Human gastrointestinal microbiota modulation with dietary prebiotics: an intimate interaction throughout life

Klaudyna Aneta Borewicz

Research output: Thesisinternal PhD, WU


The colon is the most densely colonized area within the human gastrointestinal (GI) tract, and diet is one of the most fundamental modulators of the GI microbiota in both infants and adults. The colonic microbiota can be considered an “invisible organ” influencing metabolism, normal immune and nervous system functions, and the overall health and well-being of the host.

During infancy the microbial colonization progresses through a sequence of well-orchestrated events leading to the establishment of a stable microbial ecosystem adapted for milk digestion. In breastfed infants, breastmilk is the sole source of nourishment and the source of microbes and bioactive components, such as free human milk oligosaccharides (HMOs). HMOs are believed to have evolved specifically to facilitate microbial colonization of the GI tract and to act as prebiotics by promoting growth and activity of bacterial species that are beneficial to a developing infant. We investigated faecal microbiota composition in 2-12 week old infants and detected high variability in their microbial profiles. We stratified the observed microbial patterns into three distinct microbial cluster types. As infants developed, their microbiota had a tendency to progress from a mixed community type towards faecal microbial clusters enriched in either Bifidobacterium and Bacteroides or only Bifidobacterium, and the ability of these infants to utilize HMOs also increased.

GI microbiota composition differs between breastfed and formula fed infants and today’s infant formulas are often fortified with prebiotics (mainly galactooligosaccharides (scGOS) and/or fructooligosaccharides (lcFOS)) to better mimic the functional properties of human milk with respect to its effect on GI microbiota composition and function. We investigated the composition of faecal microbiota in infants receiving either breastmilk, infant formulas fortified with prebiotics, or mixed feeding. We compared these results with results obtained from infants fed traditional formulas, which did not contain prebiotics. Infants who received formulas fortified with prebiotics showed faecal profiles that closely resembled those of healthy breastfed infants, in particular with regard to the levels of Bifidobacterium and Lactobacillus, whereas this was not observed in infants fed traditional formula. Infants fed prebiotic fortified formulas also showed an accelerated transition towards the Bifidobacterium rich faecal microbial cluster type, as compared to their breastfed counterparts. This effect was not noted in infants which received mixed feeding, for whom the transition was delayed. Thus, the type and extent of prebiotic supplementation (breastmilk HMOs vs. prebiotics in infant formula) had an impact on both speed and direction of microbial colonization.

Knowing that the HMO composition in breastmilk varies between mothers and across lactation stages, we investigated the link between maternal breastmilk HMO profiles and the microbiota composition in the faeces of corresponding infants. We did not detect strong and consistent correlations between specific breastmilk HMOs and microbial species that colonized the infant GI tract. It is likely that the microbial community in early life is shaped through a combined effect of many different milk HMOs, as well as other modulatory factors in breastmilk, including breastmilk’s own microbiota. Even though we could not predict infant microbiota profiles based on the HMO composition in maternal milk, we detected strong correlations between infant faecal microbial composition and an infant’s ability to utilize specific HMOs. There was a significant association between the cluster assignment and an infant’s ability to degrade breastmilk HMOs, with complete degradation of HMOs associated with Bifidobacterium dominated clusters and non-specific degradation associated with the mixed cluster. Constrained multivariate redundancy analysis indicated a significant association between faecal microbiota composition and gastrointestinal degradation of 2′-Fucosyllactose, Lacto-N-tetraose and Lacto-N-neotetraose, difucosyllactose, 6'Sialyllactose, Lacto-N-hexaose, Lacto-N-fucopentaose II and Lacto-N-fucopentaose III (FDR<0.05) in one month old infants. Furthermore, our study showed that an infant’s ability to degrade HMOs increased with infant age and was strongly correlated with an increase in the relative abundance of various phylotypes (OTUs), mainly within the genera Bifidobacterium, Parabacteroides, Escherichia-Shigella, Bacteroides, Actinomyces, Veillonella, Lachnospiraceae Incertae Sedis, and Erysipelotrichaceae Incertae Sedis, and to lesser extent lactobacilli. Thus, members of these taxa might play important roles in the intestinal microbial communities of infants as they were also identified as key groups in the analysis of microbial co-occurrence networks.

The exact mode of action and effect of most prebiotic supplementations on GI microbiota community structure and function is still largely unknown. There is accumulating evidence suggesting that microbial species and strains show a high degree of specificity in their preference to utilize different prebiotic compounds. This specificity, together with the advances in glycosciences, offer leads for developing prebiotic supplementations for targeted approaches in modulating gut microbiota function for a particular health, preventative, or therapeutic purpose.

Isomalto/malto-polysaccharides (IMMPs)  are a novel group of starch-derived, slowly-fermentable fibres with a prebiotic potential. We investigated the fermentation behavior and modulatory effect of IMMPs on adult faecal microbiota using an in vitro batch fermentation model. The IMMPs tested included IMMP-94 (94% α-(1→6) glycosidic linkages), IMMP-96, IMMP-27 and IMMP-dig27 (after an enzymatic removal of digestible starch segments from IMMP-27) and varied in the percentage of α-(1→6) glycosidic linkages and chain length distribution. We showed that these differences had an effect on the speed of degradation and the dynamics within the microbial community. The fermentation of α-(1→6) glycosidic linkages in IMMP-94, IMMP-96 and IMMP-dig27 started after 12 h and finished within 48 h. IMMP-27 fermentation started directly after inoculation utilizing α-(1→4) glycosidic linkages, however, the utilization of α-(1→6) linked glucoses was delayed and started only after depletion of α-(1→4) linked glucose moieties. The IMMP fermentation was accompanied by a significant increase in overall microbial diversity and the relative abundance of Bifidobacterium and Lactobacillus, as well as increased production of short chain fatty acids (SCFAs) with acetic acid and succinic acids being the major products next to propionic acid and butyric acid. During the fermentation,  polysaccharide fraction was degraded into isomalto-oligosaccharides (IMOs) mainly by extracellular enzymes. The smaller IMOs were further degraded by cell-associated enzymes. Using metatranscriptome data we showed that microbial community dynamics during fermentation also varied depending on the type of IMMP used and that the observed changes were reflected in the community gene expression profiles. Members of Bacteroides, Lactobacillus and Bifidobacterium were the predominant degraders of IMMPs, and the increased activity of these bacteria correlated with the presence of high amounts of α-(1→6) glycosidic linkages in the IMMPs tested. Furthermore, the metabolic changes as shown by the accumulation of SCFAs in the fermentation media, and the corresponding decrease in pH correlated with the microbiota activity, as measured at the metatranscriptome level.

The research presented here shows how natural prebiotics (HMOs) and prebiotic supplementations (IMMPs, scGOS/lcFOS) can influence human GI microbiota structure and function during infancy and adulthood. Developments in the field of glycosciences together with a better understanding of the mode of action of prebiotics with regard to microbial community structure and function could eventually lead to development of substrates offering attractive and safe ways to modulate microbiota to achieve specific health outcomes. Our research provided insights into both, the infant and adult large intestinal ecosystems, but additional studies are needed and should also address the long-term effects of the prebiotic supplementation on human health.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Smidt, Hauke, Promotor
Award date13 Jun 2018
Place of PublicationWageningen
Print ISBNs9789463432771
Publication statusPublished - 13 Jun 2018


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