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 |