Table 2 LEfSe analysis for bacterial taxa during antibiotic therapy in sputa samples from all 14 study patients.

From: Changes in sputum microbiota during treatment for nontuberculous mycobacterial pulmonary disease

Taxon name

Antibiotics start (%)

(n = 14)

1 mo. (%)

(n = 10)

3 mo. (%)

(n = 10)

6 mo. (%)

(n = 12)

12 mo. (%)

(n = 7)

LDA

effect size

p-value

Phylum

Fusobacteria

5.11

1.47

4.42

4.08

4.69

4.28

0.044

Spirochaetesb

1.06

0.02

0.09

0.12

0.06

3.70

 < 0.001a

Genus

Saccharimonasb

5.10

0.26

0.17

2.48

1.47

4.38

 < 0.001a

Porphyromonasb

4.94

0.53

2.70

1.06

1.70

4.28

0.027

Alloprevotella

1.08

0.02

0.89

0.78

1.26

3.92

0.049

Aggregatibacterb

0.59

0.00

0.00

0.90

0.04

3.69

0.001a

Treponemab

0.98

0.02

0.09

0.12

0.06

3.67

 < 0.001a

Dialisterb

0.35

0.01

0.03

0.16

0.13

3.24

0.001a

Parvimonasb

0.31

0.00

0.00

0.01

0.00

3.20

 < 0.001a

Species

       

Veillonella dispar

5.89

13.01

11.98

8.48

6.89

4.49

0.044

Porphyromonas endodontalisb

3.19

0.06

0.01

0.01

0.01

4.13

 < 0.001a

Fusobacterium periodonticum group

0.71

0.05

1.43

1.92

2.24

4.06

0.016

Fusobacterium nucleatum groupb

2.18

1.12

0.53

0.94

0.43

3.94

0.014

Streptococcus sinensis group

0.70

2.36

1.97

1.88

2.13

3.90

0.031

Pseudomonas aeruginosa group

0.01

0.00

0.00

0.01

0.93

3.70

0.022

Aggregatibacter aphrophilusb

0.34

0.00

0.00

0.90

0.04

3.69

0.006

Rothia aeriab

0.70

0.04

0.19

0.11

0.00

3.57

0.002

Porphyromonas gingivalisb

0.71

0.07

0.00

0.00

0.00

3.50

 < 0.001a

Haemophilus influenzae groupb

0.45

0.00

0.00

0.02

0.07

3.39

0.009

Actinomyces graevenitziib

0.47

0.01

0.00

0.15

0.26

3.36

0.043

Treponema medium groupb

0.34

0.00

0.04

0.02

0.01

3.25

0.003

Neisseria elongata groupb

0.31

0.00

0.00

0.00

0.00

3.19

 < 0.001

Rothia dentocariosab

0.36

0.35

0.08

0.17

0.00

3.19

0.015

Aggregatibacter segnisb

0.24

0.00

0.00

0.00

0.00

3.11

0.019

Treponema denticolab

0.21

0.00

0.01

0.08

0.00

3.04

0.003

Dialister pneumosintesb

0.17

0.00

0.03

0.00

0.01

3.01

 < 0.001

Parvimonas micrab

0.19

0.00

0.00

0.01

0.00

3.00

0.001

  1. LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis. LEfSe analysis included all taxa, including taxa with proportions < 1%. Taxa with an LDA effect size value > 3 were described. aAdjusted p–value < 0.05; the Benjamini–Hochberg false discovery rate was applied to correct for multiple testing, and values of less than 0.05 were considered significant. bThis indicates that the proportions of the taxa decreased over the course of antibiotic treatment. Bold font indicates that the proportions of the taxa increased over the course of antibiotic treatment.
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