Table 1 Human stool shotgun metagenome datasets used in this study
Author (Last name) | Publication year | Total from study (n) | Healthy (n) | Non-healthy (n) | Disease (n)a | Sequencing platform | Geography (Country) |
|---|---|---|---|---|---|---|---|
Ananthakrishnan | 2017 | 64 | 0 | 64 | CD (24), UC (40) | Illumina NextSeq 500 | United States |
Ang | 2021 | 22 | 22 | 0 | – | Illumina NovaSeq 6000 | United States |
Asnicar | 2021 | 568 | 568 | 0 | – | Illumina NovaSeq 6000 | United Kingdom/United States |
Backhed | 2015 | 100 | 100 | 0 | – | Illumina HiSeq 2000 | Denmark |
Costea | 2017 | 169 | 169 | 0 | – | Illumina HiSeq 2000 | Germany/Kazakhstan |
D’Souza | 2021 | 128 | 128 | 0 | – | Illumina NextSeq 500 | Netherlands |
Davies | 2020 | 44 | 0 | 44 | T2D (44) | Illumina HiSeq 2000 | New Zealand |
De Filippis | 2019 | 99 | 99 | 0 | – | Illumina HiSeq 1500/Illumina NextSeq 500 | Italy |
Dhakan | 2019 | 47 | 47 | 0 | – | Illumina NextSeq 500 | India |
Feng | 2015 | 46 | 0 | 46 | CRC (46) | Illumina HiSeq 2000 | Austria |
Franzosa | 2018 | 213 | 56 | 157 | CD (84), UC (73) | Illumina HiSeq 2000 | Netherlands/United States |
Gu | 2017 | 94 | 0 | 94 | T2D (94) | Illumina HiSeq 2500 | China |
Gupta | 2020 | 49 | 0 | 49 | RA (49) | Illumina HiSeq 4000 | United States |
He | 2017 | 86 | 40 | 46 | CD (46) | Illumina HiSeq 2000 | China |
Huttenhower; Lloyd-Priceb | 2012; 2017 | 507 | 507 | 0 | – | Illumina HiSeq 2000/Illumina Genome Analyzer II | United States |
Jacobson | 2021 | 82 | 82 | 0 | – | Illumina NovaSeq 6000 | Burkina Faso |
Jie | 2017 | 322 | 108 | 214 | ACVD (214) | Illumina HiSeq 2000 | China |
Karlsson | 2013 | 53 | 0 | 53 | T2D (53) | Illumina HiSeq 2000 | Sweden |
Kim | 2021 | 61 | 61 | 0 | – | Illumina HiSeq 4000 | South Korea |
Le Chatelier | 2013 | 88 | 88 | 0 | – | Illumina HiSeq 2000/Illumina Genome Analyzer II/Illumina Genome Analyzer IIx | Denmark |
Liu | 2016 | 110 | 110 | 0 | – | Illumina HiSeq 4000 | China/Mongolia |
Lloyd-Price | 2019 | 86 | 25 | 61 | CD (39), UC (22) | Illumina HiSeq 2000 | United States |
Lokmer | 2019 | 37 | 37 | 0 | – | Illumina HiSeq 2000 | Cameroon |
Loomba | 2017 | 86 | 0 | 86 | NAFLD (86) | Illumina HiSeq 2500 | United States |
Mehta | 2018 | 301 | 301 | 0 | – | Illumina HiSeq 2000 | United States |
Nielsen | 2014 | 159 | 82 | 77 | CD (12), UC (65) | Illumina HiSeq 2000/Illumina Genome Analyzer II/Illumina Genome Analyzer IIx | Denmark/Spain |
Obregon-Tito | 2015 | 20 | 20 | 0 | – | Illumina HiSeq 2500 | Peru/United States |
Pasolli | 2019 | 142 | 142 | 0 | – | Illumina HiSeq 2500 | Ethiopia/Madagascar |
Qi | 2019 | 43 | 43 | 0 | – | Illumina HiSeq 2500 | China |
Qin | 2012 | 369 | 183 | 186 | T2D (186) | Illumina Genome Analyzer II | China |
Qin | 2014 | 287 | 135 | 152 | LC (152) | Illumina HiSeq 2000 | China |
Rettedal | 2021 | 35 | 35 | 0 | – | Illumina HiSeq 2500 | New Zealand |
Roager | 2019 | 50 | 50 | 0 | – | Illumina HiSeq 2000 | Denmark |
Schirmer | 2016 | 385 | 385 | 0 | – | Illumina HiSeq 2000 | Netherlands |
Schirmer | 2018 | 83 | 18 | 65 | CD (39), UC (26) | Illumina HiSeq 2000 | United States |
Smits | 2017 | 38 | 38 | 0 | – | Illumina HiSeq 4000 | Tanzania |
Sun | 2021 | 42 | 42 | 0 | – | Illumina HiSeq 4000 | United States |
Tett | 2019 | 110 | 110 | 0 | – | Illumina HiSeq 2000/Illumina HiSeq 2500 | Tanzania/Ghana |
Thomas | 2019 | 160 | 61 | 99 | CRC (99) | Illumina HiSeq 2500 | Italy/Japan |
Ventura | 2019 | 48 | 24 | 24 | MS (24) | Illumina HiSeq 4000 | United States |
Vogtmann | 2016 | 81 | 30 | 51 | CRC (51) | Illumina HiSeq 2000 | United States |
Wen | 2017 | 200 | 105 | 95 | AS (95) | Illumina HiSeq 2000 | China |
Weng | 2019 | 79 | 15 | 64 | CD (40), UC (24) | Illumina HiSeq X Ten | China |
Wirbel | 2019 | 55 | 33 | 22 | CRC (22) | Illumina HiSeq 4000 | Germany |
Xie | 2016 | 130 | 130 | 0 | – | Illumina HiSeq 2000 | United Kingdom |
Yachida | 2019 | 217 | 0 | 217 | CRC (217) | Illumina HiSeq 2500 | Japan |
Yang | 2020 | 180 | 88 | 92 | CRC (92) | Illumina HiSeq X Ten | China |
Yang | 2021 | 194 | 97 | 97 | CRC (97) | Illumina NovaSeq 6000 | China |
Yassour | 2018 | 42 | 42 | 0 | – | Illumina HiSeq 2500 | Finland |
Yu | 2015 | 128 | 53 | 75 | CRC (75) | Illumina HiSeq 2000 | China |
Zeevi | 2015 | 900 | 900 | 0 | – | Illumina HiSeq 2500/Illumina HiSeq 2500/Illumina MiSeq | Israel |
Zeller | 2014 | 135 | 45 | 90 | CRC (90) | Illumina HiSeq 2000 | France/Germany |
Zhang | 2015 | 163 | 61 | 102 | RA (102) | Illumina HiSeq 2000 | China |
Zhu | 2021 | 132 | 32 | 100 | GD (100) | Illumina HiSeq 4000 | China |
