Table 1 Linkage analysis for microbial traits in the combined, diet-specific, and sex-specific models

Phylum

ASV ID

Maximum taxonomic information

Model

Left marker

Top marker

Right marker

QTL identifier

Chr

Start (Mb)

Actinobacteria

87f436ffd9de6eb9451032c6ab0c3a7e

D_5__Coriobacteriaceae UCG-002

Combined y ~ m + sex*diet

JAX00664614

backupUNC08018

UNC080237919

Asvq1

8

31.0

Actinobacteria

11c66263fce8e3ed0b6f024451a3e4f6

D_5__Enterorhabdus

Combined y ~ m + sex*diet

JAX00160641

JAX00668481

UNC080591069

Asvq2

8

36.1

Bacteroidetes

b638b1c18c30ded1d2df7558b49ee113

D_4__Muribaculaceae;D_5__uncultured bacterium

Combined y ~ m + sex*diet

UNC140463041

backupUNC14027

UNC140475528

Asvq3

14

74.3

Bacteroidetes

4e591c10e196ae155d20629952d85e34

D_4__Muribaculaceae;D_5__uncultured bacterium

Combined y ~ m + sex*diet

JAX00430230

UNC170287409

backupUNC1700

Asvq4

17

5.6

Bacteroidetes

2cc64f7f2dcfc098d317347e8d3323aa

D_4__Muribaculaceae;D_5__uncultured bacterium

Combined y ~ m + sex*diet

JAX00430230

UNC170287409

backupUNC1700

Asvq5

17

5.6

Bacteroidetes

7738a54ecc2a9056c502e19953a34adb

D_5__Alistipes

Combined y ~ m + sex*diet

backupJAX00343

UNC120435288

backupUNC1202

Asvq6

12

101.9

Bacteroidetes

ecfbbfd673f8a3e1c34718d968e6b069

D_5__Rikenella

Combined y ~ m + sex*diet

JAX00271510

UNC010409945

UNC010872195

Asvq7

1

151.9

Bacteroidetes

4cd0cd5a04c3abd39385cc354976ff4d

D_5__Rikenellaceae RC9 gut group

Combined y ~ m + sex*diet

UNC110054975

UNC110464797

JAX00311806

Asvq8

11

42.9

Firmicutes

8ab9ece30db28dd09f0e76f426a709c9

D_5__Streptococcus

Combined y ~ m + sex*diet

UNC080433052

UNC080671076

backupUNC0803

Asvq9

8

108.8

Firmicutes

8ab9ece30db28dd09f0e76f426a709c9

D_5__Streptococcus

Combined y ~ m + sex*diet

UNC080237919

JAX00671644

UNC080301746

Asvq10

8

58.6

Firmicutes

be6ee4f4c44adbe6834438d109b75853

D_5__GCA-900066575

Combined y ~ m + sex*diet

JAX00172457

JAX00173057

UNC090299874

Asvq11

9

68.4

Firmicutes

403f6d9b8d155413c40a76568324cf95

D_5__Lachnoclostridium

Combined y ~ m + sex*diet

JAX00005015

UNC010587748

backupUNC0102

Asvq12

1

70.1

Firmicutes

a122e3f0437bb8880bab1660d8e0c289

D_5__Lachnoclostridium

Combined y ~ m + sex*diet

JAX00042454

UNC130039434

backupUNC1305

Asvq13

13

21.2

Firmicutes

56f81e7c72e8c90daafad2ffad595810

D_5__Romboutsia

Combined y ~ m + sex*diet

UNC050381284

UNC050154313

backupUNC0506

Asvq14

5

66.1

Firmicutes

56f81e7c72e8c90daafad2ffad595810

D_5__Romboutsia

Combined y ~ m + sex*diet

UNC130005651

backupJAX00351

4UNC130039434

Asvq15

13

5.4

Firmicutes

b89e2f23a606787577644904f2b6aed3

D_5__Ruminiclostridium 9

Combined y ~ m + sex*diet

UNC_rs3360795

8backupUNC01062

backupJAX00013

Asvq16

1

138.0

Proteobacteria

18f60eae2c3a26bab8efa0f9823e31b4

D_5__Bilophila

Combined y ~ m + sex*diet

UNC010463165

UNC010409945

UNC010872195

Asvq17

1

144.5

Proteobacteria

18f60eae2c3a26bab8efa0f9823e31b4

D_5__Bilophila

Combined y ~ m + sex*diet

backupUNC0900

6JAX00173057

UNC090299874

Asva18

9

42.3

Phylum

ASV barcode

Maximum taxonomic information

Model

Left marker

Top marker

Right marker

QTL identifier

Chr

Start (Mb)

