Table 1.

Major categories of machine-learning methods for analysis of microbiome samples with sequencing data

Data type	Metegnome sequencing				16S rRNA
Feature type	Alignment-free		Alignment-based		OTU-based or microbial taxon-based
	(based on sequence signature features without using any database)		(based on features obtained by mapping sequence reads to annotation databases)
Type of machine learning	Supervised classification	Unsupervised clustering	Supervised classification	Unsupervised clustering	Supervised or unsupervised

The highlighted category (alignment-free supervised classification of metagenome data) is that of the current work.