Although the significance of the gut microbiome for host health is well acknowledged, the impact of host traits and environmental factors on the interindividual variation of gut microbiomes of wildlife species is not well understood. Such information is essential; however, as changes in the composition of these microbial communities beyond the natural range might cause dysbiosis leading to increased susceptibility to infections. We examined the potential influence of sex, age, genetic relatedness, spatial tactics and the environment on the natural range of the gut microbiome diversity in free-ranging Namibian cheetahs (Acinonyx jubatus). We further explored the impact of an altered diet and frequent contact with roaming dogs and cats on the occurrence of potential bacterial pathogens by comparing free-ranging and captive individuals living under the same climatic conditions. Abundance patterns of particular bacterial genera differed between the sexes, and bacterial diversity and richness were higher in older (>3.5 years) than in younger individuals. In contrast, male spatial tactics, which probably influence host exposure to environmental bacteria, had no discernible effect on the gut microbiome. The profound resemblance of the gut microbiome of kin in contrast to nonkin suggests a predominant role of genetics in shaping bacterial community characteristics and functional similarities. We also detected various Operational Taxonomic Units (OTUs) assigned to potential pathogenic bacteria known to cause diseases in humans and wildlife species, such as Helicobacter spp., and Clostridium perfringens. Captive individuals did not differ in their microbial alpha diversity but exhibited higher abundances of OTUs related to potential pathogenic bacteria and shifts in disease-associated functional pathways. Our study emphasizes the need to integrate ecological, genetic and pathogenic aspects to improve our comprehension of the main drivers of natural variation and shifts in gut microbial communities possibly affecting host health. This knowledge is essential for in situ and ex situ conservation management.

Adenovirus (AdV) infections are one of the main causes of diarrhea in young children. Enteric AdVs probably disrupt gut microbial defences, which can result in diarrhea. To understand the role of the gut microbiome in AdV-induced pathologies, we investigated the gut microbiome of a naturally AdV-infected non-human primate species, the Malagasy mouse lemur (Microcebus griseorufus), which represents an important model in understanding the evolution of diseases. We observed that AdV infection is associated with disruption of the gut microbial community composition. In AdV+ lemurs, several commensal taxa essential for a healthy gut microbiome decreased, whereas genera containing potential pathogens, such as Neisseria, increased in abundance. Microbial co-occurrence networks revealed a loss of important microbial community interactions in AdV+ lemurs and an overrepresentation of Prevotellaceae. The observation of enteric virus-associated loss of commensal bacteria and associated shifts towards pathobionts may represent the missing link for a better understanding of AdV-induced effects in humans, and also for their potential as drivers of co-infections, an area of research that has been largely neglected so far.

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Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

Astroviruses (AstV) are a major cause of diarrhoea in children. Interestingly, some wildlife species, including bats, remain phenotypically asymptomatic after infection. Disease symptoms, however, may only be less visible in bats and enteric viruses may indeed perturb their gut microbial communities. Gut microbiomes represent an important driver of immune defence mechanisms but potential effects of enteric virus-host microbiome interactions are largely unexplored. Using bats as a natural model system, we show that AstV-infections affect the gut microbiome, with the strength of the effect depending on host age. The gut microbial α- and β-diversity and the predicted microbial functional orthologs decreased in young bats but surprisingly increased in adult AstV + bats. The abundance of bacterial taxa characteristic for healthy microbiomes was strongly reduced in young AstV+ bats, possibly attributable to their immature immune system. Regardless of age, pathogen-containing genera exhibited negative interactions with several commensal taxa and increased after AstV-infection, leading to pathobiont-like shifts in the gut microbiome of all infected bats. Thus, in apparently healthy bats, AstV-infections disturb gut bacterial homeostasis, possibly increasing previously suppressed health risks by promoting co-infections. If similar processes are present in humans, the effects of enteric virus infections might have longer-term impacts extending beyond the directly observed symptoms.

Until recently, the study of major histocompability complex (MHC) mediated immunity has focused on the direct link between MHC variability and susceptibility to parasite infection. However, MHC genes can also influence host health indirectly through the sculpting of the bacterial community that in turn shape immune responses. We investigated the links between MHC class I and II gene variability gut microbiome diversity and micro- (adenovirus, AdV) and macro- (helminth) parasite infection probabilities in a wild population of non-human primates, mouse lemurs of Madagascar. This setup encompasses a plethora of underlying interactions between parasites, microbes and adaptive immunity in natural populations. Both MHC classes explained shifts in microbiome composition and the effect was driven by a few select microbial taxa. Among them were three taxa ( Odoribacter , Campylobacter and Prevotellaceae-UCG-001) which were in turn linked to AdV and helminth infection status, evidence of the indirect effect of the MHC via the microbiome. Our study provides support for the coupled role of MHC variability and microbial flora as contributing factors of parasite infection.

bPCR diagnostics detected 100% prevalence of Helicobacter in 425 wild house mice (Mus musculus) from across central Europe. Of seven species identified, the five most frequent were Helicobacter rodentium (78%), H. typhlonius (53%), H. hepaticus (41%), H. bilis (30%), and H. muridarum (1%). Double infections were more common (42%) than single (30%) and triple (21%) infections. Wild house mice could be considered potential reservoirs of Helicobacter strains for both humans and other vertebrates. The genus Helicobacter comprises more than 30 species (9). Although a few have been thoroughly studied for their impact on human and animal health (4,5,15,23) as well as on research (6), in most cases, their zoonotic potential and mode of transmission remain obscure (18), especially for intestinal helicobacters (22). In the case of rodents, most studies have been conducted with laboratory mice, and studies of wild populations across large geographical areas are virtually unknown. Therefore, screening of wild commensal rodents like the house mouse, Mus musculus, which is known to host at least 11 intestinal helicobacters (3,21,22), for the occurrence and prevalence of Helicobacter species is considered crucial for gaining insights into their ecology and epidemiology (8).In this study, 425 mice were trapped at 91 sites over a 6,500-km 2 rectangular area stretching from northeastern Germany to western Czech Republic ( Fig. 1; also, see Table S1 in the supplemental material). This area is occupied by two house mouse subspecies, Mus mus domesticus and Mus mus musculus (see references 10 and 11 for their distribution). Specifically, we asked what the prevalence and the diversity of Helicobacter spp. in natural populations of the house mouse are and also whether coinfection with several Helicobacter spp. is common in wild mice.House mice were live-trapped inside and adjacent to houses and farms from 2008 to 2010 and dissected in a field laboratory. Extreme caution was taken to avoid cross-infections and crosscontaminations (e.g., mice were housed singly until anesthetized; sterile dissection was performed a maximum of 24 h after a mouse was trapped). The colon, including feces, of each mouse was put into a sterile 30-ml screw-cap microtube containing 70% ethyl alcohol (EtOH) and stored at room temperature. DNA was isolated from fecal samples under sterile conditions at the Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, as described elsewhere (17).Using Helicobacter genus-specific primers (C97, 5=-GCT ATG ACG GGT ATC C; C98, 5=-GAT TTT ACC CCT ACA CCA), part of the 16S rRNA gene was amplified (14, 19) for each mouse sample. Escherichia coli was used as a negative and Helicobacter equorum as a positive control (provided by Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic) (1). Therefore, there is 100% prevalence of Helicobacter infection in wild house mice in our study area. The same level of Helicobacter prevalence was reported f...