Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system

Abstract

Probiotic and postbiotic treatments influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactobacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using pooled human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48-hour treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus, Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes:Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. Contrarily, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella, and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading species, whereas L. plantarum was connected with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary alterations, i.e., butyrate directly transforms microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.