Insights Into Boar Semen Under Tropical Conditions in Smallholder Production Systems: Semen Quality, Potential Microbiota Contamination and Antimicrobial Susceptibility.

This study evaluated boar semen quality, seminal microbiome composition, and antimicrobial susceptibility of bacteria isolated from seminal plasma in a tropical smallholder pig production system in Indonesia. A total of 10 ejaculates were collected from eight sexually mature boars using the gloved-hand technique from two herds located in East Nusa Tenggara (Herd A) and East Java (Herd B). Semen quality was evaluated using conventional methods in Herd A (five ejaculates from three boars) and a mobile semen analysis unit in Herd B (five ejaculates from five boars). Seminal microbiome composition (three ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was assessed using next-generation sequencing, and antimicrobial susceptibility of bacterial isolates recovered from seminal plasma (five ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was determined using the disk diffusion method. Boar semen quality from Herd A was assessed only for gross motility using subjective observation, yielding a score of 2 out of 3. In Herd B, semen quality was generally high, with a mean ejaculate volume of 232.0 ± 28.6 mL and sperm concentration of 436.9 ± 109.3 × 106/mL. Total and progressive motility were 89.5% ± 6.9% and 84.2% ± 9.5%, respectively, while the proportion of immotile spermatozoa was 10.5% ± 6.9%. Based on 16S rRNA gene sequencing, Chryseobacterium showed the highest relative abundance in semen samples from Herd A, whereas Streptococcus predominated in Herd B. Principal coordinates analysis based on Bray-Curtis dissimilarity demonstrated clear separation of seminal microbiota between herds, with Herd A samples forming a more compact cluster. LEfSe analysis further identified bacterial taxa differentially enriched between herds. Bacterial culture revealed that all semen samples were contaminated with either single or multiple bacterial species, including both Gram-negative and Gram-positive organisms. Escherichia coli and Klebsiella spp. were the most frequently detected isolates. Antimicrobial susceptibility test showed that Herd B exhibited a higher proportion of non-susceptible outcomes (58.3%) compared to Herd A (24.3%). In addition, the proportion of multidrug resistance in Herd A and Herd B were 42.9% and 83.3%, respectively. In conclusion, bacterial contamination in boar semen is unavoidable and may originate from the animal itself or the surrounding environment. Its impact on semen quality may vary depending on the bacterial load and the specific types of microorganisms present. In addition, variations in AMR and seminal microbiota between herds suggest that farm management practices may influence the microbial ecology and resistance patterns in boar semen.