Abstract Animal personality influences organismal interactions and individual habitat use. Rodents are zoonoses reservoirs and often exposed to several pathogens simultaneously, potentially resulting in interdependence of infections and susceptibility to infection. Still, entire pathogen communities are rarely investigated, even though, given rodents ubiquity in human settlements, understanding the link between animal personality and pathogenesis is an important public health issue. We investigated the association of animal personality with pathogen communities in wild rodents, analysing ectoparasite occurrence and pathogenic bacteria of 93 individuals belonging to 3 species from urban and forest areas around Potsdam, Germany. Individual personality was quantified using a combination of open-field and dark-light test. Rodents were then euthanised and screened for pathogens in the spleen through 16 S rRNA amplicon sequencing, and ectoparasites were collected. We detected 6 pathogenic bacteria and 3 ectoparasite taxa. Host species and sampling time explained most of the variation in pathogen associations, but within each genus, 7–9% of the variation was explained by animal personality. Active rodents were more likely infected by Bartonella than less active ones. Bold animals had lower tick infestation probabilities. Thus, animal personality contributes to the distribution and prevalence of pathogens in wild rodents, and should be considered in epidemiology and disease management.

Invasive species can disrupt native epidemiological processes, potentially leading to the emergence of zoonotic pathogens. The relatively recent appearance and spread of the bank vole (Clethrionomys glareolus) in Ireland provides a unique model system to study these phenomena. The depauperate small mammal community in Ireland, combined with baseline data, allows us to identify the invasion gradient of C. glareolus and its effects on rodent-borne pathogens over time. A total of 498 C. glareolus and 584 Apodemus sylvaticus were sampled, via removal trapping, across nine sites in Ireland in 2016 and 2017, with six sites revisited in 2021 and 2022. 16S rRNA metabarcoding identified 10 putative pathogenic Operational Taxonomic Units (OTUs) present in these rodents, relating to four bacterial taxa, Bartonella spp., Mycoplasma coccoides, Mycoplasma haemomuris and Mycoplasma penetrans, and one family of protozoans, Sarcocystidae. Several epidemiological processes were found to be correlated with the C. glareolus invasion; firstly, C. glareolus in Ireland exhibited patterns consistent with the enemy release hypothesis, compared to native populations in France, and the native A. sylvaticus in Ireland. Secondly, a potential dilution effect, with reduced prevalence of M. haemomuris in A. sylvaticus at the C. glareolus invasion core compared to the invasion front, was observed. Finally, C. glareolus had increased prevalence of Sarcocystidae at the invasion front when compared to the invasion core, depending on the time and stage of invasion. These findings further our understanding of pathogen dynamics during biological invasions, demonstrating that invaders affect native host-pathogen communities differently as they advance through various stages of establishment.

Despite advances in understanding infectious diseases, the persistence and re-emergence of wildlife pathogens continue to raise public and veterinary health concerns. This study investigates the relationship between biodiversity and rodent-borne diseases in Europe, focusing on habitat alterations and their impact on rodent diversity. We present host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals-wildlife interactions are likely to occur. From 2020 to 2022, 3766 specimens comprising 15 different small mammal species were analyzed. Samples were screened for bacteria via 16S rRNA sequencing or PCR, and for viral antibodies using immunofluorescent assays. Pathogens from several genera, including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus, and Orthopoxvirus, were detected at non-negligible prevalence in 11 host species. Host community composition differed between habitats, with more urban adapters in parks than in forests. Pathogen richness increased with an increase in host species diversity, supporting the "host-diversity begets parasite-diversity" hypothesis, though not with anthropization. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community driven by human impact. Host species and intrinsic factors were dominant explanatory variables for Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors influenced variations in several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus served as important connector hosts in urban spaces and temperate forests, respectively. These results improve our understanding of the complex local host-pathogen system, aiding future management decisions and supporting the public health sector.

