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US010265349B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 265 ,349 B2 Chatila et al. (45 ) Date of Patent: Apr. 23 , 2019 ( 54 ) THERAPEUTIC MICROBIOTA FOR THE (56 ) References Cited TREATMENT AND /OR PREVENTION OF FOOD ALLERGY U . S . PATENT DOCUMENTS 5 , 225 , 202 A 7 / 1993 Hodges ( 71) Applicants : THE BRIGHAM AND WOMEN ' S 5 , 733 ,575 A 3 / 1998 Mehra HOSPITAL , INC . , Boston , MA (US ) ; 5 , 951 ,977 A 9 / 1999 Nisbet CHILDREN ' S MEDICAL CENTER 6 , 139 , 875 A 10 /2000 Adams 6 ,420 ,473 B1 7 / 2002 Chittamuru CORPORATION , Boston , MA (US ) 6 ,455 ,052 B1 9 / 2002 Marcussen 6 , 569, 457 B2 5 /2003 Ullah (72 ) Inventors : Talal A . Chatila , Belmont, MA (US ) ; 8 , 460, 648 B2 6 / 2013 Borody 8 ,486 ,668 B2 7 / 2013 Ritter Lynn Bry , Jamaica Plain , MA (US ); 9 ,011 , 834 B1 4 / 2015 McKenzie et al . Georg Gerber , Boston , MA (US ) ; Azza 9 ,408 , 872 B2 8 / 2016 Borody Abdel -Gadir , Boston , MA (US ) ; Rima 9 , 433 ,652 B2 9 / 2016 Honda et al . Rachid , Belmont, MA (US ) 9 ,642 , 882 B2 5 / 2017 Honda et al. 9 ,662 , 381 B2 5 / 2017 Honda et al . 10 ,052 , 353 B2 8 / 2018 Honda et al . (73 ) Assignees : THE BRIGHAM AND WOMEN ' S 2008 /0131556 A16 / 2008 De Simone et al . HOSPITAL , INC. , Boston , MA (US ) ; 2014 / 0341921 Al 11/ 2014 Honda et al. CHILDREN ' S MEDICAL CENTER 2015 / 0004130 A11 / 2015 Faber 2016 / 0158294 AL 6 /2016 Von Maltzahn et al . CORPORATION , Boston , MA (US ) 2016 / 0317653 AL 11/ 2016 Cook et al. ( * ) Notice : Subject to any disclaimer , the term of this 2017 / 0165302 A16 /2017 Henn et al. patent is extended or adjusted under 35 U . S . C . 154 (b ) by 0 days. FOREIGN PATENT DOCUMENTS EP 0514551 A1 11/ 1992 (21 ) Appl. No. : 15 /801 ,783 EP 2027863 A1 2 /2009 WO 2001 / 060378 A2 8 / 2001 wo 2002 /018614 A1 3 / 2002 (22 ) Filed : Nov . 2 , 2017 WO 2005 /039597 A2 5 / 2005 WO WO2010062369 * 6 /2010 (65 ) Prior Publication Data Wo 2014 / 121304 AL 8 / 2014 wo WO2014 / 121298 * 8 / 2014 US 2018 /0117097 A1 May 3 , 2018 WO WO2015 /095241 * 12 / 2014 Related U . S . Application Data OTHER PUBLICATIONS Benjamini et al ., “ Controlling the False Discovery Rate: A Practical (63 ) Continuation of application NO and Powerful Approach to Multiple Testing ” , Journal of the Royal PCT/ US2016 / 060353 , filed on Nov. 3 , 2016 . Statistical Society Series B , 57 ( 1 ) 289 - 300 ( 1995 ) . Cole et al ., “ Ribosomal Database Project: data and tools for high throughput rRNA analysis ” , Nucleic Acids Res 42 ( Database issue ) (60 ) Provisional application No . 62/ 250 , 277, filed on Nov. D633 - 1642 ( 2014 ) . Published online Nov . 27 , 2013 . 3 , 2015 . Falony et al . , “ Cross - feeding between Bifidobacterium longum BB536 and acetate - converting , butyrate -producing colon bacteria (51 ) Int . CI. during growth on oligofructose ” , Appl Environ Microbiol 72 ( 12 ) A61K 39 /02 ( 2006 .01 ) 7835 - 7841 (2006 ) . A61K 35 / 742 ( 2015 . 01 ) Gerritsen et al ., “ Intestinal microbiota in human health and disease : A61K 45 /06 ( 2006 . 01 ) the impact of probiotics ” , Genes Nutr 6 ( 3 ) 209 - 240 (2011 ) . A61K 35 / 74 ( 2015 . 