US 2014.0128289A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0128289 A1 Gordon et al. (43) Pub. Date: May 8, 2014 (54) METHODS OF PROMOTING WEIGHT LOSS (60) Provisional application No. 61/076,887, filed on Jun. AND ASSOCATED ARRAYS 30, 2008, provisional application No. 61/101.011, filed on Sep. 29, 2008. (71) Applicant: The Washington University, St Louis, MO (US) Publication Classification (72) Inventors: Jeffrey I. Gordon, St. Louis, MO (US); (51) Int. C. Peter Turnbaugh, St. Louis, MO (US) CI2O I/68 (2006.01) GOIN33/569 (2006.01) (73) Assignee: The Washington University, St. Louis, (52) U.S. C. MO (US) CPC .......... CI2O 1/689 (2013.01); G0IN33/56911 (2013.01) (21) Appl. No.: 14/147,163 USPC ............................................... 506/16:506/18 (22) Filed: Jan. 3, 2014 (57) ABSTRACT Related U.S. Application Data The invention encompasses methods of modulating body fat (63) Continuation of application No. 13/002,137, filed on or weight loss. In addition, the invention encompasses arrays Mar. 29, 2011, now abandoned, filed as application that comprise biomolecules associated with an obese host No. PCT/US2009/049253 on Jun. 30, 2009. microbiome or a lean host microbiome. Second timepoit iitiative oint : Actrix:3cteria 8 is 888t::cieties 8xt::tiac:ria & 8ts: Patent Application Publication May 8, 2014 Sheet 1 of 50 US 2014/O128289 A1 SEE FIG 11 SEE FG 12 8 r: FG SEE FG 1.3 SEE FIG 1.4 SEE FG 15 Patent Application Publication May 8, 2014 Sheet 2 of 50 US 2014/O128289 A1 CONT. A FIG. 1.2 FIG 11 Patent Application Publication May 8, 2014 Sheet 3 of 50 US 2014/O128289 A1 CONT. FROM FIG. 1.1 CONT. AT FIG. 1.3 FIG 12 Patent Application Publication May 8, 2014 Sheet 4 of 50 US 2014/O128289 A1 CONT. FROM FIG. 1.2 CONT. ATFIG. 1.4 FIG 1.3 Patent Application Publication May 8, 2014 Sheet 5 of 50 US 2014/O128289 A1 CON. FROM FIG. 1.3 CONT. A FIG. 1.5 F.G. 14 Patent Application Publication May 8, 2014 Sheet 6 of 50 US 2014/O128289 A1 CONT. FROM FIG. 14 FIG 1.5 Patent Application Publication May 8, 2014 Sheet 7 of 50 US 2014/O128289 A1 A is a 8. 0.78 i 0.76 0.74 0.72 t, 3.88. 8. treated a Se: wit: yi-Yi 102 8 8.2. ea & Othese {{ 8. 88: { Nikitixer of sequences FIG 2 Patent Application Publication May 8, 2014 Sheet 8 of 50 US 2014/O128289 A1 A 0.66 raisiegt. s 8 3.8& 83 s: “s i 3 .8 *: i: .8 5 .8 3.38 featex ea: i: 888c: related C 16 v213 8.2 8 : 8. 88: t Nisixer of sexiences FIG 3 Patent Application Publication May 8, 2014 Sheet 9 of 50 US 2014/O128289 A1 Full-length 3.3. so too so 200 hitixer of seriences 28 it is 8 Nissaher of sequences FIG 3 Patent Application Publication May 8, 2014 Sheet 10 of 50 US 2014/O128289 A1 'l Full-length so o 150 Ninter of secuences FIG 3F Patent Application Publication May 8, 2014 Sheet 11 of 50 US 2014/O128289 A1 A 8. , - ,8. 8. ea e8: tireiaki &iate 0.81 .8 . .8 ..y . ses: sess treated reiated F.G. 4 Patent Application Publication May 8, 2014 Sheet 12 of 50 US 2014/O128289 A1 SEE FIG. 5, 1 SEE FIG 52 F.G. 5 SEE FIG 53 SEE FIG 54 SEE FIG 55 SEE FIG 5.6 Patent Application Publication May 8, 2014 Sheet 13 of 50 US 2014/O128289 A1 CONTAT FIG. 5.2 FIG 51 Patent Application Publication May 8, 2014 Sheet 14 of 50 US 2014/O128289 A1 CONT. FROM FIG. 5.1 3: 8:38: *:::::::::: &: CONT. A FIG. 5.3 FIG 52 Patent Application Publication May 8, 2014 Sheet 15 of 50 US 2014/O128289 A1 CONT. FROM FIG. 5.2 CON AT FIG. 5.4 FIG 53 Patent Application Publication May 8, 2014 Sheet 16 of 50 US 2014/O128289 A1 CONT. FROM FIG. 5.3 CONT. AT FIG. 5.5 F.G. 54 Patent Application Publication May 8, 2014 Sheet 17 of 50 US 2014/O128289 A1 CONT. FROM FIG. 5.4 FSX F: FE8 F8 Fly" CON. A FIG. 5.6 FIG 55 Patent Application Publication May 8, 2014 Sheet 18 of 50 US 2014/O128289 A1 CONT. FROM FIG. 5.5 FIG 56 Patent Application Publication May 8, 2014 Sheet 19 of 50 US 2014/O128289 A1 initia inepoint Second fiegint A O) o al as w 9 (0 Relative abundance (% of 16S rRNA sequences) : Actioacteria & ificates & Bacteroicieties : roteoacteria & their F G 6 Patent Application Publication May 8, 2014 Sheet 21 of 50 US 2014/O128289 A1 4.s8 83 ::::::: 88 it : : 283 : * 33 : 388 ft 38 : as : 8 83 it fisii gene s 20 30 40 50 60 70 80 90 % identity FIG 8 Patent Application Publication May 8, 2014 Sheet 22 of 50 US 2014/O128289 A1 se & 8 5 9 so s ce is 40 8 . $ox 20 20 30 40 50 . 