The emergence of infectious diseases associated with land-use changes is well-documented. However, the presence and dynamics of zoonotic pathogens in small mammals within European forests, whether from rural development or urban greening, remain underexplored. To describe zoonotic hazards in these ecosystems, and to assess the influence of biotic and abiotic factors on their distribution, we analyzed 1549 individuals from 18 small mammal species sampled across forest types representing different levels of anthropization using both targeted and broad-spectrum serological and molecular methods. We detected nine bacteria and five Apicomplexa that are potentially pathogenic to humans. Zoonotic pathogen richness and community composition varied significantly across host species, sites, and sampling periods. Richness was lower in forested urban parks, possibly due to the absence of vectors or intermediate hosts within cities. It was higher in urban adapter species, even within a given forested habitat, emphasizing the important role of specific life-history traits. Pathogen community structure was shaped by forest anthropization and host ecology, with marked differences between urban and rural forested environments and between urban adapter and dweller species within forested urban parks. The seroprevalence of key pathogens (e.g., Bartonella, Orthopoxvirus, Neoehrlichia mikurensis, and Sarcocystidae) showed spatial, temporal, and host-specific variation. Epidemiological differences between sites often exceeded those between habitat types, in particular when comparing protected and managed forests, highlighting the importance of local ecological context. Nevertheless, some patterns reflected the influence of forest anthropization and species urban adaptation strategies for certain zoonotic agents. High anthropization in forests was associated with elevated Bartonella prevalence, driven by urban-adapter species rather than forest dwellers, emphasizing local ecological interactions between hosts and pathogens. Besides, higher levels of Orthopoxvirus seroprevalence were associated with adapter species in protected forests where they might be more abundant. Altogether, these findings underscore the need for integrated and multipathogen wildlife surveillance to anticipate and mitigate disease risks at the human-environment-animal interface.

ABSTRACT African populations remain underrepresented in studies of human genetic diversity, despite a growing interest in understanding how they have adapted to the diverse environments they live in. In particular, understanding the genetic basis of immune adaptation to pathogens is of paramount importance in a continent such as Africa, where the burden of infectious diseases is a major public health challenge. In this study, we investigated the molecular variation of four Human Leukocyte Antigens (HLA) class II genes (DRB1, DQA1, DQB1 and DPB1), directly involved in the immune response to parasitic infections, in more than 1000 individuals from 23 populations across North, East, Central and West Africa. By analyzing the HLA molecular diversity of these populations in relation to various geographical, cultural and environmental factors, we identified divergent genetic profiles for several (semi‐)nomadic populations of the Sahel belt as a signature of their unique demography. In addition, we observed significant genetic structuring supporting both substantial geographic and linguistic differentiations within West Africa. Furthermore, neutrality tests suggest balancing selection has been shaping the diversity of these four HLA class II genes, which is consistent with molecular comparisons between HLA genes and their orthologs in chimpanzees (Patr). However, the most striking observation comes from linear modeling, demonstrating that the prevalence of Plasmodium falciparum, the primary pathogen of malaria in Africa, significantly explains a large proportion of the nucleotide diversity observed at the DPB1 gene. DPB1*01:01, a highly frequent allele in Burkinabé populations, is identified as a potential protective allele against malaria, suggesting that strong pathogen‐driven positive selection at this gene has shaped HLA variation in Africa. Additionally, two low‐frequency DRB1 alleles, DRB1*08:06 and DRB1*11:02, also show significant associations with P. falciparum prevalence, supporting resistance to malaria is determined by multigenic and/or multiallelic combinations rather than single allele effects.

The "dilution effect" hypothesis suggests that high host diversity can reduce the prevalence of certain zoonotic pathogens. Despite growing interest, its generality and practical relevance remain debated. In particular most previous studies have focused on large scale analyses or meta-analyses, limiting their potential use for zoonotic outbreak prevention. Here, we present an extensive field-based study of small mammals and their multiple pathogens to assess diversity-disease relationships at a local scale, revealing pathogen-specific patterns. While no significant association was detected between the prevalence of some pathogens and host diversity, others such as Orthopoxvirus and a strain of Mycoplasma haemomuris exhibited dilution effect patterns, whereas another Mycoplasma haemomuris strain and Mycoplasma coccoides displayed amplification effects. Crucially, we demonstrate that these contrasting outcomes are consistently explained by the host competence-abundance relationship. Our findings underscore the importance of host community composition and highlight the need to consider multiple pathogens when evaluating the ecological mechanisms underpinning the diversity-disease relationships. ### Competing Interest Statement The authors have declared no competing interest. The raw data have been deposited on Zenodo and are available at . BiodivERsA, https://ror.org/05cvqmv08

