Table 1. Human gut virome.

Viral type			Viral familial taxonomy	Host range	Definitive viral genera/species in human feces	Cellular tropism in humans	References
Eukaryotic virus	DNA virus	Single-stranded	Anelloviridae	Primates	Torque teno virus, Torque teno midi virus, Torque teno mini virus	Epithelial cells	Hino and Miyata, 2007; Spandole et al., 2015
			Circoviridae	Birds and mammals	Chicken anemia virus, porcine circoviruses	Monocytes, epithelial cells, and fibroblasts	Li et al., 2010
			Geminiviridae	Plants	Tomato yellow leaf curl virus	No evidence	Zhang et al., 2006
			Genomoviridae	Humans, mammals, birds, and fungi	Gemycircularvirus	Unclear	Gregory et al., 2020
			Parvoviridae	Vertebrates, insects	Human bocavirus 2-4	Epithelial cells	Emlet et al., 2020; Guido et al., 2016
		Double-stranded	Adenoviridae	Vertebrates	Enteric adenovirus 40, 41	Epithelial cells, fibroblasts, gut lymphocytes	Favier et al., 2004
			Herpesviridae	Vertebrates	Human CMV, EBV	CMV: Endothelial cells, leukocytes, and monocytes; EBV: endothelial cells, B cells	Emlet et al., 2020; Gerna et al., 2004; Stanfield and Luftig, 2017
			Iridoviridae	Amphibia, fish, invertebrates	Lymphocystis disease virus	No evidence	Gregory et al., 2020
			Papillomaviridae	Vertebrates	Human papillomavirus 6, 18, 66	Epithelial cells	Egawa et al., 2015; Popgeorgiev et al., 2013
			Polyomaviridae	Mammals and birds	BK polyomavirus, JC polyomavirus, Human polyomavirus 9, 12	Oligodendrocytes, epithelial cells	Cook, 2016; Emlet et al., 2020
			Rudiviridae	Thermophilic archaea from Crenarchaeota	Unclassified	No evidence	Gregory et al., 2020
	RNA virus	Single-stranded	Caliciviridae	Vertebrates	Human NoV, Sapovirus	Epithelial (enteroendocrine) cells, myeloid cells, and lymphoid cells in immunocompromised patients	Green et al., 2020; Karandikar et al., 2016
			Astroviridae	Vertebrates	Human astrovirus	Enterocytes, goblet cells	Kolawole et al., 2019
			Virgaviridae	Plants	Pepper mild mottle virus, Tobacco mosaic virus	No evidence	Colson et al., 2010; Zhang et al., 2006
			Picornaviridae	Vertebrates	Human cosavirus, human klassevirus/ salivirus, Aichi virus, human enterovirus, human parechovirus, Saffold cardiovirus, human echovirus, human coxsackievirus, human poliovirus, hepatitis A	Epithelial cells, neuronal cells, hepatocytes	Krishnamurthy and Wang, 2018; Rivadulla and Romalde, 2020; Tapparel et al., 2013
			Retroviridae	Vertebrates	HIV-1	T lymphocytes, macrophages	Gootenberg et al., 2017; Virgin, 2014
			Togaviridae	Humans, mammals, marsupials, birds, mosquitoes	Unclassified	Fibroblasts	Gregory et al., 2020
			Coronaviridae	Vertebrates	Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-Cov)	Tracheo-bronchial epithelial cells, type 1 pneumocytes, intestinal epithelial cells	Corman et al., 2018
			Alphaflexiviridae	Plants, fungi	Unclassified	No evidence	Gregory et al., 2020
			Iflaviridae	Insects	Unclassified	No evidence	Gregory et al., 2020
			Hepeviridae	Humans, pigs, wild boars, sheep, cows, camels, monkeys, some rodents, bats, and chickens	Hepatitis E virus	Hepatocytes, intestinal epithelial cells	Oechslin et al., 2020
		Double-stranded	Picobirnaviridae	Unclear: mammals or bacteria	Human picobirnavirus	No evidence	Malik et al., 2014
			Reoviridae	Vertebrate, invertebrates, plants, fungi	Human rotavirus	Mature enterocytes	Komoto and Taniguchi, 2014
Bacteriophages	DNA virus	Single-stranded	Microviridae	Bacteria	Chlamydia phage 1,3,4, Bdellovibrio phage phiMH2K, Chlamydia phage CPG1, Spiroplasma phage 4, Chlamydia phage CPAR39	NA	Dion et al., 2020; Székely and Breitbart, 2016
			Inoviridae	Bacteria	Unclassified	NA	Dion et al., 2020; Székely and Breitbart, 2016
		Double-stranded	Myoviridae	Bacteria, archaea	phiBCD7, Bacillus phage G, phiP-SSM4	NA	Barylski et al., 2020; Gregory et al., 2020; Guerin et al., 2018; Yutin et al., 2018
			Siphoviridae	Bacteria, archaea	Listeria phage A118, phiE125, Lactococcus phage bIL285, phiCP39-O, Clostridium phage phiCP39-O, Mycobacterium phage Athena, phage PA6, phage SM	NA	Barylski et al., 2020; Gregory et al., 2020; Guerin et al., 2018; Yutin et al., 2018
			Podoviridae	Bacteria	Enterobacteria phage P22, phage T3	NA	Barylski et al., 2020; Gregory et al., 2020; Guerin et al., 2018; Yutin et al., 2018
			crAss-like phages	Bacteria	P-crAssphage	NA	Barylski et al., 2020; Gregory et al., 2020; Guerin et al., 2018; Yutin et al., 2018
	RNA virus	Single-stranded	Leviviridae	Bacteria	Enterobacteria phage MS-2	NA	Callanan et al., 2018
		Double-stranded	Cystoviridae	Bacteria	Pseudomonas phage	NA	Callanan et al., 2018

NA, not applicable.