USOO901 1834B1 (12) United States Patent (10) Patent No.: US 9,011,834 B1 McKenzie et al. (45) Date of Patent: Apr. 21, 2015 (54) COMPOSITIONS AND METHODS 7,632,520 B2 * 12/2009 Khandelwal .................. 424/464 (71) Applicant: Seres Health, Inc., Cambridge, MA 7,731,9767,708,988 B2 6,5, 2010 CobbFarmer (US) 7,763,420 B2 7/2010 Stritzker et al. (72) Inventors: Gregory McKenzie, Arlington, MA 7.981,411 B2 7/2011 Nadeau et al. (US); Mary-Jane Lombardo 7.998.473 B2 8/2011 Boileau et al. Ncity Spid 8,034,6018,021,654 B2 10/20119/2011 RehbergerBoileau et al. Cook, Brooklyn, NY (US); Marin 8,039,006 B2 10/2011 Prato Vulic, Boston, MA (US); Geoffrey von 8, 147,482 B2 4/2012 Shimizu Maltzahn, Boston, MA (US); Brian 8, 187,590 B2 5, 2012 Farmer Goodman, Boston, MA (US); John 8,236,508 B2 8/2012 Mutharasan Grant Aunins, Doylestown, PA (US); E. R: 258 ity Matthew R. Henn, Somerville, MA 2001.0036453 A1 11, 2001 Reid (US); David Arthur Berry, Brookline, 2004/0028689 A1 2/2004 Borody MA (US); Jonathan Winkler, Boston, 2005, 0180962 A1 8, 2005 RaZ MA (US) 2006/0046246 A1 3/2006 Zeng et al. 2006,0188523 A1 8, 2006 Pei (73) Assignee: Seres Health, Inc., Cambridge, MA 2006/0233830 A1 10/2006 Wong (US) 2007/0141 139 A1 6/2007 Vandenberg 2009/O197249 A1 8, 2009 Gillevet (*) Notice: Subject to any disclaimer, the term of this 38899. A. R388 BlocaZZari et et hal. past is, G adjusted under 35 2011/0081320 A1 4/2011 Westall et al. .S.C. 154(b) by 0 days. 2011/0113863 A1 5/2011 Fuhrmann et al. 2011/O189132 A1 8/2011 Garner et al. (21) Appl. No.: 14/197,044 2011/0280840 A1 11/2011 Blaser (22) Filed: Mar. 4, 2014 2012/0020950 A1 1/2012 Davis et al. Related U.S. Application Data (Continued)Continued (63) Continuation of application No. FOREIGN PATENT DOCUMENTS PCT/US2014/014745, filed on Feb. 4, 2014. EP 0033584 A3 1, 1981 (60) Provisional application No. 61/926,918, filed on Jan. EP O433299 A4 4f1992 13, 2014, provisional application No. 61/760,584, (Continued) filed on Feb. 4, 2013, provisional application No. OTHER PUBLICATIONS 61/760,585, filed on Feb. 4, 2013, provisional application No. 61/760,574, filed on Feb. 4, 2013, Aas, J., Gessert, C.E., and Bakken, J.S. (2003), Recurrent provisional application No. 61/760,606, filed on Feb. Clostridium difficile colitis: case series involving 18 patients treated 4, 2013. with donor stool administered via a nasogastric tube. Clinical infec tious Diseases 36(5), 580-585. Int. C. Achtman, M., and Wagner, M. (2008), Microbial diversity and the (51) genetic nature of microbial species. Nat. Rev. Microbiol. 6(6), 431 AOIN 63/00 (2006.01) 440. (52) U.S. C. Accoceberry, I. et al., “One-Step Purification of Enterocytozoon CPC .................................... A61 K35/742 (2013.01) Bieneusi Spores from Human Stools by Immunoaffinity Expanded Field of Classification Search Bed Adsorption.” Journal of Clinical Microbiology, May 2001, pp. (58) 1974-1951, vol.39, No. 5. None Allen-Vercoe, E., Reid, G., Viner, N., Gloor, G.B., Hota, S., Kim, P., See application file for complete search history. Lee, C. O'Doherty, K. Vanner, S.J., Weese, J.S., et al. (2012), A Canadian Working Group report on fecal microbial therapy: micro (56) References Cited bial ecosystems therapeutics, Can. J. Gastroenterol. 