Table 1.
Human gut virome
Viral typeViral familial taxonomyHost rangeDefinitive viral genera/species in human fecesCellular tropism in humansReferences
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  
Viral typeViral familial taxonomyHost rangeDefinitive viral genera/species in human fecesCellular tropism in humansReferences
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.

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