The human intestinal microbiota has an important role in the maintenance of human health and disease pathogenesis. The aim of this research was to investigate the impact of four media on human intestinal microbiota metabolite and composition changes, we performed in vitro batch culture using intestinal microbiota samples from three fecal microbiota transplantation (FMT) donors. After 48 h culture, gut microbiota medium (GMM) had the highest production of acetic acid (73.00 ± 7.56 mM) and propionic acid (16.79 ± 1.59 mM), bacterial growth media (BGM) had the highest production of butyric acid (13.39 ± 0.56 mM). In addition, brain heart infusion (BHI) promoted (p < 0.05) the growth of
Bacteroidetes
, especially
Bacteroides
after 48 h, GMM resulted in a significant increase (p < 0.05) in
Actinobacteria
and increased the beneficial genus
Bifidobacterium
, fastidious anaerobe broth (FAB) increased
Firmicutes
population, and BGM promoted the growth of
Escherichia
–
Shigella
and
Akkermansia
. The results suggest that four media had different effects on the human intestinal microbiota metabolism and composition in vitro. These results may facilitate the culture of bacteria from the human intestinal microbiota.
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