26(7), 457-462. Allen-Vercoe, E., Strauss, J., and Chadee, K. (2011). Fusobacterium U.S. PATENT DOCUMENTS nucleatum: an emerging gutpathogen? Gut Microbes 2(5), 294-298. Anderson, K.F., Lonsway, D.R., Rasheed, J.K., Biddle, J., Jensen, B., 3,009,864 A 11, 1961 Gordon-Aldterton et al. McDougal., L.K., Carey, R.B., Thompson, A., Stocker, S., Limbago, 3,228,838 A 1/1966 Rinfret B. et al. (2007). Evaluation of Methods to Identify the Klebsiella 3,608,030 A 9, 1971 Tint pneumoniae Carbapenemase in Enterobacteriaceae, J. Clin. 4,077,227 A 3, 1978 Larson Microbiol. 45(8), 2723-2725. 4,205,132 A 5, 1980 Sandine 4,655,047 A 4, 1987 Temple (Continued) 4,689,226 A 8, 1987 Nurmi 4,839,281 A 6, 1989 Gorbach et al. Primary Examiner — Albert Navarro 5,196.205 A 3/1993 Borody (74) Attorney, Agent, or Firm — Fenwick & West LLP 5.425,951 A 6, 1995 Goodrich 5,443,826 A 8/1995 Borody (57) ABSTRACT 5,599,795 A 2f1997 McCann Disclosed herein are therapeutic compositions containing 5,648,206 A 7, 1997 Goodrich non-pathogenic, germination-competent bacterial spores, for 5,965,128 A 10/1999 Doyle et al. the prevention, control, and treatment of gastrointestinal dis 6,589.771 B1 7/2003 Marshall eases, disorders and conditions and for general nutritional 6,645,530 B1 1 1/2003 Borody health. 7.427,398 B2 9, 2008 Baillon et al. 7.628,982 B2 12/2009 Klaviniskis 28 Claims, 21 Drawing Sheets US 9,011,834 B1 Page 2 (56) References Cited (2011). Enterotypes of the human gut micreobiome. Nature 473(7346), 174-180. U.S. PATENT DOCUMENTS Atarashi, K., Tanoue, T., Oshima, K., Suda, W., Nagano, Y. Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., et al. 2012, 0021429 A1 1/2012 Rublee 2012, 0021921 A1 1/2012 Scott (2013). Treg induction by a rationally selected mixture of Clostridia 2012fOO58094 A1 3/2012 Blaser strains from the human microbiota. Nature 500(7461), 232-236. 2012fOO64592 A1 3/2012 O'Mullan et al. Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., 2012/O1286.33 A1 5/2012 Veiga et al. Momos, Y. Cheng. G., Yamasaki. S., Saito, T., Ohba, Y, et al. (2011), 2012/O128634 A1 5/2012 Veiga Induction of colonic regulator T cells by indigenous Clostridium 2012fO149584 A1 6, 2012 Ole species. Science 331(6015), 337-341. 2012fO1652.15 A1 6/2012 Andersen Backhed, F. etal (2004). The gut microbiota as an environment factor 2012/0177650 A1 7/2012 Borody 2012fO2O7726 A1 8/2012 Lipkin that regulates fat storage, PNAS, Nov. 2, 2014, pp. 15718-15723, vol. 2012fO238468 A1 9, 2012 Tuk 101, No. 44. 2012,0264.637 A1 10/2012 Brodie Bader, J., Albin, A., and Stahl, U. (2012). Spore-forming bacteria and 2012fO276.149 A1 11/2012 Littman their utilisation as probiotics. Benef Microbes 3(1), 65-75. 2012fO276201 A1 11/2012 Trachtman Bakken, J.S. (2009), Fecal bacteriotherapy for recurrent Clostridium 2012,0315249 A1 12/2012 Olmstead difficile infection. Anaerobe 15(6), 285-209. 