Table 1. Open in new tab Current...

Study	Study Population(s)	Microbiome Sample(s) and Methods	Key Findings
Fungi
⁵⁷	Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)	18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon	↑ fungal species in active CD biopsies compared with active UC and control subjects
⁶²	Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)	ITS1 sequencing of stool	↓ fungal diversity (Shannon index) in IBD
↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition
⁶⁰	Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)	ITS1, ITS2, and 16S rRNA sequencing of stool	↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli
⁵⁹	Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)	ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR	↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)	18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load	↓ fungal species count and abundance in active UC
↑ abundance of Aspergillus in active UC
⁵²	Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)	ITS2 rRNA sequencing of stool	↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission
↓ fungal species count in UC
⁶⁴	PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)	ITS2 and 16S sequencing of stool	No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals
↑ fungal diversity (Shannon) index in PSC compared with IBD remission
⁶¹	Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics	Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies	↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects
Patients with active CD (n = 7) and healthy individuals (n = 10)	↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients
⁶⁵	Patients with 3-month remission of UC (n = 31), and ileal or ileocolonic CD (n = 34), patients with active CD (n = 55), UC relatives (n = 29), CD relatives (n = 29), healthy unrelated individuals (n = 28)	Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling	↑ fungal load in relapsed CD compared with patients who remained in remission
↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed
Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse
Protozoa
⁶⁶	Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)	Culture and PCR of stool	↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive
↓ Blastocystis prevalence in both active and inactive IBD than control subjects
⁶⁷	Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)	18S rRNA sequencing of stool	↓ Blastocystis prevalence in IBD
Viruses
⁶⁸	Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)	454 pyrosequencing of stool	↓ virome diversity (Shannon index) in CD
⁶⁹	Pediatric patients with CD (n = 6), and healthy individuals (n = 6)	454 pyrosequencing of ileal and colonic biopsies, and gut washes	↑ abundances of viral species in CD, Caudovirales most abundant
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	No difference in bacteriophage species between groups
⁷⁰	Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)	454 pyrosequencing of stool	↑ abundances of Caudovirales bacteriophage species in CD and UC
⁷¹	Patients with new-onset active CD (n = 12), healthy individuals (n = 12)	454 pyrosequencing of colonic biopsies	↑ viral species in active CD
⁷²	C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)	Shotgun whole metagenome sequencing of stool	↑ abundances of Caudovirales bacteriophages species in murine colitis

Study

Study Population(s)

Microbiome Sample(s) and Methods

Key Findings

Fungi

⁵⁷

Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)

18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon

↑ fungal species in active CD biopsies compared with active UC and control subjects

⁶²

Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)

ITS1 sequencing of stool

↓ fungal diversity (Shannon index) in IBD

↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD

⁶³

Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)

Shotgun whole metagenome sequencing of stool

↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition

⁶⁰

Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)

ITS1, ITS2, and 16S rRNA sequencing of stool

↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli

⁵⁹

Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)

ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR

↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects

⁵⁸

Active UC (n = 14), healthy individuals (n = 15)

18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load

↓ fungal species count and abundance in active UC

↑ abundance of Aspergillus in active UC

⁵²

Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)

ITS2 rRNA sequencing of stool

↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission

↓ fungal species count in UC

⁶⁴

PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)

ITS2 and 16S sequencing of stool

No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals

↑ fungal diversity (Shannon) index in PSC compared with IBD remission

⁶¹

Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics

Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies

↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects

Patients with active CD (n = 7) and healthy individuals (n = 10)

↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients

⁶⁵

Patients with 3-month remission of UC (n = 31), and ileal or ileocolonic CD (n = 34), patients with active CD (n = 55), UC relatives (n = 29), CD relatives (n = 29), healthy unrelated individuals (n = 28)

Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling

↑ fungal load in relapsed CD compared with patients who remained in remission

↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed

Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse

Protozoa

⁶⁶

Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)

Culture and PCR of stool

↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive

↓ Blastocystis prevalence in both active and inactive IBD than control subjects

⁶⁷

Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)

18S rRNA sequencing of stool

↓ Blastocystis prevalence in IBD

Viruses

⁶⁸

Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)

454 pyrosequencing of stool

↓ virome diversity (Shannon index) in CD

⁶⁹

Pediatric patients with CD (n = 6), and healthy individuals (n = 6)

454 pyrosequencing of ileal and colonic biopsies, and gut washes

↑ abundances of viral species in CD, Caudovirales most abundant

⁶³

Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)

Shotgun whole metagenome sequencing of stool

No difference in bacteriophage species between groups

⁷⁰

Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)

