Although diet, alongside drugs, is a major determinant of gut microbiota composition, little is known about how food components specifically modulate the make-up of our microbiota.

A new in vitro study, led by Dr. Sylvia Duncan from the Rowett Institute at University of Aberdeen (Scotland, United Kingdom), explores how different carbohydrate substrates influence the diversity of the human colonic microbiota.

The researchers used the same human fecal inoculum from two healthy volunteers with a continuous flow of non-digestible carbohydrates within anaerobic fermenters simulating a human colon. The carbohydrate energy sources added were the only difference between the five parallel fermentor vessels, while in vitro conditions such as temperature, pH and medium composition were tightly controlled in order to minimize their impact on the microbiota.

The substrates under study included:

  • Single carbohydrates (either arabinoxylan-oligosaccharides or AXOS, pectin or inulin).
  • A 3-mix of arabinoxylan-oligosaccharides, pectin and inulin.
  • A 6-mix of arabinoxylan-oligosaccharides, pectin, inulin, resistant starch, b-glucan and galactomannan.

The substrates affected microbial diversity differently at species level, whereas no difference was detected at the phylum and family levels. Furthermore, certain species were promoted by single substrates (e.g., Bacteroides vulgatus, Bacteroides stercoris and Eubacterium eligens by pectin; Bacteroides uniformis by inulin; and Bifidobacterium longum and Bifidobacterium catenulatum by AXOS). In contrast, others (e.g., Bacteroides ovatus) grew better in the presence of mixed substrates. It should be noted, however, that the baseline fecal microbiota showed a higher diversity than at other time points during the study, i.e. diversity got lost in the model itself.

Some major shifts in microbiota profiles at the operational taxonomic unit level were also observed over the 20-day fermentation period. Interestingly, the overall effect of substrate depended on the length of time the microbiota was exposed to substrates, with the highest diversity achieved during the first 6 days.

No changes were reported in total short-chain fatty acid concentrations over time.

Meanwhile, Bacteroides ovatus and Bacteroides intestinalis/cellulosilyticus encoded large numbers of Carbohydrate Active Enzymes. This highlights the important role CAZymes play in providing a selective advantage to these species in prioritizing their degradation of the 3- and 6-mix substrate combinations over single carbohydrates.

On the whole, complex polysaccharides, including pectin and arabinoxylan-oligosaccharides, promoted greater microbiota diversity than simple polymers such as inulin.

Inulin—a simple polymer with linear chains of fructose residues—led to reduced microbial diversity over the first 6 days, when compared with both arabinoxylan-oligosaccharides and pectin alone, and the 3-mix and the 6-mix. These findings show that substrate complexity plays an important role in ensuring greater gut microbiota diversity.

In conclusion, these in vitro data show that both complexity and variety of non-digestible carbohydrates matter in promoting beneficial gut species and diversity. These findings therefore reinforce the previous idea that, for a more diverse gut microbiota when considering dietary strategies to promote optimal gut health, the more varied the number of plant substrates, the better.



Chung WSF, Walker AW, Vermeiren J, et al. Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota. FEMS Microbiol Ecol. 2019; 95(1). doi: 10.1093/femsec/fiy201.