Biology subjects

Morand, S.

Publications and source records attributed to Morand, S..

13 recordsLinked to original sources

bioRxiv2026

Exploring dog-owner microbiota and bacterial pathogens in Southeast Asia

Domestic dogs may influence human microbiota and act as reservoirs or sentinels for zoonotic bacteria, yet little is known about these dynamics in Southeast Asia. Using full-length 16S rRNA gene sequencing from rectal swabs, we analyzed microbiota from dog-owner pairs from four villages of rural Thailand (Nan province) to assess microbial diversity, shared taxa, and zoonotic potential. Dogs exhibited higher microbial and putative pathogen diversity than humans, particularly during the rainy season. While dog-owner pairs shared more bacteria than unrelated individuals, overall overlap remained limited - likely driven by their dogs free-roaming lifestyles and broader environmental exposures. However, co-occurrence of putative zoonotic pathogens such as Shigella spp. and Klebsiella pneumoniae suggests dogs could serve as useful indicators for specific public health risks, with further targeted pathogen screening needed to validate these results. Our findings highlight the value of integrating dogs into zoonotic surveillance programs, particularly in regions with free-ranging dog populations and close human-animal contact.

microbiology↗

bioRxiv2026

Pathogenic Leptospira in dogs and rodents in Tha Wang Pha, Thailand - Prevalence, diversity and linked environments

Human leptospirosis is a disease of public health importance in Thailand, but the animal species involved in the transmission cycle have not been fully uncovered. This study investigated Leptospira infection in dogs and terrestrial micromammals in rural Nan Province, Thailand, and the pathogen diversity. Sera from 95 seemingly healthy dogs and kidney samples from 399 micromammals were analyzed using real-time PCR for Leptospira detection, followed by conventional PCR and sequencing of infecting Leptospira. We investigated environmental factors associated with Leptospira infection in micromammals, using data collected during trapping. Real-time PCR revealed ongoing infection in 8.4% (8/95) of dogs and 10.0% (40/399) of terrestrial micromammals, with 12 infected species including Bandicota indica, Berylmys berdmorei, Berylmys bowersi, Mus cervicolor, Mus cookii, and Hylomys suillus. In this qPCR-positive micromammals, three pathogenic Leptospira species were identified: L. interrogans, L. weilii, and L. borgpetersenii. This represents the first confirmed detection of L. weilii in rodents in Thailand. Infected micromammals were found in agricultural and forest habitats but not in human settlements. Our study demonstrates potential complex leptospirosis epidemiology in rural Thailand, with multiple species serving as pathogenic Leptospira reservoirs across diverse habitats, and some shared pathogen diversity with human leptospirosis cases in Thailand. Free-roaming dogs may serve as bridge hosts, transmitting zoonotic Leptospira from micromammals to humans by visiting both animal habitats and human settlements. These findings emphasize the need for integrated One Health surveillance approaches to control leptospirosis in rural communities.

molecular biology↗

bioRxiv2025

Listen, who is it? A novel method for studying the nightly and annual phenologies of cave bat communities in data deficient areas of the world.

