DOCSLIB.ORG

(12) Patent Application Publication (10) Pub. No.: US 2011/0177976 A1 Gordon Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) Patent Application Publication (10) Pub. No.: US 2011/0177976 A1 Gordon Et Al 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&gt;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 &gt; 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.
Load more

Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • Doctoral Dissertation Template
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By QICHAO TU Norman, Oklahoma 2014 METAGENOMIC INSIGHTS INTO MICROBIAL COMMUNITY RESPONSES TO LONG-TERM ELEVATED CO2 A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Jizhong Zhou, Chair ______________________________ Dr. Meijun Zhu ______________________________ Dr. Fengxia (Felicia) Qi ______________________________ Dr. Michael McInerney ______________________________ Dr. Bradley Stevenson © Copyright by QICHAO TU 2014 All Rights Reserved. Acknowledgements At this special moment approaching the last stage for this degree, I would like to express my gratitude to all the people who encouraged me and helped me out through the past years. Dr. Jizhong Zhou, my advisor, is no doubt the most influential and helpful person in pursuing my academic goals. In addition to continuous financial support for the past six years, he is the person who led me into the field of environmental microbiology, from a background of bioinformatics and plant molecular biology. I really appreciated the vast training I received from the many interesting projects I got involved in, without which I would hardly develop my broad experienced background from pure culture microbial genomics to complex metagenomics. Dr. Zhili He, who played a role as my second advisor, is also the person I would like to thank most. Without his help, I could be still struggling working on those manuscripts lying in my hard drive. I definitely learned a lot from him in organizing massed results into logical scientific work—skills that will benefit me for life.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • A Metagenomic Β-Glucuronidase Uncovers a Core Adaptive Function of the Human Intestinal Microbiome
    A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome Karine Gloux, Olivier Berteau, Hanane El oumami, Fabienne Béguet, Marion Leclerc, and Joël Doré1 Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1319 Micalis, F-78352 Jouy en Josas, France Edited by Todd R. Klaenhammer, North Carolina State University, Raleigh, NC, and approved June 1, 2010 (received for review February 4, 2010) In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; XIVa), major reservoirs of BG-positive bacteria (11), are dys- E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some biosis markers in Crohn’s disease (12–15) and in intestinal carci- of the beneficial effects of dietary compounds. Despite their biolog- nogenesis (16). Nevertheless, the relative contribution of bacterial ical significance, investigations are hampered by the fact that only strains to the global intestinal BG activity remains unclear, and a few BGs have so far been studied. A functional metagenomic the molecular bases are essentially unknown. approach was therefore performed on intestinal metagenomic In the human digestive tract, bacterial BGs are known to be libraries using chromogenic glucuronides as probes. Using this strat- distributed among the Enterobacteriaceae family in some Firmi- egy, 19 positive metagenomic clones were identified but only one cutes genera (Lactobacillus, Streptococcus, Clostridium, Rumino- exhibited strong β-D-glucuronidase activity when subcloned into an coccus, Roseburia, and Faecalibacterium) and in a specific species expression vector. The cloned gene encoded a β-D-glucuronidase of Actinobacteria (Bifidobacterium dentium) (11, 17, 18). On (called H11G11-BG) that had distant amino acid sequence homolo- the basis of their sequence, BGs are highly homologous to gies and an additional C terminus domain compared with known β-galactosidases and only a few of them have been investigated β fi -D-glucuronidases.
    [Show full text]
  • Targeting the Gut Microbiome in Allogeneic Hematopoietic Stem Cell Transplantation
    medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Targeting the gut microbiome in allogeneic hematopoietic stem cell transplantation Marcel A. de Leeuw & Manuel X. Duval, GeneCreek List of Figures Contents 1 GM composition evolution across allo-HSCT . 2 I 2 Baseline GM composition and conditioning level . 3 NTRODUCTION 1 3 Top 10 variable importances estimated by the ran- dom survival forest models .............. 3 MATERIALS & METHODS 2 4 Biological safety level and aGvHD at onset . 3 DATA ANALYSIS .................. 2 5 Relative importance of regressors explaining the RESULTS 2 aGvHD status ...................... 3 OVERALL GM COMPOSITION EVOLUTION ACROSS 6 Co-exclusion by and co-occurrence with QPS species 4 ALLO-HSCT ................. 2 List of Tables CORRELATION BETWEEN CONDITIONING AND THE GM 2 BASELINE GM COMPOSITION AND SURVIVAL . 3 1 Prospective data sets used in the study . 1 AGVHD CASES, CONTROLS AND GM COMPOSITION 3 IMMUNO-MODULATING METABOLITES . 4 IN SILICO SCREENING OF THE ALLO-HSCT GM . 4 DISCUSSION 4 CONCLUSIONS 6 SUMMARY 6 DECLARATIONS 6 BIBLIOGRAPHY 7 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. Revised manuscript medRxiv preprint doi: https://doi.org/10.1101/2020.04.08.20058198; this version posted June 9, 2020.
