Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate. We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition.

中文翻译：

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抗生素使人类肠道群落从互利共生转向竞争，对真菌的影响比对细菌的影响更持久。


抗生素治疗对肠道细菌组成有明确的有害影响，但对真菌群落的影响尚不清楚。胃肠道腔内的细菌可能会限制真菌的定植和侵袭。因此，针对细菌的抗生素药物被视为真菌感染和诱发过敏的重要危险因素。然而，抗生素对肠道细菌-真菌相互作用的影响，包括真菌群落组成的破坏和恢复力，尚未在人体中进行研究。我们分析了 14 名健康人类参与者在服用 6 天抗生素后 3 个月内收集的粪便样本。我们整合了鸟枪法宏基因组学、宏转录组学、代谢组学和真菌 ITS2 测序的数据。虽然细菌群落在治疗后 3 个月内大部分恢复，但真菌群落从基线时的互利共生转变为竞争。药物干预前存在的细菌-真菌相互作用的一半在三个月后消失。在治疗过程中，真菌丰度与具有细胞生长和修复功能的细菌基因的表达相关。通过扩展宏基因组物种方法，我们发现了抑制机会性真菌病原体白色念珠菌的细菌菌株。我们在体外证明了白色念珠菌的致病性和宿主细胞损伤如何在人类肠道中通过丙酸或 5-十二碳烯酸等细菌代谢物自然控制。我们证明抗菌药物对人类肠道菌群具有长期影响。虽然细菌群落在抗菌治疗后 30 天大部分恢复，但真菌群落从互利共生转向竞争。