Impact of Antibiotic Residues on Human Gut Microbiome

The pervasive presence of antibiotic residues in the food chain, agricultural run-off and wastewater represents a growing concern for the stability and function of the human gut microbiome. Even at subinhibitory concentrations, residues of commonly used veterinary and human antibiotics can reshape microbial community structure, leading to reduced diversity, overgrowth of resistant taxa and disturbances in metabolic output. Such exposures have been linked to dysbiosis characterised by loss of key commensals, expansion of opportunistic bacteria and enrichment of antibiotic-resistance genes. Consequent alterations in short-chain fatty acids, bile acids and other microbially derived metabolites may impair mucosal integrity, modulate immune responses and predispose to chronic disorders including inflammatory bowel disease, metabolic syndrome and allergies. Experimental models, ranging from in vitro bioreactors to animal and human cohort studies, have begun to elucidate dose-dependent effects of low-level antibiotic residues and to uncover mechanistic pathways of host–microbial co-metabolism. These insights underscore the need for rigorous monitoring of environmental and dietary antibiotic residues, refinement of maximum residue limits, and development of mitigation strategies such as targeted probiotics or bacteriophages. By integrating ecotoxicological, microbiological and clinical perspectives, this body of work has global implications for food safety, public health policy and antibiotic stewardship.

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Impact of Antibiotic Residues on Human Gut Microbiome publication trend

The graph below shows the total number of articles in impact of antibiotic residues on human gut microbiome across all publications each year (not limited to Nature Index journals).

Technical terms

Dysbiosis: An imbalance in the composition or function of the gut microbial community associated with adverse health outcomes.

Subinhibitory concentration: An antibiotic dose below the minimum inhibitory concentration that does not fully prevent microbial growth but can affect microbial behaviour.

Short-chain fatty acids: Organic acids (e.g. acetate, propionate, butyrate) produced by microbial fermentation of dietary fibres, crucial for colonic health and immune modulation.

Minimum residue limit (MRL): The maximum legally permitted concentration of an antibiotic residue in food products, set to protect consumer health.

Continuous-flow bioreactor: An in vitro system that simulates gut conditions by maintaining a steady supply and removal of nutrients and microbial cultures for controlled studies.

References

1. The effect of residual antibiotics in food on intestinal microbiota: a systematic review. Frontiers in Sustainable Food Systems (2023).
2. Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model. Antibiotics (2021).
3. In vitro models to detect in vivo bile acid changes induced by antibiotics. Archives of Toxicology (2022).