MHC-I alleles mediate clearance and antibody response to the zoonotic Lassa virus in Mastomys rodent reservoirs.

West African Mastomys rodents are the primary reservoir of the zoonotic Lassa virus (LASV). The virus causes haemorrhagic Lassa fever and considerable mortality in humans. To date, the role of Mastomys immunogenetics in resistance to, and persistence of, LASV infections is largely unknown. Here, we investigated the role of Major Histocompatibility Complex class I (MHC-I) on LASV infection status (i.e., active vs. cleared infection, determined via PCR and an immunofluorescence assay on IgG antibodies, respectively) in Mastomys natalensis and M. erythroleucus sampled within southwestern Nigeria. We identified more than 190 and 90 MHC-I alleles by Illumina high throughput-sequencing in M. natalensis and M. erythroleucus, respectively, with different MHC allele compositions and frequencies between LASV endemic and non-endemic sites. In M. natalensis, the MHC allele ManaMHC-I*006 was negatively associated with active infections (PCR-positive) and positively associated with cleared infections (IgG-positive) simultaneously, suggesting efficient immune responses that facilitate LASV clearance in animals carrying this allele. Contrarily, alleles ManaMHC-I*008 and ManaMHC-I*021 in M. natalensis, and MaerMHC-I*008 in M. erythroleucus, were positively associated with active infection, implying susceptibility. Alleles associated with susceptibility shared a glutamic acid at the positively selected codon 57, while ManaMHC-I*006 featured an arginine. There was no link between number of MHC alleles per Mastomys individual and LASV prevalence. Thus, specific alleles, but not MHC diversity per se, seem to mediate antibody responses to viremia. We conclude that co-evolution with LASV likely shaped the MHC-I diversity of the main LASV reservoirs in southwestern Nigeria, and that information on reservoir immunogenetics may hold insights into transmission dynamics and zoonotic spillover risks.

Immunogenetic-pathogen networks shrink in Tome's spiny rat, a generalist rodent inhabiting disturbed landscapes.

Anthropogenic disturbance may increase the emergence of zoonoses. Especially generalists that cope with disturbance and live in close contact with humans and livestock may become reservoirs of zoonotic pathogens. Yet, whether anthropogenic disturbance modifies host-pathogen co-evolutionary relationships in generalists is unknown. We assessed pathogen diversity, neutral genome-wide diversity (SNPs) and adaptive MHC class II diversity in a rodent generalist inhabiting three lowland rainforest landscapes with varying anthropogenic disturbance, and determined which MHC alleles co-occurred more frequently with 13 gastrointestinal nematodes, blood trypanosomes, and four viruses. Pathogen-specific selection pressures varied between landscapes. Genome-wide diversity declined with the degree of disturbance, while MHC diversity was only reduced in the most disturbed landscape. Furthermore, pristine forest landscapes had more functional important MHC-pathogen associations when compared to disturbed forests. We show co-evolutionary links between host and pathogens impoverished in human-disturbed landscapes. This underscores that parasite-mediated selection might change even in generalist species following human disturbance which in turn may facilitate host switching and the emergence of zoonoses.

Wildlife gut microbiomes of sympatric generalist species respond differently to anthropogenic landscape disturbances.

BACKGROUND: Human encroachment into nature and the accompanying environmental changes are a big concern for wildlife biodiversity and health. While changes on the macroecological scale, i.e. species community and abundance pattern, are well documented, impacts on the microecological scale, such as the host's microbial community, remain understudied. Particularly, it is unclear if impacts of anthropogenic landscape modification on wildlife gut microbiomes are species-specific. Of special interest are sympatric, generalist species, assumed to be more resilient to environmental changes and which often are well-known pathogen reservoirs and drivers of spill-over events. Here, we analyzed the gut microbiome of three such sympatric, generalist species, one rodent (Proechimys semispinosus) and two marsupials (Didelphis marsupialis and Philander opossum), captured in 28 study sites in four different landscapes in Panama characterized by different degrees of anthropogenic disturbance. RESULTS: Our results show species-specific gut microbial responses to the same landscape disturbances. The gut microbiome of P. semispinosus was less diverse and more heterogeneous in landscapes with close contact with humans, where it contained bacterial taxa associated with humans, their domesticated animals, and potential pathogens. The gut microbiome of D. marsupialis showed similar patterns, but only in the most disturbed landscape. P. opossum, in contrast, showed little gut microbial changes, however, this species' absence in the most fragmented landscapes indicates its sensitivity to long-term isolation. CONCLUSION: These results demonstrate that wildlife gut microbiomes even in generalist species with a large ecological plasticity are impacted by human encroachment into nature, but differ in resilience which can have critical implications on conservation efforts and One Health strategies.

Disentangling direct from indirect effects of habitat disturbance on multiple components of biodiversity.

