Table 2.

Representative research using metagenomics sequencing to test stool samples

Reference	Subjects	Condition	Main findings
McCann et al. [105]	Elderly individuals with different levels of cognitive ability	Alzheimer's disease (AD)	Some intestinal microbes possessed the genes to produce vitamin K in the form of menaquinone (MK). Certain MK isoforms synthesized by the gut microbiome, particularly the longer chains, were positively associated with cognition
Qian et al. [106]	Idiopathic Chinese Parkinson’s disease (PD) patients and their healthy spouses living in the same household	PD	Potential diagnostic biomarkers of PD based on metagenomics sequencing results
Nicholson et al. [107]	Amyotrophic lateral sclerosis (ALS) patients and healthy controls (HC)	ALS	The relative abundance of the butyrate-producing bacteria Eubacterium rectale and Roseburia intestinalis, which play important roles in regulating inflammation and gut integrity, was lower in ALS patients than in HC
Wu et al. [108]	Healthy young, healthy elderly, and centenarians	Aging	The gut microbiota in centenarians was characterized by depletion of Faecalibacterium prausnitzii and Eubacterium rectale and enrichment of Methanobrevibacter smithii and Bifidobacterium adolescentis, compared with other groups. Functional analysis revealed that the microbiota in centenarians had a high capacity for glycolysis and fermentation to short-chain fatty-acids

Compared to 16S rRNA sequencing, researchers usually use metagenomics data for functional analysis, using databases such as Kyoto Encyclopedia of Genes and Genomes, in order to fully understand the biological meanings encoded in the genome.