Absolute abundance values reveal microbial shifts and co-occurrence patterns during gut microbiota fermentation of dietary fibres in vitro

Abstract

The compositional alterations of human colonic microbiota when fermenting dietary fibres (DF) have been well studied. However, there is a challenge in quantifying microbiota responses to DF in absolute terms, and thus the extents to which these microbes grow on diverse DF are unclear. This study aimed to compare relative and absolute abundance datasets, to investigate how human faecal microbiota altered during the in vitro fermentation of arabinoxylan, mixed-linkage beta-glucan and bacterial cellulose (representing major wheat cell wall constituents), and a physical mixture of the three. Different microbial shifts occurred per DF, where the absolute abundance of total bacteria was observed to peak at 12 h, while this trend was not observed for the relative abundance data. The DF mixtures more efficiently supported microbial growth than the individual components. Additionally, the absolute abundance of the genera Faecalibacterium, Roseburia, Anaerostipes and the Eubacterium hallii group positively correlated to butyrate production, but no significant (P < 0.05) correlations were found based on the relative abundance data. While 95 genera were common to the DF types, interestingly, their co-occurrence patterns in absolute terms vastly differed, with 45.6% specific edges unique to the BC co-occurrence network. Therefore, applying absolute quantification is recommended for experiments focusing on how microbiota respond to DF.