Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Gammaproteobacteria Gammaproteobacteria Alphaproteobacteria Gammaproteobacteria Alphaproteobacteria Alphaproteobacteria Deltaproteobacteria Deltaproteobacteria Gammaproteobacteria Gammaproteobacteria Betaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Clostridia Clostridia Clostridia Betaproteobacteria Gammaproteobacteria Gammaproteobacteria Clostridia Clostridia Clostridia Clostridia Clostridia Gammaproteobacteria Clostridia Clostridia Clostridia Clostridia Epsilonproteobacteria Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia

Corresponding class aautrla02 .%01 .%02 .%04 .%0.2% 0.1% 0.4% 0.3% 0.2% 0.3% 0.1% 0.1% 0.2% 0.2% Neisseria Parasutterella Sutterella Kerstersia Herbaspirillum Oxalobacter Cupriavidus Ralstonia Terasakiella autla2.9% 14.4% Raoultella Klebsiella Escherichia/Shigella Caenispirillum Succinivibrio Kiloniella Methylobacterium Desulfovibrio Geopsychrobacter 0.1% Acinetobacter Rhodanobacter Microvirgula Bradyrhizobium Mesorhizobium Novosphingobium Prosthecomicrobium uioocs05 .%01 .%01 .%00 .%0.1% 0.1% 0.0% 0.1% 0.1% 0.1% 0.1% 0.1% 0.5% Butyricicoccus Ruminococcus Subdoligranulum Laribacter ampiu 9.2% Haemophilus neoatr1.6% Enterobacter ctvbi .%14 .%15 .%17 .%15 .%00 .%18 .%16 .%16 .%19 .%00 .%24 .%09 1.6% 4.1% 0.9% 2.8% 2.2% 1.6% 2.4% 1.1% 1.5% 2.2% 0.0% 0.0% 1.5% 3.5% 1.9% 3.0% 2.1% 2.4% 2.7% 1.7% 0.1% 1.6% 2.7% 2.0% 0.1% 2.5% 1.8% 2.5% 0.1% 1.6% 2.6% 2.4% 0.1% 1.6% 4.1% 2.0% 0.1% 1.8% 3.4% 0.7% 0.0% 0.8% 2.9% 1.4% 0.1% 0.0% 0.0% 2.3% 0.1% 0.0% 0.1% 0.7% 3.2% 0.1% 1.5% 2.1% 1.8% 1.2% 0.4% 1.7% 0.3% 1.7% 1.3% 0.9% 0.2% 1.7% 4.6% 1.3% 0.1% 1.5% 4.0% 1.4% 0.3% 0.9% 2.9% 1.4% 0.7% 1.4% 2.2% 1.3% 1.5% 0.1% 0.1% 2.7% 0.1% 0.1% 0.1% 0.1% Ethanoligenens Anaerotruncus Acetivibrio Lactonifactor Robinsoniella Yersinia etsrpoocs01 .%11 .%12 .%17 .%10 .%00 .%01 .%15 .%16 .%10 .%12 .%00 0.0% 0.4% 0.0% 0.4% 1.8% 0.0% 1.2% 0.0% 0.8% 1.2% 1.0% 1.9% 1.2% 1.7% 1.6% 1.7% 1.6% 1.7% 1.5% 1.2% 0.0% 1.2% 0.1% 1.0% 1.0% 0.0% 0.0% 0.0% 1.0% 1.2% 1.0% 1.2% 0.3% 1.3% 1.7% 0.9% 1.1% 0.7% 1.2% 1.2% 0.9% 0.4% 1.1% 0.1% 1.0% 0.1% Peptostreptococcus Clostridium orccu 23 47 53 35 32 44 63 39 46 .%1.%1.%1.%1.%1.%1.%1.%1.%1.%64 38 73 33 12. 13.3% 0.5% 17.3% 13.8% 0.3% 6.4% 0.7% 1.0% 13.9% 0.7% 14.0% 1.1% 13.8% 11.4% 0.8% 12.8% 0.4% 13.1% 10.3% 0.0% 12.4% 0.3% 12.9% 1.3% 0.0% 14.6% 0.0% 13.9% 0.0% 16.3% 14.4% 0.0% 13.2% 13.5% 0.4% 15.3% 0.0% 14.7% 12.3% 0.1% 0.5% 0.1% Coprococcus Sporacetigenium Helicobacter Campylobacter Acetanaerobacterium Hydrogenoanaerobacterium oe .%41 .%39 .%45 .%37 .%03 .%47 .%54 .%46 .%38 .%01 .%78 .%47 4.6% 4.7% 4.9% 7.8% 5.8% 6.3% 0.1% 10.7% 11.0% 6.4% 3.6% 6.7% 3.8% 0.1% 4.6% 4.6% 5.4% 6.4% 5.4% 11.0% 9.0% 3.3% 5.0% 4.7% 3.9% 4.2% 3.1% 0.3% 9.6% 9.2% 4.3% 10.1% 3.7% 0.1% 3.8% 4.5% 9.6% 4.2% 14.3% 3.9% 13.1% 11.6% 5.0% 10.9% 4.1% 7.6% 0.6% 7.3% 9.6% 0.9% Sporobacter Faecalibacterium Dorea Marvinbryantia

