Biology subjects

Lebarbenchon, C.

Publications and source records attributed to Lebarbenchon, C..

14 recordsLinked to original sources

bioRxiv2026

Brown and Lesser noddies as epidemiological reservoirs and sentinels of avian influenza virus in the South-western Indian Ocean

Avian influenza virus (AIV) epidemiology is well-documented in temperate regions but remains poorly understood in isolated ecosystems like tropical oceanic islands. On these islands, seabirds nest in dense interspecific colonies where the role of different species as reservoirs and dispersers of AIV may vary greatly. Here, we examine the role of noddies (Anous spp.) as potential reservoirs for low pathogenic AIV and evaluate their potential as sentinel species for highly pathogenic AIV introduction on tropical oceanic islands. We analyzed blood samples from 11 seabird species across eight islands in the southwestern Indian Ocean (2015-2020). Noddies exhibited high, stable seroprevalence (30-45%), comparable to reservoir host species in temperate regions. The detection of two N7-positive noddies, sampled the same year on two distinct islands, provided direct molecular evidence that AIV actively circulates on these island colonies. While most other species showed low exposure, Bridled Terns (Onychoprion anaethetus) had exceptionally high seroprevalence (80%), though their reservoir status requires further investigation due to limited sampling. Given noddies consistent exposure and regional distribution, we recommend prioritizing islands with large noddy populations for AIV surveillance. Continued investigation of viral dynamics within and among islands is now called for to elucidate the ecological drivers of AIV maintenance and transmission.

ecology↗

bioRxiv2025

How do urban-dwelling bats cope with urbanisation? Sex-dependent plasticity of stress, microbiome and pathogen shedding

Understanding wildlifes stress and infection response patterns is crucial, especially for species like bats that are ecologically important and potential zoonotic reservoirs. While highly sensitive to habitat destruction and land use change, bats have shown adaptability in human-modified landscapes. This study investigates the impact of urbanisation on the endemic Reunion free-tailed bat (Mormopterus francoismoutoui), which roosts in a variety of rapidly urbanised habitats. We analysed 412 urine samples from 11 roosts across Reunion Island, covering a gradient of urban and agricultural land use. We measured urinary cortisol, microbiome diversity and the shedding of Leptospira bacteria and paramyxovirus. After accounting for natural cortisol level variations due to circadian rhythm, age, sex, reproduction and capture-induced stress, we found that bats roosting in agricultural and urban areas were in better condition and had lower cortisol levels, suggesting adaptation to human-modified landscapes. Less-stressed bats had more diverse urinary microbiomes and reduced pathogen shedding, suggesting that landscape modifications may indirectly alter the natural epidemiology of bat-borne infectious agents. These patterns were particularly pronounced in females, supporting sex-dependent plasticity to urbanisation in bats. Our study highlights how rapid urbanisation may elicit plastic responses in bats, with potential cascading effects on zoonotic risk of transmission.

ecology↗

bioRxiv2025

Urban bats change the menu: dietary plasticity across human-modified landscapes of a tropical island

In a rapidly urbanizing world, research on dietary habits of wildlife is essential to understand how plastic behaviors may guide evolutionary trajectories of endangered animal species. Bats are very sensitive to habitat destruction and land-use change, although some species have shown the capacity for adaptation to urban life. In this study, we tested to what extent urban insectivorous bats modify their feeding strategies in a recently human-modified tropical insular ecosystem. Using a DNA metabarcoding approach on fecal samples collected in seven roosts, we analyzed the dietary niche of free-tailed bats (Mormopterus francoismoutoui) endemic to Reunion Island. Our results revealed a wide dietary niche, including 174 arthropod species in 12 orders, among which lepidopterans were predominant. We identified several crop pests and disease vectors, highlighting the central role of this bat species for agroecology and epidemiology concerns. Our study also highlighted potential sex- and reproduction-related dietary strategies. Moreover, we found that agriculture areas, inferred from land cover surrounding bat roosts, were associated with higher relative abundance of Lepidoptera in the diet of bats. In contrast, bats roosting in urban areas increased their consumption of Blattodea. As Reunion free-tailed bats roost and thrive in human-modified landscapes, understanding the consequences of this dietary plasticity for bat health and fitness will be necessary for urban evolutionary research and conservation actions.

ecology↗

bioRxiv2025

Bat things come in threes: within-host dynamics of herpesvirus triple infection in bats

Understanding viral community ecology in bats is essential for elucidating shedding patterns and the drivers of co-infections. In this study, we explore the genetic diversity and within-host dynamics of herpesviruses (HSV) in Mormopterus francoismoutoui, a tropical insectivorous bat endemic to Reunion Island. Over three consecutive years, we collected saliva samples from seven roosts, including repeated samples from recaptured individuals. Illumina sequencing of HSV PCR-positive samples revealed a high diversity of strains (n = 20), belonging to alpha, beta and gamma-HSV subfamilies. Co-infection was frequent, with 44% of bats shedding strains from all three subfamilies. While most shedding patterns with different subfamilies appeared random, our results suggested a negative influence of gamma-HSV occurrence of the probability of co-shedding alpha-HSV. We also demonstrated a lower HSV diversity in juveniles as compared to adult bats, while pregnancy appeared to increase viral diversity--although this requires further confirmation. Longitudinal recaptures of bats revealed an accumulation of multiple HSV latent-infections over life, as the probability to be infected with a new subfamily increased with time interval between recaptures. Within-host strain dynamics were highly variable, with 79% of bats showing fluctuations in strain diversity over time--either gaining or losing strains--consistent with latency and reactivation mechanisms. These findings provide new insights into the ecological and evolutionary dynamics of herpesviruses in wild bat populations.