Swollen Shoot is a viral disease affecting cocoa trees, transmitted by several species of mealybugs (Insecta, Hemiptera, Sternorrhyncha, Pseudococcidae). These insects maintain trophobiotic relationships with a complex and species-rich assemblage of ants protecting them and natural enemies controlling their populations. Here, we provide a curated DNA barcode database to characterise this insect community. Systematic observation of 7,500 cocoa trees was conducted, coupled with the collection of mealybug colonies and associated insect communities (parasitoids, predators and ants). Natural enemies were reared from mealybug colonies collected from 1,430 cocoa trees. Specimens were identified morphologically and sequenced for fragments of the standard DNA barcode region of the COI. We recovered 17 species of mealybugs from the family Pseudococcidae. Amongst these species, eight are new to the Ivorian cocoa orchard: Dysmicoccusneobrevipes Beardsley, Ferrisiadasylirii (Cockerell), Maconellicoccusugandae (Laing), Paracoccusmarginatus Williams & Granara de Willink, Phenacoccussolenopsis Tinsley, Planococcusminor (Maskell), Pseudococcusconcavocerarii James and Pseudococcusocciduus De Lotto. Three of these species were identified for the first time in cocoa orchards in Africa: D.neobrevipes, Fe.dasylirii and Ph.solenopsis. A total of 54 ant species were identified and represented the first record of these species associated with mealybug colonies in cocoa in Côte d'Ivoire. Amongst the species associated with the mealybugs, 22 primary parasitoids, eight hyperparasitoids, 11 ladybirds beetles (Coccinellidae), seven gall midges (Cecidomyidae), one predatory lepidopteran species and four spider species were identified. Nine species of mealybugs parasitoids are newly recorded in the African cocoa orchards: Acerophagusaff.dysmicocci, Aloencyrtus sp., Anagyruskamali, Anagyrusaff.pseudococci, Aenasiusadvena, Clauseniaaff.corrugata, Gyranusoideaaff.tebygi, Zaplatycerusaff.natalensis (Encyrtidae) and Coccophaguspulvinariae (Aphelinidae) and one hyperparasitoid, Pachyneuronmuscarum (Pteromalidae). For Côte d'Ivoire in particular, besides the previously mentioned nine parasitoids and one hyperparasitoid, five additional species are recorded for the first time, including four primary parasitoids, Blepyrusinsularis (Encyrtidae), Clauseniacorrugata (Encyrtidae), Clausenia sp. (Encyrtidae), and Coccidoctonuspseudococci (Encyrtidae) and one hyperparasitoid, Cheiloneuruscyanonotus (Encyrtidae). These results significantly enhance the knowledge of the diversity of the entomofauna associated with Swollen Shoot disease and pave the way for developing control methods based on the natural regulation of its mealybug (Pseudococcidae) vectors.

Elucidating the drivers of evolution in dry environments is central to understanding how organisms respond to climate change. While research on the genomics of adaptation is growing, aridity-driven intraspecific divergence remains poorly quantified. Here, we address this gap by using genomic data from 230 individuals of the arid-adapted four-striped mouse Rhabdomys bechuanae , sampled across an aridity gradient in southern Africa, a region facing increasing aridification. Combining these data with palaeoclimatic reconstructions and present-day aridity indices, we investigate, from a spatio-temporal perspective, how intraspecific genetic variation relates to aridity. Inference of past effective population size revealed a sharp decline in the late Pleistocene, coinciding with regional aridification and potentially reflecting changes in connectivity during dry periods. Current population structure followed a pattern of isolation by distance and mirrored the aridity gradient. Genotype-Environment Association analyses identified SNPs and genes significantly associated with aridity and genetically differentiated among populations, with functions related to water and energy conservation - as expected under arid conditions - as well as neurotransmission. These findings highlight the underappreciated role for neurological processes in coping with water and resource scarcity. More broadly, our integrative genomics approach suggests that aridity shapes population connectivity and adaptation, with implications for climate resilience. ### Competing Interest Statement The authors have declared no competing interest. LabEx CeMEB, D-RANGE OSU OREME, TO contact-zones CNRS/NRF, PICS n°4841, n° 81859, LIA RhabAdapt & Drought CNRS, CNRS-MITI