Genus

CDI set 1 ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐ ‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐ ‐‐ ‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐ ‐ Recepient 0.0% 0.1% .%01 .%02 .%01 .%01 .%13 .%01 .%01 .%01 .%0.0% 0.0% 0.1% 0.1% 0.1% 0.0% 0.1% 0.1% 1.3% 0.2% 0.1% 0.1% 0.1% 0.2% 0.2% 0.1% 0.1% 1.4% 0.3% .%24 .%14 .%24 .%08 .%17 .%13 .%08 .%14 .%1.5% 1.6% 1.4% 1.3% 0.8% 0.6% 1.3% 2.3% 1.7% 0.0% 0.8% 1.5% 2.4% 1.5% 1.4% 1.4% 2.4% 1.8% .%20 .%24 .%33 .%42 .%25 .%22 .%31 .%30 .%29 .%27 .%45 .%4.2% 4.1% 4.5% 3.2% 2.7% 0.0% 2.9% 3.3% 3.0% 2.3% 3.1% 3.8% 2.2% 2.5% 2.5% 0.3% 4.2% 2.5% 3.3% 2.8% 2.4% 3.3% 2.0% 3.1% .%01 .%00 .%01 .%0.0% 0.0% 0.1% 0.1% 0.0% 0.1% 0.1% 0.0% ‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐‐‐‐‐‐ ‐ ‐‐ Donor .%12 .%1.9% 2.0% 0.0% 1.2% 1.9% 0.0% 0.5% 0.0% 0.0% ‐‐‐ ‐‐ ‐‐‐‐‐‐‐ ‐ ‐ Day 3 .%0.0% 0.2% .%0.0% 1.2% 0.0% 0.0% 0.0% ‐‐‐‐‐ ‐‐ ‐ ‐‐ ‐ Day 7 .%0.0% 0.0% .%02 0.0% 0.2% 0.4% ‐‐ ‐ ‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐ Day 14 Recepient Days 0.0% 0.0% 0.0% 0.0% ‐‐‐ ‐‐‐‐ ‐‐‐ ‐‐‐‐ Day 21 ‐ AT

0.0% ‐‐ ‐ ‐‐ ‐‐‐ ‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐ ‐‐ ‐‐ ‐‐‐ Day 28 ‐ ‐ Day 68 0.0% .%32 .%05 .%03 .%05 .%00 .%1.%01 .%17 .%0.0% 1.4% 1.7% 3.1% 0.1% 14.5% 0.0% 0.0% 0.5% 0.5% 0.1% 0.3% 0.1% 0.5% 0.0% 3.2% 0.5% .%25.8% 0.0% 0.0% .%1.%00 .%00 0.0% 0.0% 1.1% 0.0% 17.5% 0.0% 0.0% 0.8% Day 112

