# Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment

## TL;DR

This review discusses a method to amplify and study the genomes of hard-to-culture microbes directly from their natural environment using selective whole genome amplification.

## Contribution

The paper introduces and evaluates selective whole genome amplification as a novel approach for studying low-abundance microbes and pathogens.

## Key findings

- SWGA enables sequencing of low-abundance microbes directly from complex samples.
- Genomic data from SWGA helps track pathogen population dynamics and antimicrobial resistance.
- The method has limitations but offers potential for broader application in infectious disease research.

## Abstract

High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.