    [Show full text]
  • Clostridium Amazonitimonense, Clostridium Me
    ORIGINAL ARTICLE Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’, ‘Clostridium merdae’, ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’ M. T. Alou1, S. Ndongo1, L. Frégère1, N. Labas1, C. Andrieu1, M. Richez1, C. Couderc1, J.-P. Baudoin1, J. Abrahão2, S. Brah3, A. Diallo1,4, C. Sokhna1,4, N. Cassir1, B. La Scola1, F. Cadoret1 and D. Raoult1,5 1) Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France, 2) Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 3) Hopital National de Niamey, BP 247, Niamey, Niger, 4) Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal and 5) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2T, ‘Clostridium massilidielmoense’ strain MT26T, ‘Clostridium nigeriense’ strain Marseille-P2414T and ‘Clostridium merdae’ strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation. © 2017 Published by Elsevier Ltd. Keywords: ‘Clostridium amazonitimonense’, ‘Clostridium massilidielmoense’, ‘Clostridium merdae’, ‘Clostridium nigeriense’, culturomics, emerging bacteria, human microbiota, taxonogenomics Original Submission: 18 August 2017; Revised Submission: 9 November 2017; Accepted: 16 November 2017 Article published online: 22 November 2017 intestine [1,4–6].
    [Show full text]
  • Crowdsourced Study of Children with Autism and Their Typically
    bioRxiv preprint doi: https://doi.org/10.1101/319236; this version posted May 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Crowdsourced study of children with autism and their typically 2 developing siblings identifies differences in taxonomic and predicted 3 function for stool-associated microbes using exact sequence variant 4 analysis. 5 Maude M David1,2, Christine Tataru1, Jena Daniels1, Jessey Schwartz1, Jessica Keating1, Jarrad Hampton-Marcell3, Neil 6 Gottel4, Jack A. Gilbert3,4, Dennis P. Wall1,5* 7 1 Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA 8 2 Department of Microbiology, Oregon State University, Corvallis, OR, USA 9 3 Bioscience Division, The Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA 10 4 Department of Surgery, The Microbiome Center, University of Chicago, Chicago, Illinois, USA 11 5 Department of Biomedical Data Science, Stanford University, Stanford, CA, USA 12 *Corresponding Author: 13 Dennis P. Wall, Ph.D. 14 Department of Pediatrics, Division of Systems Medicine 15 Stanford University 16 1265 Welch Rd, Suite X141, Stanford, CA 94305 17 P: 650-497-0921 18 E: [email protected] 19 20 Keywords 21 Autism spectrum disorder, microbiome, crowdsource, 16S ribosomal sequencing, Clostridiales, Lachnospiraceae, butyrate 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/319236; this version posted May 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Germinants and Their Receptors in Clostridia
    JB Accepted Manuscript Posted Online 18 July 2016 J. Bacteriol. doi:10.1128/JB.00405-16 Copyright © 2016, American Society for Microbiology. All Rights Reserved. 1 Germinants and their receptors in clostridia 2 Disha Bhattacharjee*, Kathleen N. McAllister* and Joseph A. Sorg1 3 4 Downloaded from 5 Department of Biology, Texas A&M University, College Station, TX 77843 6 7 Running Title: Germination in Clostridia http://jb.asm.org/ 8 9 *These authors contributed equally to this work 10 1Corresponding Author on September 12, 2018 by guest 11 ph: 979-845-6299 12 email: [email protected] 13 14 Abstract 15 Many anaerobic, spore-forming clostridial species are pathogenic and some are industrially 16 useful. Though many are strict anaerobes, the bacteria persist in aerobic and growth-limiting 17 conditions as multilayered, metabolically dormant spores. For many pathogens, the spore-form is Downloaded from 18 what most commonly transmits the organism between hosts. After the spores are introduced into 19 the host, certain proteins (germinant receptors) recognize specific signals (germinants), inducing 20 spores to germinate and subsequently outgrow into metabolically active cells. Upon germination 21 of the spore into the metabolically-active vegetative form, the resulting bacteria can colonize the 22 host and cause disease due to the secretion of toxins from the cell. Spores are resistant to many http://jb.asm.org/ 23 environmental stressors, which make them challenging to remove from clinical environments. 24 Identifying the conditions and the mechanisms of germination in toxin-producing species could 25 help develop affordable remedies for some infections by inhibiting germination of the spore on September 12, 2018 by guest 26 form.