60 to 80 90 100 .::::::::... E."8 Bit-score w:W 38 st ''''''-::::::::::::... 8 : 383 : : 3S D *:::::::: & * - & 83 : 883 : fisii ge:38 Patent Application Publication May 8, 2014 Sheet 23 of 50 US 2014/O128289 A1 E . 8 . 2 38 : 8 : 2 3. : s 80 o::...'... S8 : 8 s identityx (xx 238 : : 3 : : 3S : *::::::::::::::::::::::::::: $8 : 3 : 883 : . 8. ::::::. 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Bacteroides stercoris M Mb Patent Application Publication May 8, 2014 Sheet 29 of 50 US 2014/O128289 A1 P2 Lean/Overweight F G. 11 Obese Bacteroides thetaiotaOmicron WP15482 Bifidobacterium adolescentis v. Bifidobacterium longum NCC2705 OO 26OO 1 O O 6 O Mb Vb Patent Application Publication May 8, 2014 Sheet 30 of 50 US 2014/O128289 A1 P3 Lean/Overweight F G. 11 Obese Coinsella aerofaciens v3.1 Dorea longicatena v2.1 100 60 Eubacterium Siraeum W3. Faecalibacterium prausnitzii M21/2 v2.1 100 Methanobrevibacter Smithii ACC3506 Patent Application Publication May 8, 2014 Sheet 31 of 50 US 2014/O128289 A1 FIG 11 P4 Lean/Overweight Obese Bacteroides distasonis ATCC8503 100: 60 . s.s. s. s. s. s.s.. .s.. .s.. .s.. .s.......s. s. s. X ‘. 1 OO 2 O ---------- ------------ ---- -------- ----------- ------- Ruminococcus torques v2.1 100 Patent Application Publication May 8, 2014 Sheet 32 of 50 US 2014/O128289 A1 3MMMMMM $83 28 388 38 388 S8: 883d 88g: B 250 208 ise 88 88. 88: 28 388 48. 838 888 88.3888g: F.G. 12 Patent Application Publication May 8, 2014 Sheet 33 of 50 US 2014/O128289 A1 C 38 38 8. 88: s: 8: 3: 38 8 * 8 8: 288 388 400 388 888 8eai i8ng: 8 ce as as as see see 8888 icegis 883 8:8s:xxx: 8-ysisex: e-vau:8x8 8waii:8x8,xits carx88,%icietityx88 FIG 12 Patent Application Publication May 8, 2014 Sheet 34 of 50 US 2014/O128289 A1 PCR-based 16S rRNA gene sequences A is: & 88%. s s 88. s: $3. s & 3% w too% & 8 x & 8 & 8 & & : : x s : x & & X: . S . S . 3. 3. i. i. i. i. i. i. i. i. k . ii. iricites 88tergicieties Actioacteria geotacteria FIG 13 x tier Patent Application Publication May 8, 2014 Sheet 35 of 50 US 2014/O128289 A1 Vicrobione sequences : 88% 8. : 3% & - 888 8 88% s 88. & s : 28% F ; : : 88% 6.8% s: 3. S. &: 20% s:------: x& x8 x: x& x8 &: x : x3 x. :. x . .. .. .. .. .. itrictites acteroisiestes Actioacteria roteoacteria FG 13 x tier Patent Application Publication May 8, 2014 Sheet 36 of 50 US 2014/O128289 A1 :: *::::::::::::::::: 8:38. e :38 388 3:383 S28. $88. 88.8 8.33s. 3883: Scy 38: 88:8 2:38: Six: assists ass 88: F.G. 14A Patent Application Publication May 8, 2014 Sheet 37 of 50 US 2014/O128289 A1 B 100 8. (8. , 0.4. ), o2 3.4 s PC1 (20%) 0. 9. 9. 0. 9. 8 0.97 0.98 OS 5 0.94 Win WS Win WS Unrelated TWin Mor pairs FIG 14. Patent Application Publication May 8, 2014 Sheet 38 of 50 US 2014/O128289 A1 3.3 8.8 I 8. g 3:38: 3888 88: 88: 88: 88:38: 83f segsex8& FIG 15 Patent Application Publication May 8, 2014 Sheet 39 of 50 US 2014/O128289 A1 Patent Application Publication May 8, 2014 Sheet 40 of 50 US 2014/O128289 A1 Bacteroidetes Firmicutes GT CE CB CAZy families FG 16B Patent Application Publication May 8, 2014 Sheet 41 of 50 US 2014/O128289 A1 3A g $&##333333333 Patent Application Publication May 8, 2014 Sheet 42 of 50 US 2014/O128289 A1 Bacterial phy :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: S ir ices & 8actero i detes Actioacter a x.