CDI set 2 0.1% 0.0% 5.5% 0.0% 0.1% ‐ ‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐ Recepient .%01 .%01 .%01 .%01 .%01 .%06 .%02 0.6% 0.2% 0.1% 0.6% 1.3% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.4% 0.1% 0.4% 0.1% 0.0% .%00 .%18 .%16 .%08 0.3% 0.8% 0.5% 1.6% 1.7% 1.8% 1.7% 0.0% 0.1% .%01 .%01 .%01 .%02 0.4% 0.2% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.0% .%00 0.0% 0.0% 0.0% .%0.1% 0.0% ‐‐‐‐‐‐‐ ‐‐‐‐‐ ‐ ‐ ‐ ‐ Donor 0.0% .%0.0% 0.3% 0.0% 0.0% 0.0% .%0.0% 1.2% ‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐ Day 3 .%00 .%02 .%01 0.1% 0.1% 0.0% 0.2% 0.0% 0.0% 0.1% 0.0% 0.9% ‐‐‐ ‐‐‐‐‐ ‐‐‐‐‐‐‐ ‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐ ‐‐‐‐ ‐ ‐ Day 7 0.0% .%00 0.0% 0.0% 0.0% .%0.0% 0.0% ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐ ‐ ‐‐‐ Day 11 0.0% .%0.0% 0.0% Recepient

Days ‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐ ‐‐‐‐ Day 18 ‐ 0.0% 0.0% AT ‐‐‐‐ ‐ Day 25 0.0% 0.1% .%11 0.8% 1.1% 0.4% ‐ ‐‐‐ ‐‐‐ ‐ ‐‐‐‐ ‐‐‐ ‐‐‐ ‐‐ Day 65 0.0% ‐‐ ‐‐ ‐‐ Day 95 .%1.%00 .%0.0% 0.2% 0.0% 15.4% 0.0% 0.0% 0.0%

‐ Day 128

CDI set 3 10.3% 0.0% 0.1% 0.1% 1.8% 0.1% 0.0% 0.1% ‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐ ‐‐‐‐ ‐ ‐ ‐ ‐ ‐ ‐‐ ‐‐‐‐‐‐ Recepient 0.0% .%01 .%01 0.0% 0.1% 0.1% 0.1% 0.2% .%10 .%09 1.6% 0.1% 0.9% 0.5% 1.4% 0.1% 1.0% 0.1% 1.2% 0.2% .%01 .%03 0.1% 0.3% 0.0% 0.1% 0.2% .%0.1% 0.7% .%06 .%03 1.5% 0.3% 2.6% 0.6% 2.1% .%01 .%00 0.0% 0.0% 0.0% 0.1% 0.1% ‐‐‐‐‐ ‐‐‐‐‐ ‐‐‐‐ ‐ ‐ ‐ ‐‐ ‐ Donor .%0.0% 0.0% .%0.0% 0.0% 0.0% .%01 .%0.0% 1.6% 0.1% 0.3% .%00 .%0.0% 0.0% 0.0% 0.0%

‐‐‐‐ Day 3 0.0% 0.0% Recepient Days ‐ ‐‐‐ ‐ Day 7 ‐ 0.0% .%1.6% 1.2% 0.0% .%0.0% 0.0% AT ‐ ‐‐ ‐‐ ‐ ‐‐ %12.6% 4%

Day 27 0.0% 0.0% 0.0% 0.0% ‐ ‐ ‐ Day 81 Clostridia Clostridia Clostridia Erysipelotrichi Erysipelotrichi Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Erysipelotrichi Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Erysipelotrichi Erysipelotrichi Clostridia Clostridia Clostridia Clostridia Erysipelotrichi Clostridia Clostridia Erysipelotrichi Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Bacilli Bacilli

