Monica-Mweetwa/16S_DuodenalMicrobiome_MalZam

This repository contains the code used to analyse 16S RNA sequencing data from duodenal samples of malnourished children in Zambia # 16S_DuodenalMicrobiome_MalZam This repository contains the code used to analyse 16S RNA sequencing data from duodenal samples of malnourished children in Zambia -in the process of an update ## Summary This repository holds the code for 2 analyses: * A retrospective cross-sectional study using samples collected during the conduct of previously reported studies on hospitalized children with SAM at the university teaching hospital (Lusaka, Zambia) and stunted children from a high-density community in Lusaka known to have with a high risk of malnutrition and enteropathy. * A meta-analysis of all publicly available duodenal microbiome 16s data on undernourished children retrieved from SRA Archive. ## Description of Datasets: ### Zambian Datasets: 1. BEECH - Duodenal samples were collected from 53 children with linear growth stunting living in an urban slum in Lusaka, Zambia. Project ID PRJEB94106 (16s paired amplicon sequenced at the Gordon Lab in Washington Uiversity) 3. EEBiomarker - Duodenal samples were collected from 24 children with SAM admitted at UTH in Lusaka, Zambia with no clinical explanation for chronic diarrhoea. Project ID PRJEB94105 (16s paired amplicon sequenced at the Gordon Lab in Washington Uiversity) ### Additional datasets for Meta-Analysis: 3. BEED Duodenal samples were collected from 36 children with linear growth stunting, living in an urban slum in Dhaka, Bangladesh, who had biopsy-confirmed EED. Project ID PRJEB32184 (16s paired amplicon sequenced at the Gordon Lab in Washington Uiversity) 5. SEEM Duodenal samples were collected from 43 children with linear growth wasting, living in Pakistan 3-6 months of age. Project ID PRJEB75181 (16s paired amplicon sequenced at the Gordon Lab in Washington Uiversity) 7. AFRIBIOTA - Duodenal samples were collected from 46 stunted children aged 2-5 years living in Bangui, Central African Republic and in Antananarivo, Madagascar. Project ID - PRJEB27868 (single-ended amplicons sequenced by Microbiome …