Finding needles in haystacks - sequencing single bacteria from complex microbiomes

Microbiomes are integral to many of the fundamental processes affecting society - from healthcare to agriculture - but the complexity and diversity harboured within these microbiomes and the roles of individual cells/species in adaptation to new environments/stresses is still largely unexplored. Traditionally, microbiome complexity is assessed using a metagenomic approach, where DNA extracted from bulk microbial pools is sequenced and the relative abundance of individual species is inferred from the data.

In this project, single-cell genomics techniques will be brought to the study of complex, real-world microbiomes. This will enable access to rare, unculturable cells, from which detailed, rich genomic information can be generated. Such cells may only constitute a tiny subfraction of the overall population but may be critical for the overall impact or function of the microbial community. The hypothesis is that the detailed whole-genome sequencing of rare microbiome components will reveal genetic diversity that cannot be observed by classical metagenomics approaches. The Macaulay lab has demonstrated the feasibility of single-cell, whole bacterial genome sequencing - with near complete genomes and single nucleotide variation data being attainable from single cells (Bawn et al. 2020).

A range of techniques will be used, including FACS, single-cell genomics, next generation sequencing and bioinformatics, to develop tools to isolate and analyse the genomes of individual cells from complex microbiomes and to apply these advances to the study of rare components of human microbiomes, revealing the extent of genetic diversity in these populations, beyond what could be observed with classical metagenomics.