Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance

Author:

Chen Jing12ORCID,Zhu Jinlin12ORCID,Lu Wenwei1234,Wang Hongchao12ORCID,Pan Mingluo12,Tian Peijun12,Zhao Jianxin124,Zhang Hao12456,Chen Wei125

Affiliation:

1. State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China

2. School of Food Science and Technology, Jiangnan University, Wuxi 214122, China

3. International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China

4. (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China

5. National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China

6. Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China

Abstract

Antibiotic treatment can lead to a loss of diversity of gut microbiota and may adversely affect gut microbiota composition and host health. Previous studies have indicated that the recovery of gut microbes from antibiotic-induced disruption may be guided by specific microbial species. We expect to predict recovery or non-recovery using these crucial species or other indices after antibiotic treatment only when the gut microbiota changes. This study focused on this prediction problem using a novel ensemble learning framework to identify a set of common and reasonably predictive recovery-associated bacterial species (p-RABs), enabling us to predict the host microbiome recovery status under broad-spectrum antibiotic treatment. Our findings also propose other predictive indicators, suggesting that higher taxonomic and functional diversity may correlate with an increased likelihood of successful recovery. Furthermore, to explore the validity of p-RABs, we performed a metabolic support analysis and identified Akkermansia muciniphila and Bacteroides uniformis as potential key supporting species for reconstruction interventions. Experimental results from a C57BL/6J male mouse model demonstrated the effectiveness of p-RABs in facilitating intestinal microbial reconstitution. Thus, we proved the reliability of the new p-RABs and validated a practical intervention scheme for gut microbiota reconstruction under antibiotic disturbance.

Funder

National Natural Science Foundation of China

Fundamental Research Funds for the Central Universities

Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province

Publisher

MDPI AG

Subject

Food Science,Nutrition and Dietetics

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