Down for the count: Cryptosporidium infection depletes the gut microbiome in Coquerel's sifakas

Abstract

Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel's sifaka (Propithecus coquereli) - an endangered, folivorous primate endemic to Madagascar - is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death. Objective: To gain a richer understanding of the pathophysiology of this pathogen while also improving captive management of endangered species, we examine the impact of cryptosporidiosis on the GMB of a flagship species known to experience a debilitating disease state upon infection. Design: Using 16S sequencing of DNA extracted from sifaka fecal samples, we compared the microbial communities of healthy sifakas to those of infected individuals, across infection and recovery periods. Results: Over the course of infection, we found that the sifaka GMB responds with decreased microbial diversity and increased community dissimilarity. Compared to the GMB of unaffected individuals, as well as during pre-infection and recovery periods, the GMB during active infection was enriched for microbial taxa associated with dysbiosis and rapid transit time. Time to recovery was inversely related to age, with young animals being slowest to recover GMB diversity and full community membership. Antimicrobial treatment during infection caused a significant depletion in GMB diversity. Conclusions: Although individual sifakas show unique trajectories of microbial loss and recolonization in response to infection, recovering sifakas exhibit remarkably consistent patterns, similar to initial community assembly of the GMB in infants. This observation, in particular, provides biological insight into the rules by which the GMB recovers from the disease state. Fecal transfaunation may prove effective in restoring a healthy GMB in animals with specialized diets.

Keywords: Enteric infection; gut microbiota; lemur; protozoan pathogen; strepsirrhine primate.

Figure 1.

(a) Photograph of a young Coquerel’s sifaka at the Duke Lemur Center; (b) drawing of the gastrointestinal tract of a Coquerel’s sifaka, reproduced with permission from John Wiley and Sons from [27].

Figure 2.

Schematic illustrating the timing of fecal sample collection relative to infection day across the study for all individuals whose initial day of infection was known, including during pre-infection (green), active infection (dark orange), and recovery (light orange) .

Figure 3.

Boxplots of mean ± quartiles weighted UniFrac distance for all pairwise comparisons within health status, including unaffected, pre-infection, infection, and recovery pairs. NS=non-significant result; ***p < 0.001.

Figure 4.

Principal coordinates (PC) analysis plots of (a) unweighted and (b) weighted UniFrac distances for all samples, including those collected from unaffected sifakas, as well as those from sifakas during pre-infection, active infection, and recovery periods.

Figure 5.

Mean ± standard error (sem) alpha and beta diversity metrics relative to infection day across the study for all of the sifakas whose initial day of infection was known. (a) Shannon index, (b) Simpson index, (c) phylogenetic diversity, and (d) weighted UniFrac distance from pre-infection (i.e. baseline).

Figure 6.

Trajectories for individual sifakas during infection and recovery relative to measures of gut microbial (a) alpha and (b) beta diversity. (a) Shannon index (solid lines) incorporates species richness and evenness, whereas phylogenetic diversity (dashed lines) quantifies taxonomic relatedness across communities. Vertical lines mark the onset of antimicrobial (orange) and antibiotic (red) treatments. (b) Principal coordinates analysis plots of UniFrac distance, weighted by relative abundance.