Table 3 Taxa that are significantly changed by rifaximin in stool samples from CVID patients.

From: RETRACTED ARTICLE: Rifaximin alters gut microbiota profile, but does not affect systemic inflammation - a randomized controlled trial in common variable immunodeficiency

Taxa

Group

Baselinea (n = 40)

2 weeksa (n = 38)

8 weeksa (n = 31)

P value interactionb

Beta2c (week 2)

Beta2c (week 8)

Bacteroidetes

No Int

0.415 (0.388–0.441)

0.385 (0.357–0.413)

0.413 (0.384–0.443)

0.012

0.28*

0.08

Rif

0.366 (0.340–0.393)

0.413 (0.385–0.441)

0.382 (0.348–0.415)

Bacteroidetes.Bacteroidia

No Int

0.414 (0.388–0.441)

0.385 (0.357–0.412)

0.413 (0.383–0.443)

0.012

0.28*

0.08

Rif

0.366 (0.340–0.393)

0.413 (0.385–0.440)

0.382 (0.348–0.415)

Bacteroidetes.Bacteroidia.Bacteroidales

No Int

0.414 (0.388–0.441)

0.385 (0.357–0.412)

0.413 (0.383–0.443)

0.012

0.28*

0.08

Rif

0.366 (0.340–0.393)

0.413 (0.385–0.440)

0.382 (0.348–0.415)

Bacteroidetes.Bacteroidia.Bacteroidales.Bacteroidaceae

No Int

0.292 (0.267–0.316)

0.265 (0.239–0.290)

0.283 (0.255–0.310)

0.009

0.25**

0.12

Rif

0.269 (0.245–0.294)

0.315 (0.289–0.340)

0.282 (0.251–0.312)

Bacteroidetes.Bacteroidia.Bacteroidales.Bacteroidaceae. Bacteroides

No Int

0.292 (0.267–0.316)

0.265 (0.239–0.290)

0.283 (0.255–0.310)

0.009

0.25**

0.12

Rif

0.269 (0.245–0.294)

0.315 (0.289–0.340)

0.282 (0.251–0.312)

Firmicutes.Clostridia.Clostridiales.Family XI.Ezakiella

No Int

−7.8E−20 (−1.3E−5–1.3E−5)

1.1E−5 (−2.2E−6–2.4E−5)

−4.3E−7 (−1.5E−5–1.4E−5)

0.029

−0.09

0.43

Rif

5.3E−6 (−7.5 E−6–1.8E−5)

5.0E−6 (−8.3E−6–1.8 E−5)

3.4E−5 (1.8E−5–5.0E−5)

Firmicutes.Clostridia.Clostridiales.Family XIII.Family XIII UCG-001

No Int

1.1E−4 (−3.9E−6–2.3E−4)

9.7E−5 (−2.2E−5–2.2E−4)

1.4E−4 (7.5E−6–2.6E−4)

0.028

0.04

0.15

Rif

2.3E−4 (1.2E−4–3.5E−4)

2.5E−4 (1.3E−4–3.7E−4)

0.001 (4.2E−4–0.001)

Firmicutes.Clostridia.Clostridiales.Lachnospiraceae. Anaerostipes

No Int

3.9E−4 (−3.7E−7–0.001)

0.001 (2.5E−4–0.001)

0.001 (0.001–0.001)

0.031

0.21

−0.25

Rif

4.9E−4 (1.0E−4–0.001)

0.001 (0.001–0.002)

4.6E−4 (−3.5E−5–0.001)

Firmicutes.Clostridia.Clostridiales.Lachnospiraceae. Lactonifactor

No Int

2.6E−5 (−9.7E−6–6.2E−5)

5.9E−5 (2.2E−5–9.6E−5)

1.2E−5 (−2.9E−5–5.2E−5)

0.0003

−0.32*

0.37*

Rif

1.0E−4 (6.4E−5–1.4E−4)

4.2E−5 (5.0E−6–8.0E−5)

1.2 E−4 (7.0E−5–1.6 E−4)

Firmicutes.Clostridia.Clostridiales.Peptococcaceae

No Int

5.3E−5 (−1.6E−5–1.2E−4)

2.5E−5 (−4.7E−5–9.6E−5)

3.1E−6 (−7.4E−5–8.0E−5)

0.023

−0.15

0.08

Rif

2.6E−4 (1.9 E−4–3.3E−4)

5.1E−5 (−2–0E−5–1.2 E−4)

1.8 E−4 (9.6 E−5–2.7 E−4)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae

No Int

0.003 (0.002–0.005)

0.005 (0.004–0.007)

0.003 (0.001–0.005)

0.012

−0.19

−0.01

Rif

0.007 (0.005–0.009)

0.003 (0.001–0.005)

0.006 (0.004–0.008)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae. Anaerotruncus

No Int

0.003 (0.002–0.005)

0.005 (0.004–0.007)

0.003 (0.001–0.005)

0.013

−0.28

0.12

Rif

0.007 (0.005–0.009)

0.003 (0.001–0.005)

0.006 (0.004–0.008)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae. Oscillibacter

No Int

1.5E−4 (6.6E−6–2.9E−4)

4.0E−4 (2.6E−4–0.001)

1.2E−4 (−3.6E−5–2.8E−4)

0.028

−0.22

0.16

Rif

1.3E−4 (−1.4E−5–2.7E−4)

5.4E−5 (−9.2E−5–2.0E−4)

1.9E−4 (8.2E−6–3.6E−4)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae. Ruminococcaceae UCG-002

No Int

0.011 (0.007–0.015)

0.017 (0.013–0.021)

0.015 (0.010–0.019)

0.014

−0.28*

−0.22

Rif

0.025 (0.021–0.029)

0.017 (0.013–0.021)

0.019 (0.014–0.025)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae. Ruminococcaceae UCG-014

No Int

0.009 (0.005–0.013)

0.011 (0.006–0.016)

0.008 (0.003–0.013)

0.018

−0.41**

−0.06

Rif

0.012 (0.008–0.018)

0.001 (−0.004–0.006)

0.007 (0.002–0.013)

Firmicutes.Clostridia.Clostridiales.Ruminococcaceae. uncultured

No Int

0.011 (0.009–0.013)

0.011 (0.009–0.013)

0.008 (0.005–0.010)

0.005

−0.08

0.28*

Rif

0.009 (0.007–0.011)

0.008 (0.001–0.006)

0.012 (0.010–0.015)

  1. aData are given in mean (95% confidence interval). bThe p value reflects the interaction between time and group from UNIANOVA. cThe beta coefficient and corresponding asterisk reflects the effect of rifaximin from linear regression with taxa at the indicated time point as dependent and treatment and baseline taxa as independent in a forced model. *P < 0.05, **P < 0.01.
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