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Particle size distribution of diet, feces, and change from diet to feces, as well as apparent digestibility (aDig, %) of selected nutrients, and novel fecal microbiome identification of mature female leopard tortoises (Stigmochelys pardalis, n = 16) fed exclusively one of three, nutritionally complete, pelleted diets were evaluated in a blind, complete randomized design study. Two diets included insoluble fiber (powdered cellulose) consisting of either 2.0 mm or 0.2 mm length. Insoluble fiber provides nutritional and physical benefits to both the animal host and the microorganisms that inhabit the gastrointestinal tract. Insoluble fiber length was used as a means of evaluating a physically effective fiber (peNDF) definition for hindgut-fermenting vertebrates. Numerical trends of each diet particle size distribution indicated a greater amount of particle recovery on the 2.0 mm sieve for the 2.0 mm diet, and a greater particle recovery on the 0.125 mm sieve for the 0.2 mm diet, both as expected based on the added fiber lengths. Fecal particle size distributions were not different between diets, however, distributions of the change in particle size from diet to feces were different between diets. Similar fecal particle size distributions across diets suggests both cellulose lengths are below the peNDF threshold of the leopard tortoise. Apparent digestibility (aDig, %) of dry matter (DM) and organic matter (OM) was not different based on diet, method, or a diet and method interaction; aDig (%) of neutral detergent fiber (aNDF) and sequential acid detergent fiber (sADF) was different based only on diet. These results suggest that while aDig (%) of OM did not change, the source of OM digestibility shifted, as both aNDF and sADF digestibility increased with the cellulose-added diets compared to the control diet. An increase in insoluble fiber digestibility suggests an "effectiveness" of the cellulose lengths. At both bacterial phyla and genera levels, fecal microbiomes were more similar between tortoises fed the cellulose-added diets versus the control diet, suggesting that the hindgut microbial communities adjusted in the hindgut of the tortoises fed the cellulose-added diets by shifting proportions of microbes, based on their role in the hindgut (i.e., cellulose digestion), to accommodate for the addition of cellulose in the two treatment diets. This may explain the similarity among fecal particle size distributions, and suggests that adaptability of the hindgut microbial communities should be considered when defining peNDF for hindgut-fermenting vertebrates.

Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.

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