Biology subjects

Gilissen, E.

Publications and source records attributed to Gilissen, E..

5 recordsLinked to original sources

bioRxiv2026

Museum specimens reveal evolutionary drivers and functions of oral microbiome in mammals

The microbiomes of wild animals, despite being integral to host survival, remain largely unexplored, particularly beyond the gut. Here, using > 450 museum-preserved dental calculus samples from 34 ecologically and phylogenetically diverse mammalian species, most of them previously unstudied, we determine the main drivers of oral microbiome evolution. We show that, similar to the gut, the oral microbiome is shaped by host ecology, particularly diet, and to a lesser extent host phylogenetic relationships. It may contribute to host adaptation, by synthesising essential micronutrients and degrading potentially harmful compounds. We also find that some oral microorganisms consistently associated with mammals throughout over evolutionary time scales and provide evidence for a likely oral origin of some rumen taxa. Together our findings demonstrate the importance of this mostly overlooked microbial community for mammalian biology.

evolutionary biology↗

bioRxiv2025

Dental calculus formation is linked to diet and phylogeny in mammals

O_LIAs a point of entry, the oral cavity serves as a potential first area of colonization of the host with environmental bacteria. As such, the oral microbial community not only affects a wide range of internal host processes, including health and digestion but may also reflect the external environment and ecology of the host. C_LIO_LIDental calculus, a mineralized form of dental plaque, preserves the DNA of the host microbiome through time, serving as a rich source of historical microbiota. Despite its potential to provide temporal information on the ecological and evolutionary processes of microbiomes, dental calculus has rarely been explored outside of humans and non-human primates. Hence, it remains unclear how ubiquitous it is across mammals. C_LIO_LIUsing natural history museum collections, we surveyed > 1600 specimens belonging to 142 species, representative of every mammalian order, to investigate the taxonomic distribution of dental calculus, and to identify factors that most strongly contribute to its formation. We found dental calculus to be abundant across mammalian taxa, with 104 of the surveyed species showing calculus deposits. C_LIO_LIHigh fiber diets were most strongly associated with calculus presence and abundance, whereas species with high protein and fat diets showed little to no calculus deposits. We also found evidence of phylogenetic signal in calculus formation, pointing to the effects of oral/dental morphology. In addition, captivity strongly affected dental calculus formation in almost all dietary categories. Using this information, we made predictions about the likelihood of finding dental calculus in unsurveyed mammalian species, with the aim of informing future investigations. C_LIO_LIOur study found that dental calculus is readily available in natural history museum collections, making it an easily accessible source of oral microbiota from wild animals. We highlight the taxonomic diversity of species presenting dental calculus and provide information and suggestions to researchers and museum curators interested in utilizing dental calculus for the study of oral microbiota, past and present. C_LI

ecology↗

bioRxiv2025

Host traits impact the outcome of metagenomic library preparation from dental calculus samples across diverse mammals

Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. While we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly due to both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing, and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.

genomics↗

bioRxiv2023

Linking the evolution of two prefrontal brain regions to social and foraging challenges in primates

The diversity of cognitive skills across primates remains both a fascinating and a controversial issue. Recent comparative studies provided conflicting results regarding the contribution of social vs ecological constraints to the evolution of cognition. Here, we used an interdisciplinary approach combining comparative cognitive neurosciences and behavioral ecology. Using brain imaging data from 16 primate species, we measured the size of two prefrontal brain regions, the frontal pole (FP) and the dorso-lateral prefrontal cortex (DLPFC), respectively involved in metacognition and working memory, and examined their relation to a combination of socio-ecological variables. The size of these prefrontal regions, as well as the whole brain, was best explained by three variables: body mass, daily traveled distance (an index of ecological constraints) and population density (an index of social constraints). The strong influence of ecological constraints on FP and DLPFC volumes suggests that both metacognition and working memory are critical for foraging in primates. Interestingly, FP volume was much more sensitive to social constraints than DLPFC volume, in line with laboratory studies showing an implication of FP in complex social interactions. Thus, our data highlights the relative weight of social vs ecological constraints on the evolution of specific prefrontal brain regions and their associated cognitive operations in primates. FundingThis work was supported by recurrent funding from CNRS to SB, SP and CG. It was also supported by the ANR-17-CE27-0005 (HOMTECH).

neuroscience↗

bioRxiv2019

Primate hippocampus size and organisation are predicted by sociality but not diet

The hippocampus is well known for its roles in spatial navigation and memory, but it is organized into regions that have different connections and functional specializations. Notably, the region CA2 has a role in social and not spatial cognition, as is the case for the regions CA1 and CA3 that surround it. Here we investigated the evolution of the hippocampus in terms of its size and organization in relation to the evolution of social and ecological variables in primates, namely home range, diet and different measures of group size. We found that the volumes within the whole cornu ammonis coevolve with group size, while only the volume of CA1 and subiculum can also be predicted by home range. On the other hand, diet, expressed as a shift from folivory toward frugivory, was shown to not be related to hippocampal volume. Interestingly, CA2 was shown to exhibit phylogenetic signal only against certain measures of group size but not with ecological factors. We also found that sex differences in the hippocampus are related to body size sex dimorphism. This is in line with reports of sex differences in hippocampal volume in non-primates that are related to social structure and sex differences in behaviour. Our findings support the notion that in primates, the hippocampus is a mosaic structure evolving in line with social pressures, where certain subsections evolve in line with spatial ability too.

evolutionary biology↗