Bacteroidetes

4e591c10e196ae155d20629952d85e34

D_4__Muribaculaceae;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

JAX00351389

JAX00042454

UNC130039434

Asvq19

13

18.2

Bacteroidetes

2cc64f7f2dcfc098d317347e8d3323aa

D_4__Muribaculaceae;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

UNC130013342

backupUNC13002

UNC130039434

Asvq20

13

12.5

Bacteroidetes

34a3b7dc9cbbb1e182c7f1085f289288

D_4__Muribaculaceae;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

UNC140463041

UNC140471593

UNC140475528

Asvq21

14

74.3

Bacteroidetes

b638b1c18c30ded1d2df7558b49ee113

D_4__Muribaculaceae;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

UNC140463041

backupUNC14027

UNC140401510

Asvq22

14

74.3

Bacteroidetes

2cc64f7f2dcfc098d317347e8d3323aa

D_4__Muribaculaceae;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

JAX00430230

UNC170009437

backupUNC1700

Asvq5

17

5.6

Bacteroidetes

d6554036e1a2bd9f0586972111720879

D_5__Rikenellaceae RC9 gut group

Diet specific y ~ sex + diet*m

UNC160227296

UNC160235091

JAX00429228

Asvq23

16

72.8

Bacteroidetes

a371498f7ad6d1368940364ff67938b6

D_5__Parabacteroides

Diet specific y ~ sex + diet*m

UNC160105631

JAX00427104

JAX00429228

Asvq24

16

72.0

Firmicutes

313437e365ff76e6d19ef1ff002d7fb9

D_5__Lactobacillus

Diet specific y ~ sex + diet*m

UNC080206141

backupUNC08155

UNC080368796

Asvq25

8

43.4

Firmicutes

8ab9ece30db28dd09f0e76f426a709c9

D_5__Streptococcus

Diet specific y ~ sex + diet*m

JAX00165590

UNC080671076

backupUNC0803

Asvq9

8

102.4

Firmicutes

8ab9ece30db28dd09f0e76f426a709c9

D_5__Streptococcus

Diet specific y ~ sex + diet*m

UNC080206141

JAX00671644

UNC080301746

Asvq10

8

43.4

Firmicutes

fc35a7e21e6a077a01e39949e08917d2

D_4__Clostridiales vadinBB60 group;D_5__uncultured bacterium

Diet specific y ~ sex + diet*m

backupUNC0600

0JAX00137865

JAX00606563

Asvq26

6

4.9

Firmicutes

6f2c4135b8fa13845d9bfdcab8aafeb2

D_4__Lachnospiraceae;D_5__uncultured

Diet specific y ~ sex + diet*m

UNC010667356

UNC010674652

UNC010475128

Asvq27

1

181.1

Phylum

ASV barcode

Maximum taxonomic information

Model

Left marker

Top marker

Right marker

QTL identifier

Chr

Start (Mb)

Bacteroidetes

7738a54ecc2a9056c502e19953a34adb

D_5__Alistipes

Sex specific y ~ diet + sex*m

UNC130013342

backupJAX00351

4UNC130039434

Asvq28

13

12.5

Phylum

Top (Mb)

End (Mb)

LOD §

Effect of B6/FVB alleles §

Effect of FVB/FVB alleles §

Top marker (% variance explained)

Sex (% variance explained)

Diet (% variance explained)

Sex * Diet (% Variance Explained)

