Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

人类将粪便资源化利用的实践已有数千年历史。好氧（嗜热）堆肥（aerobic thermophilic composting）处理市政污泥（sewage sludge）已被证实可降低机会致病菌的种群数量，并灭活原污泥中的蛔虫卵与可培养大肠杆菌（Escherichia coli），但直接堆肥原料中多数粪便细菌的归趋仍有待阐明。本研究对海地两座堆肥设施6个月内不同阶段采集的堆肥物料开展了全面的微生物群落分析，采用高密度DNA微阵列（high-density DNA microarray，PhyloChip）监测粪便微生物群（fecal microbiota）信号。研究发现，嗜热堆肥可改变初始物料的细菌群落结构：以下类群的典型粪便细菌在半数以上初始物料样本中可被检出，但在最终堆肥产物中均降至检测限以下：普雷沃菌属（Prevotella）与红蝽杆菌科（Erysipelotrichaceae）检出率完全清零；瘤胃球菌科（Ruminococcaceae）检出率下降98%~99%；毛螺菌科（Lachnospiraceae）检出率下降83%~94%，仅剩余部分未分类类群；埃希氏菌属与志贺氏菌属（Escherichia and Shigella）检出率完全清零。最终堆肥产物中，除破伤风梭菌（Clostridium tetani）外的所有机会致病菌均降至检测限以下；破伤风梭菌可能以芽孢形式存活，或在户外腐熟阶段后期被重新引入。与之相反，堆肥中常见的耐热或嗜热放线菌（Actinomycetes）与厚壁菌门（Firmicutes）类群（如高温单孢菌属Thermobifida、芽孢杆菌属Bacillus、地芽孢杆菌属Geobacillus）在高温阶段丰度显著提升。本项基于群落DNA的高温堆肥过程中人粪便微生物群归趋分析，将助力优化该工艺，为基础设施与资源匮乏地区提供可行的卫生解决方案。