evolutionary biology↗

bioRxiv2024

Role of individual and population heterogeneity in shaping dynamics of multi-pathogen excretion in an island endemic bat

Understanding processes driving pathogen transmission in bats is critical to prevent spillovers and emergence events. Although substantial research has addressed this topic, few studies have directly examined shedding dynamics (as opposed to serological studies) and co-infection patterns using fine-scale spatio-temporal datasets. Here, based on the monitoring of 5,714 Reunion free-tailed bats (Mormopterus francoismoutoui) in 17 roosts over 24 months, we studied the co-shedding dynamics of paramyxoviruses (PMV) and Leptospira bacteria (LEPTO) in urine, and herpesviruses (HSV) in saliva. We evidenced all year long shedding with high prevalence of all three infectious agents (37% - 87%), as well as an exceptionally high level of co-shedding (59%), with both positive and negative interactions between infectious agents. Shedding patterns displayed temporal synchrony among roosts, with a peak during summer months, but were not influenced by roost size. Repeated shedding in recaptured bats supports within-host persistence, though underlying mechanisms remain to be identified. Our results also showed rapid HSV infection of juveniles (< 6 months), and suggest longer protection of juveniles by maternal antibodies for PMV and LEPTO. Reproductive individuals (both during the pregnancy and mating) were associated to increased PMV and LEPTO shedding, which can result from tradeoffs between reproduction and infection in both sexes, and/or an age-related bias with the progressive infection of older juveniles during reproductive periods. This study highlights the significance of persistent shedding of multiple pathogens, including bacteria, and their intricate interactions within bat populations. Understanding how human-driven ecological changes may disrupt within-host processes and influence pathogen shedding in bats will help assessing the risk of pathogen spillover from bats to other species, including humans. Author summaryUnderstanding risks of bat-borne pathogen spillover is challenging because of the difficulty in studying shedding dynamics in wild bat populations. Here, we used an original island-endemic bat species to build up a fine-scale spatio-temporal shedding analysis of two viruses (paramyxoviruses and herpesviruses) and a bacterium (Leptospira) at both population- (roost) and individual- (through recaptured bats) levels. Shedding patterns are driven by the age of bats and associated to the reproductive periods in both females and males. Results also suggest that persistence, as well as interactions between infectious agents, are important within-host processes that contribute to the transmission of infections in bat populations. More research is essential to understand how human activities may influence these co-shedding patterns and the risk of cross- species transmission.

evolutionary biology↗

bioRxiv2023

Absence of Coronavirus in terns in the Western Indian Ocean?

We investigated coronavirus circulation in three tern species, in four islands of the Western Indian Ocean (Bird, Reunion, Europa, Juan de Nova). None of the 1513 samples tested positive by RT-PCR. We discuss the implication in term of host species range, ecological drivers of virus transmission, and diagnostic tools.

ecology↗

bioRxiv2023

Stuck on a small tropical island: wide in-situ diversification of an urban-dwelling bat

Bats are often the only mammals naturally colonizing isolated islands and are thus an excellent model to study evolutionary processes of insular ecosystems. Here, we studied the Reunion free-tailed bat (Mormopterus francoismoutoui), an endemic species to Reunion Island that has adapted to urban settings. At regional scale, we investigated the evolutionary history of Mormopterus species, as well as on Reunion Island sex-specific and seasonal patterns of genetic structure. We used an extensive spatio-temporal sampling including 1,136 individuals from 18 roosts and three biological seasons (non-reproductive/winter, pregnancy/summer, and mating), with additional samples from Mormopterus species from neighbouring islands (M. jugularis of Madagascar and M. acetabulosus of Mauritius). Complementary information gathered from both microsatellite and mitochondrial markers revealed a high genetic diversity but no signal of spatial genetic structure and weak evidence of female philopatry. Regional analysis suggests a single colonization event for M. francoismoutoui, dated around 175,000 years ago, and followed by in-situ diversification and the evolution of divergent ancestral lineages, which today form a large metapopulation. Population expansion was relatively ancient (55,000 years ago) and thus not linked to human colonization of the island and the availability of new anthropic day-roost sites. Discordant structure between mitochondrial and microsatellite markers suggests the presence of yet-unknown mating sites, or the recent evolution of putative ecological adaptations. Our study illustrates how understanding mechanisms involved in speciation can be challenging and the importance of both mitochondrial and nuclear DNA in resolving the wide in-situ diversification of an urban-dwelling bat, endemic to a small island.

genetics↗

bioRxiv2023

What can New Zealand bats tell us about Coronaviruses?

