Table 4.

Gut microbiota outcomes reported in studies¹.

Study author, year	n	Comparison diet 1	Comparison diet 2	Alpha diversity	Beta diversity	Phylum	Class	Order	Family	Genus	Species	Other/notes	Significant effects on gut microbiota?
van Faassen et al. 1987 [85]	12	Post-omnivorous	Post-vegan	—	—	—	Clostridia:↔	—	Enterobacteriaceae:↔	Anaerobes:Bifidobacteria (count):↔Bacteroides (count):↔Aerobes:Enterococci (count):↔Lactobacilli (count):↑	—	Mean counts of bacteria:Total anaerobes:↔Total aerobes:↔	Yes
	12	Post-omnivorous	Post-vegetarian	—	—	—	Clostridia:↔	—	Enterobacteriaceae:↔	Anaerobes:Bifidobacteria (count):↔Bacteroides (count):↔Aerobes:Enterococci (count):↔Lactobacilli (count):↔	—	Mean counts of bacteria:Total anaerobes:↔Total aerobes:↔	No
	12	Post-vegetarian	Post-vegan	—	—	—	Clostridia:↔	—	Enterobacteriaceae:↔	Anaerobes:Bifidobacteria (count):↔Bacteroides (count):↔Aerobes:Enterococci (count):↑Lactobacilli (count):↑	—	Mean counts of bacteria:Total anaerobes:↔Total aerobes:↔	Yes
Windey 2012 et al. [73]	20	Higher meat	Lower meat	—	—	—	—	—	—	—	—	Among 64 bandclasses, no difference was detected in the allocation of bandclass between diets.	No
Foerster et al. 2014 [86]	20	Post-red meat	Pre-red meat	—	—	—	—	—	—	—	Clostridium sp.: ↓	Band appearance of bacteria:↔ band diversity (total number of bands)↑ 5 bands appearance↓ 3 bands appearance	Yes
	20	Post-whole grain	Pre-whole grain	—	—	—	—	—	—	—	Collinsella aerofaciens: ↑	Band appearance of bacteria:↑ band diversity (total number of bands)↑ 5 bands appearance↓ 3 bands appearance
Lang et al. 2018 [87]	109	By protein sources (1) Red meat(2) White meat (3) Non-meat	By amounts of saturated fat(1) High saturated fat(2) Low saturated fat	Shannon diversity index:↔ among protein sources or between high vs low amounts of saturated fat	↔unweighted UniFrac distance: no clustering by diet	F/B ratio (log2):↔ by diet or saturated fat	NR	NR	NR	2 reported genera (Coprococcus and Ruminococcus) differed by protein sources, but pairwise comparisons between protein sources were not reported.57 genera differed by saturated fat amounts.	—	19 OTUs responded to protein source at both high and low saturated fat amounts (protein-sensitive, but not specific to protein sources). Differentially abundant OTUs: [high and low amounts of saturated fat combined] 3 between red meat vs non-meat, 1 between white meat vs non-meat, 0 between red meat vs white meat; [low saturated fat] 115, 125, 130 OTUs, respectively; [high saturated fat] 203, 198, 240 OTUs, respectively.	Yes
Hess et al. 2018 [84]	32	Post-Red meat (5d average)	Post-Mushroom (5d average)	—	—	Bacteroidetes:↓Firmicutes:↑	NR	NR	NR	Bacteroides:↓Parabacteroides:↓Coprococcus:↓Anaerostipes:↓Sutterella:↓Dorea:↑02d06:↑	—	Taxa (phylum and genus) with at least 0.05% relative abundance were reported. Relative abundances were log-transformed and controlled for false discovery rate with p<0.004.	Yes
Schmedes et al. 2018 [71]	19	Post-lean seafood	Pre-lean seafood	—	—	Firmicutes:↔Bacteroidetes:↔F/B ratio:↔	—	—	—	Clostridium cluster IV:↔	—	The following results were described and not reported in details: the dataset included "42 bacterial OTU groups at the genera level, 8 bacterial OTU groups at the family level, 2 bacterial OTU groups at the order level, 1 bacterial OTU group at the class level, and 1 bacterial OTU group at the domain level”.	Yes
	19	Post-non-seafood	Pre-non-seafood	—	—	Firmicutes:↔(p=0.1)Bacteroidetes:↔(p=0.1)F/B ratio:↔(p=0.1)	NR	NR	NR	Clostridium cluster IV:↓ (greater reduction than lean-seafood group)	—
