US 2011 0206654A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0206654 A1 Hodin et al. (43) Pub. Date: Aug. 25, 2011 (54) METHODS OF MODULATING Related U.S. Application Data GASTRONTESTINAL TRACTFLORA LEVELS WITH ALKALINE PHOSPHATASE (60) Provisional application No. 61/093,129, filed on Aug. 29, 2008. (75) Inventors: Richard A. Hodin, Newton, MA (US); Madhu S. Malo, Burlington, Publication Classification MA (US) (51) Int. Cl. (73) Assignee: THE GENERAL, HOSPITAL A638/46 (2006.01) CORPORATION, Boston, MA CI2N 9/16 (2006.01) (US) A6IPI/00 (2006.01) (21) Appl. No.: 13/060,863 (52) U.S. Cl. ........................................ 424/94.6; 435/196 (22) PCT Fled: Aug. 27, 2009 (57) ABSTRACT (86) PCT NO.: PCT/USO9/55216 This invention relates generally to a therapeutic use of alka S371 (c)(1), line phosphatase to modulate gastrointestinal tract flora levels (2), (4) Date: May 5, 2011 in Subject. C 7 e 4 ---. W. Mouse Stoo B Mac Brucella MacConkey Agar Plates Media Aerobic Condition) B D WT AP-KO n . 1 ^: O Š AP-KO Mouse Stool Brucella MacConkey Agar Plates Media (Anaerobic Condition) Patent Application Publication Aug. 25, 2011 Sheet 1 of 7 US 2011/0206654 A1 F.G. 1 W &ws s IAP-KOS ls S 4 S.Š 3 WT Mouse Stoo LB BH Mac Brucella MacConkey Agar Plates Media (Aerobic Condition) D 12 SS 9 : AP-KO Mouse Stool Brucella MacConkey Agar Plates Media (Anaerobic Condition) Patent Application Publication Aug. 25, 2011 Sheet 2 of 7 US 2011/0206654 A1 FIG 2 $2$3$?2 8?duesdødsweeg38),jojaquumN A. Dipnil Hae il hipa TRFP Enzyme AADs Ordination with Combined Layout Patent Application Publication Aug. 25, 2011 Sheet 3 of 7 US 2011/0206654 A1 FIG. 3 B : 800 as Hyperthyroid Hyperthyroic: f Hypothyroid Hypothyroid f -- s is s Week 8, 2 S 2: 32 Wek disorsenatoriousnesser-rea transacowrierstores T3 if Saire (i.p., Daily T3 or Sairie ip. Daily Alkaline Phosphatase Activity Growth on 8 Agar Plates (Aerotic Cottlitions C O 3 as Hyperthyroid O E. Hyperthyroid Hypothyroid E. Hypothyroid is f : . s s S 5 13 g ii. i.P s se g 5 S 11 l al 1. s Week 6 6 2 24 32 Week O S 2 is 2 2s 32 -sorcemeteorollowesterestauromulo quantularlawuwukuruuth T3 or SaÉire (i.p., aly T3 or Satire (i.p., Oasty) Growth on FiacConkey Agar Plates Growth on Bruceiia Agar Plates (Aerobic Conditions} (Anaerobic Conditions) Patent Application Publication Aug. 25, 2011 Sheet 4 of 7 US 2011/0206654 A1 FIG. 4 A. 8 & C. Peset in Sto: 3 3 as 3 g 2 2 . C. 1 2 3 4 5 5, 7, 8 9 31, E. coli Po Day B a cAP n = 6 C g 5 Es cAP p<0.002 s: s S 3 E. coli Po Š i. s Day -1 0 1 2 3 4 5 & 789 10 cAPFWehicle -- - - - - - - - - - - - - Streptomycin - - - - - - - - - - - - - C is clAp" n = 6 & 5 a ciAP p<0.015 4 3S 3 3 u. 2 s fay - -6-5-4-3-2-1 Q 1 2 3 4 5 capiwehicle - - - - - - - - - - - - - - Antibiotics + -- + - - - - - - - - - - - Patent Application Publication Aug. 25, 2011 Sheet 5 of 7 US 2011/0206654 A1 FIG. 5 100 - 79 5 - -- clAP Buffer" 123 -s- CAP Buffer O . - -- Patent Application Publication Aug. 25, 2011 Sheet 6 of 7 US 2011/0206654 A1 F.G. 6 3 O O O 2 5 O O 2OOO ... 