Skip to main content

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