454 pyrosequencing of stool

↑ abundances of Caudovirales bacteriophage species in CD and UC

⁷¹

Patients with new-onset active CD (n = 12), healthy individuals (n = 12)

454 pyrosequencing of colonic biopsies

↑ viral species in active CD

⁷²

C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)

Shotgun whole metagenome sequencing of stool

↑ abundances of Caudovirales bacteriophages species in murine colitis

Study	Study Population(s)	Microbiome Sample(s) and Methods	Key Findings
Fungi
⁵⁷	Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)	18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon	↑ fungal species in active CD biopsies compared with active UC and control subjects
⁶²	Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)	ITS1 sequencing of stool	↓ fungal diversity (Shannon index) in IBD
↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition
⁶⁰	Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)	ITS1, ITS2, and 16S rRNA sequencing of stool	↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli
⁵⁹	Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)	ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR	↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)	18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load	↓ fungal species count and abundance in active UC
↑ abundance of Aspergillus in active UC
⁵²	Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)	ITS2 rRNA sequencing of stool	↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission
↓ fungal species count in UC
⁶⁴	PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)	ITS2 and 16S sequencing of stool	No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals
↑ fungal diversity (Shannon) index in PSC compared with IBD remission
⁶¹	Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics	Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies	↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects
Patients with active CD (n = 7) and healthy individuals (n = 10)	↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients
⁶⁵	Patients with 3-month remission of UC (n = 31), and ileal or ileocolonic CD (n = 34), patients with active CD (n = 55), UC relatives (n = 29), CD relatives (n = 29), healthy unrelated individuals (n = 28)	Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling	↑ fungal load in relapsed CD compared with patients who remained in remission
↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed
Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse
Protozoa
⁶⁶	Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)	Culture and PCR of stool	↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive
↓ Blastocystis prevalence in both active and inactive IBD than control subjects
⁶⁷	Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)	18S rRNA sequencing of stool	↓ Blastocystis prevalence in IBD
Viruses
⁶⁸	Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)	454 pyrosequencing of stool	↓ virome diversity (Shannon index) in CD
⁶⁹	Pediatric patients with CD (n = 6), and healthy individuals (n = 6)	454 pyrosequencing of ileal and colonic biopsies, and gut washes	↑ abundances of viral species in CD, Caudovirales most abundant
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	No difference in bacteriophage species between groups
⁷⁰	Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)	454 pyrosequencing of stool	↑ abundances of Caudovirales bacteriophage species in CD and UC
⁷¹	Patients with new-onset active CD (n = 12), healthy individuals (n = 12)	454 pyrosequencing of colonic biopsies	↑ viral species in active CD
⁷²	C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)	Shotgun whole metagenome sequencing of stool	↑ abundances of Caudovirales bacteriophages species in murine colitis

Study

Study Population(s)

Microbiome Sample(s) and Methods

Key Findings

Fungi

⁵⁷

Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)

18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon

↑ fungal species in active CD biopsies compared with active UC and control subjects

⁶²

Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)

ITS1 sequencing of stool

↓ fungal diversity (Shannon index) in IBD

↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD

⁶³

Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)

Shotgun whole metagenome sequencing of stool

↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition

⁶⁰

Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)

ITS1, ITS2, and 16S rRNA sequencing of stool

↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli

⁵⁹

Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)

ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR

↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects

⁵⁸

Active UC (n = 14), healthy individuals (n = 15)

18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load

↓ fungal species count and abundance in active UC

↑ abundance of Aspergillus in active UC

⁵²

Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)

ITS2 rRNA sequencing of stool

↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission

↓ fungal species count in UC

⁶⁴

PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)

ITS2 and 16S sequencing of stool

No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals

↑ fungal diversity (Shannon) index in PSC compared with IBD remission

⁶¹

Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics

Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies

↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects

Patients with active CD (n = 7) and healthy individuals (n = 10)

↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients

⁶⁵

Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling

↑ fungal load in relapsed CD compared with patients who remained in remission

↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed

Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse

Protozoa

⁶⁶

Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)

Culture and PCR of stool

↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive

↓ Blastocystis prevalence in both active and inactive IBD than control subjects

⁶⁷

Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)

18S rRNA sequencing of stool

↓ Blastocystis prevalence in IBD

Viruses

⁶⁸

Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)

454 pyrosequencing of stool

↓ virome diversity (Shannon index) in CD

⁶⁹

Pediatric patients with CD (n = 6), and healthy individuals (n = 6)

454 pyrosequencing of ileal and colonic biopsies, and gut washes

↑ abundances of viral species in CD, Caudovirales most abundant

⁶³

Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)

Shotgun whole metagenome sequencing of stool

No difference in bacteriophage species between groups

⁷⁰

Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)

454 pyrosequencing of stool

↑ abundances of Caudovirales bacteriophage species in CD and UC

⁷¹

Patients with new-onset active CD (n = 12), healthy individuals (n = 12)

454 pyrosequencing of colonic biopsies

↑ viral species in active CD

⁷²

C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)

Shotgun whole metagenome sequencing of stool

↑ abundances of Caudovirales bacteriophages species in murine colitis

Table 1.