Corresponding class oeui .%36 .%42 .%43 .%48 .%00 .%31 .%45 .%27 .%41 4.4% 4.1% 4.2% 2.7% 2.7% 4.5% 3.0% 3.1% 6.1% 0.0% 4.2% 4.8% 4.0% 4.3% 4.8% 4.2% 2.9% 3.6% 0.4% Anaerofilum Roseburia Thermotalea Solobacterium Holdemania Anaerosporobacter Dialister Allisonella Acidaminococcus Desulfitobacterium Oribacterium Lachnobacterium Geosporobacter Bulleidia ailbce .%32 .%25 .%26 .%22 .%01 .%28 .%43 .%39 .%44 .%01 .%07 .%33 3.2% 3.3% 4.3% 0.7% 3.0% 0.1% 3.4% 4.4% 4.2% 3.9% 3.7% 4.3% 2.6% 2.8% 3.0% 0.1% 2.5% 2.2% 1.4% 2.6% 2.9% 2.5% 2.4% 3.2% 0.2% Oscillibacter Papillibacter Mitsuokella Megasphaera Anaerofustis Mogibacterium uatru .%20 .%25 .%10 .%06 .%01 .%10 .%13 .%14 .%02 .%00 .%06 .%18 1.7% 1.8% 1.2% 0.6% 1.0% 0.0% 0.8% 0.2% 0.4% 1.4% 0.6% 1.3% 1.2% 1.0% 1.7% 0.1% 1.3% 0.6% 0.4% 1.0% 0.9% 2.5% 0.3% 2.0% 0.0% Anaerovorax Eubacterium Parvimonas Mahella 0.6% 0.5% 0.4% 0.4% 0.6% 0.5% 0.1% 0.5% 0.1% Anaerococcus Howardella neotps02 .%24 .%20 .%23 .%17 .%20 .%13 .%18 .%17 .%11 .%38 .%22 .%2.7% 1.9% 2.2% Acidaminobacter 17. 2.8% Garciella 14.2% 3.8% 20.3% 23.7% 0.0% 18.9% 0.3% 1.1% 20.0% 1.3% 23.3% 1.7% 26.6% 21.4% 1.6% 27.6% 1.8% 26.2% 17.3% 2.1% 19.2% 1.3% 16.3% 1.8% 4.4% 2.0% 0.1% 15.7% 19.6% 19.1% 16.4% 1.7% 17.4% 1.8% 14.6% 20.5% 2.3% 18.8% 2.2% 4.5% 2.0% 2.0% 2.4% 1.9% 0.2% Blautia Pseudobutyrivibrio Butyrivibrio Anaerostipes orbclu .%08 .%15 .%14 .%10 .%03 .%10 .%18 .%20 .%11 .%01 .%21 .%14 1.8% 1.4% 1.3% 2.1% 2.6% 0.1% 1.3% 1.1% 1.6% 2.0% 1.6% 1.8% 1.3% 1.0% 1.0% 0.3% 1.3% 1.0% 1.7% 1.4% 1.2% 1.5% 1.8% 0.8% 0.1% Catenibacterium Coprobacillus Phascolarctobacterium etccu .%0.0% 0.1% Peptococcus Fusibacter Lutispora Turicibacter Clostridiisalibacter Allobaculum Desulfitibacter aoaarbce 0.0% Caloranaerobacter Anaerovirgula Zymophilus eloel .%00 0.1% 0.0% 1.1% Veillonella Succiniclasticum eel .%00 0.0% 0.0% 0.1% Gemella Staphylococcus