Human habitat disturbance affects both species diversity and intraspecific genetic diversity, leading to correlations between these two components of biodiversity (termed species-genetic diversity correlation, SGDC). However, whether SGDC predictions extend to host-associated communities, such as the intestinal parasite and gut microbial diversity, remains largely unexplored. Additionally, the role of dominant generalist species is often neglected despite their importance in shaping the environment experienced by other members of the ecological community, and their role as source, reservoir and vector of zoonotic diseases. New analytical approaches (e.g. structural equation modelling, SEM) can be used to assess SGDC relationships and distinguish among direct and indirect effects of habitat characteristics and disturbance on the various components of biodiversity. With six concrete and biologically sound models in mind, we collected habitat characteristics of 22 study sites from four distinct landscapes located in central Panama. Each landscape differed in the degree of human disturbance and fragmentation measured by several quantitative variables, such as canopy cover, canopy height and understorey density. In terms of biodiversity, we estimated on the one hand, (a) small mammal species diversity, and, on the other hand, (b) genome-wide diversity, (c) intestinal parasite diversity and (d) gut microbial heterogeneity of the most dominant generalist species (Tome's spiny rat, Proechimys semispinosus). We used SEMs to assess the links between habitat characteristics and biological diversity measures. The best supported SEM suggested that habitat characteristics directly and positively affect the richness of small mammals, the genetic diversity of P. semispinosus and its gut microbial heterogeneity. Habitat characteristics did not, however, directly impact intestinal parasite diversity. We also detected indirect, positive effects of habitat characteristics on both host-associated assemblages via small mammal richness. For microbes, this is likely linked to cross species transmission, particularly in shared and/or anthropogenically altered habitats, whereas host diversity mitigates parasite infections. The SEM revealed an additional indirect but negative effect on intestinal parasite diversity via host genetic diversity. Our study showcases that habitat alterations not only affect species diversity and host genetic diversity in parallel, but also species diversity of host-associated assemblages. The impacts from human disturbance are therefore expected to ripple through entire ecosystems with far reaching effects felt even by generalist species.

Las perturbaciones antropogénicas sobre los hábitats naturales pueden afectar tanto a la diversidad de las especies como a la diversidad genética intraespecífica, dando lugar a correlaciones entre estos dos elementos de la biodiversidad (denominados correlación de la diversidad genética de las especies, SGDC por sus siglas en inglés). Sin embargo, todavía queda sin explorar si las predicciones de la SGDC afectan a las comunidades de parásitos y microorganismos intestinales asociadas al hospedador. Adicionalmente, el rol que juegan las especies generalistas, especialmente aquéllas dominantes, suele ser descuidado, a pesar de la importancia de control que ejercen sobre la estructura de la comunidad, y su rol como fuente, reservorio y vector de enfermedades zoonóticas. Para poder evaluar las relaciones de SGDC y distinguir entre los efectos directos e indirectos que tienen las características del hábitat y las perturbaciones sobre los distintos componentes de la biodiversidad, se pueden utilizar nuevos enfoques analíticos como por ejemplo los modelos de ecuaciones estructurales (SEM, por sus siglas en inglés). Considerando seis modelos específicos y biológicamente sólidos, recopilamos las características del hábitat de 22 sitios ubicados en cuatro paisajes distintos situados en el centro de Panamá. Cada paisaje difería en el grado de perturbación antropogénica y fragmentación, medido por diferentes variables cuantitativas, como la cobertura del dosel, la altura del dosel y la densidad del sotobosque. En términos de biodiversidad, por un lado estimamos (1) la diversidad de especies de pequeños mamíferos y, por otro lado (2) la diversidad del genoma completo, (3) la diversidad de parásitos intestinales, y (4) la heterogeneidad de las comunidades microbianas del intestino de la especie generalista más dominante, la rata espinosa de Tomes Proechimys semispinosus. Para evaluar los vínculos entre las características del hábitat y las medidas de diversidad biológica se utilizó el modelado SEM. El SEM mejor apoyado sugirió que las características del hábitat afectan directa y positivamente a la abundancia de pequeños mamíferos, a la diversidad genética de P. semispinosus y a la heterogeneidad microbiana intestinal. Sin embargo, se observó que las características del hábitat no tienen un efecto directo en la diversidad de parásitos intestinales. Aparte de estos efectos directos, detectamos efectos indirectos y positivos de las características del hábitat en ambos conjuntos asociados al hospedador (diversidad de parásitos y microorganismos intestinales) a través de la abundancia de pequeños mamíferos. En el caso de las comunidades microbianas, esto está probablemente relacionado con la transmisión interespecífica, especialmente en hábitats compartidos y/o antropogénicamente alterados; mientras que la diversidad de hospedadores mitiga las infecciones de parásitos. El SEM reveló un efecto indirecto adicional pero negativo sobre la diversidad de parásitos intestinales a través de la diversidad genética de los hospedadores. Nuestro estudio muestra que los patrones de SGDC se filtran a través de las varias capas de diversidad biológica, añadiendo los ensamblajes asociados al hospedador como componentes biológicos afectados por las alteraciones del hábitat.

Human encroachment into wildlife gut microbiomes.