01) (Continued ) A61K 35 / 741 ( 2015 .01 ) A61K 35 / 744 ( 2015 .01 ) Primary Examiner — Jennifer E Graser A61K 35 / 745 ( 2015 .01 ) (74 ) Attorney , Agent, or Firm — Nixon Peabody LLP ; A61P 37 / 08 ( 2006 .01 ) David S . Resnick ; Mark J . FitzGerald A61K 9 / 00 ( 2006 . 01) A61K 9 / 19 ( 2006 .01 ) (52 ) U . S . CI. ( 57 ) ABSTRACT CPC .. .. A61K 35 / 742 (2013 . 01 ) ; A61K 9 /0053 Disclosed are methods and compositions for the prevention (2013 .01 ) ; A61K 35 / 74 ( 2013 .01 ) ; A61K and treatment of food allergy . In particular, described herein 35 / 741 (2013 . 01 ) ; A61K 35/ 744 ( 2013 . 01 ) ; are microbial consortia , including minimal microbial con A61K 35 / 745 (2013 .01 ) ; A61K 45 / 06 sortia , that can prevent and/ or cure food allergy . In certain ( 2013 . 01 ) ; A61P 37 / 08 ( 2018 .01 ) ; A61K 9 / 19 embodiments , the consortia comprise certain members of (2013 . 01 ) ; YO2A 50/ 473 (2018 .01 ) the taxa Clostridiales and /or Bacteroidetes. (58 ) Field of Classification Search None See application file for complete search history . 27 Claims, 52 Drawing Sheets US 10 , 265 ,349 B2 Page 2 References Cited Open Biome FMT capsules F30 and G3: available on the web at (56 ) openbiome. org / fmtcapsules / . Petrof et al . , “ Stool substitute transplant therapy for the eradication OTHER PUBLICATIONS of Clostridium difficile infection : ' RePOOPulating the gut” ,Microbiome 1 ( 1 ) 3 ( 2013 ). Schloss et al . , “ Introducing mothur: open - source , platform Helm et al. , “ A neonatal swine model for peanut allergy ” , J Allergy independent , community - supported software for describing and Clin Immunol 109 ( 1 ) 136 - 142 ( 2002 ) . comparing microbial communities ” , Appl Environ Microbiol 75 ( 23 ) Kozich et al. , “ Development of a dual- index sequencing strategy 7537 - 7541 ( 2009 ) . and curation pipeline for analyzing amplicon sequence data on the Smith et al. , “ The microbial metabolites, short - chain fatty acids, MiSeq Illumina sequencing platform ” , Appl Environ Microbiol regulate colonic Treg cell homeostasis ” , Science 341 (6145 ) 569 79 ( 17 ) 5112 -5120 ( 2013 ) . 573 (2013 ) . Lara - Villoslada et al. , “ Short -chain fructooligosaccharides, in spite Yamashita et al ., “ Production of alpha - linked galactooligosac of being fermented in the upper part of the large intestine , have charide (alpha - GOS ) by alpha- galactosidase from Aspergillus niger APC -9319 and its physical and physiological properties ” , Journal of anti - inflammatory activity in the TNBS model of colitis ” , European Applied Glycoscience 51 ( 2 ) : 115 - 121 ( 2004 ) . English Abstract Journal of Nutrition 45 ( 7 ) 418 -425 ( 2006 ) . Only . Mathias et al. , “ IgE -mediated systemic anaphylaxis and impaired Faith et al ., “ Identifying Gut Microbe -Host Phenotype Relation tolerance to food antigens in mice with enhanced IL - 4 receptor ships Using Combinatorial Communities in Gnotobiotic Mice ” , Sci . signaling ” , J Allergy Clin Immunol 127 ( 3 ) 795 -805 ( 2011 ) . Transl . Med . 