Genus

CDI set 1 ‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐‐‐ ‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐ ‐‐ ‐‐ ‐‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ Recepient .%00 .%00 0.0% 0.0% 0.1% 0.0% 0.0% .%00 .%0.0% 0.2% 0.0% 0.0% .%01 .%00 .%01 .%01 .%01 .%00 .%01 .%01 .%0.1% 0.0% 0.1% 0.1% 0.1% 0.1% 0.0% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.0% 0.1% 0.1% 0.1% .%21 .%29 .%30 .%2.6% 6.6% 3.0% 4.7% 2.9% 4.1% 2.1% 2.9% .%02 .%03 .%08 0.0% 0.8% 0.1% 0.3% 0.1% 0.2% 0.4% .%00 0.0% 0.0% 0.0% .%0.0% 0.0% .%03 .%19 .%03 .%39 .%26 .%45 .%20 .%18 .%2.6% 2.1% 1.8% 2.2% 2.0% 1.5% 4.5% 2.3% 2.6% 0.0% 3.9% 1.3% 0.3% 1.5% 1.9% 2.1% 0.3% 1.2% .%0.0% 0.0% 0.0% .%00 .%0.0% 0.1% 0.0% 0.0% .%03 .%08 .%02 .%0.9% 0.3% 0.2% 0.9% 0.8% 1.1% 0.3% 1.2% 0.0% .%01 .%01 0.0% 0.1% 0.2% 0.1% 0.1% 0.0% 0.1% 0.0% 0.0% 0.0% 0.0% 0.0% .%00 .%13 0.0% 1.3% 1.1% 0.0% 0.6% 0.0% .%02 .%14 .%06 .%0.7% 0.8% 0.6% 0.7% 1.4% 0.5% 0.2% 0.7%

‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐ Donor 0.0% 0.0% .%00 0.0% 0.0% 0.0% 0.0% ‐ ‐‐‐ ‐ ‐‐‐‐‐‐‐ ‐‐ ‐ ‐ Day 3 .%00 .%00 .%00 .%00 .%00 .%00 .%00 .%00 .%00 .%00 .%0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.1% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% .%00 0.0% 0.0% 0.0% 0.0% 0.0% ‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐ ‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐ ‐ ‐ Day 7 0.0% 0.0% .%01 .%0.0% 0.0% 0.1% 0.0% 0.0% ‐‐ ‐ ‐‐‐‐‐ ‐‐ ‐‐ ‐ ‐‐‐‐‐ Day 14 Recepient Days 0.0% ‐‐‐ ‐‐‐ ‐‐‐ ‐‐‐‐ ‐‐‐ ‐‐‐ ‐‐‐ ‐‐‐‐ Day 21 ‐ AT

0.0% ‐ ‐‐ ‐ ‐ ‐ Day 28 .%0.1% 0.0% .%2.1% 0.0% .%0.0% 0.1% .%00 .%00 0.5% 0.0% 0.1% 0.0% 0.8% ‐‐ ‐‐ ‐‐ ‐‐ Day 68 0.2% 0.0% 0.1% 0.0% 0.0% 0.0% ‐‐ ‐ Day 112

CDI set 2 1.4% .%00 1.5% 0.0% 4.7% 0.0% ‐ ‐ ‐ ‐ ‐ ‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐ Recepient 0.0% .%30 .%09 .%33 .%31 4.4% 3.1% 1.8% 3.3% 1.1% 0.9% 3.8% 3.0% 5.7% .%01 .%00 .%02 .%00 0.1% 0.0% 0.0% 0.2% 0.0% 0.0% 0.1% 0.1% 0.5% .%0.0% 0.0% 0.0% 0.1% 0.0% 0.0% .%01 .%14 .%14 .%15 0.9% 1.5% 0.8% 1.4% 1.6% 1.4% 0.9% 0.1% 0.0% .%12 .%17 .%22 .%20 1.9% 2.0% 1.8% 2.2% 1.8% 1.7% 0.8% 1.2% 1.0% 0.0% .%00 0.0% 0.0% 0.0% .%02 .%01 .%01 .%01 0.4% 0.1% 0.1% 0.1% 0.1% 0.1% 0.2% 0.2% 0.4% .%0.0% 0.0% .%04 .%05 .%03 .%02 0.2% 0.2% 0.2% 0.3% 0.3% 0.5% 0.2% 0.4% 0.1% .%0.0% 0.0% 0.0% .%00 0.0% 0.0% 0.0% .%00 .%02 .%01 .%01 0.1% 0.1% 0.1% 0.1% 0.1% 0.2% 0.0% 0.0% 0.0% 0.0% .%08 .%06 .%06 .%04 0.5% 0.4% 0.7% 0.6% 0.9% 0.6% 1.2% 0.8% 0.9% .%0.0% 0.0% ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ Donor .%0.0% 0.0% .%00 0.0% 0.0% 0.0% ‐‐ ‐‐‐‐‐ ‐‐‐‐‐‐‐‐ ‐ ‐ Day 3 .%06 .%04 .%07 0.9% 0.7% 0.5% 0.4% 0.6% 0.6% 0.0% 0.0% .%01 .%01 .%00 0.1% 0.0% 0.1% 0.1% 0.1% 0.1% 0.0% ‐‐‐‐ ‐ ‐ ‐‐ ‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐ Day 7 .%02 .%02 .%0.3% 0.1% 0.2% 0.3% 0.2% 0.1% 0.0% .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% ‐‐‐‐‐ ‐ ‐ ‐‐‐ Day 11 .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% .%00 .%0.0% 0.2% 0.0% 0.5% Recepient

