US 20110177976A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2011/0177976 A1 Gordon et al. (43) Pub. Date: Jul. 21, 2011 (54) METHODS FOR PROMOTING WEIGHT Related U.S. Application Data LOSS AND ASSOCATED ARRAYS (60) Provisional application No. 61/076,887, filed on Jun. (75) Inventors: Jeffrey I. Gordon, St. Louis, MO 30, 2008, provisional application No. 61/101.011, (US); Peter Turnbaugh, St. Louis, filed on Sep. 29, 2008. MO (US) Publication Classification (73) Assignee: THE WASHINGTON (51) Int. Cl. UNIVERSITY, St. Louis, MO C40B 40/08 (2006.01) (US) C40B 40/10 (2006.01) (21) Appl. No.: 13/002,137 (52) U.S. Cl. ............................................. 506/17:506/18 (22) PCT Fled: Jun. 30, 2009 (57) ABSTRACT (86) PCT NO.: PCT/USO9/49253 Methods of modulating body fat or weight loss are presented Nucleic acid and protein microarrays that comprise biomol S371 (c)(1), ecules associated with an obese host microbiome or a lean (2), (4) Date: Mar. 29, 2011 host microbiome are utilized for analysis. Patent Application Publication Jul. 21, 2011 Sheet 1 of 50 US 2011/0177976 A1 SEE FIG 11 SEE FIG 12 F.G. 1 SEE FIG 1.3 SEE FIG 1.4 SEE FG 15 Patent Application Publication Jul. 21, 2011 Sheet 2 of 50 US 2011/0177976 A1 CONTAT FIG. 12 FIG 11 Patent Application Publication Jul. 21, 2011 Sheet 3 of 50 US 2011/0177976 A1 CONT FROM FG 11 CONT. A. F.G. 1.3 F.G. 12 Patent Application Publication Jul. 21, 2011 Sheet 4 of 50 US 2011/0177976 A1 CONT FROM FIG. 12 CONT. AT F.G. 14 F.G. 13 Patent Application Publication Jul. 21, 2011 Sheet 5 of 50 US 2011/0177976 A1 CONT. FROM FG 1.3 CONTAT FIG. 15 F.G. 14 Patent Application Publication Jul. 21, 2011 Sheet 6 of 50 US 2011/0177976 A1 CONT. FROM FG 14 FG 15 Patent Application Publication Jul. 21, 2011 Sheet 7 of 50 US 2011/0177976 A1 0.82 0.80 .8 i . r i . i.88 88 treated a Seif vice ity; it 122 102 8 k s 2 4. 2 2 2000 4000 6000 8000 10000 Number of sequences FIG 2 Patent Application Publication Jul. 21, 2011 Sheet 8 of 50 US 2011/0177976 A1 A 0.66 B ors Fisii-ie:gth ,83 8 8,8: & s 0.63 8,82 36 5 8,8 .38 treated Relate: w unrelated Reiate C 16 v213 i 12 s -sa 8 as: e 8 . 4. (it 8. 8. Nitroer of sequences FIG 3 Patent Application Publication Jul. 21, 2011 Sheet 9 of 50 US 2011/0177976 A1 D 8. Full-length 4 Elean 2.5-3 III it obese 2 11 II g 1.5 I i s 100 s 200 Niniber of sequences 4000 S 8 isier of sectieces FIG 3 Patent Application Publication Jul. 21, 2011 Sheet 10 of 50 US 2011/0177976 A1 'l Full-length s so to so 20 Number of sequences FIG 3F Patent Application Publication Jul. 21, 2011 Sheet 11 of 50 US 2011/0177976 A1 A 8 .8 3.8 . ear e8. tireiated eated .8 ,8. .8 . .8- Cese Othese treated reiated FIG 4 Patent Application Publication Jul. 21, 2011 Sheet 12 of 50 US 2011/0177976 A1 SEE FIG 51 SEE FIG 52 FIG 5 SEE FIG 53 SEE FIG 54 SEE FIG 55 SEE FIG 56 Patent Application Publication Jul. 21, 2011 Sheet 13 of 50 US 2011/0177976 A1 CON. A FG, 5.2 FIG 51 Patent Application Publication Jul. 21, 2011 Sheet 14 of 50 US 2011/0177976 A1 CONT FROM FG, 5.1 F832 . kees F838: CON AT FIG. 5.3 FIG 52 Patent Application Publication Jul. 21, 2011 Sheet 15 of 50 US 2011/0177976 A1 CON FROM FIG. 5.2 CONT. AT FIG. 54. F.G. 5.3 Patent Application Publication Jul. 21, 2011 Sheet 16 of 50 US 2011/0177976 A1 CONT FROM FG 53 CONTAT FIG 5.5 F.G. 54 Patent Application Publication Jul. 21, 2011 Sheet 17 of 50 US 2011/0177976 A1 CONT. FROM FG, 5.4 F FS: CONT. ATFG. 5.6 FIG 55 Patent Application Publication Jul. 21, 2011 Sheet 18 of 50 US 2011/0177976 A1 CONT FROM FIG 55 FIG 5.6 Patent Application Publication Jul. 21, 2011 Sheet 19 of 50 US 2011/0177976 A1 initial timepoint Second timepoint O 1O 2 30 4, 5 6.O 70 30 O CO. O. 10 20 30 40 50 60 7O 8O 90 OO Relative abundance (% of 16S rRNA sequences) ... Actioacteria Frictes Eacterocetes Proteobacteria. Other FG 6 Patent Application Publication Jul. 21, 2011 Sheet 20 of 50 US 2011/0177976 A1 8: *&^ 88% of itivitiais ::::: *: 83% of it civicas *::::::::::: Ricycities / 8: w8 88% fiftivisitas / 8.338 civicas 88: 8:::iii.33s 38: 4. 