Abstract
<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>
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