The emergence of infectious diseases associated with land-use changes is well-documented. However, zoonotic risks originating from European forests, whether from rural development or urban greening, remain underexplored. To assess and mitigate zoonotic hazards in these ecosystems, we analyzed 1,549 individuals from 18 small mammal species sampled along a forest anthropization gradient using both targeted and broad-spectrum serological and molecular methods. We detected nine bacteria and several Apicomplexa that are potentially pathogenic to humans. Zoonotic pathogen richness and community composition varied significantly across host species, sites and sampling periods. Richness was lower in forested urban parks, possibly due to the absence of vectors or intermediate hosts within cities. It was higher in urban adapter species, even within a given forested habitat, emphasizing the important role of specific life-history traits. Pathogen community structure was similarly shaped by forest anthropization and host ecology, with marked differences between urban and rural forested environments and between urban adapter and dweller species within forested urban parks. The (sero-)prevalence of key pathogens (e.g., Bartonella, Orthopoxvirus, Neoehrlichia mikurensis , Sarcocystidae) showed spatial, temporal, and host-specific variation. Site-level differences often exceeded those between general habitat types, highlighting the importance of local ecological context. Nevertheless, some patterns reflected the influence of forest anthropization and species urban adaptation strategies for certain zoonotic agents. Forest anthropization had a positive impact on Bartonella prevalence, for urban adapter species within parks, emphasizing a potential dilution effect of these pathogens. Besides, higher levels of Orthopoxvirus seroprevalence were associated with adapter species, in protected forests where they might be more abundant. Altogether, these findings underscore the need for integrated and multi-pathogen wildlife monitoring to anticipate and mitigate disease risks at the human– environment–animal interface. ### Competing Interest Statement The authors have declared no competing interest. 2018-2019 BiodivERsA joint call, BiodivERsA3 ERA-Net COFUND programme

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. ### Competing Interest Statement The authors have declared no competing interest. French National Research Agency, ANR JCJC SEXIBAT Université de la Réunion - BIOST, MOLOSS-EAT

As human activities drive biodiversity decline, effective biomonitoring is more crucial than ever to track species distribution changes and inform conservation and restoration actions. Environmental DNA (eDNA) metabarcoding has emerged as a promising tool for the simultaneous detection of multiple taxa. However, while substrates play a crucial role in eDNA studies, limited research has compared substrate performance for terrestrial vertebrate detection, leaving a critical gap in empirical knowledge for large-scale application. This study evaluates and compares the effectiveness of three easy-to-collect substrates: soil, leaf swabs, and spider webs, for broad terrestrial vertebrate eDNA monitoring. Specifically, we examined taxonomic richness overlaps among substrates, their effects on wild vertebrate detection probabilities, and within-sample PCR repeatability. We analysed 120 samples from the Landes Forest, an intensively managed temperate forest in Western France, and included additional control samples from the Montpellier zoo to validate our detection capabilities. Using metabarcoding with 12S-V5 and 16S mam primers, we identified 63 taxa at the genus or species level. Our findings highlight the advantages of substrates that passively accumulate airborne DNA (leaf swabs and spider webs) over soil, and position spider webs as a suitable choice for maximising detection probabilities in rapid eDNA surveys, emphasising their potential for efficient, scalable biomonitoring. Further research is needed to identify factors affecting eDNA detectability from these substrates, aiming to standardise procedures and move from proof-of-concept to broad use by researchers and managers.

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the occurrence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11 host species from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), multiple regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors (study year and site; host habitat, species, sex and age class) contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover, we detected positive associations between several pathogens, including Bartonella , Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species.

Aphids (Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, complicating our understanding of aphid trait evolution. In this work, we aimed to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from aphid obligate endosymbiont, Buchnera aphidicola. We obtained data from these three sources for a subset of aphid species, facilitating a comparative analysis of their signal. Our analyses confirm the monophyly of most subfamilies, validating current taxonomic classifications. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera are fully resolved but disagree with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep timescales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.

