Table 1.

The overview of pros and cons of current widely used methods for dissecting microbiome.

Methods	Advantages	Disadvantages	Solution
Amplicon sequencing	(1) Relatively low cost; (2) Taxonomic annotations of uncultured microbial communities.	(1) Low resolution: cannot identify microbes at species or stain level; (2) Cannot realize functional annotations of microbial communities.	(1) Combined with metagenomics; (2) Use PICRUSt to obtain predicted metagenomics and functional annotations.
Metagenomic sequencing	(1) Taxonomic and functional annotations of uncultured microbial communities; (2) Obtain the full genetic repertoire of the microbial communities.	(1) Difficulties in metagenome assembly and taxonomically and functionally assign accurately; (2) Lack of high genome coverage; (3) Cannot link all the functional genes of one microbe to its phylogeny.	(1) Long-read sequencing and improved algorithms for assembly; (2) Combined with single-cell sequencing.
Single-cell sequencing	(1) Taxonomic and functional annotations of uncultured microbes at cell level; (2) Generate a high-quality genome for microbes with low abundance; (3) Dissect virus-host interactions of uncultured microbes.	(1) Difficulties in cell sorting; (2) Easily influenced by contaminated DNA; (3) Uneven read coverage, chimeric reads caused by MDA.	(1) Combined with metagenomics; (2) Improved experimental operation and various computational approaches to control DNA contamination and errors caused by MDA.