Bacteria colonize stallion semen during collection and processing which may cause disease in inseminated females or negatively affect sperm quality during storage prior to insemination. Antibiotics are added to semen extenders to control the growth of these bacteria but may induce antimicrobial resistance. Research into alternatives to antibiotics for this purpose requires knowledge of which bacteria are present in semen. Not all bacteria in semen, however, can be identified by conventional microbiological techniques. The objectives of the study were to: i) determine which bacteria are present in stallion semen using metagenomics; and ii) investigate individual differences in bacterial content in semen from all stallions on one premises. Bacterial DNA was extracted from ejaculates from seven stallions (one ejaculate per stallion) and bacteria were identified using 16S sequencing. In total, 83 bacterial genera were identified, varying from 25 to 52 among different individuals. There was a negative correlation (r = -0.81212; P < 0.05) between the presence of Treponema spp. and Advenella spp. In conclusion, most of the bacteria present in stallion semen could be identified to genus level by 16S sequencing even when present at a low frequency. This method of identification may help to clarify individual variation in bacterial content and its potential effects on fertility.

细菌在收集和加工过程中定植于种马的精液中，这可能会导致受精雌性疾病或在受精前储存期间对精子质量产生负面影响。将抗生素添加到精液稀释剂中以控制这些细菌的生长，但可能会引起抗菌素耐药性。为此目的研究抗生素的替代品需要了解精液中存在哪些细菌。然而，并非精液中的所有细菌都可以通过常规微生物技术识别。该研究的目的是： i) 使用宏基因组学确定种马精液中存在哪些细菌；ii) 在一个场所调查所有种马精液中细菌含量的个体差异。从七匹种马的精液中提取细菌 DNA（每匹种马精液一匹），并使用 16S 测序鉴定细菌。总共确定了 83 个细菌属，不同个体之间从 25 到 52 不等。呈负相关（r = -0.81212; P  < 0.05) 在密螺旋体属的存在之间。和Advenella spp。总之，即使以低频率存在，也可以通过16S测序将种马精液中存在的大多数细菌鉴定到属水平。这种鉴定方法可能有助于阐明细菌含量的个体差异及其对生育能力的潜在影响。