti...

From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bi-directional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions, by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requi...

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens...

Multiple large-scale restoration strategies are emerging globally to counteract ecosystem degradation and biodiversity loss. However, restoration often remains insufficient to offset that loss. To address this challenge, we propose to focus restoration science on the long-term (centuries to millennia) re-assembly of degraded ecosystem complexity in...

Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associat...

The application of DNA sequencing‐based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological qu...

Hill numbers provide a powerful framework for measuring, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. In order to facilitate the implementation of Hill numbers into such analyses, whether focusing on diet reconstruction, microbial community profiling or more general...

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated microorganisms. Whereas amplicon sequencing has traditionally been used to characterise the microbiome, the increasing number of published population genomics datase...

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host’s biology, health and associated microorganisms. Whereas amplicon sequencing has traditionally been used to characterise the microbiome, the increasing number of published population genomics datase...

1. A few of the >1300 bat species recognised worldwide are known to consume fish to various extents. However, empirical information about how and how much different bat species capture and consume fish is limited, and is probably distorted due to the biases introduced by occasional observations. 2. In this review, we aim to synthesise the knowledge...

Plecotus macrobullaris (Kuzjakin, 1965) is a medium-sized chiropteran commonly called the alpine long-eared bat, and 1 of the 11 Palearctic species recognized in the genus Plecotus. It has the characteristic long ears of plecotine bats, and externally its most conspicuous diagnostic characteristic is the inverted triangular-shaped pad most individu...

Niche partitioning through foraging is a mechanism likely involved in facilitating the coexistence of ecologically similar and co-occurring animal species by separating their use of resources. Yet, this mechanism is not well understood in flying insectivorous animals. This is particularly true of bats, where many ecologically similar or cryptic spe...

Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquacultu...

Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis workflows to ensure reliable results. We explore how decisions regarding study design, laboratory set-up, and bioinformatic processing affect the final results, and provide guidelines for reliable study of environment...

The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary n...

Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from...

Behavioral plasticity is a key feature allowing animals to broaden their dietary niche when novel food resources become available, and long-fingered bats provide an appropriate model system to study the underpinnings of behavioral plasticity, since although generally being an insectivorous species, some individuals have been reported to catch fish....

Schematic illustration of the operation of the (A) stationary and (B) temporary targets. (B.1) When the fishing line was pulled the fish was submerged, and (B.2) when the fishing line was released the buoyancy of the cork caused the emergence of the upper lip of the fish. (PDF)

Differences in the feet insertion depth between different bats (insectivorous vs. piscivorous) and target types (stationary vs. temporary). This feature was classified into three categories: touching the water with the toes (toes), insertion of half of the foot into the water (half foot) and submersion of more than half of the foot into the water (...

The principal component analysis (PCA) between attacks on stationary (blue) and temporary (yellow) targets by (A) piscivorous individuals and (B) insectivorous individuals. The ellipses are drawn at a confidence level of 0.95. PC1 explains 47% of the variation, and the PC2 17%, for a cumulative proportion of 65%. (PDF)

Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied , particularly for taxa that are difficult to sample such as bats. Aiming to estim...

Consensus Bayesian tree generated in MrBayes 3.2.5 (Huelsenbeck & Ronquist, 2001; Ronquist et al. 2012) from sequences of mitochondrial COI gene (657 bp) of Myotis species, applying the substitution model HKY+I. The numbers of each node respectively indicate the posterior probability and the bootstrap percentage in the analogous ML tree, separated...

Consensus Bayesian tree generated in MrBayes 3.2.5 (Huelsenbeck & Ronquist, 2001; Ronquist et al. 2012) from sequences of mitochondrial COI gene (657 bp) of phyllostomid species, applying the substitution model HKY+I. The numbers of each node respectively indicate the posterior probability and the bootstrap percentage in the analogous ML tree, sepa...

List of public sequences of the mitochondrial DNA gen cytochrome oxidase I (COI) used in this study for comparison. (DOCX)

Number of males and females captured for each species. (DOCX)

List of sequences of the mitochondrial DNA gene cytochrome oxidase I (COI) obtained from bats at Valle del Silencio (Costa Rica) and uploaded to GenBank. (DOCX)

Sequences obtained from each species with the two sets of primers used, namely, UTyr and C1L705 (Hassanin et al. 2012), and the cocktail C_VF1LFt1+C_VR1LRt1 (Ivanova et al. 2012). For each set of primers we respectively indicate de amount of samples analysed, in how many of them we got the whole fragment of COI sequenced (657 bps), and the sequence...

This article is a comprehensive summary of the PhD presented by Antton Alberdi at the University of the Basque Country (UPV/EHU), on december 5th, 2014, under the supervision of Dr. Inazio Garin and Dr. Joxerra Aihartza. The thesis was awarded by the Spanish Society of Mammalogist (SECEM) in 2015, as the best thesis about Iberian mammals. DOI: 10.7...

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sap...

Conservation efforts for endangered animals commonly focus on the protection of foraging habitats, aiming to ensure sufficient food availability. However, the diet of many species is based on animals that undergo habitat shifts across ontogenetic life stages, yielding considerable differences between the lifelong habitat requirements of both predat...

Several insectivorous bats have included fish in their diet, yet little is known about the processes underlying this trophic shift. We performed three field experiments with wild fishing bats to address how they manage to discern fish from insects and adapt their hunting technique to capture fish. We show that bats react only to targets protruding...

AimWe used an integrative approach to reconstruct the evolutionary history of the alpine long-eared bat, Plecotus macrobullaris, to test whether the variable effects of Pleistocene climatic oscillations across geographical regions led to contrasting population-level demographic histories within a single species.LocationThe Western Palaearctic.Metho...