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在促进小鼠微生物群恢复方面,饮食比微生物移植更有效。

Diet outperforms microbial transplant to drive microbiome recovery in mice.

作者信息

Kennedy M S, Freiburger A, Cooper M, Beilsmith K, St George M L, Kalski M, Cham C, Guzzetta A, Ng S C, Chan F K, DeLeon O, Rubin D, Henry C S, Bergelson J, Chang E B

机构信息

Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA.

Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.

出版信息

Nature. 2025 Apr 30. doi: 10.1038/s41586-025-08937-9.


DOI:10.1038/s41586-025-08937-9
PMID:40307551
Abstract

A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth, which in turn increases risk for a wide array of metabolic, immune and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment, although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.

摘要

高脂、低纤维的西式饮食(WD)会引发微生物群失调,其特征是分类多样性和代谢广度降低,进而增加患一系列代谢、免疫和全身疾病的风险。最近的研究表明,WD会损害微生物群对抗生素治疗等急性干扰的恢复力,尽管对损害机制以及抗生素后长期失调对宿主的具体影响知之甚少。在这里,我们描述了正常饮食(RC)或WD喂养的小鼠在抗生素治疗后肠道微生物群恢复其分类和功能特征的轨迹,发现只有RC喂养的小鼠经历了快速的连续恢复过程。代谢模型表明,RC饮食促进了互营交叉喂养相互作用的发展,而在WD喂养的小鼠中,一个优势分类群垄断了现成的资源,而不释放互营副产物。干预实验表明,合适的饮食资源环境对于微生物群的快速和强劲恢复既是必要的也是充分的,而微生物移植则不然。此外,WD喂养的小鼠抗生素后长期失调使它们易受肠道病原体鼠伤寒沙门氏菌的感染。我们的数据对将粪便微生物群移植(FMT)作为解决失调问题的策略的广泛热情提出了挑战,并表明特定的饮食干预至少是有效FMT的必要先决条件,并且可能提供一种更安全、更自然且侵入性更小的替代方案。

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引用本文的文献

[1]
Emerging concepts and shifting paradigms for understanding the microbial basis of inflammatory bowel diseases.

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[2]
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[3]
Applying ecological principles to microbiome engineering.

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[4]
Post-antibiotics microbiome restoration driven by diet.

Nat Rev Gastroenterol Hepatol. 2025-6-11

[5]
Inflammatory Bowel Disease Drivers Revealed in Human Organ Chips.

medRxiv. 2024-12-8

本文引用的文献

[1]
Pectin supplementation accelerates post-antibiotic gut microbiome reconstitution orchestrated with reduced gut redox potential.

ISME J. 2024-1-8

[2]
Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential.

Nat Commun. 2023-8-24

[3]
Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization.

Cell Rep. 2023-8-29

[4]
Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis.

Microbiol Spectr. 2023-8-17

[5]
Key determinants of success in fecal microbiota transplantation: From microbiome to clinic.

Cell Host Microbe. 2023-5-10

[6]
dbCAN3: automated carbohydrate-active enzyme and substrate annotation.

Nucleic Acids Res. 2023-7-5

[7]
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.

Nat Biotechnol. 2023-9

[8]
Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations.

Nat Ecol Evol. 2023-1

[9]
The microbiome and gut homeostasis.

Science. 2022-7

[10]
Salmonella enterica serovar Typhimurium chitinases modulate the intestinal glycome and promote small intestinal invasion.

PLoS Pathog. 2022-4

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