Supplementary Table 1: Extraction of Nucleic Acids and Output of Promethion Sequencing DNA/Cdna Input (Total Output Individual Group (Ng) Ng) (Mb) 1 Raw DNA 47.25 77

Supplementary table 1: Extraction of nucleic acids and output of PromethION sequencing DNA/cDNA Input (total Output Individual Group (ng) ng) (Mb) 1 raw DNA 47.25 77

2 raw DNA 50.4 48

3 raw DNA 23.63 57

4 raw DNA 123.3 203

5 raw DNA 129.6 67 1,185.6 amplified 1 2,100 1,700 DNA/cDNA amplified 2 2,570 892 DNA/cDNA amplified 3 1.700 1,500 DNA/cDNA amplified 4 2,130 2,200 DNA/cDNA amplified 5 1,200 1,900 DNA/cDNA Note: the quantity of DNA/cDNA(ng) is separately measured after terminal repair and gel extraction

Supplementary table 2: The identification of viral family and species in gut

Individual 1 Individual 2 Individual 3 Individual 4 Individual 5 Inoviridae yes yes yes yes yes Siphoviridae yes Genomoviridae yes Family Podoviridae yes yes yes Microviridae yes Alphaflexiviridae yes Virgaviridae yes Cactus virus X yes Pitaya virus X yes Uncultured phage WW-nAnB strain 3 yes yes yes yes yes Lambdavirus,Escherichia virus Lambda yes Tobacco mild green mosaic virus yes Species Chicken stool-associated gemycirc yes uncultured crAssphage yes yes yes uncultured phage WW-nAnB yes yes yes Uncultured phage WW-nAnB strain 2 yes Parabacteroides phage YZ-2015a yes Pseudomonas phage PaP2 yes Note: character 'yes' represents the existence of this virus in the individual

Supplementary table 3: The number of identified certain contigs NCBI GVD NCBI NT Individual Group (minimap2) (minimap2) (Blastn) 1 raw DNA 0 0 0

2 raw DNA 0 0 0

3 raw DNA 0 1 8

4 raw DNA 0 0 0

5 raw DNA 0 0 0 amplified 1 0 3 5 DNA/cDNA amplified 2 0 1 0 DNA/cDNA amplified 3 1 2 10 DNA/cDNA amplified 4 0 2 0 DNA/cDNA amplified 5 0 5 0 DNA/cDNA Note: NCBI, NCBI viruses genome database; GVD, The human Gut Virome database; NCBI NT, NCBI nucleotide database