Dataset and R code for article "Topical emollient therapy with sunflower seed oil alters the skin microbiota of young children with severe acute malnutrition in Bangladesh: a randomised, controlled study"

Fischer, N

, Darmstadt, GL, Shahunja, K, Crowther, JM, Kendall, L, Gibson, RA, Ahmed, T and Relman, DA (2021). Dataset and R code for article "Topical emollient therapy with sunflower seed oil alters the skin microbiota of young children with severe acute malnutrition in Bangladesh: a randomised, controlled study". [Dataset]. Stanford Digital Repository. https://purl.stanford.edu/dk954yp6586

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A detailed description of the data analysis, along with all analysis code and raw data used to go from sequences to final results and figures.

Keywords

Bangladesh; Microbiota; Severe acute malnutrition; Sunflower oil

Item Type	Dataset
Resource Type	Resource Type Resource Description Software R script
Description of data capture	Background: Topical emollient therapy with sunflower seed oil (SSO) reduces risk of sepsis and mortality in very preterm infants in low- or middle-income countries (LMICs). Proposed mechanisms include modulation of skin and possibly gut barrier function. The skin and gut microbiota play important roles in regulating barrier function, but the effects of emollient therapy on these micro-biotas are poorly understood. Methods: We characterised microbiota structure and diversity with 16S rRNA gene amplicon sequence data and ecological statistics in 20 children with severe acute malnutrition (SAM) aged 2-24 months, at four skin sites and in stool, during a randomised, controlled trial of emollient therapy with SSO in Bangladesh. Microbes associated with therapy were identified with tree-based sparse discriminant analysis. Results: The skin microbiota of Bangladeshi children with SAM was highly di-verse and displayed significant variation in structure as a function of physical distance between sites. Microbiota structure differed between the study groups (P = 0.005), was more diverse in emollient-treated subjects–including on the forehead which did not receive direct treatment–and changed with each day (P = 0.005) at all skin sites. Overall, Prevotellaceae were the most differentially affected by emollient treatment; several genera within this family became more abundant in the emollient group than in the controls across several skin sites. Gut microbiota structure was associated with sample day (P = 0.045) and subject age (P = 0.045), but was not significantly affected by emollient treatment (P = 0.060). Conclusions: Emollient therapy altered the skin microbiota in a consistent and temporally coherent manner. We speculate that therapy with SSO enhances skin barrier function in part through alterations in the microbiota, and through systemic mechanisms. Strategies to strengthen skin and gut barrier function in populations at risk, such as children in LMICs like Bangladesh, might include deliberate manipulation of their skin microbiota. Trial registration ClinicalTrials.gov: NCT02616289.
Capture method	Unknown
Date	25 November 2021
Language(s) of written materials	English
Creator(s)	Fischer, N , Darmstadt, GL, Shahunja, K, Crowther, JM, Kendall, L, Gibson, RA, Ahmed, T and Relman, DA
LSHTM Faculty/Department	Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology (-2023)
Participating Institutions	Stanford University School of Medicine, Stanford, California, United States; International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh; JMC Scientific Consulting Ltd, Egham, Surrey, United Kingdom; GlaxoSmithKline R&D, Global Health Catalyst, Stevenage, United Kingdom; Veterans Affairs Palo Alto Health Care System 154T, Palo Alto, California, United States
Funders	Project Funder Grant Number Funder URI GSK / Save the Children partnership GlaxoSmithKline UNSPECIFIED http://dx.doi.org/10.13039/100004330 UNSPECIFIED Thrasher Research Fund 61147865-120965 http://dx.doi.org/10.13039/100005627 UNSPECIFIED Stanford University UNSPECIFIED http://dx.doi.org/10.13039/100005492 UNSPECIFIED Chan Zuckerberg Initiative UNSPECIFIED http://dx.doi.org/10.13039/100014989
Date Deposited	25 Jan 2024 12:45
Last Modified	25 Jan 2024 12:45
Publisher	Stanford Digital Repository