ContextBats are the only mammals who have conquered the skies and the leading mammals in terms of total biomass with the exception of humans and domestic mammals. However, the ecology of many bat species is still unknown, especially in poorly sampled regions such as Central Africa. AimsWe present the first application of an acoustic method for studying the nocturnal activity patterns and annual phenology of bat activity of cave bat communities in regions where no bat acoustic classifier exists. MethodsIn two caves (Mont Belo and Boundou) in the Republic of Congo, which are home to several species of insectivorous bats throughout the year, we set up a passive acoustic monitoring (PAM) over a period of 19 months. To identify the massive recordings collected, we used a sonotype classifier. To assign a species name or species group to the different sonotypes identified by the classifier, we collected local reference calls by capturing bats at the cave entrances. This enabled us to identify two bat groups and three species despite the absence of local call libraries. The capture sessions also allowed us to collect information about the reproductive condition of the individuals, which we interpreted in relation to the annual phenology of bat activity. To quantify bat activity, we defined the activity of each acoustic group as the number of bat passes, where a bat pass corresponds to the detection of one or several echolocation calls within a five-second interval. This standardized measure allowed us to quantify nightly and seasonal variations in activity. Key resultsThe nightly activity displayed strong peaks in the evening and the morning, except during the long rainy season, when a tri- or quadri-modal activity was detected. This more evenly distributed activity throughout the night is related to the period of juvenile rearing (gestation, parturition and lactation). For all acoustic groups, we also observed a higher activity during the rainy seasons and the short dry season, compared to the long dry season. This high activity is linked to the lactation period, the independence of young bats and potentially the mating period. Finally, the reproductive activity of insectivorous bat species is synchronized with the period of high resource availability. ConclusionThis study represents the first long-term acoustic monitoring of cave bats in the Republic of Congo. This was allowed by the use of a classifier built without any pre-existing regional call data, highlighting a practical pathway for studying bat activity in other data-deficient regions. ImplicationsInformation about the biological status of individuals captured at the monitored caves in association with the cave annual activity phenology produced with this method are key to progress in the understanding of the ecology and the conservation issues of cave bat communities, which are particularly threatened globally.

ecology↗

bioRxiv2023

Ecological factors shaping the ectoparasite community assembly of the Azara Grass Mouse, Akodon azarae (Rodentia: Cricetidae)

Parasites are integral members of the global biodiversity. They are useful indicators of environmental stress, food web structure and diversity. Ectoparasites have the potential to transmit vector-borne diseases of public health and veterinary importance and to play an important role in the regulation and evolution of host populations. The interlinkages between hosts, parasites and the environment are complex and challenging to study, leading to controversial results. Most previous studies have been focused on one or two parasite groups, while host are often co-infected by different taxa. The present study aims to assess the influence of environmental and host traits on the entire ectoparasite community composition of the rodent Akodon azarae. A total of 278 rodents were examined and mites (Mesostigmata), lice (Phthiraptera), ticks (Ixodida) and fleas (Siphonaptera) were determined. A Multi Correspondence Analyses was performed in order to analyse interactions within the ectoparasite community and the influence of environmental and host variables on this assembly. We found that environmental variables have a stronger influence on the composition of the ectoparasite community of A. azarae than the host variables analysed. Minimum temperature was the most influential variable among the studied. In addition, we found evidence of agonistic and antagonistic interactions between ticks and mites, lice and fleas. The present study supports the hypothesis that minimum temperature play a major role in the dynamics that shape the ectoparasite community of A. azarae, probably through both direct and indirect processes. This finding becomes particularly relevant in a climate change scenario.

ecology↗

bioRxiv2021

Rats in the city: implications for zoonotic disease risk in an urbanizing world

Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we began to explore the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the abundance and diversity of reservoir hosts (rodents), ectoparasite vectors (ticks), and microbial pathogens across a gradient of urbanization in Malaysian Borneo. We found that although rodent species diversity decreased with increasing urbanization, two species appeared to thrive in anthropogenic environments: the invasive urban exploiter, Rattus rattus and the native urban adapter, Sundamys muelleri. R. rattus was strongly associated with the presence of built infrastructure across the gradient and dominated the urban rodent community where it was associated with high microbial diversity and multi-host zoonoses capable of environmental transmission, including Leptospira spp., and Toxoplasma gondii. In contrast, S. muelleri was restricted to sites with a significant vegetative component where it was found at high densities in the urban location. This species was strongly associated with the presence of ticks, including the medically important genera Ambylomma, Haemaphysalis, and Ixodes. Overall, our results demonstrate that the response to urbanization varies by species at all levels: host, ectoparasite, and microbe. This may lead to increased zoonotic disease risk in a subset of environments across urban and urbanizing landscapes that can be reduced through improved pest management and public health messaging.

ecology↗

bioRxiv2020

Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ)

