Table 4 Log2 fold change abundance of bacterial species in fecal samples of children with CeD

1

Clostridium sp. L2-50

– 2.0120

8.85^–20

3.43^–17

2

Ruminococcus sp. SR1/5

– 0.2670

9.89^–20

3.43^–17

3

Streptococcus sp. SR4

0.0787

2.91^–13

6.75^–11

4

Actinomyces sp. oral taxon 175

2.0207

1.80^–12

3.12^–10

5

Clostridiales bacterium VE202-07

0.7391

3.68^–11

5.11^–09

6

Actinomyces sp. ICM39

– 1.6899

1.01^–10

1.16^–08

7

Bacteroides sp. 1_1_30

– 0.9884

1.39^–10

1.37^–08

8

Alistipes inops

– 5.4881

4.50^–10

3.90^–08

9

Desulfovibrio piger

– 0.7593

7.71^–10

5.94^–08

10

Actinomyces sp. ICM58

– 5.2606

3.41^–09

2.24^–07

11

Bifidobacterium angulatum

– 1.3309

3.55^–09

2.24^–07

12

Actinobaculum massiliense

4.2776

6.03^–09

3.49^–07

13

Bacteroides clarus

– 3.5549

6.67^–09

3.56^–07

14

Oscillibacter sp. KLE 1745

1.8464

3.35^–08

1.66^–06

15

Lactobacillus acidophilus

0.8589

3.69^–08

1.69^–06

16

Prevotella sp. P5-119

– 3.6227

4.01^–08

1.69^–06

17

Burkholderiales bacterium 1_1_47

– 3.2591

4.14^–08

1.69^–06

18

Coprobacter fastidiosus

– 4.7198

6.62^–08

2.55^–06

19

Tannerella sp. 6_1_58FAA_CT1

– 2.9135

7.82^–08

2.85^–06

20

Blautia hydrogenotrophica

4.3470

1.11^–07

3.88^–06

21

Coriobacteriaceae bacterium BV3Ac1

2.8402

1.51^–07

4.99^–06

22

Phascolarctobacterium succinatutens

0.1041

2.10^–07

6.63^–06

23

Citrobacter freundii

– 3.9256

3.56^–07

1.07^–05

24

Leuconostoc pseudomesenteroides

– 4.7313

5.15^–07

1.49^–05

25

Parasutterella excrementihominis

– 2.8930

1.38^–06

3.84^–05

26

Coprobacillus sp. D6

0.7717

2.13^–06

5.69^–05

27

[Ruminococcus] gnavus

1.4824

2.73^–06

7.03^–05

28

Klebsiella variicola

– 3.4290

3.35^–06

8.32^–05

29

Actinomyces sp. HPA0247

0.3485

4.56^–06

0.0001

30

[Clostridium] spiroforme

– 0.9840

8.71^–06

0.0002

31

Bacteroides eggerthii

– 3.4963

1.24^–05

0.0002

32

Megasphaera massiliensis

2.4114

2.15^–05

0.0004

33

Clostridiales bacterium VE202-26

2.0418

2.29^–05

0.0004

34

Megasphaera sp. BL7

– 3.4443

2.52^–05

0.0005

35

Actinotignum schaalii

2.0700

3.82^–05

0.0007

36

Enterococcus avium

0.8707

7.96^–05

0.0015

37

Eggerthella sp. 1_3_56FAA

– 0.3357

8.57^–05

0.0016

38

Corynebacterium pyruviciproducens

5.6575

8.87^–05

0.0016

39

Eubacterium limosum

– 0.2074

0.0001

0.0018

40

Bifidobacterium breve

– 0.6821

0.0001

0.0028

41

Mitsuokella jalaludinii

0.7105

0.0001

0.0028

42

Weissella confusa

– 2.7298

0.0002

0.0037

43

Streptococcus pneumoniae

1.8511

0.0002

0.0042

44

Lactobacillus plantarum

– 1.0534

0.0002

0.0043

45

