Supplemental Materials

Fecal microbiota transfers in ulcerative colitis, a retrospective microbiome analysis Marcel A. de Leeuw & Manuel X. Duval, GeneCreek

Contents

Supplemental materials 1 supplemental dataset ...... 1 FMT driven change in microbiota ...... 1 donor microbiome phenotypes ...... 1 responder and non-responder associated taxa ...... 2 responder associated species ...... 3

Bibliography 6

List of Figures S1 Chao species richness change through FMT ...... 1 S2 Strict anaerobe proportion change through FMT ...... 1 S3 Donor microbiome assessment, data set ERP013257 ...... 2 S4 Post-FMT class composition, non-responders ...... 2 S5 Post-FMT class composition, responders ...... 3

List of Tables S1 Profiling data sets used in the study ...... 1 S2 Class level taxa associated with responder and non-responder status, post FMT ...... 3 S3 Interconnected species associated with responder status, post FMT ...... 4 S4 Additional species associated with responder status, post FMT ...... 5 S5 Species associated with non-responder status, post FMT ...... 6

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Supplemental materials supplemental dataset

Table S1: Profiling data sets used in the study. N: number of patients, n: number of samples, 16S: variable regions covered.

BioProject SRA N n type 16S publication PRJNA450340 SRP183770 79 201 stool V4 [1]

FMT driven change in microbiota Several publications have reported dysbiosis in UC is reduced through FMT. This principle is illustrated using data set SRP108284 and Chao species richness in figure 1. The improvement reaches statistical significance in the samples collected in the second week after a single FMT, but washes out subsequently in the fourth week. 0.029 200 0.0044

150

100

Chao species richness 50

Baseline Donor Week 2 Week 4 Figure S1: Chao species richness change through FMT. Data set SRP108284, 20 patients with single FMT

Just like species diversity, the strict anaerobe proportion can be modified through FMT, figure 2. The two donors used in study SRP198502 were selected based on fecal butyrate concentration [2] and had a high propor- tion of strict anaerobes. 0.0032 0.013 1.6e−08 1.0

0.5 Strict anaerobe proportion Strict anaerobe 0.0 Baseline Donor FMT Placebo Figure S2: Strict anaerobe proportion change through FMT. Data set SRP198502, longitudinal randomized study with 6 FMT and 6 placebo. donor microbiome phenotypes Plotting the relation between phylogenetic diversity and oxygen tolerance for donor samples, we found these are related and separate responder and non-responder associated donors, Fig. S3. Phylogenetic diversity shows

1/6 Manuscript under review important variance around the donor means. response NR PR RE

12.5

10.0

7.5

phylogenetic diversity 5.0

−0.4 −0.3 −0.2 −0.1 oxygen tolerance Figure S3: Donor microbiome assessment, data set ERP013257. Lines connect samples from the same donor. NR: nonresponders, PR: partial responders, RE: responders. responder and non-responder associated taxa The following treemaps document the relative abundance post-FMT of classes in non-responders and responders, respectively Fig. S4 and S5. Verrucomicrobia Fusobacteria Firmicutes β-proteo bacteria Bacilli Negativicutes Erysipe Proteo lotrichia bacteria Actino γ-proteo bacteria bacteria

Firmicutes

Clostridia Bacteroidetes

Figure S4: Post-FMT class composition, non-responders. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742.

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Fusobacteria

Erysipelo Firmicutes α-pb Verruco Bacilli β-proteo trichia Negativicutes microbia bacteria Proteo bacteria Actino γ-proteo bacteria bacteria Firmicutes

Clostridia

Bacteroidetes

Figure S5: Post-FMT class composition, responders. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742.

At the class level, DESeq2 analysis detects the following post-FMT taxa as differentially abundant between non-responders and responders, Table S2

Table S2: Class level taxa associated with responder and non-responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.05.

taxon log2FC association p__Spirochaetes -7.0 NR c__Lentisphaeria -6.9 NR c__Methanobacteria -2.2 NR p__Actinobacteria -2.0 NR c__Negativicutes -1.5 NR unknown 2.6 RE c__Verrucomicrobiae 2.8 RE c__Flavobacteriia 4.8 RE c__Alphaproteobacteria 5.7 RE c__Sphingobacteriia 5.7 RE responder associated species The following, esssentially gram negative, aerobic and facultative species are associated with responder status and are tightly interconnected, 3.

