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( 12 ) United States Patent 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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