Actinomyces cardiffensis

– 0.1851

0.0004

0.0068

46

Bacteroides faecichinchillae

– 2.1328

0.0004

0.0068

47

Lactobacillus mucosae

0.6968

0.0005

0.0077

48

Alistipes sp. HGB5

0.9527

0.0005

0.0081

49

Peptoniphilus harei

2.6088

0.0006

0.0083

50

Kocuria rhizophila

1.5647

0.0006

0.0083

51

Haemophilus haemolyticus

1.8040

0.0007

0.0098

52

Bacteroides gallinarum

– 0.9100

0.0007

0.0098

53

[Eubacterium] siraeum

– 1.1823

0.0008

0.0103

54

Scardovia inopinata

2.6347

0.0008

0.0104

55

Dialister succinatiphilus

– 0.6384

0.001

0.011

56

Eggerthella sp. YY7918

– 2.9586

0.001

0.012

57

Bifidobacterium merycicum

– 1.2398

0.001

0.012

58

Alistipes onderdonkii

– 1.8638

0.001

0.012

59

Lachnospiraceae bacterium oral taxon 500

2.4268

0.001

0.013

60

Alistipes sp. AL-1

– 2.0624

0.001

0.013

61

Kandleria vitulina

– 1.1850

0.001

0.014

62

Actinomyces turicensis

1.7418

0.001

0.015

63

Kallipyga massiliensis

1.4601

0.001

0.015

64

Prevotella timonensis

2.3958

0.002

0.018

65

Alistipes indistinctus

– 0.9069

0.002

0.018

66

Streptococcus parauberis

– 1.4411

0.002

0.021

67

Streptococcus dysgalactiae

3.0429

0.002

0.021

68

Acinetobacter junii

1.3684

0.002

0.022

69

Prevotella bergensis

2.2901

0.002

0.022

70

Anaerococcus prevotii

1.3590

0.002

0.023

71

Bifidobacterium biavatii

0.1734

0.002

0.023

72

Weissella cibaria

– 3.1430

0.003

0.026

73

Peptostreptococcus anaerobius

1.7918

0.003

0.026

74

Gardnerella vaginalis

1.5445

0.003

0.026

75

Eggerthia catenaformis

– 1.3356

0.003

0.027

76

Bifidobacterium thermophilum

– 0.8901

0.003

0.027

77

Bacteroides finegoldii

– 2.9953

0.003

0.027

78

Atopobium vaginae

1.5527

0.003

0.028

79

Mitsuokella multacida

2.0038

0.003

0.028

80

Anaerostipes sp. 3_2_56FAA

– 4.0899

0.003

0.028

81

Catonella morbi

1.5910

0.003

0.028

82

Ruminococcus gauvreauii

1.5330

0.003

0.029

83

Streptococcus anginosus

1.5551

0.004

0.031

84

Dialister invisus

– 0.8902

0.004

0.031

85

Dialister micraerophilus

2.4775

0.004

0.032

86

Sharpea azabuensis

– 1.5192

0.004

0.033

87

Lactobacillus gasseri

2.1423

0.004

0.033

88

Coprobacillus sp. D7

0.5299

0.004

0.033

89

Escherichia sp. 1_1_43

0.9507

0.004

0.033

90

Anaerococcus obesiensis

1.2936

0.004

0.033

91

Clostridium celatum

1.5093

0.005

0.037

92

Clostridium paraputrificum

2.9282

0.005

0.037

93

Actinomyces dentalis

1.3394

0.005

0.038

94

Coprococcus sp. HPP0074

1.9454

0.005

0.038

95

[Clostridium] saccharogumia

1.2495

0.006

0.040

96

Enterobacter cloacae complex 'Hoffmann cluster IV'