Days ‐ ‐ ‐ ‐ ‐‐ ‐ ‐‐‐‐‐ Day 18 ‐ 0.0% .%00 0.0% 0.0% 0.0% 0.0% 0.0% AT ‐‐ Day 25 0.0% 0.0% 0.0% ‐‐ ‐ ‐ ‐‐‐ ‐ ‐ ‐‐‐ Day 65 .%0.0% 0.0% ‐ ‐ ‐ Day 95 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% ‐‐‐‐‐‐ ‐ ‐‐‐‐ ‐‐ Day 128

CDI set 3 2.6% .%01 .%0.2% 0.0% 0.1% 3.7% .%00 0.1% 0.0% 0.0% 0.1% ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐‐‐‐ ‐‐ ‐‐‐ ‐ ‐ ‐ ‐ ‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐ ‐ Recepient 0.1% .%43 .%24 4.0% 2.4% 4.1% 4.3% 3.6% .%08 .%35 3.4% 3.5% 7.5% 0.8% 1.6% 0.0% .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.0% 0.2% .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.1% .%0.0% 0.0% .%0.0% 0.0% .%17 .%14 1.4% 1.4% 1.4% 1.7% 2.2% 0.0% .%00 .%01 0.0% 0.1% 0.0% 0.0% 0.0% .%02 .%06 0.7% 0.6% 0.5% 0.2% 0.9% .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.0% .%01 .%25 2.3% 2.5% 0.8% 0.1% 0.8% 0.2% .%00 0.0% 0.0% 0.0% 0.1% .%0.0% 0.0% 0.0% 1.3% .%01 .%12 0.8% 1.2% 0.8% 0.1% 0.6% 0.0% ‐ ‐ Donor 0.0% 0.0% 0.0% .%00 .%0.0% 0.0% 0.0% 0.0% ‐‐‐‐ ‐‐ ‐‐‐‐ ‐‐‐‐ ‐ ‐‐‐‐ ‐‐‐‐ ‐‐‐‐ ‐‐‐‐ Day 3 0.0% .%00 0.0% 0.0% 0.0% .%02 0.6% 0.2% 0.1% Recepient Days ‐ ‐‐‐ ‐‐ ‐‐‐ ‐‐ ‐‐‐ ‐ Day 7 ‐ 0.0% .%0.0% 0.6% .%0.0% 0.0% 0.2% AT ‐ ‐‐ ‐