2013, OO17999 A1 1/2013 Fremont Bakken, J.S., Borody, T., Brandt, L.J., Brill, J.V. Demarco, D.C., 2013/0022575 A1 1/2013 Cassity 2013,0045274 A1 2/2013 Hlavka Frankos, M.A., Kelly, C. Khoruts, A., Louie, T., Martinelli, L.P., et 2013,0045874 A1 2, 2013 Ehrlich al. (2011). Treatin Clostridium difficile infection with fecal 2013, O149339 A1 6, 2013 Honda microbiota transplantation. Clin. Gastroenterol. Hepatol. 9(12), 2013/014.9375 A1 6, 2013 Geall 1044-1049. 2013,0266539 A1 10/2013 Borody Barreau, M., Pagnier, I., and La Scola, B. (2013). Improving the 2014/0045744 A1 2/2014 Gordon Identification of anaerobes in the clinical microbiology laboratory through MALDI-TOF mass spectrometry. Anaerobe 22, 123-125. FOREIGN PATENT DOCUMENTS Bauer, T.M. et al., “Derivation and Validation of Guidelines for Stool Cultures for Enteropathogenic Bacteria. Other Than Clostridium dif EP 1107772 B1 4/2006 EP 1631312 B1 9, 2008 ficile in Hospitalized Adults.”The Journal of the American Medical EP 2337569 A2 6, 2011 Association, Jan. 17, 2001, pp. 313-319. EP 2338989 A1 6, 2011 Ben-Amor, K., Heilig, H. Smidt, H. Vaughan, E.E., Abee, T., and De EP 2519108 A1 11 2012 Vos, W.M. (2005). Genetic diversity of viable, injured, and dead fecal EP O47982O B1 T 2014 bacteria assessed by fluorescene-activated cell sorting and 16S rRNA WO WO 20O2/OO7741 A1 1, 2002 gene analysis, Applied and Environmental Microbiology 71 (8), WO WO 2005/110445 A2 11/2005 4679-4689. WO WO 2006/O12586 A2 2, 2006 WO WO 2008/O76696 A2 6, 2008 Berstad, A. et al., “Fecal Fat Determination with a Modified Titration WO WO 2008/083157 A2 T 2008 Method.” Scandinavian Journal of Gastroenterology, 2010, pp. 603 WO WO 2010/030997 A1 3, 2010 607, vol. 45. WO WO 2010/062369 A2 6, 2010 Bhatia, A et al., "Proionibacterium Acnes and Chronic Diseases.”The WO WO 2010, 124387 A1 11, 2010 Infectious Etiology of Chronic Diseases: Defining the Relationship, WO WO 2010, 151842 A2 12/2010 Enhancing the Research, and Mitigating the Effects: Workship Sum WO WO 2011/005756 A1 1, 2011 mary. Knobler, S.L. et al. (eds.), 2004, pp. 74-80, may be down WO WO 2011/022542 A2 2, 2011 loaded at <URL:http://www.nap.edu/catalog/11026.html>. WO WO 2011022660 A1 2, 2011 WO WO 2011/033310 A1 3, 2011 Bidawid, S., Farber, J.M., Sattar, S.A., and Hayward, S. (2000). Heat WO WO 2011/043654 A1 4/2011 inactivation of hepatitis. A virus in dairy foods, J. Food Prot. 63(4), WO WO 2011/046616 A3 4/2011 522-528. WO WO 2011, 103123 A2 8, 2011 Bloedt, K., Riecker, M., Poppert, S., and Wellinghausen, N. (2009). WO WO 2011, 107482 A2 9, 2011 Evaluation of new selective culture media and a rapid flourescence in WO WO 2011, 113801 A1 9, 2011 situ hybridization assay for identification of Clostridium difficile WO WO 2011 107481 A2 9, 2011 from stool samples, J Med Microbiol 58(7), 874-877.
Details
-
File Typepdf
-
Upload Time-
-
Content LanguagesEnglish
-
Upload UserAnonymous/Not logged-in
-
File Pages116 Page
-
File Size-