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Table 3 Estimation (%) and enrichment of motility, stress, antibiotics and toxic resistance genes in wastewater genomes

From: Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system

Subsystem

Gene

n

% of genomes with gene†

q-value*

Odds ratio

TP

BP

TP/BP

BP/TP

Single-copy genes ‡

 

5

100

100

ns

1.0

1.0

Heavy metal resistance

       

Arsenate reductase (glutaredoxin)

arsC

1

50

17

0.000

2.8

0.4

Arsenic efflux pump protein

arsB

1

24

10

0.000

2.4

0.4

Arsenic resistance protein

arsH

1

37

5

0.000

7.4

0.1

Arsenical pump-driving (ATPase)

arsA

1

15

28

0.000

0.5

1.9

Arsenite oxidase

aoxB

1

10

8

ns

1.3

0.8

Cadmium-transporting (ATPase)

cadA

1

3

14

0.000

0.2

4.5

Chromate transport protein

chrA

1

40

50

0.034

0.8

1.3

Copper-translocating P-type (ATPase)

copA

1

>100

>100

ns

1.1

0.9

CZC resistance protein

czcD

1

>100

75

0.006

1.6

0.6

Mercuric reductase

merA

1

80

33

0.000

2.4

0.4

Antibiotics & toxicity resistance

       

Beta-lactamase

ampC

1

>100

>100

0.000

1.8

0.6

Beta-lactamase (MRSA)

mecA

1

0

0

nd

0

0

Dihydrofolate reductase

folA

1

80

47

0.034

1.6

0.6

Pterin binding enzyme

sul

1

83

66

0.003

1.3

0.8

Multidrug efflux system protein

acrB

1

>100

>100

0.000

1.4

0.7

Dioxygenase (Bleomycin resistance)

bleO

1

>100

>100

0.000

2.3

0.4

Aminoglycoside-3’-adenylyltransferase

aadA

1

40

>100

0.000

0.3

3.2

Antiholin-like protein (murein hydrolase)

lrgA

1

4

37

0.000

0.1

9.6

Antiholin-like protein (murein hydrolase)

lrgB

1

17

39

0.001

0.4

2.5

Streptomycin adenylyltransferase

ant1

1

0

3

0.031

0.0

nd

Drug resistance transporter

cflA

1

61

37

0.000

1.6

0.6

MFS transporter (DHA2)

emrB

1

>100

57

0.000

3.6

0.3

D-alanine--D-alanine ligase

vanA

1

76

81

ns

0.9

1.1

Multi antimicrobial extrusion protein

norM

1

6

40

0.000

0.2

6.6

Multidrug efflux transporter

mexF

1

16

6

0.043

2.7

0.4

RND efflux system (transporter)

cmeB

1

53

>100

0.000

0.5

2.1

RND efflux system (membrane protein)

cmeA

1

18

46

0.005

0.4

2.5

RND efflux system (lipoprotein)

cmeC

1

19

60

0.020

0.3

3.1

Protein secretion systems

       

Type I

--

1

nd

nd

0.000

1.5

0.7

Type III

--

10

nd

nd

0.001

0.8

1.8

Type IV

--

5

nd

nd

0.000

3.1

1.4

Type V

--

3

nd

nd

0.001

1.7

0.6

Type VI

--

10

nd

nd

0.000

2.8

0.7

Motility & Chemotaxis systems

       

motility/chemotaxis

--

74

nd

nd

0.000

0.7

2.7

Stress systems

       

stress response

--

276

nd

nd

0.000

2.2

1.8

  1. *Indicate components that are significantly different between the two samples (q < 0.05) based on the Fisher’s exact test using corrected q-values (Storey’s FDR multiple test correction approach).
  2. ‡Housekeeping genes: gyrA, gyrB, recA, rpoA and rpoB.
  3. †Direct comparison between the frequency of different functional genes, either within or between metagenomes, was not established since length and copy number of the gene was not incorporated in the formula.
  4. TP: top pipe.
  5. BP: bottom pipe.
  6. NS: not significant.
  7. ND: not determine.
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BMC Microbiology

ISSN: 1471-2180

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