Day 27 0.0% 0.0% 0.0% 0.0% ‐ ‐ 6% Day 81 Actinobacteria Mollicutes Bacilli Bacilli Bacilli Bacilli Spirochaetes Actinobacteria Actinobacteria Verrucomicrobiae Fusobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Spirochaetes Spirochaetes Lentisphaeria Actinobacteria Bacteroidia Actinobacteria Actinobacteria Bacteroidia Fusobacteria Bacteroidia [Numbers represent Corresponding class cumulative atccu .%18 .%00 .%01 .%00 .%28 .%00 .%01 .%03 .%02 .%03 .%02 .%01 0.3% 0.1% 0.1% 0.3% 0.2% 0.3% 1.6% 1.6% 1.6% 1.3% 0.3% 0.2% 1.8% 1.9% 1.1% 0.5% 0.2% 0.0% 23.6% 0.2% 0.0% 3.4% 0.3% 0.5% 3.0% 0.7% 0.0% 0.9% 0.1% 0.0% 1.0% 0.6% 0.0% 0.9% 0.0% 0.0% 0.6% 0.2% 0.0% 0.3% 2.8% 0.0% 0.5% 0.8% 1.9% 17.9% 0.0% 0.0% 8.9% 0.0% 2.4% 0.2% 0.2% 0.1% 0.1% 2.2% 0.0% 0.1% 0.6% 0.0% 0.1% 0.6% 0.1% 0.1% 1.2% 1.8% 0.0% 3.8% 0.1% 0.1% 0.6% 0.1% 25.4% 0.1% 6.6% Collinsella Haloplasma Lactococcus Streptococcus Enterococcus Lactobacillus iioatru 64 .%97 .%61 .%1.%78 .%31 .%69 .%78 .%76 .%31 .%23 .%55 .%00 0.0% 0.0% 0.2% 5.5% 8.9% 2.3% 6.4% 3.1% 0.8% 7.6% 5.4% 7.8% 4.0% 6.9% 3.3% 3.1% 6.3% 7.8% 12.0% 7.1% 6.1% 6.4% 9.7% 6.6% 16.4% Brachyspira Bifidobacterium Corynebacterium kemni .%09 .%3.3% 3.2% 0.9% 0.1% Akkermansia Cetobacterium Fusobacterium Slackia Adlercreutzia odnbce .%00 .%00 .%0.1% 0.0% 0.0% 0.0% 0.0% 0.0% Gordonibacter Eggerthella rvtla0.8% Prevotella Tannerella lsie .%04 .%09 .%08 .%07 0.7% 0.7% 0.4% 0.8% 1.5% 0.9% 0.6% 0.4% 0.0% Barnesiella Alistipes Odoribacter atrie .%21 .%38 .%55 .%52 .%02 .%12 .%01 .%06 .%01 .%00 .%08 .%75 7.8% 7.5% 3.5% 0.8% 0.2% 0.0% 0.9% 0.1% 0.1% 0.6% 0.1% 0.1% 5.7% 1.2% 4.3% 0.2% 3.6% 5.2% 3.7% 5.5% 4.5% 3.8% 3.6% 2.1% 0.2% Parabacteroides Bacteroides Leptonema Leptospira Victivallis Actinomyces Paraprevotella Rothia Brachybacterium uyiioa .%0.0% 0.0% Butyricimonas Rikenella abundances

Genus of members

CDI set 1 of particular ‐‐‐‐ ‐‐‐‐‐‐‐‐ ‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐ ‐‐ ‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐ Recepient .%0.0% 0.0% .%04 .%01 .%01 .%0.9% 0.3% 0.1% 0.5% 0.1% 1.2% 0.4% 3.9% .%00 .%01 .%01 .%0.1% 0.2% 0.1% 0.2% 0.1% 0.2% 0.0% 0.1% .%08 .%06 .%09 .%0.3% 0.4% 0.9% 0.5% 0.6% 0.8% 0.8% 0.5% .%09 .%07 .%03 .%0.4% 0.4% 0.3% 0.8% 0.7% 0.6% 0.9% 0.2% .%04 .%09 .%06 .%0.6% 1.0% 0.6% 1.5% 0.9% 0.5% 0.4% 0.9% 0.1% 0.0% ‐ genus Donor 0.0% in ‐‐‐‐‐‐ ‐‐‐‐‐‐‐ ‐

Day 3 a sample; .%0.1% 0.1% 0.0% 0.0% 0.0% ‐‐‐‐‐ ‐ Day 7 abundances .%0.0% 0.0% ‐‐ ‐‐‐ ‐‐‐‐‐ ‐ ‐‐‐‐ ‐ Day 14 Recepient Days .%00 .%3.1% 0.0% 0.0% 1.0% .%0.0% 0.0% 0.0% ‐‐ ‐

