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Table 2 Summary statistics and metadata fields for the full dataset, partitioned for analyses by internal or external microbiomes of terrestrial and freshwater host organisms

From: Host-associated microbiomes are predicted by immune system complexity and climate

Metadata field

Description

Full dataset

Internal

External

Marine_external

Samples

sample runs included in this study

15,790

741

1193

266

sOTU

exact sequence variants (sub-operational taxonomic units)

175,709

17,544a

28,410a

5.077a

Publications (by doi)

digital object identifier accession number of published studies

51

23

13

6

Host Kingdom

https://www.itis.gov or http://www.eol.org

2

2

2

2

Host Phyllum

https://www.itis.gov or http://www.eol.org

8

3

2

4

Host Class

https://www.itis.gov or http://www.eol.org

16

7

5

8

Host Order

https://www.itis.gov or http://www.eol.org

80

26

23

27

Host Family

https://www.itis.gov or http://www.eol.org

177

65

52

45

Host Genus

https://www.itis.gov or http://www.eol.org

427

171

106

58

Host species name

full scientific name of host organism

654

204

239

78

Host taxid

taxa id number for the host species from NCBI Taxonomy Browser

640

197

236

78

Collection timestamp

date of sampling in DD/MM/YYYY format

1069

143

173

108

Countries

country from which samples were collected

46

26

18

20

Latitude range (deg)

latitude in decimal degrees

-43.53 to 60.17

-37.94 to 60.17

-39.84 to 52.28

-43.14 to 51.73

Longitude range (deg)

longitude in decimal degrees

-157.79 to 174.83

-121.79 to 152.31

-122.83 to 138.94

-157.79 to 174.83

Elevation range (m)

GPS coordinates used to estimate elevation if not stated in study

-490 to 3955

-3 to 3955

17 to 3837

-490 to 25

microbial_habitat_type

internal, external, and whole organism

3

internal and whole organism

external

external

internal_habitat_type

digestive-associated, oral, nasal, lung, reproductive, leaf internal, root internal, and n/a

8

1

n/a

n/a

digestive_habitat_type

foregut, fecal, cloacal, intestine, stomach, other and n/a

7

5

n/a

n/a

external_habitat_type

leaf surface, root surface, animal surface, gill, and n/a

5

n/a

4

3

surrounding_habitat

freshwater, marine, terrestrial

3

freshwater,terrestrial

freshwater,terrestrial

marine

lifestage

adult, juvenile/pupae, larvae, and infant

4

4

3

2

sampling_month

month when the samples were collected

12

12

12

12

trophic_diet

scaled 0=primary producers, 1=herbivore, 2=omnivore, 3=carnivore, 4=detritivore/scavenger

5

5

n/a

n/a

preservation_method

sample storage by direct freeze, ethanol, RNA-later, or other

4

4

3

2

extraction_method

name of DNA extraction kit

15

5

6

2

biogeo_realm

https://en.wikipedia.org/wiki/Biogeographic_realm

7

6

5

4

Worldclim2 bioclimatic variables

http://worldclim.org/version2; Fick et al 2017

n/a

8

8

n/a

Marine geophysical variables

http://marspec.weebly.com/about.html; Sbrocco et al 2013

n/a

n/a

n/a

11

Immune Complexity (binary)

inferred from host class information

n/a

2

2

n/a

Immune Complexity (ordinal)

scale based on Flajnik et al 2018;

n/a

1-9

1-9

n/a

  1. asOTUs after rarefaction at 1000 reads per sample