Call for postdoctoral candidates interested in applying for a Marie Curie Individual Fellowship 2022 projects in microbiota in the vertebrate dietary/metabolic adaptation

Project title: Role of host-gut microbes symbiosis in the adaptation of an insular vertebrate, the Balearic wall lizard Podarcis lilfordi

This project aims to understand the role of the gut microbiota in the vertebrate dietary/metabolic adaptation. For this purpose, we will use Balearic Wall lizard Podarcis lilfordi, an endemic species of the Balearic Islands, to explore the role of gut microbial communities in conferring insular adaptation to the limited resource availability using population-level analyses and targeting both composition and functional profile of the gut microbiome in relation to host ecology and genetics.

The study system

Island populations of small vertebrates provide a simplified model for the study of host-microbiome functional complementarity due to their isolated nature, small sizes, reduced selective pressures (no major predators or competitors), and overall smaller ecological networks. These closed systems allow to fully monitor both host genetics and microbiome variation at population level, and to explore the holobiont (host and gut microbes) local adaptation to resource-poor ecosystems that constitute small islands.

The Lilford’s wall lizard (Podarcis lilfordi, Günther, 1874) represents an extremely suitable and interesting model for this purpose. P. lilfordi is a medium-size lizard endemic of the Balearic archipelago that originated during the re-flooding of the Mediterranean at the end of the Messinian Salinity Crisis. Currently the species distribution is limited to the Cabrera National Park and several islets surrounding Mallorca and Menorca, prompting its listing as ‘Endangered’ by the IUCN. All populations share a similar genetic structure and inhabit comparable habitats, but differ in density, coloration, body shape, body size and life-history traits, indicating a gradual process of divergence and adaptation to their local environments. The species is largely omnivorous, having adapted to the scarce resources provided by these islets. Although there are records of local extinctions due to genetic drift, most islet populations persist despite large fluctuations in their populations.

Adaptive morphological and life history traits recorded in these lizards are likely sourced from important standing genetic variation, rather than novel mutations, which provides the basis for fast evolutionary responses. Whether part of this standing genetic variation is provided by the gut microbes is a central question in the hypothesis of an extended genotype/phenotype scenario and for conservation purposes of these populations.

Although examples of the role of microbes in the host phenotype are increasing, integrative studies in natural systems and at population-level scale remain rare. Wild animals provide necessary critical systems to address the key eco-evolutionary aspects of this symbiosis and the short and long-term contribution of these communities to the host adaptation

Previous work and data available

The hosting group has been studying the P. lilfordi since 2015 and has pioneered the studies of the gut microbiota in the Balearic lizards. Using a portion of the 16S rRNA gene as a bacterial marker on both intestine and fecal samples, results from the group have shown a remarkable conservation of the microbial taxonomic profiles among distinct populations of both Mallorca and Menorca archipelagos, suggesting strong host genotypic effects in shaping these communities and a strict host-microbes interdependency. They also showed that microbial differences among populations begin to be visible at high levels of taxonomic resolution (from genus to strain), hinting to a progressive differentiation of both the host and associated microbes, resulting into a holobiont local profile for each islet (Baldo et al., 2018, FEMS).

More recently and in collaboration with the G. Tavecchia’s team from the Mediterranean Institute for Advanced Studies (IMEDEA) in Mallorca, the group has focused the study on three neighboring populations/islets on the South of Mallorca (Na Moltona (NM), Na Guardis (NG) and En Curt (EC)) subject of a long-term capture-mark-recapture demographic study since 2009. All captured specimens have been photo-identified through their pattern of ventral scales, and sex, age, and morphometrics data recorded twice a year (spring and fall). This has provided unprecedented individual-level and longitudinal data for natural populations, showing that the three populations differ in demographic parameters and life history traits such as body growth rate, fecundity, survival, and density. Recently, the group has integrated demographic data with host diet (by stable isotopes), host genetics (microsatellites and Single Nucleotide Polymorphism, SNPs) and gut microbiota to begin to explore the eco-evo dynamics of these populations under a holobiont perspective. Based on fecal sampling from a subset of specimens of NG and NM populations along two seasons (spring and fall) and two years and the characterization of the gut microbiota by a portion of 16S rRNA we have shown that the gut microbiome is plastic and cycles along seasons in a similar fashion in two Mallorcan islets (controlling for sex and age). While few candidate taxa involved in seasonality were identified, their functional impact remains unclear, due to lack of strain resolution.

The main hypothesis of this project is that this microbiome seasonal reconfiguration provides the host with metabolic flexibility to adjust to energy requirements and resource availability during seasonal fluctuations, as recently proposed in mammals. To reach strain resolution and to understand the functional profile of these microbial communities, the gut microbiota of a total of 180 specimens spanning the wide range of distribution of the Balearic lizard have been now fully sequenced with 16S full length using Oxford Nanopore sequencing technologies (ONT) with a Minion available in the group. Data is ready to be analyzed.

Finally, the group has now sequenced the genome of P. lilfordi (first draft available, in collaboration with the Centro Nacional de Análisis Genómico CNAG, https://www.biogenoma.cat/especie/podarcislilfordi/) and began exploring trait selection by SNP mapping to the genome (under analysis by CNAG collaborators and PhD student in the hosting group). Data will be interpreted in light of the extensive demographic data available.