8. 8: 88: 888 288 300 88:38: {:f3>8888&is&isis: FIG 7 Patent Application Publication Jul. 21, 2011 Sheet 21 of 50 US 2011/0177976 A1 * SO 8 it r:- 58 ft &x 28 it - 258 • 3 38 : * : : 338 338 : fiti gee 20 30 40 50 60 to 80 90 % identity F.G. 8 Patent Application Publication Jul. 21, 2011 Sheet 22 of 50 US 2011/0177976 A1 4.88 2 &&3. s * st 20 30 40 50... 60 to 80 90 100 3. c. 8 "it Bit-score wxw 388 it ''''''. 238 it * 3: : :::::::::::: 38 it D *::::::::::*: ) t S8 ri S8 it 8 frigee 8. s 4. 2 Patent Application Publication Jul. 21, 2011 Sheet 23 of 50 US 2011/0177976 A1 E - e 0.8 to.6. as 0.4 0.2 * 8 838 it 2 3 4 5 6 8 * i38 st &M 2 % identity -- an F S8 ft 8 frigee S ,3.k8 a. rw8xxx::::::::::::::::M 2 3 4 5 S 3 38 Bit-score FIG 8 Patent Application Publication Jul. 21, 2011 Sheet 24 of 50 US 2011/0177976 A1 . .2 * 38 ::::::::::::: 33 as 5 t 8 futi gene .8 4. 0.2 . 2 3 4 8 8 % identity FIG 8 Patent Application Publication Jul. 21, 2011 Sheet 25 of 50 US 2011/0177976 A1 f to.8 in0.6 a a 0.4 s 0.2 20 30 40 50 6070 80 90 100 Bit-score it futi gene FIG 8 Patent Application Publication Jul. 21, 2011 Sheet 26 of 50 US 2011/0177976 A1 6"50MET Patent Application Publication Jul. 21, 2011 Sheet 27 of 50 US 2011/0177976 A1 s {x& Bacteroidetes xT& S. ki Firicites x & S S S S & so ss so "ss" to vs " so as "go 'gs too Percent icientity to reference geitones FIG 10 Patent Application Publication Jul. 21, 2011 Sheet 28 of 50 US 2011/0177976 A1 Lean/Overweight F G. 1. 1. Obese Alistipes putrednis v2.1 1 O O 6 O 2 O Bacteroides fragilis NCTC9343 100 60 20.: Bacteroides fragilis YCH46 ----------------is: Bactero ides ovatus V2. 100 3-c.c. ::::::::::::8.4.4.4.4.4.4.4.4.4.4.4.4.4,8.4.4.4.4.8 6 O 2 O ser ---. Bacteroides sterCoris v2.1 100 60 20. Patent Application Publication Jul. 21, 2011 Sheet 29 of 50 US 2011/0177976 A1 lean?Overweight F G. 11 Obese Clostridium leptum v3.1 100: 60 Mb Mb Patent Application Publication Jul. 21, 2011 Sheet 30 of 50 US 2011/0177976 A1 Lean/Overweight F G. 1 1. Obese Collinsella aerofaciens v3.1 100: w s s s 6O :s s s s Methanobrevibacter Smithii ACC35061 Patent Application Publication Jul. 21, 2011 Sheet 31 of 50 US 2011/0177976 A1 Lean/Overweight FIG 11 Obese Bacteroides distasonis ACC8503 Ruminococcus gnavus v. 100 Ruminococcus obeum v3.1 1 OO 6 O 2 O Patent Application Publication Jul. 21, 2011 Sheet 33 of 50 US 2011/0177976 A1 C 388S: s 3. 3. 2. 3. 38 S. S} React eigii; D 23: 38 88& S. 838 e88 > Sample Sarpie2 s. As threshot: e-waites:8 8-waite<18 8waitext e-wak-ex8, hitscorex$8%icientity-38 FG, 12 Patent Application Publication Jul. 21, 2011 Sheet 34 of 50 US 2011/0177976 A1 A A 83% 83% ($3. :: % 3% 8. 38% 88: 33% % 1% 8: 3. 38% & & 2 & 3 8 8 & & 38 &: 8S - 8S S . is . is. k-. 3 . & . is is i. riricites Bacterchitiates Acticeacteria oteobacteria FIG. 13 « Other Patent Application Publication Jul. 21, 2011 Sheet 35 of 50 US 2011/0177976 A1 Vicrobiore sequences D 38% 83. 88% 48%. 88: 8. 8%, 88: 28% 8% i s i s s s firictites Bactercitietes Actiidacteria prote acteria FG 13 x tet Patent Application Publication Jul. 21, 2011 Sheet 36 of 50 US 2011/0177976 A1 88::::::::::::::::: *x-ext: 2: fs 88.8 Kerence gast gessssss :8S ra&A fragments -------------- 2: is FS2& 3. 28 3x3 E8 28. 48 F: SR 3R8s; Sox 323s scs s as: 88: F.G. 14A Patent Application Publication Jul. 21, 2011 Sheet 37 of 50 US 2011/0177976 A1 B 1. 8 2 -8, 8 -0.4 -8.2. { 0.2 0.4 . PC1 (20%) 9.9.3.9.9. 56789. 9 4 Win WS Win vs Unreated TWi Non pairs FIG 14. Patent Application Publication Jul. 21, 2011 Sheet 38 of 50 US 2011/0177976 A1 8 8 8. 388 8:8 S{{: 20000 25000 8.338 of $88:38:ces FG 15 Patent Application Publication Jul. 21, 2011 Sheet 39 of 50 US 2011/0177976 A1 W79?,"50MET Patent Application Publication Jul.