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Table 4 Summary of the LMM outcomes testing for the effects of host fish species, habitats, and diets on alpha diversity (Chao1, Shannon entropy, PD) and beta diversity (PCoA 1–5) of the gut and skin microbiome bacterial communities across 17 species of fish and three habitats of the Great Lakes

From: Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome

Model

Variables

Sum Sq

Mean Sq

F value

Gut samples

 Shannon entropy ~ Habitats + Diet + Fishname + (1|Locations), REML = FALSE

Diet

25.6

3.65

4.26***

 

Habitats

6.2

3.10

3.61*

 

Fish species

16.4

1.64

1.91*

 Chao1 ~ Habitats + Fishname + (1|Locations), REML = FALSE

Habitats

4.7

0.27

4.44***

Fish species

1

0.51

8.25***

 PD ~ Fishname + (1|Locations), REML = FALSE

Fish species

3.3

0.17

3.97***

 Axis.1 ~ Habitats + Diet + Fishname + (1|Locations), REML = FALSE

Diet

3630

518

1.98

Fish species

13,546

1354

5.17***

Habitats

1095

547

2.09

 Axis.2 ~ Diet + (1|Locations), REML = FALSE

Diet

11,736

1676

7.56***

 Axis.3 ~ Habitats + Fishname + (1|Locations), REML = FALSE

Habitats

2686

1343

9.97***

Fish species

1108

651

4.84***

 Axis.4 ~ Fishname + (1|Locations), REML = FALSE

Fish species

16,933

891.22

3.40***

 Axis.5 ~ Fishname + (1|Locations), REML = FALSE

Fish species

5303

279.14

3.27***

Skin samples

 Shannon entropy ~ Diet + (1|Locations), REML = FALSE

Diet

6.3

0.79

0.81

 Chao1 ~ Fishname + (1|Locations), REML = FALSE

Fish species

1.2

0.07

1.20

 PD ~ Diet + Fishname + Habitats + (1|Locations), REML = FALSE

Diet

0.46

0.05

1.30

 

Fish species

0.44

0.05

1.36

 Axis.1 ~ Fishname + (1|Locations), REML = FALSE

Fish species

13,286

830.37

3.99***

 Axis.2 ~ Diet + Fishname + (1|Locations), REML = FALSE

Diet

4932

616.50

5.04***

 

Fish species

4037

504.69

4.13***

 Axis.3 ~ Habitats + Diet + Fishname + (1|Locations), REML = FALSE)

Diet

954

744.36

6.13***

 

Habitats

1904

952.19

7.85***

 

Fish species

1986

331.05

2.72*

 Axis.4 ~ Fishname + Weight + (1|Locations), REML = FALSE)

Fish species

19,372

1210.8

14.32***

 Axis.5 ~ Fishname + (1|Locations), REML = FALSE)

Fish species

7985

499.06

4.92***

  1. Significance codes: 0.01 < P ≤ 0.05*, 0.001 < P ≤ 0.01**, P ≤ 0.001***
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Microbiome

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