Microbial profiling of five traditional Chinese medicines: culture-based identification vs. 16S rRNA sequencing

<b>Introduction.</b> Traditional Chinese medicines (TCMs) may carry microbial hazards, yet conventional inspection methods often underestimate their diversity and risks.<b>Hypothesis.</b> Culture-based methods may overlook significant microbial diversity and potential pathogens compared with sequencing approaches.<b>Aim.</b> This study aimed to compare culture-based identification (VITEK-2) with 16S rRNA high-throughput sequencing for microbial detection in selected TCMs.<b>Methodology.</b> Thirty batches of five southern TCM samples, including <i>Areca catechu</i>, <i>Alpinia oxyphylla</i>, <i>Eugenia caryophyllata</i>, <i>Pogostemon cablin</i> and <i>Morinda officinalis</i>, were analysed for microbial contamination according to the 'Pharmacopoeia of the People's Republic of China' (2020 Edition). Culture-based isolates were identified using VITEK-2, and microbial communities were profiled by 16S rRNA sequencing.<b>Results.</b> Culture-based methods identified bile salt-resistant Gram-negative bacteria in 12 out of 30 batches (40%), comprising seven genera spanning two phyla, including <i>Enterobacter cloacae</i>, <i>Pseudomonas aeruginosa</i>, <i>Cronobacter sakazakii</i> and <i>Klebsiella pneumoniae</i>. Sequencing identified 795 genera across 26 phyla, revealing far greater diversity, though DNA signatures of some cultured taxa (e.g. <i>Enterobacter</i> in <i>M. officinalis</i> and <i>Leclercia</i> in <i>Areca catechu</i>) were undetected. Microbial composition varied significantly among TCMs.<b>Conclusion.</b> Sequencing uncovered substantially broader microbial diversity than culture-based methods, while both approaches identified pathogenic and opportunistic microbes. These findings emphasize the critical need for more rigorous microbial surveillance and stringent quality control of TCMs to protect public health.