The current Covid-19 pandemic emphasizes the dramatic consequences of emerging zoonotic pathogens and stimulates the need for an assessment of the evolution and natural cycle of such microbes in a One Health framework. A number of recent studies have revealed an astonishing diversity of bat-borne Coronaviruses, including in insular environments, which can be considered as simplified biological systems suited for the exploration of the transmission cycles of these viruses in nature. In this work, we present two new lineages of alpha Coronaviruses detected by screening the only two extant New Zealand bat species: the lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus). Infection prevalence reaching 60% in long-tailed bats makes this host-pathogen model relevant for the investigation of maintenance mechanisms in a bat reservoir with peculiar physiological adaptations to temperate climates. A phylogenetic analysis shows that these viral lineages do cluster with Coronaviruses hosted by bat sister species from Australia, supporting co-diversification processes and confirming that the evolution of these viruses is tightly linked to that of their hosts. These patterns provide an interesting framework for further research aiming at elucidating the natural history and biological cycles of these economically-devastating zoonotic viruses.

ecology↗

bioRxiv2023

Migratory patterns of two major influenza virus host species on tropical islands

Animal migration is a major driver of infectious agent dispersal. Duck and seabirds migrations, for instance, play a key role in the spatial transmission dynamics and gene flows of avian influenza viruses (AIV), worldwide. On tropical islands, brown and lesser noddies (Anous stolidus and A. tenuirostris) may be important AIV hosts, but the lack of knowledge on their migratory behaviour limits our understanding of virus circulation in island networks. Here we show that high connectivity between islands generated by post-breeding behaviours could be a major driver in the spread and the maintenance of AIV among tropical islands. Tracking data highlight two types of behaviours during the non-breeding season: birds either staying in the vicinity of their breeding ground (on Bird Island, Seychelles), or moving to and roosting on other islands in the Indian Ocean. Differences in roosting places are detected between migrant birds, ranging from the Tanzanian coast to the Maldives archipelago and Tromelin Island. Epidemiological data further support that brown and lesser noddies are major hosts for AIV, although significant variation of seroprevalence between species suggest that other drivers are involved in virus infection and transmission dynamics.

ecology↗

bioRxiv2022

Synchronicity of viral shedding in molossid bat maternity colonies

Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated to major increase in the prevalence of bats shedding viruses. The synchronicity of such shedding pulses, however, is yet to be assessed, between viruses but also maternity colonies. Based on 3422 fresh faeces collected every two to five weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs), and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection dates, and therefore by the seasonality of parturition. We highlight that virus shedding patterns are reproducible among years and colonies for CoVs and at a lesser extent for PMVs, but not for AstVs. We also report 1% of bats harbouring double infections, mostly CoVs and PMVs, but none shedding simultaneously AstVs, CoVs and PMVs.

ecology↗

bioRxiv2020

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, "MyCoV", which provides a method for attributing subgenus and assessing the reliability of the attribution. Importance StatementThe analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package MyCoV which classifies user generated sequences.

evolutionary biology↗

bioRxiv2019

Astrovirus in Reunion Free-tailed Bat (Mormopterus francoismoutoui)

Astroviruses (AstVs) are RNA viruses infecting of a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from June 21st 2016 to September 4th 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. A phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

ecology↗

bioRxiv2019

Bat coronavirus phylogeography in the western Indian Ocean

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% {+/-} 4.9%) as compared to those sampled on islands (4.5% {+/-} 1.5%). Phylogenetic analyses revealed a large diversity of - and {beta}-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. ImportanceThis is the first study to report the presence of coronaviruses (CoVs) in bats in Mayotte, Mozambique and Reunion Island, and in insectivorous bats in Madagascar. Eight percent of the tested bats were positive for CoVs, with higher prevalence in continental Africa than on islands. A high genetic diversity of - and {beta}-CoVs was found, with strong association between bat host and virus phylogenies, supporting a long history of co-evolution between bats and their associated CoVs in the Western Indian Ocean. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.

evolutionary biology↗

bioRxiv2019

Exploring the infection dynamics of a bacterial pathogen on a remote oceanic island reveals annual epizootics impacting an albatross population

Oceanic islands with reduced species richness provide an opportunity to investigate the emergence, maintenance and transmission of infectious diseases threatening wildlife. On Amsterdam Island, in the southern Indian Ocean, massive and recurrent mortality of the nestlings of Indian yellow-nosed albatross (Thalassarche carteri) has been attributed to avian cholera caused by Pasteurella multocida, a bacterial pathogen of likely human introduction. To understand the annual dynamics of pathogen prevalence, we measured the shedding of bacterial DNA by the albatrosses during four successive breeding seasons. The screening of 583 bird swabs by Real-Time PCR revealed an intense circulation of P. multocida during each study year, with a steady increase of infection prevalence across the breeding season. In the three years of highest pathogen prevalence, the epizootics were associated with massive die-offs of nestlings, inducing low annual fledging success (< 20%). These findings and developed PCR protocol have crucial applications for refining wildlife conservation plans aiming at controlling this disease.

ecology↗