Current data from the hosting group include an unprecedented dataset of individual-level data for these three islets/populations of wild lizards, spanning:

- Gut microbiomics (partial 16S of 230 specimens, full length 16S of 180 specimens of several islets).

- Host genomics (the P. lilfordi genome and SNPs of 96 specimens).

- Demography (population size, survival and fecundity, past 10 years).

- Host metadata (sex, age, body size, body growth rates, GPS locations).

- Trophic ecology (stable isotopes, COI metabarcoding under development).

- Island ecology (biotic index, plant and animal diversity).

Question and objectives of the project

Major Question

Does the gut microbiome plasticity confer the lizard metabolic optimization to limited resources availability and dietary flexibility to cope with seasonal changes, thus contribute to the resilience of these small populations?

As genomic adaptive processes are unlikely to provide a rapid enough solution to cope with this environmental stress, our starting hypothesis is that microbiome diversity and plasticity might contribute to the host dietary adjustment, increasing its fitness landscape, by boosting the host ecological adaptation.

Objectives

To address the above question, we will mainly focus on three neighbouring populations of P. lilfordi (NG, NM and EC) with a gradient of environmental and genetic complexity and complement the extensive individual-level data available (demography, metadata, diet) with the profiling of the gut microbiota (16S rRNA and metagenomes), diet (metabarcoding) and a first screening of the fecal metabolites.

The project will specifically target the following objectives, depending on time and skills of the candidate:

1. Establishment of population- and seasonal- differences in gut microbiome composition using full-gene 16S sequence analysis (alpha/beta diversity, community structure, microbial persistence and plasticity). To reach this objective we already count with available 16-full length ONT data from 180 specimens of the three populations (2 years, 2 seasons sampling). Additional sampling will be performed over the following years, during the fall and spring campaigns.

2. Predictive functional profiling of the gut microbiota to understand metabolic contribution of gut microbes to the lizard trophic ecology (16S full length ONT data from multiple populations, already available).

3. Lizard diet fine characterization by fecal metabarcording and to correlate population and seasonal differences in gut microbiota (compositional and functional) with lizard dietary changes. To raise hypotheses about possible microbial candidates involved in the digestion of specific dietary components (particularly plant material). Protocols for metabarcoding is currently being optimized in the host lab.

4. Contrast both diet and microbial composition data with individual-level host metadata. Identification of possible variations in diet and microbial composition (within same lizard population) depending on host sex and/or age. Metadata is available and a database is currently under construction for easier management.

5. Shotgun metagenomics of subset of individuals to generate a functional profile of the microbiome by pathway reconstruction. Identification of possible genes involved in host adaptation to the environment and production of vitamins and cofactors devoid in lizard diet. Validation of expression of key genes by qPCR. Feces will be collected during the fall 2022 and sequencing outsourced at an external centre (e.g., Novogene).

6. Targeted metabolomics in lizard stool to detect stable metabolites involved in host-microbiota functional interactions. Feces will be collected during the fall 2022. This protocol is new, and data will be generated during the project.

Description of host research group and institution

Group webpage: http://www.ub.edu/evok/

The candidate will join a highly active department at the University of Barcelona (UB), a top-ranked university worldwide with access to all facilities necessary to the development of this project. Morevoer, Barcelona offers a multidisciplinary and active scientific environment with several sequencing centers and important scientific institutes, organizing seminars and courses on topics related to this project.

The project will be a collaboration with the UB and the Mediterranean Institute for Advanced Studies (IMEDEA, Mallorca). The PI of the host research group (Laura Baldo) has 20 years of experience in the study of microbial symbiosis and has pioneered the study of gut microbiota through metagenomics in iconic natural animal systems, including the cichlids fishes and the Balearic lizard. The host research group has well-equipped lab, with an Oxford Nanopore Sequencer fully operative for the most up-to-date sequencing technology in this field

The current project builds on current available data on the three well-researched Mallorcan populations under study since 2009 (and ongoing) by collaborators from IMEDEA (G. Tavecchia). The IMEDEA group is specialized on demographic modelling and the evolution of life-history traits in lizards (https://animaldemography.blogspot.com/). The PI and IMEDEA were recently granted funding to sequence the P. lilfordi genome (assembly now available, https://www.biogenoma.cat/especie/podarcis-lilfordi/) and to study the resilience of these populations by demographic modelling, SNPs and microbiome analysis (PERSIL, by Govern de les Illes Balears, in progress). Researchers from the University of Lund in Sweden (N. Feiner, and T. Uller, working team) have recently joined the genome project and are currently performing RNAseq analyses for genome annotation (http://feiner-uller-group.se/).

Support for applicants

The International Research Projects Offfice at the University of Barcelona offers support to applicants (eligibility check, info sessions, feedback on the draft proposal) and has recently launched a Mentoring programme specifically designed for MSCA applicants (subject to availability)

The project manager from IRBiIo offers support the applicant during the writing proposal with the supervisor and the International Research Project Office.

Requeriments and Skills:
We look preferentially for candidates with experience on microbiota studies and amplicon metagenomics. The candidate should have good bioinformatics and statistical skills (i.e. processing of Illumina Miseq amplicon data and/or ONT, multivariate statistical analyses), and be familiar with R programming or other languages. We look for a highly motivated candidate with a large interest in microbes, ecology and evolution.


Required Education Level: PhD or equivalent

Required documents: CV and motivation letter

CONTACT: