Table 3.
Composition analysis of the included studies.
| Author | OTU | Chao1 | Abundance coverage |
Evenness | Shannon | Simpson | Inverse Simpson |
Faith | Beta Diversity |
Relative abundance |
|---|---|---|---|---|---|---|---|---|---|---|
| Bai et al., 2022 (29) | NS | C higher than P | C higher than P | Bray-Curtis: S Weighted UniFrac: S |
Phylum level: Higher Bacteroidetes, Actinobacteria, Firmicutes, Probacteria in P. Firmicutes also higher in C. Family level: Higher unidentified family Lachnospiraceae, unidentified family Erysipelotrichaceae in P than C. Higher unidentified family Christensenellaceae, unidentified family Lachnospiraceae, and unidentified family Ruminococcaceae in C. Genus level: Higher Bacteroides, Parabacteroides, and Odoribacter, Eggerthella and Varibaculum, SMB53, Lachnospira, Dorea, Veillonella, Anaerotruncus, Butyricicoccus, Eubacterium, Coprobacillus, Sutterella in P than C. Higher Anaerostipes and Oribacterium in C. |
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| Berlinberg et al., 2021 (30) | NS | NS | NS | NS | Bray-Curtis: NS | Species level: Higher Bifidobacterium adolescentis and Porphyromonas bennonis in P. Higher Streptococcus anginosus and Bacteroides dorei in C. |
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| Braundmeier-Fleming et al., 2016 (31) | Species level: lower E. sinensis, C. aerofaciens, F. prausnitzii, O. splanchnicus, and L. longoviformis in P. | |||||||||
| Chen et al., 2019 (32) | NS at genus and species level | Decreased in P compared to C | Phylum level: higher Firmicutes in P. Genus level: lower Faecalibacterium in P. Species level: higher Faecalibacterium prausnitzii, Bifidobacteriumadolescentis, and Methanobrevibacter smithii in C. Higher Blautia hydrogenotrophica, Clostridium asparagiforme, Clostridium clostridioforme, Clostridium bolteae, Clostridium citroniae, Clostridium hathewayi, Clostridium ramosum, Clostridium spiroforme, Clostridium symbiosum, Eggerthella lenta, Flavonifractor plautii, Lachnospiraceae bacterium, and Ruminococcus gnavus in P. Higher Bacteroides clarus, Bacteroides intestinalis, Bacteroides salyersiae, Bacteroides stercoris, Butyrivibrio crossotus, Clostridium sp. L2_50, Coprococcus catus, Eubacterium hallii, Eubacterium ramulus, Odoribacter splanchnicus, Peptostreptococcaceae noname unclassified, Prevotella copri, Ruminococcus callidus, Ruminococcus champanellensis, Ruminococcus obeum, and Sutterella wadsworthensis in C. |
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| Clos-Garcia et al., 2019 (33) | NS | NS | NS | NS | NS | P lower than C | Phylum level: Bacteroidetes and Firmicutes both increased and decreased, Actinobacteria reduced in P. Family level: Higher Rikenellaceae in P. Lower unassigned genus in Bacteroidaceae and Lachnospiraceae families, Bifidobacteriaceae and Erysipelotichaceae in P. Genus level: Lower Bacteroides, Bifidobacterium, Eubacterium and Clostridium in P. Higher Dorea, Roseburia and Alistipes in P. |
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| Frémont et al., 2013 (34) | NS | Genus level: Higher Lactonifactor and Alistipes in Norwegian P. Higher Roseburia, Syntrophococcus, Holdemania and Dialister in Norwegian C. Higher Lactonifactor in Belgian P. Higher Asaccharobacter in Belgian C. | ||||||||
