DOCSLIB.ORG

WO 2014/121304 Al 7 August 2014 (07.08.2014) P O P C T

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

(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 2014/121304 Al 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: 1A, Cambridge, MA 02142 (US). GOODMAN, Brian; c/o C12N 1/00 (2006.01) Seres Health, Inc., 161 First Street, Suite 1A, Cambridge, MA 02 142 (US). (21) International Application Number: PCT/US2014/014747 (74) Agents: HUBL, Susan T. et al; Fenwick & West LLP, Silicon Valley Center, 801 California Street, Mountain (22) International Filing Date: View, CA 94041 (US). 4 February 2014 (04.02.2014) (81) Designated States (unless otherwise indicated, for every English (25) Filing Language: kind of national protection available): AE, AG, AL, AM, (26) Publication Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (30) Priority Data: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 61/760,574 4 February 2013 (04.02.2013) US HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 61/760,585 4 February 2013 (04.02.2013) US KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,606 4 February 2013 (04.02.2013) us MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,584 4 February 2013 (04.02.2013) us OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/798,606 15 March 2013 (15.03.2013) us SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/926,918 13 January 2014 (13.01.2014) us TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (71) Applicant: SERES HEALTH, INC. [US/US]; 161 First ZW. Street, Suite 1A, Cambridge, MA 02 142 (US). (84) Designated States (unless otherwise indicated, for every (72) Inventors: AFEYAN, Noubar, B.; c/o Seres Health, Inc., kind of regional protection available): ARIPO (BW, GH, 161 First Street, Suite 1A, Cambridge, MA 02142 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, MCKENZIE, Mary-Jane, Lombardo; c/o Seres Health, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (US). LITCOFSKY, Kevin, Daniel; c/o Seres Health, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Inc., 161 First Street, Suite 1A, Cambridge, MA 02142 MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (US). COOK, David, N.; c/o Seres Health, Inc., 161 First TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, SN, Street, Suite 1A, Cambridge, MA 02142 (US). AFEYAN, KM, ML, MR, NE, TD, TG). Noubar, B.; c/o Seres Health, Inc., 161 First Street, Suite [Continued on nextpage] (54) Title: COMPOSITIONS AND METHODS C, i rt r S 6 7 o Figure 6 (57) Abstract: Provided are defined bacterial compositions for the maintenance or restoration of a healthy microbiota in the gastrointestinal tract of a mammalian subject, and methods for populating the gastrointestinal tract of a subject. Provided also are bacterial formulations for oral or gastric administration to a mammalian subject in an effective amount for prevention or treatment of a gastrointestinal disease, disorder or condition. w o 2014/121304 Al II II II I III IIII II I ll ll III II ill II I II Published: — with sequence listing part of description (Rule 5.2(a)) — with international search report (Art. 21(3)) — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) TITLE [001] Compositions and Methods RELATED APPLICATIONS [002] This application is related to U.S. Provisional Application No. 61/760,584, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,585, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,574, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/760,606, filed on Feb. 4 , 2013, and to U.S. Provisional Application No. 61/926,928, filed on Jan. 13, 2014, which are each incorporated by reference in its entirety for all purposes. REFERENCE TO A SEQUENCE LISTING [003] This application includes a Sequence Listing submitted electronically as a text file named 25968PCT_CRF_sequencelisting.txt, created on Feb. 4 , 2014, with a size of 9 11,051 bytes. The sequence listing is incorporated by reference. BACKGROUND [004] Mammals are colonized by microbes in the gastrointestinal (Gl) tract, on the skin, and in other epithelial and tissue niches such as the oral cavity, eye surface and vagina. The gastrointestinal tract harbors an abundant and diverse microbial community. It is a complex system, providing an environment or niche for a community of many different species or organisms, including diverse strains of bacteria. Hundreds of different species may form a commensal community in the Gl tract in a healthy person, and this complement of organisms evolves from the time of birth to ultimately form a functionally mature microbial population by about 3 years of age. Interactions between microbial strains in these populations and between microbes and the host, e.g. the host immune system, shape the community structure, with availability of and competition for resources affecting the distribution of microbes. Such resources may be food, location and the availability of space to grow or a physical structure to which the microbe may attach. For example, host diet is involved in shaping the Gl tract flora. [005] A healthy microbiota provides the host with multiple benefits, including colonization resistance to a broad spectrum of pathogens, essential nutrient biosynthesis and absorption, and immune stimulation that maintains a healthy gut epithelium and an appropriately controlled systemic immunity. In settings of 'dysbiosis' or