In the Anthropocene, humans, domesticated animals, wildlife, and their environments are interconnected, especially as humans advance further into wildlife habitats. Wildlife gut microbiomes play a vital role in host health. Changes to wildlife gut microbiomes due to anthropogenic disturbances, such as habitat fragmentation, can disrupt natural gut microbiota homeostasis and make animals vulnerable to infections that may become zoonotic. However, it remains unclear whether the disruption to wildlife gut microbiomes is caused by habitat fragmentation per se or the combination of habitat fragmentation with additional anthropogenic disturbances, such as contact with humans, domesticated animals, invasive species, and their pathogens. Here, we show that habitat fragmentation per se does not impact the gut microbiome of a generalist rodent species native to Central America, Tome's spiny rat Proechimys semispinosus, but additional anthropogenic disturbances do. Indeed, compared to protected continuous and fragmented forest landscapes that are largely untouched by other human activities, the gut microbiomes of spiny rats inhabiting human-disturbed fragmented landscapes revealed a reduced alpha diversity and a shifted and more dispersed beta diversity. Their microbiomes contained more taxa associated with domesticated animals and their potential pathogens, suggesting a shift in potential metagenome functions. On the one hand, the compositional shift could indicate a degree of gut microbial adaption known as metagenomic plasticity. On the other hand, the greater variation in community structure and reduced alpha diversity may signal a decline in beneficial microbial functions and illustrate that gut adaption may not catch up with anthropogenic disturbances, even in a generalist species with large phenotypic plasticity, with potentially harmful consequences to both wildlife and human health.

Mammalian deltavirus without hepadnavirus coinfection in the neotropical rodent Proechimys semispinosus.

Hepatitis delta virus (HDV) is a human hepatitis-causing RNA virus, unrelated to any other taxonomic group of RNA viruses. Its occurrence as a satellite virus of hepatitis B virus (HBV) is a singular case in animal virology for which no consensus evolutionary explanation exists. Here we present a mammalian deltavirus that does not occur in humans, identified in the neotropical rodent species Proechimys semispinosus The rodent deltavirus is highly distinct, showing a common ancestor with a recently described deltavirus in snakes. Reverse genetics based on a tandem minus-strand complementary DNA genome copy under the control of a cytomegalovirus (CMV) promoter confirms autonomous genome replication in transfected cells, with initiation of replication from the upstream genome copy. In contrast to HDV, a large delta antigen is not expressed and the farnesylation motif critical for HBV interaction is absent from a genome region that might correspond to a hypothetical rodent large delta antigen. Correspondingly, there is no evidence for coinfection with an HBV-related hepadnavirus based on virus detection and serology in any deltavirus-positive animal. No other coinfecting viruses were detected by RNA sequencing studies of 120 wild-caught animals that could serve as a potential helper virus. The presence of virus in blood and pronounced detection in reproductively active males suggest horizontal transmission linked to competitive behavior. Our study establishes a nonhuman, mammalian deltavirus that occurs as a horizontally transmitted infection, is potentially cleared by immune response, is not focused in the liver, and possibly does not require helper virus coinfection.

Pathogen-associated selection on innate immunity genes (TLR4, TLR7) in a neotropical rodent in landscapes differing in anthropogenic disturbance.

Toll-like receptors (TLRs) form part of the innate immune system and can recognize structurally conserved pathogen-associated molecular pattern (PAMP) molecules. Their functional importance in the resistance to pathogens has been documented in laboratory experimental settings and in humans. TLR diversity, however, has been rarely investigated in wildlife species. How the genetic diversity of TLRs is associated with various pathogens and how it is shaped by habitat disturbance are understudied. Therefore, we investigated the role of genetic diversity in the functionally important parts of TLR4 and TLR7 genes in resistance towards gastrointestinal nematodes and Hepacivirus infection. We chose a generalist study species, the rodent Proechimys semispinosus, because it is highly abundant in three Panamanian landscapes that differ in their degree of anthropogenic modification. We detected only two TLR7 haplotypes that differed by one synonymous single-nucleotide polymorphism (SNP) position. The TLR4 variability was higher, and we detected four TLR4 haplotypes that differed at one synonymous SNP and at three amino acid positions within the leucine-rich repeat region. Only TLR4 haplotypes had different frequencies in each landscape. Using generalized linear models, we found evidence that nematode loads and virus prevalence were influenced by both specific TLR4 haplotypes and landscape. Here, the variable "landscape" served as a surrogate for the important influential ecological factors distinguishing landscapes in our study, i.e. species diversity and host population density. Individuals carrying the common TLR4_Ht1 haplotype were less intensely infected by the most abundant strongyle nematode. Individuals carrying the rare TLR4_Ht3 haplotype were all Hepacivirus-positive, where those carrying the rare haplotype TLR4_Ht4 were less often infected by Hepacivirus than individuals with other haplotypes. Our study highlights the role of TLR diversity in pathogen resistance and the importance of considering immune genetic as well as ecological factors in order to understand the effects of anthropogenic changes on wildlife health.