1. Most species in ecological communities are rare whereas only a few are common. This distributional paradox has intrigued ecologists for decades but the interpretation of species abundance distributions remains elusive. 2. We present Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ) as an R package. FuzzyQ shifts the focus from the prevailing species-categorization approach to develop a quantitative framework that seeks to place each species along a rare-commonness gradient. Given a community surveyed over a number of sites, quadrats, or any other convenient sampling unit, FuzzyQ uses a fuzzy clustering algorithm that estimates a probability for each species to be common or rare based on abundance-occupancy information. Such as probability can be interpreted as a commonness index ranging from 0 to 1. FuzzyQ also provides community-level metrics about the coherence of the allocation of species into the common and rare clusters that are informative of the nature of the community under study. 3. The functionality of FuzzyQ is shown with two real datasets. We demonstrate how FuzzyQ can effectively be used to monitor and model spatio-temporal changes in species commonness, and assess the impact of species introductions on ecological communities. We also show that the approach works satisfactorily with a wide range of communities varying in species richness, dispersion and abundance currencies. 4. FuzzyQ produces ecological indicators easy to measure and interpret that can give both clear, actionable insights into the nature of ecological communities and provides a powerful way to monitor environmental change on ecosystems. Comparison among communities is greatly facilitated by the fact that the method is relatively independent of the number of sites or sampling units considered. Thus, we consider FuzzyQ as a potentially valuable analytical tool in community ecology and conservation biology.

ecology↗

bioRxiv2020

The accelerated infectious disease risk in the Anthropocene: more outbreaks and wider global spread

The greatly accelerated economic growth during the Anthropocene has resulted in astonishing improvements in many aspects of human well-being, but has also caused the acceleration of risks, such as the interlinked biodiversity and climate crisis. Here, we report on another risk: the accelerated infectious disease risk associated with the number and geographic spread of human infectious disease outbreaks. Using the most complete, reliable, and up-to-date database on human infectious disease outbreaks (GIDEON), we show that the number of disease outbreaks, the number of diseases involved in these outbreaks, and the number of countries affected have increased during the entire Anthropocene. Furthermore, the spatial distribution of these outbreaks is becoming more globalized in the sense that the overall modularity of the disease networks across the globe has decreased, meaning disease outbreaks have become increasingly pandemic in their nature. This decrease in modularity is associated with tremendous increases in mobility, especially in air traffic. We also show that those countries and regions which are most central within these disease networks tend to be countries and global regions with higher GDPs. Therefore, one cost of greater economic growth and the associated increased global mobility is the increased risk of disease outbreaks and their wider spread. Finally, the recent global outbreaks of Covid-19 and monkeypox allowed us to demonstrate that the time of first occurrence in each country was correlated with each countrys centrality value in the disease network. We briefly discuss three different scenarios of how mobility may develop in the future which decision-makers might discuss in light of our results.

ecology↗

bioRxiv2019

Diversity and complexity of the large surface protein family in the compacted genomes of various Pneumocystis species

Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins, and provide detailed description of the classification, unique characteristics and phylogenetic relatedness of five Msg families. We further describe the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety of functions for this superfamily, not only conferring antigenic variation to allow immune evasion but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting to specific host niches or environmental conditions. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology.

molecular biology↗

bioRxiv2019

Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli mice allows protection from multiple retroviruses

Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. To begin to understand how restriction factors evolve, we surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice (Mus caroli, M. cervicolor and M. cookii). The presence of flanking repeats suggested it arose by LINE-mediated retrotransposition. A high degree of natural variation was observed in both Fv1 and Fv7, including numerous single nucleotide polymorphisms resulting in altered amino acids, as well as insertions and deletions that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes with activities directed against feline foamy virus (FFV), equine infectious anemia virus (EIAV) and MLV. It seems likely, at least in the case of M. caroli, that the observed gene duplication confers protection against multiple viruses not possible with a single restriction factor. We suggest that EIAV-, FFV- and MLV-like viruses are endemic within these populations, driving the evolution of the Fv1 and Fv7 genes.\n\nAuthor SummaryDuring the passage of time all vertebrates will be exposed to infection by a variety of different kinds of virus. To meet this threat, a variety of genes for natural resistance to viral infection have evolved. The prototype of such so-called restriction factors is encoded by the mouse Fv1 gene, which acts to block the life cycle of retroviruses at a stage between virus entry into the cell and integration of the viral genetic material into the nuclear DNA. We have studied the evolution of this gene in certain species of wild mice from South East Asia and describe an example where a duplication of the Fv1 gene has taken place. The two copies of the gene, initially identical, have evolved separately allowing the development of resistance to two rather different kinds of retroviruses, lentiviruses and spumaviruses. Independent selection for resistance to these two kinds of retrovirus suggests that such mice are repeatedly exposed to never-before-reported pathogenic retroviruses of these genera.