Major advances in the understanding of infectious diseases have been achieved in the last decades. However, the persistence and re-emergence of pathogens continue to raise public and veterinary health concerns, of which the recent COVID-19 pandemic may be one of the most dramatic examples. Understanding the impact of habitat alterations and concomitant biodiversity loss on pathogen transmission and emergence from wildlife remains challenging. Here, we aim to elucidate the interlinkages between biodiversity and rodent-borne diseases at local and European scales. We present recently collected host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals – wildlife interactions are likely to occur. 3766 specimens were analyzed during the period from 2020 to 2022 comprising 15 different small mammal species. Different organ tissues of each specimen were screened for bacteria by either 16S rRNA amplicon sequencing or specific PCR. The presence of antibodies to different families of viruses was screened using immunofluorescent assays. A multitude of pathogens of zoonotic potential from several genera including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira , Orthohantavirus and Orthopoxvirus were detected at non-negligible prevalence in 11 different terrestrial mammal species. A shift in host community composition was observed along the anthropization gradient with more urban adapters in more anthropized sites. Pathogen richness increased with an increase in host species diversity, following the “host-diversity begets parasite-diversity” hypothesis. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community along the anthropization gradient. Host species and host intrinsic factors were dominant explanatory variables for endoparasitic Mycoplasma species and Sarcocystidae , while extrinsic environmental and climatic factors where influential in explaining variations in occurrences of several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus were important connector host species in respectively urban green spaces and temperate forests. Increased host diversity, but not anthropization, correlated with a richer pathogen community. These results ultimately lead to an increased understanding of the complex host-pathogen system at the local landscape that can aid future management decisions and support the public health sector. ### Competing Interest Statement The authors have declared no competing interest.

Aphids (Hemiptera: Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this considerable research interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, particularly at deep nodes, complicating our understanding of aphid trait evolution. In this work, we aimed to produce new data to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species that were added to 31 published mitochondria. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from the primary aphid obligate endosymbiont , Buchnera aphidicola . We obtain data from these three sources for a subset of 51 aphid species, facilitating a comparative analysis of their phylogenetic signals. Our analyses confirm the monophyly of subfamilies, validating current taxonomic classifications, except for Eriosomatinae and Calaphidinae. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera appear fully resolved but exhibit some discordance with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep phylogenetic scales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.### Competing Interest StatementThe authors have declared no competing interest.

Gaining meaningful insights into bacterial communities associated with animal hosts requires the provision of high-quality nucleic acids. Although many studies have compared DNA extraction methods for samples with low bacterial biomass (e.g. water) or specific PCR inhibitors (e.g. plants), DNA extraction bias in samples without inherent technical constraint (e.g. animal samples) has received little attention. Furthermore, there is an urgent need to identify a DNA extraction methods in a high-throughput format that decreases the cost and time for processing large numbers of samples. We here evaluated five DNA extraction protocols, using silica membrane-based spin columns and a 96-well microplate format and based on either mechanical or enzymatic lysis or a combination of both, using three bacterial mock communities and Illumina sequencing of the V4 region of the 16SrRNA gene. Our results showed that none of the DNA extraction methods fully eliminated bias associated with unequal lysis efficiencies. However, we identified a DNA extraction method with a lower bias for each mock community standard. Of these methods, those including an enzymatic lysis showed biases specific to some bacteria. Altogether, these results again demonstrate the importance of DNA extraction standardization to be able to compare the microbiome results of different samples. In this attempt, we advise for the use of the 96-well DNeasy Blood and Tissue kit (Qiagen) with a zirconia bead-beating procedure, which optimizes altogether the cost, handling time and bacteria-specific effects associated with enzymatic lysis.