6 ( 220 ) : 220ra11 ( 2014 ) . Matsen et al ., " pplacer: linear timemaximum - likelihood and Bayes Kailasapathy et al. , “ Survival and therapeutic potential of probiotic ian phylogenetic placement of sequences onto a fixed reference organisms with reference to Lactobacillus acidophilus and tree ” , BMC Bioinformatics 11 :538 ( 2010 ) . Bifidobacterium spp ” , Immunology and Cell Biology 78 : 80 - 88 Mcmurdie et al. , " phyloseq : an R package for reproducible inter ( 2000 ) . active analysis and graphics of microbiome census data ” , PLoS One Prakash et al ., " Gut microbiota : next frontier in understanding 8 ( 4 ) e61217 ( 2013 ) . human health and development of biotherapeutics ” , Biologics : “ Medical Physiology /Gastrointestinal Physiology / Secretions” , avail Targets and Therapy 5 :71 - 86 (2011 ) . able at: en .wikibooks . org /wiki /Medical _ Physiology /Gastrointestinal Hopkins et al. " Changes in predominant bacterial populations in Physiology /Secretions ( Printed Feb . 8 , 2018 ) . human faeces with age and with Clostridium difficile infection ” , Noval Rivas et al. , “ A microbiota signature associated with experi Journal of Medical Microbiology 51 ( 4 ) : 448 -452 (2002 ) . mental food allergy promotes allergic sensitization and anaphy Song et al. ““ “ Bacteroides goldsteinii sp . nov. ” isolated from clinical laxis ” , J Allergy Clin Immunol 131 ( 1 ) 201- 212 ( 2013 ) . specimens of human intestinal origin . " , Journal of Clinical Micro Noval Rivas et al. , “ Regulatory T Cell Reprogramming toward a biology 43 ( 9 ) : 4522 -4527 ( 2005 ) . Th2 - Cell - like Lineage Impairs Oral Tolerance and Promotes Food Allergy ” , Immunity 42 ( 3 ) 512 -523 ( 2015 ) . * cited by examiner U . S . Patent Apr . 23 , 2019 Sheet 1 of 52 US 10 , 265, 349 B2 ooooootruturarteanUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU DC Mast Cell ILC2 ILC2 oooos FIG . 1 atent Apr . 23 , 2019 Sheet 2 of 52 US 10 , 265, 349 B2 . ITIM(Y->Mutationmice:4raF709IL- GainoffunctiontheIL-4R IL-4Ra )IL-4Ra PPPPPPPPPPPPPPPPPPPPPP FIG.2 (IL-4 IL-4and13Geneexpression mi OO JAKU OUT Proliferation Differentiation yor are : STATO TypeIIL-4R: STATG Nucleus atent Apr . 23 , 2019 Sheet 3 of 52 US 10 ,265 , 349 B2 Temperaturedrop -OVAspecificIgEserum -MastcellscountsSI (5mgOVA) -TotalIgEserum Challenge -MCP1 (250ug/10ug) 3 FIG.3 OVA-SEB WeeksOS DOOR 2x Y MY poo Www DOOR toooo w DolgoDOG DopoCOOR . WTmice PEN 89103 tent Apr . 23 , 2019 Sheet 4 of 52 US 10 ,265 , 349 B2 OVA SEB SEB Let PBSOVA PBS LPF/ cells Mast Nbr )ml / ug ( 1 - MMCP 114raF709 OVA SEB OVA SEB AWT PBS PBS )ml / ug ( IgE Total )ml / ug ( IgE- OVA FIG.4 114raF709+OVA-SEB Time(min) 6050403020100 WT+PBS SEBOVA-WT+O #114raF709+PBS ) °C( Temperature A U . S . Patent Apr . 23 , 2019 Sheet 5 of 52 US 10 ,265 , 349 B2 OVA SEB SEB UPBSOVA PBS - - - - - - - - LLLLLL 2.57 2.04T Na mana mana o ) x104 ( 1l4raF709 IFN + CD4 % IF + CD4 Nbr SEB SEB WT2. PBSOVA nh LOPBSMOVA FIG.4(cont) ) x105 ( 41 - IL + CD4 % + 4- IL *CD4 Nbr GOTOVO 1.6+0%oolella 1.5+04% OVA-SEB . ?????????????? IFN-Y olisikolloids IL4raf709 10*.3?02% buildinBucurestil. itustilul huuksusluk 01707675,%bullulilu .Judulluisul BAY Y U . S . Patent Apr . 23 , 2019 Sheet 6 of 52 US 10 , 265, 349 B2 IL4raF709OVA-SEB WeWO Spleenwwwwwwwwwwwwwwwww 15.1+04% LUVY 8.7+01% WIDA maryamsportgagerieor ola ginagamitngayong777TTTT ?????????????????????????????????????????????????????????????????????????????????????????????????????.
