Dataset Information

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.

ABSTRACT: Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.

SUBMITTER: Nanetti E

PROVIDER: S-EPMC11233967 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature

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The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.

Nanetti Enrico E Scicchitano Daniel D Palladino Giorgia G Interino Nicolò N Corlatti Luca L Pedrotti Luca L Zanetti Federica F Pagani Elena E Esposito Erika E Brambilla Alice A Grignolio Stefano S Marotti Ilaria I Turroni Silvia S Fiori Jessica J Rampelli Simone S Candela Marco M

iScience 20240606 7

Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (<i>Capra ibex</i>) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome th ...[more]

PMID: 38989465

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Project description:BackgroundThe cyst-forming coccidia of the genus Sarcocystis (Sarcocystidae) are widespread protists of mammals, particularly of domestic and wild ruminants. Research on genus Sarcocystis in wild members of the subfamily Caprinae is, however, rather limited. Sarcocystis in the Alpine ibex (Capra ibex) have only been investigated in depth once and then solely by morphological techniques. In the current investigation we aimed to morphologically and genetically characterise Sarcocystis species of Alpine ibex in Austria.MethodsSarcocysts detected in the diaphragm and myocardium muscles were morphologically described using light microscopy and transmission electron microscopy (TEM). Isolated sarcocysts were molecularly identified and characterised at the level of the 18S ribosomal RNA (rRNA) gene and cytochrome c oxidase I gene (cox1). The obtained sequences were subjected to phylogenetic analysis.ResultsThree Sarcocystis species, namely S. capracanis, S. cornagliai and S. rossii n. sp., were found in Alpine ibex. For the first time, we genetically characterised S. cornagliai, which is most closely related to Sarcocystis species that are transmitted by corvid birds. Sarcocysts of S. rossii n. sp. were found to be ribbon-shaped, with pointed tips. Hair-like protrusions about 5 μm in length were observed on sarcocyst walls. Observation of toluidine blue-stained semi-thin sections revealed that the sarcocyst of S. rossii n. sp. was thin-walled. Using TEM, cyst walls were observed to be similar to type 7a, with thin hair-like villar protrusions on the cyst wall, which were filled with many fine electron-dense granules. The ground substance layer was particularly thin, measuring 0.2-0.4 μm. The cox1 sequences of S. rossii n. sp. had the highest similarity to those of Sarcocystis arieticanis and Sarcocystis hircicanis. Sarcocystis rossii n. sp. had a close phylogenetic relationship with species that use canids as definitive hosts.ConclusionsThis study confirms the role of the Alpine ibex as an intermediate host of three Sarcocystis species and sets a new host record for S. capracanis. It also provides the first molecular data on Sarcocystis from Alpine ibex and on S. cornagliai. In addition, a new species, S. rossii, was identified and described. Phylogenetic analyses suggested corvid birds and canids as potential definitive hosts for S. cornagliai and S. rossii n. sp., respectively.

Project description:BackgroundDefining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions.ResultsWe tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Previous studies based on large sample sizes taken from its principal populations have revealed that the Iberian ibex has a remarkably small MHC DRB1 diversity (only six remnant alleles) as a result of recent population bottlenecks and a marked demographic decline that has led to the extinction of two recognized subspecies. Extending on the geographic range to include non-studied isolated Iberian ibex populations, we sequenced a new MHC DRB1 in what seemed three small isolated populations in Southern Spain (n = 132). The findings indicate a higher genetic diversity than previously reported in this important gene. The newly discovered allele, MHC DRB1*7, is identical to one reported in the domestic goat C. aegagrus hircus. Whether or not this is the result of ancient polymorphisms maintained by balancing selection or, alternatively, introgressions from domestic goats through hybridization needs to be clarified in future studies. However, hybridization between Iberian ibex and domestic goats has been reported in Spain and the fact that the newly discovered allele is only present in one of the small isolated populations and not in the others suggests introgression. The new discovered allele is not expected to increase fitness in C. pyrenaica since it generates the same protein as the existing MHC DRB1*6. Analysis of a microsatellite locus (OLADRB1) near the new MHC DRB1*7 gene reveals a linkage disequilibrium between these two loci. The allele OLADRB1, 187 bp in length, was unambiguously linked to the MHC DRB1*7 allele. This enabled us to perform a DRB-STR matching method for the recently discovered MHC allele.ConclusionsThis finding is critical for the conservation of the Iberian ibex since it directly affects the identification of the units of this species that should be managed and conserved separately (Evolutionarily Significant Units).

Dataset Information

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.

Publications

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.

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