Skip to main content

Table 2 Differentially abundanta classes and genera between controls and CA cases, HP cases, and SSA cases

From: The gut microbiota in conventional and serrated precursors of colorectal cancer

  

CA cases vs. controls

HP cases vs. controls

SSA cases vs. controls

Taxon

Mean countb

Fold change (95% CI)

q c

Fold change (95% CI)

q c

Fold change (95% CI)

q c

Class

 Firmicutes; Bacilli

506.3

2.11 (1.6, 2.78)

2.45E−06

1.23 (0.78, 1.94)

1.00

0.79 (0.49, 1.3)

0.79

 Firmicutes; Erysipelotrichi

305.8

0.92 (0.79, 1.07)

0.57

1.1 (0.85, 1.41)

1.00

0.68 (0.52, 0.89)

0.09

 Proteobacteria; Gammaproteobacteria

394.4

1.81 (1.19, 2.76)

0.04

0.32 (0.16, 0.63)

0.02

0.43 (0.21, 0.88)

0.18

Genus

 Actinobacteria; Actinobacteria; Actinomycetales; Actinomycetaceae; Actinomyces

9.1

1.69 (1.32, 2.17)

0.0006

1.24 (0.82, 1.87)

0.99

1.07 (0.7, 1.64)

0.98

 Actinobacteria; Actinobacteria; Actinomycetales; Corynebacteriaceae; Corynebacterium

1.0

3.73 (1.88, 7.4)

0.002

0.78 (0.28, 2.22)

0.99

0.86 (0.3, 2.5)

0.98

 Firmicutes; Bacilli; Lactobacillales; Streptococcaceae; Streptococcus

422.2

2.38 (1.76, 3.21)

1.35E−06

1.26 (0.78, 2.05)

0.99

0.72 (0.43, 1.21)

0.65

 Firmicutes; Clostridia; Clostridiales; NA; NAd

2624.0

1.44 (1.26, 1.65)

6.31E−06

1.18 (0.94, 1.47)

0.92

0.98 (0.77, 1.25)

0.98

 Firmicutes; Clostridia; Clostridiales; [Mogibacteriaceae]; NAd

16.2

0.78 (0.65, 0.94)

0.06

0.85 (0.63, 1.15)

0.99

0.89 (0.65, 1.22)

0.88

 Firmicutes; Clostridia; Clostridiales; [Tissierellaceae]; Peptoniphilus

1.6

3.41 (1.83, 6.35)

0.002

0.55 (0.21, 1.46)

0.99

0.85 (0.32, 2.28)

0.98

 Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Anaerostipes

45.7

1.23 (0.98, 1.54)

0.30

1.96 (1.36, 2.84)

0.03

1.02 (0.69, 1.52)

0.98

 Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Dorea

216.1

1.19 (1.05, 1.35)

0.06

1.09 (0.88, 1.34)

0.99

1 (0.8, 1.25)

0.99

 Firmicutes; Clostridia; Clostridiales; Veillonellaceae; Phascolarctobacterium

115.4

1.91 (1.24, 2.96)

0.04

1.12 (0.57, 2.22)

0.99

0.85 (0.41, 1.76)

0.98

 Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; Coprobacillus

10.8

0.59 (0.39, 0.88)

0.07

0.36 (0.19, 0.68)

0.07

1.03 (0.53, 2.01)

0.98

 Proteobacteria; Betaproteobacteria; Burkholderiales; Alcaligenaceae; Sutterella

430.2

2.06 (1.52, 2.78)

8.60E−05

0.84 (0.52, 1.37)

0.99

0.97 (0.58, 1.65)

0.98

 Tenericutes; Mollicutes; RF39; NA; NAd

36.4

0.42 (0.22, 0.78)

0.06

1.1 (0.44, 2.77)

0.99

1.06 (0.4, 2.81)

0.98

  1. CA, conventional adenoma, HP hyperplastic polyp, SSA sessile serrated adenoma
  2. aDifferential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
  3. bCounts were normalized by dividing raw counts by DESeq2 size factors
  4. cFDR-adjusted p value. FDR adjustment was conducted at each level (i.e., class, genus) separately
  5. dNA: unclassified genus