evolutionary biology↗

bioRxiv2019

Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand

Scrub typhus, caused by a bacterial pathogen (Orientia spp.), is a potentially life-threatening febrile illness widely distributed in the Asia-Pacific region and is emerging elsewhere. The infection is transmitted by the larval stage of trombiculid mites (\"chiggers\") that often exhibit low host specificity. Here, we present an analysis of chigger ecology for 38 species sampled from 11 provinces of Thailand and microbiomes for eight widespread species. In total, >16 000 individual chiggers were collected from 1 574 small mammal specimens belonging to 18 species across four horizontally-stratified habitat types. Chigger species richness was positively associated with higher latitudes, dry seasonal conditions, and host maturity; but negatively associated with increased human land use. Human scrub typhus incidence was found to be positively correlated with chigger species richness. The bacterial microbiome of chiggers was highly diverse, with Sphingobium, Mycobacterium, Neisseriaceae and various Bacillales representing the most abundant taxa. Only Leptotrombidium deliense was found to be infected with Orientia. {beta}-diversity, but not -diversity, was significantly different between chigger species and geographic regions, although not between habitat types. This first field survey of the chigger microbiome provides a framework for future studies on interactions between pathogens and other symbionts in these understudied vectors.

microbiology↗

bioRxiv2018

Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species

Emerging infectious diseases arising from pathogen spillover from mammals to humans comprise a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines. However, the species that share pathogens most widely with other mammals, and the role of different wildlife groups in sharing viruses with humans remain poorly identified. To address this challenge, we applied network analysis and Bayesian hierarchical models to a global database of mammal-virus associations. We show that domesticated mammals and some primates hold the most central positions in networks of known mammal-virus associations. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses, while the frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than DNA viruses. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses with other host species, while network centrality of Primates scored relatively high for sharing DNA viruses. Ungulates hold central positions for sharing both RNA and DNA viruses. Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change.

ecology↗

bioRxiv2018

Objective Classification of Neocortical Pyramidal Cells

A consensus on the number of morphologically different types of pyramidal cells (PCs) in the neocortex has not yet been reached, despite over a century of anatomical studies. This is because of a lack of agreement on the subjective classifications of neuron types, which is based on expert analyses of neuronal morphologies: the shapes of somata, dendrites, and axons. Even for neurons that are visually different to non-experts, there is no common ground to consistently distinguish morphological types. We found that objective classification is possible with methods from algebraic topology, and that the dendritic arbor is sufficient for reliable identification of distinct types of PCs. We also provide a solution for the more challenging problem of whether two similar neurons belong to different types or to a continuum of the same type. Using this scheme, we objectively identify seventeen types of PCs in the rat somatosensory cortex. Our topological classification does not require expert input, is stable, and helps settle the long-standing debate on whether cell-types are discrete or continuous morphological variations of each other.

neuroscience↗

bioRxiv2016

Evolutionary history of the brown rat: out of southern East Asia and selection

The brown rat (Rattus norvegicus) is found wherever humans live and transmits many diseases, and its breeding produced the laboratory rat used widely in medical research. Here, we sequenced whole genomes from 118 rats to explore the origin and dispersal routes of the brown rat and the domestication of the laboratory rat. We showed that brown rats migrated about 3600 years ago from southern East Asia, rather than Northern Asia as formerly suggested, to the Middle East and then to Europe and Africa. Many genes involved in the immune system experienced positive selection in the wild brown rat, while genes involved in the nervous system and energy metabolism showed evidence of artificial selection during the domestication of laboratory strains. Our findings demystify the puzzling origin and migration of brown rats and reveal the impact of evolution and domestication on this animal.

evolutionary biology↗