1.3726

0.006

0.040

97

Streptococcus sinensis

1.2504

0.006

0.042

98

Mageeibacillus indolicus

– 1.2756

0.007

0.047

99

Bacteroides stercorirosoris

– 1.5318

0.007

0.048

100

Bifidobacterium saguini

2.2018

0.007

0.048

101

Lactobacillus ultunensis

2.0939

0.008

0.048

102

Klebsiella sp. 10,982

– 1.2026

0.008

0.048

103

Klebsiella michiganensis

5.7397

0.008

0.048

104

Megasphaera micronuciformis

– 0.3100

0.008

0.050

105

Anaeroglobus geminatus

2.7566

0.009

0.054

106

Corynebacterium pseudodiphtheriticum

1.1915

0.009

0.055

107

Clostridiales bacterium VE202-09

– 3.922

0.010

0.059

108

Christensenella minuta

– 0.3566

0.010

0.059

109

Leuconostoc mesenteroides

0.0528

0.010

0.061

110

Bacteroides barnesiae

– 2.0367

0.011

0.062

111

Corynebacterium argentoratense

– 0.7247

0.012

0.071

112

Intestinimonas butyriciproducens

0.3570

0.013

0.075

113

Propionibacterium acidifaciens

1.9602

0.014

0.079

114

Klebsiella pneumoniae

– 1.3439

0.016

0.084

115

Streptococcus constellatus

0.6456

0.017

0.095

116

Anaerococcus vaginalis

1.0155

0.018

0.097

117

Enorma massiliensis

1.2870

0.018

0.097

118

Lachnospiraceae bacterium 2_1_58FAA

1.4788

0.019

0.099

119

Ruminococcaceae bacterium D16

– 0.8005

0.020

0.105

120

Bacteroides salanitronis

0.0412

0.020

0.105

121

Akkermansia muciniphila

– 0.4313

0.021

0.111

122

Bifidobacterium minimum

– 2.4337

0.022

0.112

123

Candidatus Saccharibacteria oral taxon TM7x

1.1047

0.022

0.112

124

Shigella sp. SF-2015

1.7508

0.024

0.119

125

Bifidobacterium callitrichos

– 0.0551

0.024

0.119

126

Lachnospiraceae bacterium 1_4_56FAA

– 0.3516

0.025

0.124

127

Bifidobacterium gallinarum

0.2816

0.026

0.126

128

Lachnospiraceae bacterium 9_1_43BFAA

2.1702

0.027

0.128

129

Turicibacter sp. HGF1

1.9376

0.027

0.128

130

Leucobacter chironomi

– 0.9613

0.027

0.128

131

Slackia exigua

1.4279

0.027

0.128

132

Streptococcus pyogenes

1.9995

0.028

0.128

133

Bulleidia extructa

1.0910

0.028

0.129

134

Streptococcus mutans

1.2386

0.028

0.130

135

bacterium LF-3

1.1778

0.030

0.135

136

Morococcus cerebrosus

0.9367

0.030

0.136

137

Klebsiella oxytoca

1.8890

0.030

0.136

138

Raoultella ornithinolytica

– 4.1641

0.031

0.137

139

Enterococcus saccharolyticus

0.1371

0.031

0.137

140

Mucispirillum schaedleri

– 1.0032

0.032

0.138

141

Butyricimonas synergistica

0.1619

0.032

0.138

142

Eubacterium ramulus

– 0.9600

0.033

0.142

143

Prevotella sp. BV3P1

4.9067

0.034

0.144

144

Parabacteroides goldsteinii

1.2363

0.035

0.150

145

Haemophilus pittmaniae

0.2372

0.036

0.152

146

Oribacterium sinus

0.9714

0.036

0.152

147

Pseudoramibacter alactolyticus

0.1447

0.037

0.153

148

Olsenella profusa

2.2762

0.038

0.156

149

Bacteroides pyogenes

– 4.6019

0.038

0.158

150

Streptococcus sp. SR1

0.9154

0.039

0.160

151

candidate division TM7 single-cell isolate TM7b

1.1954

0.040

0.161

152

Eikenella corrodens

– 0.9100

0.041

0.165

153

Enterobacter sp. MGH 38

– 5.7753

0.042

0.165

154

Streptococcus oralis

1.0494

0.042

0.165

155

Lactobacillus casei group

– 0.8741

0.043

0.168

156

Desulfovibrio desulfuricans

– 1.1163

0.043

0.169

157

Escherichia fergusonii

– 1.4098

0.044

0.169

158

Paraclostridium bifermentans

0.9890

0.044

0.169

159

Citrobacter koseri

0.8884

0.045

0.169

160

Granulicatella elegans

– 0.3866

0.045

0.169

161

Succinivibrio dextrinosolvens

– 2.7856

0.046

0.171

162

Streptococcus thermophilus

– 0.8128

0.046

0.171

163

Prevotella buccae

0.8820

0.046

0.171

164

Lactobacillus jensenii

– 0.4273

0.046

0.171

165

butyrate-producing bacterium SM4/1

– 2.8000

0.047

0.171

166

Atopobium sp. ICM42b

– 0.9230

0.047

0.171

167

Bifidobacterium longum

0.9381

0.048

0.176

168

Parabacteroides johnsonii

1.6349

0.049

0.176

169

Collinsella intestinalis

1.0310

0.049

0.177