    [Show full text]
  • ( 12 ) United States Patent
    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
    [Show full text]
  • Interactions Between Host Genetics and Gut Microbiota Determine Susceptibility to CNS Autoimmunity
    Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity Theresa L. Montgomerya,1, Axel Künstnerb,c,1, Josephine J. Kennedya, Qian Fangd, Lori Asariand, Rachel Culp-Hille, Angelo D’Alessandroe, Cory Teuscherd, Hauke Buschb,c, and Dimitry N. Krementsova,2 aDepartment of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05401; bMedical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; cInstitute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany; dDepartment of Medicine, Immunobiology Division, University of Vermont, Burlington, VT 05401; and eDepartment of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO 80045 Edited by Dennis L. Kasper, Harvard Medical School, Boston, MA, and approved August 26, 2020 (received for review February 23, 2020) Multiple sclerosis (MS) is an autoimmune disease of the central circulation to directly impact distal sites, including the brain (11, nervous system. The etiology of MS is multifactorial, with disease 12). With regard to MS, a number of recent case-control studies risk determined by genetics and environmental factors. An emerg- have demonstrated that the gut microbiome of MS patients differs ing risk factor for immune-mediated diseases is an imbalance from that of their healthy control counterparts. Some broad fea- in the gut microbiome. However, the identity of gut microbes as- tures, such as decreased abundance of putative short-chain fatty sociated with disease risk, their mechanisms of action, and the acid (SCFA)-producing bacteria and expansion of Akkermansia, interactions with host genetics remain obscure. To address these have been observed consistently across several studies (13–19).
    [Show full text]
  • MICRO-ORGANISMS and RUMINANT DIGESTION: STATE of KNOWLEDGE, TRENDS and FUTURE PROSPECTS Chris Mcsweeney1 and Rod Mackie2
    BACKGROUND STUDY PAPER NO. 61 September 2012 E Organización Food and Organisation des Продовольственная и cельскохозяйственная de las Agriculture Nations Unies Naciones Unidas Organization pour организация para la of the l'alimentation Объединенных Alimentación y la United Nations et l'agriculture Наций Agricultura COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS Chris McSweeney1 and Rod Mackie2 The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. 1 Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, 306 Carmody Road, St Lucia Qld 4067, Australia. 2 University of Illinois, Urbana, Illinois, United States of America. This document is printed in limited numbers to minimize the environmental impact of FAO's processes and contribute to climate neutrality. Delegates and observers are kindly requested to bring their copies to meetings and to avoid asking for additional copies. Most FAO meeting documents are available on the Internet at www.fao.org ME992 BACKGROUND STUDY PAPER NO.61 2 Table of Contents Pages I EXECUTIVE SUMMARY .............................................................................................. 5 II INTRODUCTION ............................................................................................................ 7 Scope of the Study ...........................................................................................................
    [Show full text]
  • Depression and Microbiome—Study on the Relation and Contiguity Between Dogs and Humans
    applied sciences Article Depression and Microbiome—Study on the Relation and Contiguity between Dogs and Humans Elisabetta Mondo 1,*, Alessandra De Cesare 1, Gerardo Manfreda 2, Claudia Sala 3 , Giuseppe Cascio 1, Pier Attilio Accorsi 1, Giovanna Marliani 1 and Massimo Cocchi 1 1 Department of Veterinary Medical Science, University of Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Italy; [email protected] (A.D.C.); [email protected] (G.C.); [email protected] (P.A.A.); [email protected] (G.M.); [email protected] (M.C.) 2 Department of Agricultural and Food Sciences, University of Bologna, Via del Florio 2, 40064 Ozzano Emilia, Italy; [email protected] 3 Department of Physics and Astronomy, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-051-209-7329 Received: 22 November 2019; Accepted: 7 January 2020; Published: 13 January 2020 Abstract: Behavioral studies demonstrate that not only humans, but all other animals including dogs, can suffer from depression. A quantitative molecular evaluation of fatty acids in human and animal platelets has already evidenced similarities between people suffering from depression and German Shepherds, suggesting that domestication has led dogs to be similar to humans. In order to verify whether humans and dogs suffering from similar pathologies also share similar microorganisms at the intestinal level, in this study the gut-microbiota composition of 12 German Shepherds was compared to that of 15 dogs belonging to mixed breeds which do not suffer from depression. Moreover, the relation between the microbiota of the German Shepherd’s group and that of patients with depression has been investigated.
    [Show full text]