Single-cell metagenomics: challenges and applications

Abstract

With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.

Keywords: bioinformatics; metagenomics; single-cell genomics.

Figure 1

Workflow of single-cell metagenomics

Figure 2

Multiple displacement amplification process and chimera types. (A) Primer Phi29 DNA polymerase annealing to the DNA and extension by Phi29 DNA polymerase. Phi29 DNA polymerase can displace downstream 5′-termini DNA strand to extend the growing 3′-termini strand by a simple branch migration reaction, and 3′-termini can be displaced as well in a similar way. (B) Four types of chimeric rearrangements. I: the second segment is inverted from its original orientation and directly joined after the first segment. II: the second segment is inverted from its original orientation and directly joined before the first segment. III: two directed segments are directly joined. IV: two directed segments are reversely joined