Open in new tab

Current insights from high-throughput sequencing of the nonbacterial microbiome in IBD

Study	Study Population(s)	Microbiome Sample(s) and Methods	Key Findings
Fungi
⁵⁷	Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)	18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon	↑ fungal species in active CD biopsies compared with active UC and control subjects
⁶²	Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)	ITS1 sequencing of stool	↓ fungal diversity (Shannon index) in IBD
⁶²		ITS1 sequencing of stool	↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition
⁶⁰	Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)	ITS1, ITS2, and 16S rRNA sequencing of stool	↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli
⁵⁹	Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)	ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR	↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)	18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load	↓ fungal species count and abundance in active UC
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)		↑ abundance of Aspergillus in active UC
⁵²	Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)	ITS2 rRNA sequencing of stool	↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission
⁵²		ITS2 rRNA sequencing of stool	↓ fungal species count in UC
⁶⁴	PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)	ITS2 and 16S sequencing of stool	No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals
⁶⁴		ITS2 and 16S sequencing of stool	↑ fungal diversity (Shannon) index in PSC compared with IBD remission
⁶¹	Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics	Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies	↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects
⁶¹	Patients with active CD (n = 7) and healthy individuals (n = 10)		↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients
⁶⁵	Patients with 3-month remission of UC (n = 31), and ileal or ileocolonic CD (n = 34), patients with active CD (n = 55), UC relatives (n = 29), CD relatives (n = 29), healthy unrelated individuals (n = 28)	Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling	↑ fungal load in relapsed CD compared with patients who remained in remission
			↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed
			Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse
Protozoa
⁶⁶	Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)	Culture and PCR of stool	↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive
⁶⁶		Culture and PCR of stool	↓ Blastocystis prevalence in both active and inactive IBD than control subjects
⁶⁷	Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)	18S rRNA sequencing of stool	↓ Blastocystis prevalence in IBD
Viruses
⁶⁸	Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)	454 pyrosequencing of stool	↓ virome diversity (Shannon index) in CD
⁶⁹	Pediatric patients with CD (n = 6), and healthy individuals (n = 6)	454 pyrosequencing of ileal and colonic biopsies, and gut washes	↑ abundances of viral species in CD, Caudovirales most abundant
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	No difference in bacteriophage species between groups
⁷⁰	Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)	454 pyrosequencing of stool	↑ abundances of Caudovirales bacteriophage species in CD and UC
⁷¹	Patients with new-onset active CD (n = 12), healthy individuals (n = 12)	454 pyrosequencing of colonic biopsies	↑ viral species in active CD
⁷²	C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)	Shotgun whole metagenome sequencing of stool	↑ abundances of Caudovirales bacteriophages species in murine colitis

