The influence of dietary factors on gut microbiota composition of Peruvian infants and young children

Background and aims: Complementary feeding practices play a fundamental role in modulating the infant and young child (IYC) gut microbiota. Despite this knowledge, very few studies have considered the association between specific dietary factors and the IYC gut microbiota composition. Sub-optimal complementary feeding practices also play a role in micronutrient deficiencies, such as iron deficiency anaemia (IDA). IDA is highly prevalent among IYC populations in low- and middle-income countries and is a persistent public health issue across IYC populations in Peru. In response, the Peruvian Ministry of Health have set out to combat IDA through a national programme which includes the provision of preventative and therapeutic iron supplementation. IDA and iron supplementation may also impact the gut microbiota of IYC. This research explored the role of dietary factors, including dietary intake, anaemia status and iron supplementation intake, during the complementary feeding period on the gut microbiota composition in peri-urban Peruvian IYC.

Methods: Cross-sectional analysis of dietary data, including anaemia status, iron supplementation intake, 24h quantitative dietary intake data via maternal recall and dietary patterns with gut microbiota composition data was carried out on IYC aged 6.0-23.9 months from two peri-urban sites in Lima and Huánuco, Peru. Dietary intake and dietary patterns were assessed in a sample of n=242 IYC. Analysis of the association between dietary factors and gut microbiota composition was assessed in a sub-sample of n=77 IYC. The gut microbiota was analysed using 16S rRNA gene amplicon sequencing. IYC anaemia was determined by haemoglobin concentration. Dietary patterns were derived by principal component analysis.

Results: The gut microbiota of peri-urban Peruvian IYC was dominated by Bacteroidota and Bacillota phyla, with genera from these two phyla, namely Bacteroides, Faecalibaterium and Prevotella, the most abundant across samples. The results from this thesis observed a high prevalence of anaemia across the sample. Of concern is the low adherence to current policies across the country surrounding the provision if iron supplements to IYC. More than half of the sample reported that they were not consuming iron supplements and a large proportion of anaemic IYC were also not consuming iron supplements. The role that iron, or lack thereof, may play in the gut microbiota composition was studied. IYC with anaemia had a greater abundance of Paraprevotella, Alloprevotella, Raoultella and a lower abundance of Providencia, Eubacterium, iii Intestinimonas and Campylobacter, compared to IYC without anaemia. Consumption of iron supplements in the previous month was associated with a greater abundance of Helicobacter, Fusobacterium, Odoribacter and Providencia and a lower abundance of Paraprevotella, Acidaminococcus, Catenibacterium, Raoultella, Alloprevotella, Eubacterium, Klebsiella and Anaerotruncus, compared to IYC not consuming iron supplements. Characterisation of the complementary feeding indicators of IYC in peri-urban Peru, indicated that adherence to current guidelines is mixed. A large proportion of the IYC were meeting diet quality indicators (minimum dietary diversity, minimum meal frequency and minimum acceptable diet), however consumption of unhealthy foods and sugar-sweetened beverages is concerningly high. Distinct dietary patterns were also observed, namely (i) Varied, (ii) High infant formula and pulses, nuts and seeds, and (iii) Transitioning. This thesis demonstrated limited evidence of the differential influence of the complementary diet (macronutrient intake and dietary patterns) on the IYC gut microbiota. Intake of vegetable protein was positively associated with alpha diversity, as well as the genera Lactobacillus and Clostridium_XIVb. Total sugar intake was negatively associated with Streptococcus, and saturated fat intake was associated with beta diversity. Adherence to the ‘Varied’ diet was positively associated with alpha diversity as well as increased abundance of Butyricicoccus, Ruminococcus2, Paraprevotella, Anaerostipes and Subdoligranulum and a lower abundance of Providencia. Adherence to the ‘High infant formula and pulses nuts and seeds’ pattern was inversely associated with Alloprevotella, Paraprevotella and positively associated with Lactobacillus. Finally, adherence to the ‘Transitioning’ pattern was associated with lower abundance of Ruminococcus2 and increased abundance of Akkermansia, Paraprevotella and Alloprevotella.

Conclusion: This thesis provides insight into the complementary feeding practices and the gut microbiota of IYC from low-income peri-urban households in a middle-income country. The observed associations between dietary intake, anaemia status and iron supplementation with the peri-urban Peruvian IYC gut microbiota serve as useful preliminary evidence, which warrants further investigation.