Pagliai et al. 2020 [74]	23	Post-Mediterranean diet	Pre-Mediterranean diet	Richness; inverse Simpson’s, Gini-Simpson’s, Shannon’s indices; evenness, dominance:Phylum-level:↔Class-level:↔Order-level:↔Family-level:↔Genus-level:↔	(1) Weighted Unifrac (PCoA)(2) Bray-Curtis dissimilarity metrics(3) Principle component analysis (PCA) & co-inertia analysis (CIA):No clearly separated clustering by diet.LEfSe tool: no discriminating characteristics by diet.PERMANOVA: no difference in microbiota composition by diet at any taxonomic level.	F/B ratio:↔F/P ratio:↔Other phyla:↔	Betaproteobacteria:↓ (p=0.05)	Burkholderiales:↓ (p=0.05)	Alcaligenaceae:↓ (p=0.05)	Enterorhabdus:↑Lachnoclostridium:↑Parabacteroides:↓Parasutterella:↓ (p=0.05)	—	—	Yes
	23	Post-vegetarian diet	Pre-vegetarian diet	Richness; inverse Simpson’s, Gini-Simpson’s, Shannon’s indices; evenness, dominance:Phylum-level:↔Class-level:↔Order-level:↔Family-level:↔Genus-level:↔		F/B ratio:↔F/P ratio:↔Euryarchaeota:↑ (abundance median increased from 0 to 1)Other phyla:↔	Methanobacteria:↑ (abundance median increased from 0 to 1)	Methanobacteriales:↑ (abundance median increased from 0 to 1)	Clostridiaceae_1:↓Methanobacteriaceae:↑ (abundance median increased from 0 to 1)	Anaerostipes:↑Clostridium_sensu_stricto_1:↓Methanobrevibacter:↑ (abundance median increased from 0 to 1)Odoribacter:↓Streptococcus:↑Tyzzerella_3: abundance median=0, interquartile range ↑	—	—
	23	Pre-Post change of Mediterranean diet	Pre-Post change of vegetarian diet	Order-level richness: median=1, interquartile range↑Genus-level richness:↓All other parameters:↔		F/B ratio:↔F/P ratio:↔Other phyla:↔	—	—	Clostridiaceae_1:↑	Anaerostipes:↓Clostridium_sensu_stricto_1:↑Enterorhabdus:↑Slackia: abundance median=0, interquartile range ↑Veillonella:↑	—	—
Crimarco et al. 2020 [88]	36	Animal diet	Plant diet	—	Bray-Curtis dissimilarity:↔	NR	NR	NR	NR	Volcano plot of taxa with between-group difference in abundance:Lachnospiraceae sp: mixedRuminococcus sp.:↑Roseburia sp.:↑Ruminococcaceae sp.:↓	Volcano plot of taxa with between-group difference in abundance:H. parainfluenzae:↓	—	Yes
	36	Post-animal	Pre-animal	—		—	—	—	—	—	—	—
	36	Post-plant	Pre-plant	—		—	—	—	—	—	—	—
Kahleova et al. 2020 [89]	84	Post-omnivorous	Pre-omnivorous	Abundance-weighted phylogenetic diversity measure:↑	—	↔	—	—	—	Methanobrevibacter (read counts and %):↑Eubacterium (read counts):↑	Bacteroides fragilis (read counts and %):↓	—	Yes
	84	Post-vegan	Pre-vegan	Abundance-weighted phylogenetic diversity measure: ↔	—	Bacteroidetes (read counts):↑Proteobacteria (%):↓	—	—	—	Bifidobacterium (read counts):↑Anaerostipes (read counts):↑	Faecalibacterium prausnitzii (read counts&%):↑Bacteroides fragilis (read counts and %):↓	—
	168	Post-pre change in omnivorous	Post-pre change in vegan	Abundance-weighted phylogenetic diversity measure:↑	—	↔	—	—	—	↔	Faecalibacterium prausnitzii (%):↓Bacteroides fragilis (read counts and %):↑	—
Meslier et al. 2020 [92]	62	Post-Mediterranean diet (wk4)	Post-omnivorous diet (wk4)	—	Separate diversity (N-integrative supervised analysis)Dissimilarity by adherence to MedD diet 0-4wk	NR	NR	NR	NR	NR	77 species differed at week 4, primarily:↓ species:Ruthenibacterium lactatiformans, Flavonifractor plautii, Parabacteroides merdae, Ruminococcus torques, Ruminococcus Gnavus, Streptococcus thermophilusi, Streptococcus thermophilus↑ species: 5 members of Faecalibacterium prausnitzii and 7 members of taxa Roseburia and Lachnospiraceae	—	Yes
	62	Post-Mediterranean diet (wk8)	Post-omnivorous diet (wk8)	—							44 species differed at week 8. Information on detailed species was not extracted.	—
	32	Post-omnivorous diet (wk4/wk8)	Pre-omnivorous diet	—							14 species differed at week 4 compared to baseline, 19 differed at week 8 compared to week 4. Information on detailed species was not extracted.	—
	30	Post- Mediterranean diet (wk4/wk8)	Pre- Mediterranean diet	—							69 species differed at week 4 compared to baseline, 17 differed at week 8 compared to week 4. Information on detailed species was not extracted.	—
