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Table 1 Studies from which bacterial 16S rRNA sequence datasets included in our meta-analysis were sourced, in chronological order. For each study, bibliographical references (including PubMed ID; PMID), as well as helminth parasite(s) and vertebrate host species under investigation, sequence data repository and corresponding accession number, are provided. The numbers of samples from helminth-infected and -uninfected hosts from each study included in the meta-analysis, and of raw and high-quality reads subjected to (re)processing are also included. Results from dataset (re)processing using MGnify are available in ENA MGnify (https://www.ebi.ac.uk/metagenomics/) using the accession numbers provided

From: MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

PMID

Ref.

Host

Parasite

Type of infection

Type/site of sampling

16S rRNA hypervariable region

Pipeline

Ref. DB

ENA Accession

MGnify accession

Sample size

Raw read count

High-quality read count

Uninfected

Infected

Uninfected

Infected

Uninfected

Infected

23925654

[39]

Hamster (Mesocricetus auratus)

Opisthorchis viverrini

Experimental

Colon

V7-V9

CloVR-16S

RDP

PRJNA188112

MGYS00003431

4

4

179,193

189,399

149,780

157,744

24795483

[40]

Human (Homo sapiens)

Necator americanus

Experimental

Faeces

V1-V3 V3-V5

QIIME

Greengenes

PRJNA244913

MGYS00003191

8

8

106,832

103,428

86,737

83,780

26377648

[25]

Mouse (Mus musculus)

Nippostrongylus brasiliensis

Experimental

Small intestine

V3-V4

QIIME

Greengenes

PRJNA255974

MGYS00003192

10

9

77,836

71,752

77,836

71,752

25942314

[41]

Mouse

Trichuris muris

Experimental

Caecum, faeces

V4

QIIME

Greengenes

PRJEB6560

MGYS00001732

80

60

3,253,762

2,438,665

3,034,081

2,306,376

26150661

[35]

Wild yellow-necked mouse (Apodemus flavicollis)

Multiparasites

Natural

Stomach, small intestine, caecum, colon

V1-V3

QIIME

Greengenes

PRJEB8312

MGYS00003181

38

93

1,790,824

4,990,294

1,723,425

4,865,341

25934152

[42]

Cat (Felis catus) Dog (Canis lupus familiaris)

Multiparasites

Natural

Faeces

V4

MR DNA

Greengenes

PRJNA276586

MGYS00003432

14

48

587,641

2,002,497

500,349

1,657,742

27912797

[43]

Cat

Toxocara cati

Natural

Faeces

V3-V4

QIIME

Greengenes

PRJNA349988

MGYS00003433

21

24

4,121,930

6,206,792

3,365,062

4,999,740

27827438

[44]

Human

N. americanus

Experimental

Small intestine

V3-V4

QIIME

Greengenes

PRJNA316208

MGYS00003180

12

12

7,855,514

6,597,567

7,025,186

5,918,376

26853110

[36]

Alpine goat (Capra aegagrus hircus)

Haemonchus contortus

Experimental

Abomasum

V3-V4

QIIME

Greengenes

PRJNA518079

MGYS00004556

5

12

1,213,261

3,302,574

1,196,878

3,263,552

28892494

[45]

Human

Multiparasites

Natural

Faeces

V3-V4

QIIME

Greengenes

PRJEB21999

MGYS00003147

22

11

8,388,179

4,934,705

7,777,849

4,506,626

30353019

[46]

Human

Strongyloides stercoralis

Natural

Faeces

V3-V4

QIIME2

Greengenes

PRJEB28700

MGYS00003148

11

20

1,946,889

2,578,359

1,873,123

2,487,145

30104612

[28]

Mouse

Schistosoma mansoni

Experimental

Small and large intestine

V4

QIIME

Greengenes

PRJEB29315

MGYS00003460

40

40

1,405,122

1,369,830

1,405,120

1,369,830

30149004

[47]

Mouse

Metagonimus yokogawai

Experimental

Caecum

V3-V4

Mothur

EzBioCloud

PRJNA481634

MGYS00003893

7

8

3,335,612

1,405,858

3,194,586

1,351,499

30323795

[48]

Human

Clonorchis sinensis

Natural

Faeces

V3-V4

QIIME

Greengenes

PRJNA486437

MGYS00003894

42

47

5,010,319

5,131,918

4,814,736

4,997,256

30643702

[49]

Human

Multiparasites

Natural

Faeces

V4

Mothur

RDP

PRJNA487588

MGYS00003908

6

16

88,768

338,701

86,195

328,849