Antibiotic subsistence in bacteria represents an alternative resistance machinery, while paradoxically, it is also a cure for environmental resistance. Antibiotic-subsisting bacteria can detoxify antibiotic-polluted environments and prevent the development of antibiotic resistance in environments. However, progress toward efficient in situ engineering of antibiotic-subsisting bacteria is hindered by the lack of mechanistic and predictive understanding of the assembly of the functioning microbiome. By top–down manipulation of wastewater microbiomes using sulfadiazine as the single limiting source, we monitored the ecological selection process that forces the wastewater microbiome to perform efficient sulfadiazine subsistence. We found that the community-level assembly selects for the same three families rising to prominence across different initial pools of microbiomes. We further analyzed the assembly patterns using a linear model. Detailed inspections of the sulfonamide metabolic gene clusters in individual genomes of isolates and assembled metagenomes reveal limited transfer potential beyond the boundaries of the Micrococcaceae lineage. Our results open up new possibilities for engineering specialist bacteria for environmental applications.

细菌中的抗生素存在代表了一种替代的抗性机制，而自相矛盾的是，它也是一种治疗环境抗性的方法。抗生素存在的细菌可以解毒抗生素污染的环境，并防止环境中抗生素耐药性的发展。然而，由于缺乏对功能性微生物组组装的机制和预测性理解，阻碍了对抗生素生存细菌进行有效原位工程改造的进展。通过使用磺胺嘧啶作为单一限制源自上而下地操纵废水微生物组，我们监测了迫使废水微生物组进行有效磺胺嘧啶生存的生态选择过程。我们发现，社区水平的集会选择了相同的三个家族，这些家族在不同的初始微生物组库中崛起。我们使用线性模型进一步分析了组装模式。对分离株个体基因组和组装的宏基因组中磺胺类代谢基因簇的详细检查揭示了超出基因组边界的有限转移潜力微球菌科谱系。我们的研究结果为环境应用的工程专业细菌开辟了新的可能性。