| Giloteaux et al., 2016 (35) | C: 1486.5 (456.5) P: 1204.3 (351.2) S |
C: 2918.4 (884.9) P: 2363.5 (705) S |
C: 5.9 (0.9) P: 5.3 (0.9) S |
C: 73.4 (19.0) P: 61.7 (16.7) S |
Weighted UniFrac: NS Unweighted UniFrac: NS |
Phylum level: lower Firmicutes in P. Higher Proteobacteria in P. Family level: higher Enterobacteriaceae, Prevotellaceae in P. Lower Ruminococcaceae, Bacteroidaceae, Rickenellaceae, Bifidobacteriaceae in P. Genus level: Higher Oscillospira, Lactococcus, Anaerotruncus, Coprobacillus and Eggerthella in P. Higher Faecalibacterium and Bifidobacterium in C. |
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| Guo et al., 2023 (36) | NS | P lower then C | P lower then C | Bray-Curtis: S | Species level: Lower F. prausnitzii, E. rectale, and C. secundus in P. Higher R. lactatiformans, C. bolteae, R. gnavus, E. ramosum, C. scindens, Blauti sp. N6H1.15, S. intestinalis, T. nexilis, and Lachnoclostridium sp. YL32 in P. |
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| Janulewicz et al., 2019 (37) | P: 576 (SD: 12.9) C: 415 (SD: 83.1) S |
P: 4.03 (SD: 0.15) C: 3.79 (SD: 0.23) S (family level) |
Phylum level: NS Family level: higher Lachnispiracae in C compared to P. Genus level: Higher Dialister in C than P. Ruminococcus higher in P than C. |
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| Kitami et al., 2020 (38) | NS | NS | Genus level: Higher Blautia, Coprobacillus, Eggerthella in P. Higher Collinsella, Faecalibacterium and Lachnospira in C. | |||||||
| Kopchak et al., 2022 (39) | Species level: higher frequency of Alceligenes spp, Clostridium coccoides, Clostridium propionicum, Eggerthella lenta, Pseudonocardia spp, Rhodococcus spp, Micromycetes spp (campesterol and sitosterol), Herpes simplex for P than C. | |||||||||
| Lupo et al., 2021 (40) | P: 215.6 (78) C: 221.4 (60.8) NS |
P: 453.4 (194.7) C: 422 (151.2) NS |
P: 17.7 (11.1) C: 13.3 (7.3) NS |
Phylum level: Higher Bacteroidetes in P. Higher Firmicutes in C. Class level: Higher Bacteroidia in P. Higher Clostridia in C. Order level: Higher Clostridiales in C. Higher Bacteroidales in P. Family level: Lower Lachnospiraceae in P. Higher Bacteroidaceae, Barnesiellaceae in P. Genus level: Lower Anaerostipes in P. Higher Bacteroides and Phascolarctobacterium in P. Species level: Higher Bacteroides ovatus and Bacteroides uniformis in P. |
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| Mandarano et al., 2018 (41) | C: 18.1 (SE: 6.9) P: 14.1 (SE: 7.8) NS |
C: 26.6 (SE: 10.7) P: 20.6 (SE: 10.9) NS |
C: 2.8 (SE: 1.2) P: 2.3 (SE: 1.2) NS |
C: 6.7 (SE:2.1) P: 6.0 (SE:2.4) NS |
Weighted UniFrac: NS Unweighted UniFrac: NS |
Phylum level fungi: lower Ascomycota in P. Higher Basidiomycota, Stramenopiles and Zygomycota in P. Class level: higher Agaricomycetes, Tremellomycetes in P. Order level: lower Saccharomycetales in P. Higher Agaricales, Boletales, Polyporales, Tremellomycetes unknown, Malasseziales, Entomophthorales, Mucorales, Pleurosigma, Eustigmatales, Peronosporales, Cystofilobasidiales in P. Tremellales, Sporidiobolales and Ustilaginales only observed in C. Species level: Higher Blastocystis in P. |