Understanding how environmental gradients shape the spatial patterns of intraspecific genetic diversity is a central issue in ecological and evolutionary sciences. In riverine ecosystems, there is generally an increase in neutral genetic diversity downstream, as well as an increase in genetic differentiation among upstream populations. However, selective pressures may vary markedly along the upstream–downstream gradient, which could modify these patterns, but this has rarely been tested empirically. Here, we investigated how environmental gradients in a river network could shape the spatial patterns of intraspecific genetic diversity and differentiation in both neutral SNP markers and functional genetic markers putatively under natural selection (candidate SNPs associated with physiological functions and immune Major Histocompatibility Complex (MHC) loci) in wild brown trout populations. First, we showed that both the distance from the confluence and the centrality on the river network could explain the variation in genetic diversity and differentiation. Second, we found that both neutral and functional markers followed a similar pattern, with a higher genetic diversity and a lower genetic differentiation among populations that were more central and/or near to the confluence. This study highlights the importance of considering both the spatial and hydrological factors of a river network to understand and predict the role of dendritic connectivity in the spatial patterns of genetic diversity and differentiation in wild fish populations.

Despite its central role in host fitness, the gut microbiota may differ greatly between individuals. This variability is often mediated by environmental or host factors such as diet, genetics, and infections. Recently, particular attention has been given to the interactions between gut bacteriota and helminths, as these latter could affect host susceptibility to other infections. Further studies are still required to better understand the three-way interactions between gut bacteriota, helminths and other parasites, especially because previous findings have been very variable, even for comparable host-parasite systems. In our study, we used the V4 region of the 16S rRNA gene to assess the variability of gut bacteriota diversity and composition in wild populations of a small mammal, the bank vole Myodes glareolus. Four sites were sampled at a regional geographical scale (100 km) along a North-South transect in Eastern France. We applied analyses of community and microbial ecology to evaluate the interactions between the gut bacteriota, the gastro-intestinal helminths and the pathogenic bacteria detected in the spleen. We identified important variations of the gut bacteriota composition and diversity among bank voles. They were mainly explained by sampling localities and reflected the North/South sampling transect. In addition, we detected two main enterotypes, that might correspond to contrasted diets. We found geographic variations of the Firmicutes/Bacteroidetes ratio, that correlated positively with body mass index. We found positive correlations between the specific richness of the gut bacteriota and of the helminth community, as well as between the composition of these two communities, even when accounting for the influence of geographical distance. The helminths Aonchotheca murissylvatici, Heligmosomum mixtum and the bacteria Bartonella sp were the main taxa associated with the whole gut bacteriota composition. Besides, changes in the relative abundance of particular gut bacteriota taxa were specifically associated with other helminths ( Mastophorus muris, Catenotaenia henttoneni, Paranoplocephala omphalodes and Trichuris arvicolae) or pathogenic bacteria. Especially, infections with Neoehrlichia mikurensis, Orientia sp, Rickettsia sp and P. omphalodes were associated with lower relative abundance of the family Erysipelotrichaceae (Firmicutes), while coinfections with higher number of bacterial infections were associated with lower relative abundance of a Bacteroidales family (Bacteroidetes). These results emphasize complex interlinkages between gut bacteriota and infections in wild animal populations. They remain difficult to generalize due to the strong impact of the environment on these interactions, even at regional geographical scales. Abiotic features, as well as small mammal community composition and within host parasite coinfections, should now be considered to better understand the spatial variations observed in the relationships between gut bacteriota, gastro-intestinal helminths and bacterial infections.

Crocidura olivieri is a large-sized shrew species showing a clear trend towards commensalism in West Africa, where it co-occurs and interacts with a number of rodent species in indoor small mammal communities. Among the rodents present is the house mouse Mus musculus , a major invasive species worldwide. We here test the hypothesis that M. musculus could be part of the diet of C. olivieri in a number of localities of Senegal where the two species are known to coexist. We use a metabarcoding approach based on the high-throughput sequencing of a 133 bp fragment of the COI gene, on DNA extracted from digestive tracts and faeces of a sample of 108 shrews. Beside insects of various groups (ants, beetles and cockroaches especially) representing usual items of shrew’s diet, and traces of domestic mammals and poultry that were probably scavenged, several species of rodents were evidenced. Among them, M. musculus was by far the best represented species, found in 17 of the 54 shrews where at least one prey taxon was identified. This finding tends to confirm the potential role of C. olivieri as predator of house mice, while highlighting the capacity of this species to adapt its diet to environmental conditions.