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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

PMIDRef.HostParasiteType of infectionType/site of sampling16S rRNA hypervariable regionPipelineRef. DBENA AccessionMGnify accessionSample sizeRaw read countHigh-quality read count
UninfectedInfectedUninfectedInfectedUninfectedInfected
23925654[39]Hamster (Mesocricetus auratus)Opisthorchis viverriniExperimentalColonV7-V9CloVR-16SRDPPRJNA188112MGYS0000343144179,193189,399149,780157,744
24795483[40]Human (Homo sapiens)Necator americanusExperimentalFaecesV1-V3 V3-V5QIIMEGreengenesPRJNA244913MGYS0000319188106,832103,42886,73783,780
26377648[25]Mouse (Mus musculus)Nippostrongylus brasiliensisExperimentalSmall intestineV3-V4QIIMEGreengenesPRJNA255974MGYS0000319210977,83671,75277,83671,752
25942314[41]MouseTrichuris murisExperimentalCaecum, faecesV4QIIMEGreengenesPRJEB6560MGYS0000173280603,253,7622,438,6653,034,0812,306,376
26150661[35]Wild yellow-necked mouse (Apodemus flavicollis)MultiparasitesNaturalStomach, small intestine, caecum, colonV1-V3QIIMEGreengenesPRJEB8312MGYS0000318138931,790,8244,990,2941,723,4254,865,341
25934152[42]Cat (Felis catus) Dog (Canis lupus familiaris)MultiparasitesNaturalFaecesV4MR DNAGreengenesPRJNA276586MGYS000034321448587,6412,002,497500,3491,657,742
27912797[43]CatToxocara catiNaturalFaecesV3-V4QIIMEGreengenesPRJNA349988MGYS0000343321244,121,9306,206,7923,365,0624,999,740
27827438[44]HumanN. americanusExperimentalSmall intestineV3-V4QIIMEGreengenesPRJNA316208MGYS0000318012127,855,5146,597,5677,025,1865,918,376
26853110[36]Alpine goat (Capra aegagrus hircus)Haemonchus contortusExperimentalAbomasumV3-V4QIIMEGreengenesPRJNA518079MGYS000045565121,213,2613,302,5741,196,8783,263,552
28892494[45]HumanMultiparasitesNaturalFaecesV3-V4QIIMEGreengenesPRJEB21999MGYS0000314722118,388,1794,934,7057,777,8494,506,626
30353019[46]HumanStrongyloides stercoralisNaturalFaecesV3-V4QIIME2GreengenesPRJEB28700MGYS0000314811201,946,8892,578,3591,873,1232,487,145
30104612[28]MouseSchistosoma mansoniExperimentalSmall and large intestineV4QIIMEGreengenesPRJEB29315MGYS0000346040401,405,1221,369,8301,405,1201,369,830
30149004[47]MouseMetagonimus yokogawaiExperimentalCaecumV3-V4MothurEzBioCloudPRJNA481634MGYS00003893783,335,6121,405,8583,194,5861,351,499
30323795[48]HumanClonorchis sinensisNaturalFaecesV3-V4QIIMEGreengenesPRJNA486437MGYS0000389442475,010,3195,131,9184,814,7364,997,256
30643702[49]HumanMultiparasitesNaturalFaecesV4MothurRDPPRJNA487588MGYS0000390861688,768338,70186,195328,849
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