Study	Study Population(s)	Microbiome Sample(s) and Methods	Key Findings
Fungi
⁵⁷	Active CD (n = 31), active UC (n = 26), non-IBD intestinal inflammation (n = 15), healthy individuals (n = 32)	18S rRNA–based amplification, denaturing gradient gel electrophoresis, and clone library analysis of stool and biopsies from inflamed colon	↑ fungal species in active CD biopsies compared with active UC and control subjects
⁶²	Pediatric IBD (26 CD, 4 UC, and 2 indeterminate colitis), healthy adult and pediatric control subjects (n = 90)	ITS1 sequencing of stool	↓ fungal diversity (Shannon index) in IBD
⁶²		ITS1 sequencing of stool	↑ abundance of Cyberlindnera jadinii and C. parapsilosis and ↓ abundance of Cladosporium cladosporioides in IBD
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	↑ abundance of C. jadinii, S. cerevisiae, Clavispora lusitaniae, C. albicans, and Kluyveromyces marxianus in active CD, which decreased following 8 weeks of exclusive enteral nutrition
⁶⁰	Active and inactive CD (n = 20), CD relatives (n = 28), unrelated healthy individuals (n = 21)	ITS1, ITS2, and 16S rRNA sequencing of stool	↑ abundance of C. tropicalis in CD patients, positively correlated with Serratia marcescens and Escherichia coli
⁵⁹	Active CD (n = 16), inactive CD (n = 7), healthy individuals (n = 10)	ITS2 rRNA sequencing of ileo-colonic biopsies with quantitative PCR	↑ fungal load of both inflamed and inflamed mucosa in active CD compared with inactive CD and healthy control subjects
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)	18S and ITS2 rRNA sequencing of biopsies from inflamed colon; quantitative PCR of 18S rRNA for fungal load	↓ fungal species count and abundance in active UC
⁵⁸	Active UC (n = 14), healthy individuals (n = 15)		↑ abundance of Aspergillus in active UC
⁵²	Active CD and UC patients (n = 106), inactive CD and UC patients (n = 129), healthy individuals (n = 38)	ITS2 rRNA sequencing of stool	↑ abundance of C. albicans and ↓ abundance of S. cerevisiae and Malassezia sympodialis in active IBD compared with remission
⁵²		ITS2 rRNA sequencing of stool	↓ fungal species count in UC
⁶⁴	PSC patients with IBD in remission (n = 27), PSC patients without IBD (n = 22), IBD patients in remission without PSC (n = 33), and healthy individuals (n = 30)	ITS2 and 16S sequencing of stool	No difference in fungal diversity (Shannon and Chao1 indices) between IBD remission and healthy individuals
⁶⁴		ITS2 and 16S sequencing of stool	↑ fungal diversity (Shannon) index in PSC compared with IBD remission
⁶¹	Mice injured by colonic biopsies and treated with antibiotics to impair healing, control mice injured but not treated with antibiotics	Quantitative PCR of ITS of murine mucosal wounds and patient ileal biopsies	↑ Debaryomyces hansenii abundance in mucosal wounds of antibiotic-treated mice compared with control subjects
⁶¹	Patients with active CD (n = 7) and healthy individuals (n = 10)		↑ D. hansenii abundance in inflamed mucosa of CD patients compared with uninflamed mucosa in same patients
⁶⁵	Patients with 3-month remission of UC (n = 31), and ileal or ileocolonic CD (n = 34), patients with active CD (n = 55), UC relatives (n = 29), CD relatives (n = 29), healthy unrelated individuals (n = 28)	Quantitative PCR of ITS2 and 16S rRNA of stool, random forest predictive modelling	↑ fungal load in relapsed CD compared with patients who remained in remission
			↑ fungal load in relapsed UC compared with UC remission, CD remission, and CD relapsed
			Fungal and bacterial load combined with clinical markers (C-reactive protein and fecal calprotectin) and demographic data distinguished UC from CD and could predict relapse
Protozoa
⁶⁶	Active and inactive CD and UC patients (n = 100), healthy individuals (n = 96)	Culture and PCR of stool	↓ Blastocystis and Dientamoeba fragilis prevalence in active CD and UC than inactive
⁶⁶		Culture and PCR of stool	↓ Blastocystis prevalence in both active and inactive IBD than control subjects
⁶⁷	Patients with active CD (n = 76) and UC (n = 31), healthy individuals (n = 616)	18S rRNA sequencing of stool	↓ Blastocystis prevalence in IBD
Viruses
⁶⁸	Patients with active (n = 10) and inactive (n = 1) ileocolonic CD, healthy individuals (n = 8)	454 pyrosequencing of stool	↓ virome diversity (Shannon index) in CD
⁶⁹	Pediatric patients with CD (n = 6), and healthy individuals (n = 6)	454 pyrosequencing of ileal and colonic biopsies, and gut washes	↑ abundances of viral species in CD, Caudovirales most abundant
⁶³	Pediatric active CD (n = 90), healthy pediatric control subjects (n = 26)	Shotgun whole metagenome sequencing of stool	No difference in bacteriophage species between groups
⁷⁰	Patients with CD (n = 18), UC (n = 42), healthy individuals (n = 12)	454 pyrosequencing of stool	↑ abundances of Caudovirales bacteriophage species in CD and UC
⁷¹	Patients with new-onset active CD (n = 12), healthy individuals (n = 12)	454 pyrosequencing of colonic biopsies	↑ viral species in active CD
⁷²	C57BL6/J Rag1^-/- mice with colitis induced by injection of CD4+ CD45RB^High T cells (n = 3) and control mice injected with saline (n = 3)	Shotgun whole metagenome sequencing of stool	↑ abundances of Caudovirales bacteriophages species in murine colitis

Abbreviations: CD, Crohn’s disease; IBD, inflammatory bowel disease; PCR, polymerase chain reaction; PSC, primary sclerosing cholangitis; rRNA, ribosomal RNA; UC, ulcerative colitis.

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