Actinobacteria

41.0

58.6

5.88^a

 − 15.95

 − 30.70

5.79***

4.88***

2.37***

0.26

Actinobacteria

51.0

62.8

4.66^b

 − 4.95

18.19

4.45***

1.98**

8.59***

0.01

Bacteroidetes

76.0

83.1

4.16^b

 − 4.74

16.50

3.41***

0.07

22.92***

 < 0.01

Bacteroidetes

7.1

19.6

4.97^b

8.82

26.77

4.26***

0.2

19.09***

0.11

Bacteroidetes

7.1

19.6

4.32^b

 − 3.12

18.84

3.98***

0.05

13.67***

0.12

Bacteroidetes

105.1

116.6

5.15^b

2.79

19.26

3.72***

1.57**

25.28***

5.04***

Bacteroidetes

180.2

193.3

4.05^b

14.52

26.93

4.08***

1.37*

5.83***

0.11

Bacteroidetes

47.3

56.3

4.17^b

 − 17.71

 − 20.93

3.57***

0.04

19.7***

0.13

Firmicutes

117.1

122.5

5.44^a

3.49

20.68

3.14***

0.91**

43.41***

1.57***

Firmicutes

69.3

84.1

5.03^b

11.74

20.72

2.92***

0.97**

43.19***

1.29**

Firmicutes

76.4

80.8

4.5^b

 − 18.84

 − 25.37

4.52***

0.78

6.08***

0.04

Firmicutes

102.4

115.9

4.41^b

5.60

 − 18.11

4.25***

1.13*

6.65***

2.75***

Firmicutes

37.5

48.5

4.05^b

 − 18.36

 − 4.08

3.38***

0.08

24.50***

0.23

Firmicutes

96.8

119.7

4.13^b

9.48

22.51

3.67***

7.26***

5.22***

4.21***

Firmicutes

18.4

37.5

4.17^b

 − 9.90

 − 23.14

3.72***

7.16***

5.22***

4.23***

Firmicutes

155.9

186.3

4.25^b

21.51

13.00

3.98***

1.85**

10.65***

1.19*

Proteobacteria

180.2

193.3

4.13^b

19.85

19.71

3.69***

0.15

17.47***

0.12

Proteobacteria

76.4

80.8

4.49^b

 − 15.24

 − 24.35

3.97***

0.16

17.81***

0.11

Phylum

Top (Mb)

End (Mb)

LOD ⌘

Effect of

American B6/FVB

alleles ⌘

Effect of

American FVB/FVB alleles ⌘

Top marker (% variance explained)

Sex (% variance

explained)

Diet (% variance explained)

Top marker * diet (% variance explained)

Bacteroidetes

21.2

37.5

4.42^b

 − 41.61

 − 22.57

2.04**

0.19

19.27***

3.72***

Bacteroidetes

19.7

37.5

4.23^b

 − 39.27

 − 42.36

2.65**

0.05

13.85***

3.78***

Bacteroidetes

77.5

83.1

4.28^b

2.04

37.54

2.42***

0.18

37.42***

2.74***

Bacteroidetes

76.0

79.3

4.25^b

 − 6.75

35.00

3.41***

0.07

22.92***

3.34***

Bacteroidetes

6.2

19.6

4.27^b

4.24

44.19

3.79***

0.05

13.67***

3.77***

Bacteroidetes

79.6

96.5

4.03^b

 − 43.76

 − 38.57

2.02**

0.8

10.28***

3.76***

Bacteroidetes

87.6

96.5

4.04^b

 − 30.20

 − 51.51

0.86

0.02

3.91***

4.11***

Firmicutes

80.5

97.8

4.13^b

24.13

52.27

0.9

2.06**

1.73**

4.22***

Firmicutes

117.1

122.5

5.98^a

4.91

42.32

3.14***

0.91**

43.41***

3.34***

Firmicutes

69.3

84.1

4.33^b

24.52

39.92

2.92***

0.97**

43.19***

2.45***

Firmicutes

10.5

33.5

4.33^b

 − 19.90

 − 52.94

0.4

0.1

1.51**

4.56***

Firmicutes

187.2

191.6

4.71^b

 − 41.34

 − 50.88

2.33**

1.15*

12.54***

4.21***

Phylum

Top (Mb)

End (Mb)

LOD ⌘

Effect of

male B6/FVB

alleles ⌘

Effect of male FVB/FVB alleles ⌘

Top marker (% variance explained)

Sex (% variance

explained)

Diet (% variance

explained)

Top marker * sex (% variance explained)

Bacteroidetes

18.4

37.5

5.72^a

 − 15.36

32.02

0.44

1.66

25.35***

4.41***