Here a cycle of endophytic‐enteric‐soil‐endophytic microbes is proposed which has relevance for health and comprises the fate of animal faeces as natural microbial inoculants for plants that constitute bacterial sources for animal guts.

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Background The volcano rabbit is the smallest lagomorph in Mexico, it is monotypic and endemic to the Trans-Mexican Volcanic Belt. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Romerolagus diazi consumes large amounts of grasses, seedlings, shrubs, and trees. Pines and oaks contain tannins that can be toxic to the organisms which consume them. The volcano rabbit microbiota may be rich in bacteria capable of degrading fiber and phenolic compounds. Methods We obtained the fecal microbiome of three adults and one young rabbit collected in Coajomulco, Morelos, Mexico. Taxonomic assignments and gene annotation revealed the possible roles of different bacteria in the rabbit gut. We searched for sequences encoding tannase enzymes and enzymes associated with digestion of plant fibers such as cellulose and hemicellulose. Results The most representative phyla within the Bacteria domain were: Proteobacteria, Firmicutes and Actinobacteria for the young rabbit sample (S1) and adult rabbit sample (S2), which was the only sample not confirmed by sequencing to correspond to the volcano rabbit. Firmicutes, Actinobacteria and Cyanobacteria were found in adult rabbit samples S3 and S4. The most abundant phylum within the Archaea domain was Euryarchaeota. The most abundant genera of the Bacteria domain were Lachnoclostridium (Firmicutes) and Acinetobacter (Proteobacteria), while Methanosarcina predominated from the Archaea. In addition, the potential functions of metagenomic sequences were identified, which include carbohydrate and amino acid metabolism. We obtained genes encoding enzymes for plant fiber degradation such as endo 1,4 β-xylanases, arabinofuranosidases, endoglucanases and β-glucosidases. We also found 18 bacterial tannase sequences.

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<p><strong>Background:</strong> The excess of antimicrobials and anthelmintics cause important dysbiosis processes in equines, as well as resistance phenomena mainly in the communities of bacteria, archaea, protozoa, and helminths. The study of the equine microbiome is becoming more and more relevant to understand the biotic processes of the gastrointestinal tract. In colon and cecum, the role of cyathostomins as part of the microbiome is still unexplored. While interaction with certain bacterial groups may be key to the understanding of parasitism. <strong>Objective:</strong> To characterize the microbiota in feces of yearling naturally infected with cyathostomins in a quarter-horse farm in Sierra de Lobos, Guanajuato, Mexico. <strong>Methodology:</strong> Weights were measured and obtained the parasite burden in feces, from which samples were transfer and processing in the laboratory for DNA extraction and later sent for sequencing and analysis. <strong>Results:</strong> Average weight of the colts was 399 kg, and the average weight of the fillies was 432 kg. All horses were high shedders:  1,390 ± 698 egg per gram of feces. Alpha and beta diversity analyses indicated no differences within the microbial community between colts and fillies. Main bacteria at Phyla in both groups (females; males) were Bacteroidetes (37%; 37%), Firmicutes (46%; 37%), Verrucomicrobia (4%; 10%), Spirochaetes 5%; 4%) and Proteobacteria (1%; 3%). At Class level the principal identified groups were Bacteroidia (31%; 31%), Clostridia (43%; 35%), at Order level are Bacteroidales (31%; 31%) and Clostridiales (43%; 35%). Main bacteria at Family level were Ruminococcaceae (19%; 11%), Lachnospiraceae (15%; 6%) and non-assigned family Bacteriodales (19%; 21%). The most abundant non-assigned bacterial Genra were Bacteroidales (26%; 27%), Ruminococcaceae (10%; 5%) y Lachnospiraceae (9%; 6%); the assigned bacterial Genra were <em>Clostridium</em> (5%; 9%) and <em>Treponema</em> (4% y 3%).  The most abundant non-assigned bacterial Species were<em> Methanocorpusculaceae</em> sp (19%; 22%), <em>Pedobacter</em> sp (10%; 5%), <em>Bacteroidales</em> sp (9% y 6%) and <em>Prevotella</em> sp (4% y 3%); the assigned bacterial species were <em>Fibrobacter succinogenes</em> (2%; 1%), <em>Succinispira mobilis</em> (1%; 1%).  <strong>Implications:</strong> It is suggested that environmental factors and feeding are aspects that regulate the parasitic burden and the bacterial composition in this studied population. This is a short communication of the finding of the components of the microbiota and is relevant in Mexico for future studies, however it is imperative to explore the composition of the metacommunity of a horse free of cyathostomines. <strong>Conclusion:</strong> Considering that these nematodes are in the cecum and colon, where this microbiota was inferred, and that it is not known whether this interaction is beneficial or detrimental, the study of the microbiome is imperative. In the study, no horse presented clinical signs or colic due to the presence of nematodes.</p>