Changes in the human nasal microbiome following exposure to pig farm environment: a prospective cohort study. Human Nasal Microbiome in pig farm environment

Based on 16S rRNA gene sequence analysis, we detected a temporary shift of the nasal microbiome of MRSA-negative human visitors after a one-hour exposure in a pig farm. On the other hand, long time occupationally exposed pig farm workers were found to have a wide range of microbial communities. Analysis of microbial community clustering revealed five community state types (CSTs) among the samples of short time visitors and pig farm workers. Two of the CSTs were found only in pigs, short time visitors at farm, and in some farm workers. Remaining three CSTs were found in visitors’ at home and in farmers which shows the microbial transition in short time visitors, and diverse microbial communities in farm workers. There were neither phylogenetic nor statistical differences in the microbial diversity of farm workers at different time points during an entire week. The observed differences in the dynamics of the nasal microbiomes between farm workers and short-time visitors are important factors in understanding the overall risk of transmission of the microbiome, including LA-MRSA, from pig farms to household members and the general population.

基于16S核糖体RNA（16S rRNA）基因序列分析，我们发现，在猪场暴露1小时后，耐甲氧西林金黄色葡萄球菌（Methicillin-resistant Staphylococcus aureus, MRSA）阴性人类访客的鼻腔微生物组会出现暂时性偏移。另一方面，长期职业暴露的猪场工作人员体内的微生物群落组成更为多样。微生物群落聚类分析显示，在短期暴露访客与猪场工作人员的样本中，共存在5种群落状态类型（community state types, CSTs）。其中2种群落状态类型仅在猪、猪场短期暴露访客以及部分猪场工作人员的样本中被检出。其余3种群落状态类型则见于居家访客与猪场工作人员体内，这一结果表明短期暴露访客的鼻腔微生物组发生了菌群转变，而猪场工作人员则具备更为多样化的微生物群落。在一整周内的不同时间点采集的猪场工作人员样本中，其微生物多样性既未出现系统发育层面的差异，也无统计学意义上的显著差异。本研究观察到的猪场工作人员与短期暴露访客之间鼻腔微生物组动态变化的差异，是理解微生物组（包括畜牧相关耐甲氧西林金黄色葡萄球菌（Livestock-associated Methicillin-resistant Staphylococcus aureus, LA-MRSA））从猪场向家庭成员及普通人群传播的整体风险的关键因素。