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  • W O 2017/079450 Al 11 May 2017 (11.05.2017) W IPOI PCT

    W O 2017/079450 Al 11 May 2017 (11.05.2017) W IPOI PCT

    (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 W O 2017/079450 Al 11 May 2017 (11.05.2017) W IPOI PCT (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61K35/741 (2015.01) A61K 35/744 (2015.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, A61K 35/745 (2015.01) A61K35/74 (2015.01) DO, DZ, EC, EE, EG, ES, Fl, GB, GD, GE, GH, GM, GT, C12N1/20 (2006.01) A61K 9/48 (2006.01) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, A61K 45/06 (2006.01) KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (21) International Application Number: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, PCT/US2016/060353 SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (22) International Filing Date: TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 3 November 2016 (03.11.2016) ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated,for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (30) Priority Data: TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 62/250,277 3 November 2015 (03.11.2015) US TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, Fl, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, (71) Applicants: THE BRIGHAM AND WOMEN'S HOS- LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, PITAL [US/US]; 75 Francis Street, Boston, Massachusetts SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, 02115 (US).
  • Bacterial Involvements in Ulcerative Colitis: Molecular and Microbiological Studies

    Bacterial Involvements in Ulcerative Colitis: Molecular and Microbiological Studies

    BACTERIAL INVOLVEMENTS IN ULCERATIVE COLITIS: MOLECULAR AND MICROBIOLOGICAL STUDIES Samia Alkhalil A thesis submitted in partial fulfilment of the requirements for the award of the degree of Doctor of Philosophy of the University of Portsmouth Institute of Biomedical and biomolecular Sciences School of Pharmacy and Biomedical Sciences October 2017 AUTHORS’ DECLARATION I declare that whilst registered as a candidate for the degree of Doctor of Philosophy at University of Portsmouth, I have not been registered as a candidate for any other research award. The results and conclusions embodied in this thesis are the work of the named candidate and have not been submitted for any other academic award. Samia Alkhalil I ABSTRACT Inflammatory bowel disease (IBD) is a series of disorders characterised by chronic intestinal inflammation, with the principal examples being Crohn’s Disease (CD) and ulcerative colitis (UC). A paradigm of these disorders is that the composition of the colon microbiota changes, with increases in bacterial numbers and a reduction in diversity, particularly within the Firmicutes. Sulfate reducing bacteria (SRB) are believed to be involved in the etiology of these disorders, because they produce hydrogen sulfide which may be a causative agent of epithelial inflammation, although little supportive evidence exists for this possibility. The purpose of this study was (1) to detect and compare the relative levels of gut bacterial populations among patients suffering from ulcerative colitis and healthy individuals using PCR-DGGE, sequence analysis and biochip technology; (2) develop a rapid detection method for SRBs and (3) determine the susceptibility of Desulfovibrio indonesiensis in biofilms to Manuka honey with and without antibiotic treatment.
  • Microbiota and Drug Response in Inflammatory Bowel Disease

    Microbiota and Drug Response in Inflammatory Bowel Disease

    pathogens Review Microbiota and Drug Response in Inflammatory Bowel Disease Martina Franzin 1,† , Katja Stefanˇciˇc 2,† , Marianna Lucafò 3, Giuliana Decorti 1,3,* and Gabriele Stocco 2 1 Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] 2 Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] (K.S.); [email protected] (G.S.) 3 Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-3785362 † The authors contributed equally to the manuscript. Abstract: A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in Citation: Franzin, M.; Stefanˇciˇc,K.; the treatment of IBD can be either beneficial or disadvantageous.