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Table S3: Interconnected species associated with responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001.

taxon class log2FC gram oxygen Corynebacterium kroppenstedtii Actinobacteria 8.5 positive anaerobe Micrococcus luteus Actinobacteria 7.3 positive aerobe Altererythrobacter dongtanensis Alphaproteobacteria 3.1 negative aerobe Brevundimonas terrae Alphaproteobacteria 9.2 negative aerobe Brevundimonas vesicularis Alphaproteobacteria 5.2 negative aerobe Hyphomicrobium zavarzinii Alphaproteobacteria 7.1 negative aerobe Mesorhizobium thiogangeticum Alphaproteobacteria 10.5 negative aerobe Methylobacterium adhaesivum Alphaproteobacteria 7.1 negative aerobe Methylobacterium populi Alphaproteobacteria 10.8 negative aerobe Rubellimicrobium thermophilum Alphaproteobacteria 10.4 negative aerobe Sphingobium subterraneum Alphaproteobacteria 10.6 negative aerobe Sphingomonas kwangyangensis Alphaproteobacteria 9.6 negative aerobe Sphingomonas melonis Alphaproteobacteria 7.1 negative aerobe Sphingopyxis ginsengisoli Alphaproteobacteria 11.9 negative aerobe Xanthobacter autotrophicus Alphaproteobacteria 8.1 negative facultative Staphylococcus epidermidis Bacilli 5.2 positive facultative Delftia tsuruhatensis Betaproteobacteria 3.2 negative aerobe Limnobacter thiooxidans Betaproteobacteria 6.6 negative obligate aerobe Massilia timonae Betaproteobacteria 7.1 negative aerobe Methyloversatilis universalis Betaproteobacteria 3.9 negative facultative Piscinibacter aquaticus Betaproteobacteria 5.5 negative facultative Ralstonia pickettii Betaproteobacteria 10.5 negative aerobe Sphaerotilus natans Betaproteobacteria 8.4 negative facultative Acinetobacter calcoaceticus Gammaproteobacteria 5.2 negative aerobe Acinetobacter johnsonii Gammaproteobacteria 9.6 negative aerobe Acinetobacter junii Gammaproteobacteria 6.8 negative microaerophile Acinetobacter lwoffii Gammaproteobacteria 8.9 negative facultative Methylomonas methanica Gammaproteobacteria 8.7 negative aerobe Pseudomonas aeruginosa Gammaproteobacteria 11.1 negative facultative Pseudomonas fluorescens Gammaproteobacteria 7.6 negative aerobe Pseudomonas putida Gammaproteobacteria 5.7 negative aerobe Stenotrophomonas maltophilia Gammaproteobacteria 13.1 negative aerobe Sediminibacterium goheungense Sphingobacteriia 9.1 negative aerobe

Additional species, more loosely interconnected are associated with responder status, table 4.

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Table S4: Additional species associated with responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001.

taxon class log2FC gram oxygen Gordonibacter urolithinfaciens Actinobacteria 6.3 positive anaerobe Abiotrophia defectiva Bacilli 9.6 positive facultative Lactobacillus algidus Bacilli 7.3 positive microaerophile Lactobacillus mucosae Bacilli 3.5 positive anaerobe Staphylococcus simulans Bacilli 7.2 positive facultative Bacteroides rodentium Bacteroidia 14.2 negative anaerobe Parabacteroides goldsteinii Bacteroidia 11.7 negative obligate anaerobe Porphyromonas catoniae Bacteroidia 5.2 negative anaerobe Porphyromonas uenonis Bacteroidia 7.5 negative obligate anaerobe Prevotella buccae Bacteroidia 5.0 negative anaerobe Neisseria flavescens Betaproteobacteria 3.7 negative aerobe Oxalobacter formigenes Betaproteobacteria 10.2 negative anaerobe Eubacterium infirmum Clostridia 7.0 positive anaerobe Oribacterium asaccharolyticum Clostridia 6.7 positive anaerobe Oscillibacter ruminantium Clostridia 10.4 negative anaerobe Peptoniphilus lacrimalis Clostridia 5.7 positive anaerobe Ruminococcus champanellensis Clostridia 4.2 positive anaerobe Leptotrichia trevisanii Fusobacteriia 8.3 negative aerobe Haemophilus influenzae Gammaproteobacteria 9.9 negative microaerophile Dialister invisus Negativicutes 3.2 positive anaerobe Dialister propionicifaciens Negativicutes 5.3 negative anaerobe Negativicoccus succinicivorans Negativicutes 8.5 negative microaerophile

