Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides

Abstract

The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants ( n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis ( B. infantis ) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum . Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III ( Se+, Le -) (22%) than in most previously studied populations, with an enrichment in 2′-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis , and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation

“…Inulin supplementation led to lower Bacteroides relative abundance in D2 microbiota, potentially due to the competitive advantage of inulin-degrading Bifidobacterium taxa. Our in vitro finding supports the negative association detected between Bacteroides fragilis and two Bifidobacterium species in fecal metagenomes from the same Kenyan infant population [ 59 ].…”

“…Acacia gum-degrading taxa could be absent or at low prevalence in the gut microbiota of partially breast-fed Kenyan infants aged 6–10 months. This was indeed confirmed in a recently published metagenomic study of fecal samples of the same Kenyan infant population, which detected genes for only three of the five bacterial enzymes for acacia gum degradation (GH43, GH16, and GH27) at low gene prevalence and abundance [ 59 ]. Previously published bifidogenic and SCFA-promoting effects of acacia gum were mainly reported in studies with human adult feces [ 32 , 34 , 60 ]; in vitro studies involving American infant feces also did not detect acacia gum fermentation [ 62 , 63 ].…”

Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants

“…Overall, 224 different bacterial genera were present in the stool samples, with the most dominant genera being Bifidobacterium, Escherichia/Shigella, Klebsiella, Bacteroides, Streptococcus, Clostridium sensu stricto 1, Clostridioides, Akkermansia, Veillonella, Romboutsia, Enterococcus, Faecalibacterium, Erysipelatoclostridium, Pediococcus, and Intestinibacter (Figure b). While the prevalence of Bifidobacterium was like in several other studies, ,,− some findings differentiate our cohort. For instance, levels of potentially pro-inflammatory or pathogenic bacteria including Escherichia/Shigella and Klebsiella were remarkably high and persistent in stool of some NIs at month 1 postdelivery.…”

Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition

“…To date, most research addressing the HMO-bacteria relationship in the infant gut focused on a single time point 20 . A longitudinal cohort study is needed in order to examine how changes in HMO composition impact the infant gut microbiome over time.…”