Microbiomes and Resistomes in Household Environments with Soil Floors and Domestic Animal Cohabitation: A Study in Rural Bangladesh

In low-income countries, inadequate housing (e.g., soil floors) and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to pathogen and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as fuel and fertilizer. We extracted DNA and performed shotgun metagenomic sequencing to detect pathogens and ARGs.