Both Thai studies demonstrated high diversity within the gut microbial populations in managed Asian elephants, with many similarities to predominant microbiomes described for both semi-wild and managed Asian elephants elsewhere, as well as African elephants (Klinsawat et al., 2023). However, some unique microbes were identified by Klinsawat et al. (2023), and particular differences in microbiomes in elephants fed predominantly local palms (Caryota urens) compared with Napier grass (Pennisetum purporeum)-based diets may have broader health and nutrition implications for the species. 

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Thus, age of the animal can play a huge role in gut microbiome diversity, with diet likely playing the predominant role. Both Ilmberger et al. (2014) and Kambe et al. (2020) demonstrated that elephant calves have a much less diverse microbiome compared with older individuals, but changes can develop rapidly in the very young calf.

In an elephant study (with a single individual), Kambe et al. (2020) documented radical differences in microbial diversity, community composition, and specific taxa (order) between mother and calf. Enterobacteroidales and Lactobacillales were initially found in the infant; since lactic acid bacteria stimulate gut immunity and barrier in other species, these may be critically important components of the early elephant calf gut development. Milk substrates positively correlated with those particular microbial constituents include the sugars lactose, rhamnose, sorbitol, fucose, and sorbose, along with protein constituents asparagine and threonine, as well as the hormone estradiol-17ß (Lactobacillales only).

These sugar components in milk appeared in highest quantities up to about Day 7 of lactation; later (Days 22-37) milk samples analyzed higher in specific amino acid (aspartic acid) and lipid (palmitic acid) components.  Concurrent with these changes in milk constituents, by Day 6, Bacteroidales predominated and by Day 29, Clostridiales was identified as the primary bacterial order in the calf, which also positively correlated with milk palmitic acid content. 

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By one month of a milk-based diet, the calf microbiome more closely resembled phyla proportions found in the mother. Interestingly, this calf was observed practicing coprophagy at Day 26, which may also have contributed to the changeover in gut microbes. In other species, oligosaccharides are involved in the increase of lactic acid bacteria in the gut environment; oligosaccharides and glucosamine have been identified in Asian elephant milks (Uemura et al., 2006; Takatsu et al., 2017) and may also play a role in elephant calf gut microbiome development. 

Detailed analyses that correlate diet chemistry and fecal bacteria may help us better understand the relationship(s) of dietary constituents in milk to optimize the gut microbiome, development, and associated health of elephant calves, beginning at birth.

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In the earliest published elephant microbiome report comparing the gut microbiome in a three-week-old (milk-fed) calf versus a six-year-old elephant, Ilmberger et al. (2014) also documented Bacteroidetes and Firmicutes as predominant phyla. Proteobacteria species, however, were found in a high proportion in the calf feces of their study – likely due to dietary substrate differences.

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These authors found many unique microbial carbohydrase enzymes in both samples analyzed, and suggested that Bacteroidetes species seemed to play a critical role in carbohydrate utilization in elephants, perhaps warranting focus in future targeted probiotic blends for elephants. Unpublished data (Paine and Choudhury) demonstrated significant differences in microbiome between a newborn calf and its mother, which the authors attributed to microbial exposure in the birth canal, as well as milk, resulting in an early dominance of Firmicutes in the calf. 

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A later microbiome study of Zhang et al. (2019) with three free-range elephants in China reported that Firmicutes species were found in greater abundance than Bacteroidetes species, and a number of unique carbohydrases were detected in fecal samples.  Fibrobacteres species also detected in this study increased proportionately with age (and presumably dietary fiber), but overall microbiome diversity decreased.

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These authors found evidence for greater hemicellulose- than cellulose-degrading enzymes in the microbial metagenomic evaluation of samples, and suggested hemicellulose as the primary energy source for elephants from this locale. Diets consumed by elephants in this study comprised bamboo and plantain; it’s possible that the microbes and metagenomics of this particular population may reflect that unique landscape/habitat and diet rather than a broader elephant microbiome generalization. Bamboo, as a grass, typically contains a higher hemicellulose component than other plant types, thus microbial adaptation to hemicellulose (a substrate which can also be partially hydrolyzed by stomach acids prior to microbial exposure in the hindgut) appears to be a useful adaptive digestive strategy.

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In adult elephants, environment and accompanying diet have been shown to influence microbial species abundance as well as, in some cases, diversity. African savannah elephants (Loxodonta africana) display a majority Firmicutes species typically associated with grazing hindgut fermenters, whereas the microbiome of African forest elephants (L. cyclotis) was dominated by Proteobacteria, similar to more frugivorous species (Budd et al. 2020).

Specific community composition, but not microbial diversity, was seen to change in free-range compared to captive Asian elephants; diversity increased in one study with animals stressed by translocation, with an increase in Bacteroidetes species and decrease in Proteobacteria seen in response to both anthropogenic activities described. Additionally, as mentioned above, effects of management activities (a specific deworming agent, Albendazole) temporarily impacted the gut microbiome, decreasing Firmicutes and Spirochaetes while increasing Proteobacteria proportions; direct and indirect effects of the medication were documented but the microflora resorted to pre-treatment levels within 3 weeks (Moustafa et al., 2021).  

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In an unpublished study, Paine and Choudhury reported the wild Asian elephant gut microbiome collected from animals (n=9) in grasslands of the Brahmaputra Valley was dominated by Firmicutes (23%-47%) and Bacteroidetes (20-60%) species, and differed significantly from captive adults which displayed Thermoplasmata (~40%), Cyanobacteria (~45%) and Methanobacteria (~10%). The wild elephants also displayed a unique range of soil microbes in fecal samples, that may be associated with plants (and/or other substrates) consumed in natural environments. Imbalances in the microbiome may be involved in some of the GI-related medical problems that we see in adult as well as neonatal elephants.

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As we begin to better understand more about the elephant microbiome, we may be able to use this knowledge therapeutically to optimize health and nutrition. While a healthy gut microbiome is critical to digestive function and immunity, increasing evidence links specific microbial interaction to endocrine control of metabolic and reproductive hormones which, in turn regulate physiological responses, metabolism, mood, growth and development, and reproduction.

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We need to acknowledge species-specific genetics, environmental and dietary factors that impact the gut microbiome, and better understand relationships among microflora, endocrine hormones and overall health in situational management of gut dysbiosis. Such issues are not trivial and can have lifelong impacts regarding health of the individual, and provide relevant information for niche identification, rehabilitation and conservation of the species.

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From a practical starting perspective, faunation or transfaunation can occur naturally through exposure during birth, suckling, normal dietary consumption, and/or coprophagy. In response to dysbiosis, animals can be orally transplanted with gut microbiota from other healthy individuals through fecal harvest following discontinuation of antimicrobials (Mullen et al., 2018) with or without freezer storage for future use in animal treatment/management. Feeding inulin (a prebiotic) may also help to restore the gut microbiome in elephants with colic (Bo et al., 2023).  

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