Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals

Abstract

Soil-derived microorganisms have been sampled intensively throughout the last decades in order to discover bacterial strains that produce new antibiotics. The increasing emergence of multidrug-resistant bacteria and the constant high demand for new antibiotic classes are leading to the sampling and investigation of new microbiomes that contain antimicrobial producers. Human-associated microbiomes are therefore gaining more and more attention. This chapter presents a detailed description of how human microbiomes can be sampled and how microbiota members from skin and nasal samples can be isolated. Different methods for antimicrobial compound screening are presented.

Keywords: Antimicrobial compound; ESKAPE pathogens; Isolation of bacterial strains; Microbiome sampling; Nose; Skin; Staphylococcus.