Non-human primates are being used in translational research involving infectious, immune-mediated, metabolic and other disorders where the scientific objectives cannot be fully accomplished by the use of other animal models [
43,
67,
68,
69]. The gut microbiomes of two biologically distinct (GS and healthy) groups of captive rhesus macaques were for the first time compared. A recent work by Yasuda and colleagues demonstrated that rhesus stool microbiome is a suitable proxy for both large and small intestine microbiomes [
70]. In the present study, representative stool samples were characterized by amplifying V4 region of the 16S rRNA gene [
19,
32,
34,
35,
37]. It was hypothesized that disease progression in GS macaques is associated with a loss of gut microbial diversity which can potentially lead to increased epithelial permeability thereby exacerbating intestinal inflammation [
25,
26,
27,
28,
29]. Our findings clearly demonstrate that microbiomes in GS and healthy macaques differ significantly while on long-term (≥one year) conventional, gluten-containing diet, i.e., GD. Since the gut microbiomes of GS macaques have not been studied before, findings reported here are novel and provide directions for potential future studies. The GS macaques can be used in preclinical studies to evaluate if novel dietary or other therapeutic interventions can reverse gut dysbiosis. In studies with unrelated, chronic bacterial colitis-affected macaques, an overgrowth of
Pasteurellaceae and
Enterobacteriaceae, as well as decreased microbial diversity was observed. Taken together, our findings also corroborate that gluten sensitivity can contribute to chronic bacterial enterocolitis e.g., one of the major health concerns of polyfactorial origin in captive macaques [
24,
44,
71,
72].
As noted by McKenna and colleagues [
19], a distinctive feature of the macaque gut microbiome is the abundance of intestinal Spirochetes from the
Treponema lineage. In agreement with those observations, in the present study, intestinal Spirochetes were abundant in healthy controls, while GS macaques had lower loads of these bacteria. This finding suggests that a thriving population of intestinal Spirochetes is indeed an indicator of robust health in macaques. It is also consistent with the findings of Zeller and Takeuchi [
73], who pointed out the presence of intestinal Spirochetes in healthy macaques. Our group previously reported that intestinal Spirochetes, despite their high prevalence, were not among intestinal bacteria linked with chronic enterocolitis [
44].
One of the key similarities between human and rhesus gut microbiomes is that
Firmicutes and
Bacteroidetes are the two prominent phyla. It was established that the ratio between these two can be in humans affected by “western” and “low-calorie/high-fiber” types of diets [
74,
75]. Consistent with these findings,
Firmicutes followed by
Bacteroidetes, were amongst the most abundant phyla represented in our study macaques. Nonetheless, several differences in composition were observed between GS and healthy control macaques. While GS macaques exhibited dysbiosis, several groups of intestinal bacteria were differentially abundant when compared with healthy controls. The over-abundant groups included two major families belonging to the phylum
Firmicutes, i.e.,
Streptococcaceae and
Lactobacillaceae. Previously, it was reported by Caminero et al., that both
Lactobacillaceae and
Streptococcaceae play an important role in metabolism of gluten [
39]. While it is obvious that the presence of
Streptococcaceae represents potential to contain pathogenic strains, the biological significance underlying the increased presence of
Lactobacillaceae in GS macaques is less certain. Clearly,
Lactobacillus spp. have the capacity to degrade gluten resulting in decreased immunotoxicity of its major immunogens such as the 33-mer of alpha-gliadin [
76]. At the same time, however, the full pathogenic potential of dysbiotic bacterial taxa including
Lactobacillaceae,
Streptococcaceae and others in GS individuals still needs to be elucidated. Interestingly, and in concordance with our study, Ardeshir and colleagues (2014) independently reported that chronic intestinal enterocolitis is in rhesus macaques associated with an over-abundance of intestinal
Lactobacillaceae [
24], suggesting that not all of the
Lactobacilli spp. act as a health-promoting probiotics. According to their study,
Lactobacillaceae overgrowth can be reduced in macaques by inulin treatment [
24]. Less abundant taxa in GS macaques were mostly represented by
Coriobacteriaceae that belong to phylum
Actinobacteria.
Actinobacteria were recognized as the producers of host-beneficial metabolites with antibacterial, antifungal, immunomodulatory and other functions [
66,
77]. Reduced abundance of
Bacteroidetes has been previously reported in human celiac infants [
33]. Similar studies that utilized different technologies, and focused on different types of (biopsy) samples, have not always produced consistent results [
32,
34,
35,
37]. In our study, a few of the bacterial taxa belonging to
Bacteroidetes were less abundant in GS macaques while others, namely
Prevotella sp., were overabundant compared to healthy controls. One group of patients where GS occurs with higher frequency and in parallel with neurodevelopmental disorders, are the patients with Autism Spectrum Disorder [
78,
79]. It has been reported that Autism and Parkinson’s disease patients lack beneficial gut microflora [
80,
81]. In this context, we previously reported that up-regulation of the Autism Spectrum Disorder-associated gene CADPS2, and other neurodevelopmental disorder-related genes (BACE2 and DSCR5) were detected in GS macaques [
82]. Despite that these associations and links are still largely under-explored, they offer clues for potential future studies.
While microbial dysbiosis is a hallmark of chronic inflammatory diseases of the gastrointestinal tract, the potential mechanisms underlying these alterations remain unknown. A recent study demonstrated that fecal miRNAs secreted by intestinal epithelial cells could enter luminal bacterial cells and regulate their growth via post-transcriptional gene regulation [
42]; suggesting a critical mechanism by which the host could not only shape but also potentially dysregulate its intestinal microbiome. Additionally, miRNAs have also been demonstrated to regulate the intestinal epithelial barrier in inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) via post-transcriptional regulation of TJ proteins [
54,
83]. Notable miRNAs associated with inflammation in our study included miR-203 and miR-29b that have previously been reported to be upregulated in IBD and IBS [
54,
55,
56]. More importantly, the inverse relationship between miR-203, -204 and -29b expression and their predicted/validated claudin-1 target protein expression, suggests an important post-transcriptional mechanism regulating the intestinal epithelial barrier that could promote translocation of dysbiotic intestinal bacteria leading to adverse systemic inflammation/immune dysregulation in GS macaques and celiac disease patients. Similarly, dysregulation of miR-204 and miR-23a/b has been reported in various other inflammatory conditions [
58,
59,
60,
61].