1500 1 OOO. 500 O 50 100 200 400 clAP in Drinking Water (UIml) Patent Application Publication Aug. 25, 2011 Sheet 7 of 7 US 2011/0206654 A1 FIG. 7 --:::::: Day clAPIVehicle r Streptomycin - tù cAPVehicle -- - - - - - - - - - - - - - - - - Streptomycin - - - - - - - - - - - - - - - - US 2011/0206654 A1 Aug. 25, 2011 METHODS OF MODULATING Nguyen, Arch Intern Med 162:2177, 2002; Bartlett, N Engl J GASTRONTESTINAL TRACTFLORA Med, 346:334, 2002; McFarland, Dig Dis, 16:292, 1998: LEVELS WITH ALKALINE PHOSPHATASE Wistrom et al., J Antimicrob Chemother, 47:43, 2001; Mar teau et al., Aliment Pharmacol Ther; 20 Suppl 4:18, 2004: CROSS REFERENCE TO RELATED Seksik et al., Gut, 52:237, 2003; Kleessen, Scand J Gastro APPLICATION enterol, 37:1034, 2002: Brenchley et al., Nat Med, 12:1365, 0001. This application claims priority from U.S. Provi 2006; Mai and Morris, J Nutr. 134:459, 2004; Seksik et al., sional Application Ser. No. 61/093,129, filed on Aug. 29. Gut, 52:237, 2003; Marteau et al., Aliment Pharmacol Ther 2008, which is incorporated herein by reference in its entirety. 20 Suppl 4:18, 2004; Kleessen et al., Scand.J Gastroenterol, 37: 1034, 2002: Pool-Zobel et al., Br. J Nutr 87 Suppl2:S273, FEDERALLY SPONSORED RESEARCHOR 2002). Epidemiological studies have also linked altered com DEVELOPMENT position of the intestinal microbiota with the development of rheumatoid arthritis, eczema, and other allergic diseases 0002 The research described in this application was made (Lupp and Finlay, Curr Biol, 15:R235, 2005; Toivanen, Ann with U.S. Government support under grant numbers Rheum Dis, 62:807, 2003) and aberrant microbiota during R01DK050623 and R01 DK47186 awarded by the National childhood may predispose one to the development of inflam Institutes of Health. The Government may have certain rights matory gut diseases and diarrhea (Juntunen et al., Clin Diagn in this invention. Lab immunol, 8:293, 2001; Arvola et al., Pediatrics, 104:e64, 1999). TECHNICAL FIELD 0006. However, the fundamental mechanisms that govern 0003. This invention relates to methods of modulating the normal homeostatic number and composition of the intes levels of gastrointestinal tract flora with alkaline phosphatase. tinal microbiota remain poorly understood. Factors that have been implicated in influencing the gastrointestinal tract flora BACKGROUND include antimicrobial peptides, age, nutrition, immune status, 0004 Through millions of years of evolution, metazoans luminal pH, fecal transit time, interactions among compo have developed mechanisms that maintain a mutually benefi nents of the flora, available fermentable materials, medica cial symbiotic relationship with commensal microbiota. tions, stress, general living conditions, etc. (Collins and Gib Intestinal microbes play a pivotal role in maintaining human son, Am J Clin Nutr, 69:1052S, 1999; Gibson and Fuller, J health and wellbeing (Marchesi and Shanahan, Curr Opin Nutr; 130:391S, 2000). Infect Dis, 20:508, 2007: Blaut and Clavel, J Nutr; 137:751S, SUMMARY 2007; Turnbaugh et al., Nature, 444:1027, 2006: Dethlefsen et al., Trends Ecol Evol., 21:517, 2006; Lupp and Finlay, Curr 0007. This invention is based, at least in part, on the dis Biol, 15:R235, 2005; Backhed et al., Science, 307:1915, covery that administering, e.g., orally, an alkaline phos 2005; Mai and Morris, Jr., JNutr. 