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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 Manuscript under review Manuscript under review 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. 2/6 Manuscript under review 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. 3/6 Manuscript under review 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. 4/6 Manuscript under review 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. 5/6 Manuscript under review 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
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    ii Antibiotic Use Guidelines for Companion Animal Practice (2nd edition) iii Antibiotic Use Guidelines for Companion Animal Practice, 2nd edition Publisher: Companion Animal Group, Danish Veterinary Association, Peter Bangs Vej 30, 2000 Frederiksberg Authors of the guidelines: Lisbeth Rem Jessen (University of Copenhagen) Peter Damborg (University of Copenhagen) Anette Spohr (Evidensia Faxe Animal Hospital) Sandra Goericke-Pesch (University of Veterinary Medicine, Hannover) Rebecca Langhorn (University of Copenhagen) Geoffrey Houser (University of Copenhagen) Jakob Willesen (University of Copenhagen) Mette Schjærff (University of Copenhagen) Thomas Eriksen (University of Copenhagen) Tina Møller Sørensen (University of Copenhagen) Vibeke Frøkjær Jensen (DTU-VET) Flemming Obling (Greve) Luca Guardabassi (University of Copenhagen) Reproduction of extracts from these guidelines is only permitted in accordance with the agreement between the Ministry of Education and Copy-Dan. Danish copyright law restricts all other use without written permission of the publisher. Exception is granted for short excerpts for review purposes. iv Foreword The first edition of the Antibiotic Use Guidelines for Companion Animal Practice was published in autumn of 2012. The aim of the guidelines was to prevent increased antibiotic resistance. A questionnaire circulated to Danish veterinarians in 2015 (Jessen et al., DVT 10, 2016) indicated that the guidelines were well received, and particularly that active users had followed the recommendations. Despite a positive reception and the results of this survey, the actual quantity of antibiotics used is probably a better indicator of the effect of the first guidelines. Chapter two of these updated guidelines therefore details the pattern of developments in antibiotic use, as reported in DANMAP 2016 (www.danmap.org).
  • WO 2018/064165 A2 (.Pdf)

    WO 2018/064165 A2 (.Pdf)

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.