Kohnert et al. 2021 [91]	53	Post-pre change in omnivorous	Post-pre change in vegan	NR	Bray-Curtis dissimilarity: no clustering.	NR	NR	NR	NR	↑ generaBacteroides, Clostridium, Faecalibacterium, Roseburia↓ genera:Bacteroides, Blautia, Dialister, Faecalibacterium, Ruminococcus	Differences in species were observed at ASV level.Information on detailed species was not extracted.	Unweighted UniFrac distances showed two separate clusters, but not clearly between two diets.	Yes
	27	Post-omnivorous	Pre-omnivorous	Chao1, Shannon, Inverse Simpson, Fisher’s index:↔	Bray-Curtis dissimilarity: no clustering	NR	NR	NR	NR	↑ genera:Alistipes, Bacteroides, Blautia, Clostridium, Faecalibacterium (unspecified species), Megamonas, Roseburia, Ruminococcus↓ genera:Bacteroides, Bifidobacterium, Blautia, Dialister, Faecalibacterium, Gemminger, Phascolarctobacterium, Prevotella, Ruminococcus, Sutterella			Yes
	26	Post-vegan	Pre-vegan	Chao1, Shannon, Inverse Simpson, Fisher’s index:↔	Bray-Curtis dissimilarity: no clustering	NR	NR	NR	NR	↑ genera:Alistipes, Bacteroides, Blautia, Coprococcus, Dialister, Dorea, Faecalibacterium (unspecified species), Phascolarctobacterium, Ruminococcus↓ genera:Akkermansia, Bacteroides, Bifidobacterium, Clostridium, Coprococcus, Faecalibacterium, Roseburia, Ruminococcus			Yes
McKenna et al. 2021 [90]	28	wk1-higher red meat (high)	Pre-high	Faith’s phylogenetic diversity and Shannon: ↔	Unweighted UniFrac: significant between-group differenceWeighted UniFrac:↔DEICODE metrics:↔	NR	NR	Betaproteobacteriales:↑	—	↓ genera:Akkermansia, unclassified genus of family Eggerthellaceae, Ruminococcaceae UCG-010, Megasphaera, Veillonella↑ genera:Catenibacterium	—	—	Yes
	28	Post-high	wk1-high					—	—	↓ genera:Catenibacterium↑ genera:Akkermansia, unclassified genus of family Eggerthellaceae, Veillonella	—	—
	28	Post-high	Pre-high					Betaproteobacteriales:↑	—	Megasphaera:↓	—	—
	22	wk1-Lower red meat (MOD)	Pre-MOD	Faith’s phylogenetic diversity and Shannon: ↔	Unweighted UniFrac: significant between-group differenceWeighted UniFrac:↔DEICODE metrics:↔	NR	NR	Mollicutes RF39:↓	Lachnospiraceae:↑	↓ genera:Streptococcus↑ genera:Coprococcus 2, Holdemanella, Acidaminococcus	—	—
	22	Post-MOD	wk1-MOD					Mollicutes RF39:↑	—	↓ genera:Acidaminococcus, Holdemanella, Catenibacterium↑ genera:Veillonella	—	—
	22	Post-MOD	Pre-MOD					—	Lachnospiraceae:↑	↓ genera:Blautia, Catenibacterium↑ genera:Coprococcus 2	—	—
	50	Post-MOD	Post-high	Faith’s phylogenetic diversity and Shannon: ↔	Unweighted UniFrac: significant between-group differenceWeighted UniFrac:↔DEICODE metrics:↔	NR	NR	—	Ruminococcaceae:↓	↓ genera:HoldemanellaI, Acidaminococcus↑ genera:Megasphaera, metagenome	—	—
	50	wk1-MOD	wk1-high					Mollicutes RF39:↓	—	↑ genera:Ruminiclostridium 5, Oscillibacter, Megasphaera, metagenome, Lactobacillus, Veillonella, uncultured genus of family Eggerthellaceae	—	—
	50	Pre-MOD	Pre-high					Betaproteobacteriales:↑	Enterobacteriaceae:↑	↓ genera:[Eubacterium] eligens group, Ruminococcaceae UCG-013, Coprococcus 2, Holdemanella, Acidaminococcus, Slackia, uncultured genus of family Eggerthellaceae↑ genera:Streptococcus, Catenibacterium, metagenome, Dielma	—	—
Bratlie et al. 2021 [93]	9	Post-cod	Pre-cod	—	No clear separation between diets pre-intervention.Trend of separation between diets post-intervention, especially between post-salmon and post-control.	NR	NR	Post-Cod & Post-Salmon compared to Post-Control (bacterial counts):Bacteroidales:↓Clostridiales:↓Selenomonadales:↓	NR	NR	NR	—	Yes
	13	Post-salmon	Pre-salmon
	11	Post-control	Pre-control

¹Higher abundance (↑), lower abundance (↓), or comparable abundances (↔). NR, data measured but not reported; OTU, operational taxonomic unit; ASV, amplicon sequence variant.