Association between clinical and environmental factors and the gut microbiota profiles in young South African children

Abstract

Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population. This includes the determination of the influence of demographic, clinical and environmental factors on the microbiota in a setting, and elucidates possible bias introduced by these factors, prior to further investigations. Little is known about the microbiota of children in South Africa after infancy. We provide a detailed description of the gut microbiota profiles of children from urban Cape Town and describe the influences of various clinical and environmental factors in different age groups during the first 5 years of life. Prevotella was the most common genus identified in the participants, and after infancy, the gut bacteria were dominated by Firmicutes and Bacteroidetes. In this setting, children exposed to antibiotics and indoor cooking fires were at the most risk for dysbiosis, showing significant losses in gut bacterial diversity.

Fungal diversity in the gut microbiome of young South African children

“…A study in neonates found that the diversity and structure of fungi in the gut were unaffected by sex, whereas another study that included both adults and children found that the gut mycobiota in females had increased richness and abundance [ 11 , 13 ]. This disparity in diversity between girls and boys was not detected in the bacterial microbiota of our study population [ 17 ]. The lower degree of diversity in girls may be a consequence of different diets, play activities and socialisation, medication use or immunological responses.…”

“…The children included in the study had a median age of 32 months (interquartile range [IQR]:15—43), 52.2% were boys and only one child was HIV-positive. The full set of participant demographics and exposures to different clinical and environmental factors that were investigated, as outlined in the methods section, have been published as part of a study describing the bacterial microbiota in the same samples, based on 16S rRNA gene sequencing [ 17 ].…”

“…Evidence suggests that deficiencies in micronutrients such as vitamin A may disrupt microbiota development, but published works focus on the bacterial microbiota [ 21 – 23 ]. Unlike fungal diversity, bacterial richness in this study population was not associated with vitamin A supplementation, but the bacterial community compositions trended toward significant dissimilarity [ 17 ]. There were no substantial differences in fungal alpha diversity between age groups; however, the fungal community compositions were shown to differ significantly between the younger (< 2 years) and older (4 to < 5 years) age groups, mostly attributed to the shift in the dominant genera, Candida and Saccharomyces .…”

“…TB-CHAMP aims to assess the efficacy and safety of levofloxacin as preventive therapy in children exposed to multidrug-resistant (MDR) tuberculosis (TB) within the household. This sub-study was a continuation of previous work that explored the bacterial gut microbiota of the children at their baseline visit, before randomisation into the treatment or placebo groups [ 17 ].…”

“…The study population has been described previously [ 17 ]. Briefly, children from the Cape Town metropolitan area under the age of 5 years who were residing in the same household as an enrolled adult index case (≥ 18 years of age) with bacteriologically confirmed pulmonary MDR-TB were eligible.…”