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Cotton serves as a vital economic driver within the agricultural sector of Mississippi. The seeds of cotton are rich in fat and protein content, making them a cost-effective alternative to soybean meal and other expensive protein sources. Additionally, cottonseed is the primary source of gossypol, a phenolic compound with significant potential for natural parasite control. The rumen microbiota, a diverse community of microorganisms, has a pivotal role in nutrient digestion and detoxification. However, the impact of cottonseed on rumen microbial ecosystems remains largely unexplored. The aim of this study is to investigate the effects of cottonseed supplementation on the rumen microbiota of meat goats with and without the challenge of parasites. Forty female weaned Boer x Spanish crossed meat goats were assigned to one of the four treatments (n = 10 per treatment) in a 2 x 2 factorial design consisting of control group (CON), parasite challenge group (P), cottonseed supplementation (0.5% body weight) without parasite challenge group (CS-NP), and CS supplementation with parasite challenge group (CS-P). The parasite challenge was performed with a dose of 4,000 infective third-stage larvae of Haemonchus contortus per animal. After 25 d following the first dose, the treatments were applied for 10 wk. The goats were slaughtered at the end of the experiment, and rumen digesta samples were collected for microbiota analysis using high-resolution full-length 16S rRNA gene amplicon sequencing. The results revealed that the parasite challenge significantly reduced the number of bacterial species in the rumen (P = 0.032), regardless of cottonseed supplement. Anaeromassilibacillus senegalensis, which has been isolated from kwashiorkor (severe protein malnutrition) patient, Hungateiclostridium aldrichii, and Mogibacterium diversum were enriched in rumen of P group, while Anaerocella delicata and the rumen lipolytic organism Anaerovibrio lipolyticus were reduced compared with the CON group [linear discriminant analysis (LDA) scores > 3.6]. Cottonseed supplementation did not affect the number of bacterial species in the rumen of parasite-challenged goats, but it did lead to an increase of Anaerovibrio lipolyticus (P = 0.008) and a reduction of Anaeromassilibacillus senegalensis (P = 0.007). Moreover, cottonseed supplementation tended to increase the number of bacterial species in the rumen of meat goats without parasite challenge (P = 0.08) and increased the relative abundance of butyrate-producing bacteria such as Pseudobutyrivibrio xylanivorans and Intestinimonas butyriciproducens, along with the butanol-producing bacteria Clostridium saccharoperbutylacetonicum (LDA scores > 2). Conversely, cottonseed supplementation inhibited cellulolytic bacteria Fibrobacter succinogenes, polysaccharide-degrading bacteria Butyrivibrio proteoclasticus, and several Prevotella species, including P. oris, P. loescheii, P. copri, and P. albensis (LDA score > 2). In conclusion, parasite challenge affects the rumen microbial diversity and certain bacterial species that utilize protein and lipids, and cottonseed supplementation partially restores the altered rumen microbial ecosystem of the parasite-challenged meat goats. [ABSTRACT FROM AUTHOR]