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| Minerbi et al., 2019 (42) | NS | NS | Bray-Curtis: S | Species level: Lower F. prausnitzii and B. uniformis in P. Higher Intestinimonas butyricipro ducens, Flavonifractor plautii, Butyricoccus desmolans, Eisenber giella tayi, and Eisenbergiella massiliensis in P. | ||||||
| Nagy-Szakal et al., 2017 (43) | Bray-Curtis: C lower than P. | Family level: lower Lachnospiraceae and Porphyromonadaceae in P, while higher Clostridiaceae. Genus level: lower Dorea, Faecalibacterium, Coprococcus, Roseburia, and Odoribacter in P, while higher Clostridium and Coprobacillus. Species level: lower Faecalibacterium prausnitzii, Faecalibacterium cf., Roseburia inulinivorans, Dorea longicatena, Dorea formicigenerans, Coprococcus catus, Odoribacter splanchnicus, Ruminococcus obeum, and Parabacteroides merdae in P, while higher Clostridium asparagiforme, Clostridium symbiosum, and Coprobacillus bacterium in P. |
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| Reichenberger et all., 2013 (44) | P: mean 280.45 (195-392 range) C: mean 328.63 (145-591 range) S |
P: 520.76 (SE: 44.18) C: 651.75 (SE: 54.12) S |
P: 3.89 (SE: 0.15) C: 4.12 (SE: 0.12) S |
Unweighted UniFrac matrix: S (since clustering is successful based on disease state) | Phylum level: Firmicutes 64.8% in C and 44% in P, Proteobacteria 0.078% in C and 5.1% in P. | |||||
| Sheedy et al., 2009 (45) | Species level: Higher E. Coli in C. Higher E. faecalis, S. sanguinis in P. | |||||||||
| Shukla et al., 2015 (46) | Phylum level: Higher Bacteroidetes (P 27.71% vs C 22.43%), lower Firmicutes (P 58.40% vs 65.29%) and lower Actinobacteria (P 0.58% vs C 1.06%) in P. | |||||||||
| Weber et al., 2022 (47) | P: 194.85 (SD: 42.98) C: 197.99 (SD: 49.69) NS |
P: 183.37 (50.84) C: 187.96 (44.04) NS |
P: 212.46 (139.9) C: 185.53 (41.58) NS |
P: 0.73 (0.05) C: 0.73 (0.05) NS |
P: 5.58 (0.56) C: 5.58 (0.56) NS |
P: 0.15 (0.04) C: 0.14 (0.05) NS |
P: 16.07 (SD:2.71) C: 16.13 (2.98) NS |
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| Yong et al., 2023 (48) | NS | NS | NS | Weighted UniFrac: NS Unweighted UniFrac: NS Bray-Crutis: NS |
Phylum level: no difference. Class level: Higher Tissierellia in P1 and P2 than C. Order level: Higher Tissierellales in P1 and P2 than C. Family level: Higher Peptoniphilaceae and Eubacteriaceae in P1 than C. Higher Peptoniphilaceae in P2 than C. Genus level: Higher Olsenella in P1 than C. Higher Hungatella, Clostridium_g6, Eggerthella and Longicatena in P2 than C. Higher Catenibacterium, PAC000195_g, Fusicantenibacter, Agathobacter, Eubacterium_g4, Roseburia, Lachnospiraceae_uc, Eubacterium_g21 in C than P1. Higher PAC001134_g, Catenibacterium, PAC000692_g, Holdemanella, PAC001137_g, PAC000195_g, Agathobacter, Eubacterium_g4, Roseburia, Frisingicoccus, Faecalibacterium, Dorea and Lachnospira in C than P2. |
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| Zhao et al. (49) | P: 323.05 C: 321.9 |
P: 327.86 C: 327.51 |
P: 336.72 C: 335.62 |
P: 5.26 C: 5.84 |
P: 0.91 C: 0.96 |
Weighted UniFrac: S | Phylum level: lower Firmicutes in P, and higher Probacteria in P. Genus level: higher Anaerostipes, Erysipelatoclostridium, Holdemanella, Sarcina, Streptococcus, and Weissella in P. Lower Faecalibacterium, Romboutsia, and Subdoligranulum in P. |
C, controls; NA, not applicable; NS, non-significant; P, patients; S, significant.