P1321 Inflammatory bowel disease and the rural to urban microbiome transition in Zambia
Authors: Hodges P , Mweetwa M , Kayamba V , O’Keefe S , Ocvirk S , Neuhaus K , Kelly P 
Published: January 2025

Abstract

Background
Existing evidence suggests that incidence of Inflammatory Bowel Disease (IBD) is increasing in geographical regions where it has traditionally been viewed as uncommon, including sub-Saharan Africa.(1) The nutrition transition that has occurred alongside rapid urbanisation in this region is one possible explanation for this. For instance, a shift towards a ‘Western-style’ diet may lead to subsequent changes in the intestinal microbiota resulting in a ‘pro-inflammatory’ environment. To investigate this hypothesis, we examined the faecal microbiota across several different sectors of Zambian society. We included IBD patients as well as healthy rural and urban controls.

Methods
Stool samples were collected from four groups: IBD patients (n=14); healthy urban controls of high socioeconomic status (SES) (n=16); urban controls of low SES (n=20); and rural controls (n=20). IBD patients and urban controls were all resident in the capital city of Lusaka and surrounding peri-urban area. Rural controls were recruited from a village in Northern Zambia. Stool samples were aliquoted into cryovials and frozen at -80°C within 6 hours of being passed. 16S rRNA gene amplicon sequencing was conducted at the ZIEL - Core Facility Microbiome of the Technical University of Munich. Analysis of 16S rRNA gene amplicon sequencing results was done using IMNGS2.org, an updated version of IMNGS (2), which now includes TIC (3), and Rhea (4) in R v4.1.2.

Results
Shannon effective number indicated reduced alpha diversity in rural controls compared to all other groups. (Figure 1A) The PCoA in Figure 1B shows the separation of the faecal microbiomes of the rural controls from the other groups, suggesting a lack of species abundant in the urban populations.(Figure 1B) At the genus level, several genera were significantly more abundant in the rural controls as opposed to other groups, notably Butyricicoccus, Enterorhabdus, Senegalimassilia, and the Eubacterium-eligens group.

Conclusion
There is a clear separation in the faecal microbiota of rural Zambian village dwellers compared to urban groups, with the urban high SES group closely overlying the IBD group in PCoA, suggesting that there may be factors specific to the urban high SES lifestyle that predispose the microbiota in healthy individuals to an IBD-associated composition. We have demonstrated underrepresentation of the butyrate-producing Butyricicoccus in IBD patients when compared with healthy rural controls, consistent with previous data that butyrogenic bacteria are underrepresented in the microbiota of IBD patients.

References
1.Ng SC, Shi HY, Hamidi N, Underwood FE, Tang W, Benchimol EI, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. 2018;390(10114):2769-78.
2.Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, et al. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Scientific Reports. 2016;6:33721.
3.Kioukis A, Pourjam M, Neuhaus K, Lagkouvardos I. Taxonomy Informed Clustering, an optimized method for purer and more informative clusters in diversity analysis and microbiome data processing. Frontiers in Bioinformatics. 2022;2(864597).
4.Lagkouvardos I, Fischer S, Kumar N, Clavel T. Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. Peerj. 2017;5:e2836.

Figure 1 A Alpha-diversity (Shannon index) B Principal coordinate analysis derived from Bray-Curtis dissimilarities C Relative abundance of genera