Table Info

Table 2.

Restrictions of exclusionary diets and their effects on the microbes

Diet	Food inclusion	Food exclusion	UC or CD	Microbial changes	SCFA	BA	Trp	References
EEN	Liquid formula	Solid food	CD	Reduced diversity Decrease in Bacteroides/Prevotella ratio ↑ Firmicutes ↑ Alistepes ↓ Faecalibacterium ↓ Proteobacteria ↑ Roseburia ↑ Oscillibacter ↓ Haemophilus ↓ Veillonella ↓ Prevotella ↓ Anarostipes	Decrease in SCFA (returned to baseline with reintroduction of solid food)	Decrease of PBA and increase in SBA (returned to baseline after reintroduction of solid food)	Decrease in kynurenine and quinolic acid Increase in serotonin metabolites ↑ Melatonin ↑ N-acetylserotonin	[84–92]
CDED	Include: chicken, eggs, potatoes, bananas, and apple (these are mandatory)	Exclude: wheat, dairy, animal fat, processed foods, and red meat	CD	↑ Firmicutes ↑ Clostridiales ↑ Clostridia ↑ Ruminococcuss ↑ Roseburia ↑ Oscillibacter ↓ Haemophilus ↓ Veillonella ↓ Prevotella ↓ Anarostipes ↓ Gammaproteobacteria	No changes in SCFA	No changes in BA	Decrease in kynurenine and quinolic acid Increase in serotonin metabolites ↑ Melatonin ↑ N-acetylserotonin	[87, 91, 92]
PEN	Liquid formula and solid food	N/A	CD	N/A	N/A	N/A	Decrease in kynurenine and increase in serotonin	[91, 92]
FODMAP	Include: certain fruits and vegetables	Exclude: certain vegetables and fruits, wheat products, mushrooms, and honey	CD and UC	↑ Ruminococcus torques ↓ Bifidobacterium (Bifidobacterium longum and adolescentis ↓ Clostridium cluster XIVa ↓ Akkermansia muciniphila ↓ Faecalibacterium prausnitzii	Decrease in SCFA and no changes seen	Decrease in BAs	Higher concentration of 3-indole propionic acid	[108, 109, 112]
SCD	Include: fruits, meat and vegetables	Exclude: grains, potatoes, corn, processed meat, and dairy	CD and UC	↑ Roseburia ↑ Eubacterium eligens ↑ Blautia ↑ Lachnospiraceae ↑ Eubacterium ↑ Ruminoccocus ↑ Subdoligranulum ↓ Bacteroides ↓ Parabacteroides ↑ F. prausnitzii ↑ Clostridium	N/A	N/A	N/A	[114, 116]
MD	Include: vegetables, fruit, whole grain, nuts, olive oil, and fish	Exclude: high red meat intake, processed foods, sugar, and processed meat	CD and UC	↑ Roseburia ↑ Lachnospira ↑ Prevotella ↑ Ruminococcuss bromii ↑ Flavonifractor plautii ↑ Butyricicoccus ↑ Faecalibacterium prausnitzii ↑ Clostridium cluster ↑ Bacteroidetes ↓ Proteobacteria ↓ E. coli ↓ Proteobacteria ↓ Bacillaceae ↓ R. torques ↓ R. gnavus ↓ Bilophila wadsworthia	Increase of SCFA Decrease in BCFA	Decrease in BAs	Decrease of tryptophan and increase of IPA, ILA, IAA [132]	[128, 130]
PBD	Daily intake of fruits, legumes, vegetables, potatoes, and yogurt	Avoid sweets	CD and UC	↑ Roseburia ↑ Ruminococcus ↑ Streptococcus thermophiles ↑ Bacteroides thetaiotaomicron ↑ Clostridium clostridioforme ↑ F. prausnitzii ↑ Prevotella ↑ Lachnospira ↓ Clostridium cluster XIVa ↓ Alistepes ↓ Proteus mirabilis Clostridium XIV ↑ Bacteroides ↑ Prevotella	Higher levels of SCFA	Lower BAs	Lower kynurenine in serum High levels of Trp	[125, 136, 139, 140]

EEN: exclusive enteral nutrition; CDED: Crohn’s disease exclusion diet; PEN: partial enteral nutrition; FODMAP: fermentable oligo-, di-, mono-saccharide and polyol; SCD: specific carbohydrate diet; MD: Mediterranean diet; PBD: plant-based diet; UC: ulcerative colitis; CD: Crohn’s disease; SCFA: short chain fatty acids; BCFA: branched chain fatty acids; BA: bile acids; Trp: tryptophan; PBA: primary bile acids; SBA: secondary bile acids; IPA: indole-3-propionic acid; ILA: indole-3-lactic acid; IAA: indole-3-acetic acid. ↑: increase in relative abundance; ↓: decrease in relative abundance; N/A: not applicable

Declarations

Acknowledgments

We thank Prof. B. Witteman (emeritus from Wageningen University and Research, Wageningen, The Netherlands) for stimulating discussions during the preparation of the manuscript, and Dr. T. Dinse (University College Roosevelt, Middelburg, The Netherlands) for correcting the language and style of the manuscript.

Author contributions

HM: Conceptualization, Investigation, Writing—original draft, Writing—review & editing. GR: Validation, Writing—review & editing, Supervision. Both authors read and approved the submitted version.

Conflicts of interest

Not applicable.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

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Open Exploration maintains a neutral stance on jurisdictional claims in published institutional affiliations and maps. All opinions expressed in this article are the personal views of the author(s) and do not represent the stance of the editorial team or the publisher.

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