134:459, 2004: Falk et al., phatase, e.g., an intestinal alkaline phosphatase, to a subject Microbiol Mol Biol Rev, 62:1157, 1998). Mucosa-associated in a therapeutically effective amount, can rapidly restore gas bacteria, in conjunction with the mucus-layer and the epithe trointestinal tract microbiotato normal levels and/or function, lium, provide a direct selective barrier between the gutlumen e.g., lost during antimicrobial treatment, and can thus safely and systemic sites, allowing the absorption of nutrients, and easily reduce one or more symptoms such as diarrhea, water, and electrolytes, while inhibiting the translocation of e.g., antibiotic-associated diarrhea (AAD), with little or no pathogenic microbes or toxins. The microbiota synthesizes side effects. The new methods are effective for a variety of Vitamins, detoxifies toxins, and also provides additional Subjects including humans and animals. Such as laboratory energy for the epithelial cells by fermentation of otherwise animals, e.g., mice, rats, rabbits, or monkeys, or domesticated non-digestible food components, such as fiber and starch. and faun animals, e.g., cats, dogs, goats, sheep, pigs, cows, Commensal organisms also participate in the maturation and horses, and birds, e.g., chickens and turkeys. maintenance of the gastrointestinal tract immune system, 0008. In one aspect, the invention features methods of keeping the intestinal epithelia in a state of physiological modulating gastrointestinal tract flora levels in a Subject, Such inflammation that appears to be critical for a rapid response as a human or animal Subject. The methods include adminis against potentially harmful bacteria. tering to the Subject an amount of an alkaline phosphatase 0005. The human gastrointestinal tract harbors approxi effective to increase the number of commensal bacteria in the mately 10' bacteria that are composed of between 300 and gastrointestinal tract, decrease the number of pathogenic bac 1,000 different species (Kullberg, Nature, 453:602, 2008: teria in the gastrointestinal tract, or both increase the number Baba et al., J. Leukoc Biol, 84:468, 2008). A reduction in the of commensal bacteria and decrease the number of patho normal levels and function of flora that occur naturally in the genic bacteria in the gastrointestinal tract of the Subject. gastrointestinal tract of animals and in humans can cause 0009. In another general aspect, the invention features various symptoms. Dysbiosis, defined as dysregulation of the methods of reducing one or more symptoms of antibiotic normal homeostasis of the intestinal microbiota, has been associated diarrhea (AAD) or Clostridium difficile-associated implicated in the pathogenesis of myriad disease conditions, disease (CDAD) in a subject, the methods including admin including, but not limited to, antibiotic-associated diarrhea istering, e.g., orally, to the Subject an amount of an alkaline (AAD), Clostridium difficile-associated disease (CDAD), phosphatase, e.g., intestinal alkaline phosphatase, effective to acquired immunodeficiency syndrome (AIDS), hypothyroid reduce one or more symptoms of AAD or CDAD. ism, food poisoning, obesity, inflammatory bowel disease 0010. In another aspect, the invention features methods of (IBD), irritable bowel syndrome (IBS), and colorectal carci modulating gastrointestinal tract flora levels in a Subject by noma (Dethlefsen et al., Trends Ecol Evol., 21:517, 2006: administering alkaline phosphatase at or at about the same Schroeder, Am Fam Physician, 71:921, 2005; Hurley and time as a diagnosis of aberrant levels of gastrointestinal tract US 2011/0206654 A1 Aug.