Day 21 less AT

0.0% than ‐‐ ‐ ‐ ‐‐‐ ‐ Day 28

0.05% 0.1% .%0.0% 0.0% ‐‐‐‐‐‐ ‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐‐ Day 68 are

0.1% 0.0% 0.0% .%01 .%0.0% 0.1% 0.1% 0.0% shown ‐‐ Day 112 as CDI set 2

0.0%; .%01 0.0% 0.1% 0.5% ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐‐‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐ ‐‐‐‐‐‐‐‐‐ ‐‐‐‐‐‐‐‐‐‐ ‐

Recepient " ‐ " designates .%02 0.2% 0.2% 0.1% .%04 .%07 .%07 .%06 1.1% 0.6% 0.5% 0.7% 0.3% 0.7% 0.2% 0.4% 1.9% .%01 0.0% 0.1% 0.0% .%02 .%03 .%03 .%01 0.2% 0.1% 0.3% 0.3% 0.2% 0.3% 0.1% 0.2% 0.1% 0.0% .%14 .%02 .%04 .%00 0.2% 0.0% 0.1% 0.4% 0.1% 0.2% 2.1% 1.4% 1.1% .%10 .%03 .%05 .%00 0.3% 0.0% 0.2% 0.5% 0.3% 0.3% 1.9% 1.0% 0.8% .%07 .%01 .%06 .%02 0.2% 0.2% 0.0% 0.6% 0.1% 0.1% 1.3% 0.7% 0.8% .%04 .%00 .%08 .%00 0.2% 0.0% 0.1% 0.8% 0.1% 0.0% 2.3% 0.4% 1.5% .%29 .%42 .%37 .%24 .%01 .%44 .%49 3.8% 4.9% 0.8% 4.4% 0.7% 0.1% 3.1% 2.4% 5.0% 3.7% 5.2% 4.2% 3.3% 2.9% 1.5% 0.0% .%00 .%0.0% 0.4% 0.0% 0.0% Donor 0.0% ‐ ‐‐‐‐‐‐‐

no Day 3 members 0.0% 0.0% ‐‐ ‐‐‐ ‐ ‐‐‐‐‐‐‐ ‐ Day 7 0.0% detected ‐‐ ‐‐‐‐‐‐ ‐ ‐ Day 11 .%00 .%00 0.0% 0.0% 0.0% 0.0% 0.0% .%0.0% 0.0% 0.0% Recepient

Days ‐‐ ‐ ‐‐‐‐‐ ‐ ] Day 18 ‐ .%0.3% 0.2% .%00 .%0.2% 0.0% 0.0% 0.0% AT ‐‐‐ Day 25

‐‐ Day 65 0.0%

‐ Day 95 0.1% .%0.0% 0.0% 0.0% 0.0%

‐‐‐‐ Day 128

CDI set 3 71 .%03 0.0% 0.3% 0.0% 17.1% ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐ ‐‐‐‐‐‐ ‐ ‐‐ Recepient .%20 .%08 2.7% 0.8% 0.8% 2.0% 3.6% .%00 .%00 0.1% 0.0% 0.0% 0.0% 0.1% .%07 .%02 0.3% 0.2% 0.4% 0.7% 0.4% .%03 .%01 0.2% 0.1% 0.3% 0.3% 0.3% .%0.0% 0.0% .%01 .%13 0.5% 1.3% 0.5% 0.1% 0.1% .%01 .%19 1.2% 1.9% 0.5% 0.1% 0.1% .%01 .%13 0.9% 1.3% 0.6% 0.1% 0.0% .%01 .%21 0.8% 2.1% 0.3% 0.1% 0.1% 0.0% .%0.0% 0.3% 0.0%

‐‐‐ Donor .%00 .%0.0% 0.1% 0.0% 0.0% ‐‐‐‐ ‐‐‐‐ Day 3 0.0% Recepient Days ‐‐‐ ‐ Day 7 ‐ 0.4% 0.0% .%0.0% 0.0% 0.0% AT ‐‐ ‐‐

Day 27 ‐ ‐ ‐ Day 81