A large number of mostly non-connected species are associated with non-responder status, table 5.

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Table S5: Species associated with non-responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001.

taxon log2FC | taxon log2FC Acidaminococcus fermentans -3.51 Hungatella hathewayi -3.59 Actinomyces lingnae -6.05 Lactobacillus fermentum -14.61 Actinomyces turicensis -4.99 Lactobacillus gasseri -5.04 Aggregatibacter aphrophilus -12.75 Lactobacillus paracasei -9.77 Alistipes massiliensis -11.51 Lactobacillus plantarum -5.99 Allisonella histaminiformans -13.21 Lactobacillus pontis -6.63 Anaerococcus vaginalis -3.50 Lactobacillus reuteri -11.78 Anaerofustis stercorihominis -5.02 Lactobacillus rhamnosus -3.67 Anaerostipes caccae -13.03 Lactobacillus ruminis -11.02 Bacteroides acidifaciens -8.31 Lactobacillus sanfranciscensis -8.07 Bacteroides eggerthii -10.45 Lactonifactor longoviformis -6.37 Bacteroides intestinalis -13.79 Leptotrichia wadei -9.52 Bacteroides massiliensis -4.26 Megamonas funiformis -16.97 Bacteroides nordii -12.78 Megasphaera massiliensis -15.30 Bacteroides plebeius -15.51 Mitsuokella multacida -10.21 Bifidobacterium dentium -12.28 Morganella morganii -12.49 Blautia glucerasea -4.53 Paraprevotella clara -14.98 Butyricimonas faecihominis -9.48 Pediococcus acidilactici -13.60 Butyricimonas paravirosa -11.58 Peptostreptococcus anaerobius -12.46 Butyricimonas virosa -12.36 Peptostreptococcus stomatis -10.89 Campylobacter concisus -3.81 Phascolarctobacterium succinatutens -11.00 Campylobacter hominis -5.59 Porphyromonas asaccharolytica -11.88 Catenibacterium mitsuokai -16.65 Prevotella corporis -4.99 Cellulosilyticum lentocellum -7.91 Prevotella melaninogenica -8.37 Clostridium aldenense -6.46 Prevotella stercorea -12.64 Clostridium butyricum -8.18 Prevotella veroralis -4.18 Clostridium ghonii -10.41 Proteus mirabilis -11.45 Clostridium neonatale -7.78 Romboutsia sedimentorum -10.68 Clostridium nexile -16.68 Roseburia faecis -15.75 Clostridium perfringens -7.16 Ruminococcus callidus -3.97 Corynebacterium durum -5.67 Slackia isoflavoniconvertens -12.54 Dialister pneumosintes -7.31 Streptococcus anginosus -11.32 Eikenella corrodens -8.92 Streptococcus equinus -15.04 Eisenbergiella tayi -3.40 Streptococcus gallolyticus -8.51 Enterobacter cloacae -16.11 Streptococcus mutans -12.36 Enterococcus raffinosus -6.57 Streptococcus peroris -6.81 Faecalicoccus pleomorphus -8.48 Streptococcus pneumoniae -6.18 Haemophilus sputorum -9.66 Streptococcus sanguinis -8.75 Holdemanella biformis -3.81 Veillonella ratti -10.84 Howardella ureilytica -13.37 Weissella confusa -9.53

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