A Shotgun Metagenomics Investigation into Labeling Inaccuracies in Widely Sold Probiotic Supplements in the USA

While probiotics are generally considered safe, concerns persist regarding the accuracy of labels on these supplements and their potential contribution to the spread of antibiotic resistance genes. Given that probiotics are predominantly ingested with a view towards obtaining particular health benefits. The objective of this study is to assess the composition of 50 widely available probiotic supplements in the USA using shotgun metagenome sequencing. The study also determines the potential resistome profile, and the functional characteristics of these products. This study finds that 67% of products does not contain any labeling inaccuracies. Antimicrobial Resistance Genes (ARGs) are identified in several products, particularly Bacillus‐based products carrying between 10 and 56 genes. The risk posed by the presence of these ARGs requires further study. Functional analysis reveals differences in metabolic profiles among probiotic supplements, indicating the importance of strain‐level selection for personalized probiotics. This study provides updated and comprehensive analysis to evaluate a snapshot of the USA market. The study demonstrates that label inaccuracies occur on approximately one third of popular dietary supplement products sold in the USA, supporting the need for improved approaches to marketing and quality control. Further, the risk of antibiotic resistance, especially in Bacillus‐based formulations, should be assessed. The study analyzes 50 Over‐the‐Counter (OCT) probiotic supplements using shotgun metagenomics, finding 33% has labeling inaccuracies. Thirteen supplements have unlisted microorganisms, six lacks listed strains and three have both issues. Potential antimicrobial resistance genes are common, particularly in Bacillus‐based supplements. Findings underscore the need for quality control and transparency to safeguard public health.