disrupted symbiosis, microbiota functions can be lost or deranged, resulting in increased susceptibility to pathogens, altered metabolic profiles, or induction of proinflammatory signals that can result in local or systemic inflammation or autoimmunity. Thus, the intestinal microbiota plays a significant role in the pathogenesis of many diseases and disorders, including a variety of pathogenic infections of the gut. For instance, subjects become more susceptible to pathogenic infections when the normal intestinal microbiota has been disturbed due to use of broad-spectrum antibiotics. Many of these diseases and disorders are chronic conditions that significantly decrease a subject's quality of life and can be ultimately fatal. [006] Manufacturers of probiotics have asserted that their preparations of bacteria promote mammalian health by preserving the natural microflora in the Gl tract and reinforcing the normal controls on aberrant immune responses. See, e.g., U.S. Patent No. 8,034,601 . Probiotics, however, have been limited to a very narrow group of genera and a correspondingly limited number of species; as such, they do not adequately replace the missing natural microflora of the Gl tract in many situations. [007] Thus, there is a need for a method of populating a subject's gastrointestinal tract with a diverse and useful selection of microbiota in order to alter a dysbiosis. In response to the need for durable, efficient, and effective compositions and methods for treatment of Gl diseases by way of restoring or enhancing microbiota functions, Applicants address these and other shortcomings of the art by providing compositions and methods for treating subjects. SUMMARY OF THE INVENTION [008] Disclosed herein are therapeutic compositions comprising a bacterial population comprising at least three but fewer than nine bacterial strains selected from the group consisting of Escherichia coli, Enterococcus faecalis, Clostridium innocuum, Clostridium ramosum, Clostridium bifermentans, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaiotaomicron, and Blautia producta, wherein the composition is formulated for oral or gastric administration to a mammalian subject in an effective amount for prevention or treatment of a gastrointestinal disease, disorder or condition. In some embodiments, the bacterial strains are not a colonic bacterium and/or are not obtained from a fecal culture. In some embodiments, at least one Bacteroides species is detectably present in the mammalian subject prior to administration of the composition or, in other embodiments at least one Bacteroides species is not detectably present in the mammalian subject prior to administration of the composition, but is detectably present in the mammalian subject at least one hour after administration of the composition. In some embodiments, the mammalian subject has not received at least two doses of vancomycin, metronidazole and/or or similar antibiotic compound within one week prior to administration of the therapeutic composition. In some embodiments, a single administration is substantially effective to reduce C. difficile and/or C. difficile toxin content in a mammalian subject to whom the composition is administered. In some embodiments, one strain of E. coli is present in amounts at least 2 , 5 , 10 , 50, 100 or more than 100 times greater than any other strain of E. coli present in the composition. In some embodiments, at least three bacterial strains are not present in the composition in equal ratios or are present in a ratio equivalent to the ratio of the bacterial strains in a reference mammalian subject. In some embodiments, at least one of the bacterial strains is provided in a concentration of greater than 1x1 09 viable bacteria per gram of composition or is provided in a concentration of less than 1x108 viable bacteria per gram of composition.
Recommended publications
  • Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis

    Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis

    GBE Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis Ciaran O’Flynn1,*, Oliver Deusch1, Aaron E. Darling2, Jonathan A. Eisen3,4,5, Corrin Wallis1,IanJ.Davis1,and Stephen J. Harris1 1 The WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, United Kingdom Downloaded from 2The ithree Institute, University of Technology Sydney, Ultimo, New South Wales, Australia 3Department of Evolution and Ecology, University of California, Davis 4Department of Medical Microbiology and Immunology, University of California, Davis 5UC Davis Genome Center, University of California, Davis http://gbe.oxfordjournals.org/ *Corresponding author: E-mail: ciaran.ofl[email protected]. Accepted: November 6, 2015 Abstract Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and at University of Technology, Sydney on January 17, 2016 plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions char- acterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to syn- thesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood.
  • ( 12 ) United States Patent

    ( 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 .
  • The Salivary Microbiome Is Consistent Between Subjects

    The Salivary Microbiome Is Consistent Between Subjects

    www.nature.com/scientificreports OPEN The salivary microbiome is consistent between subjects and resistant to impacts of short-term Received: 19 April 2017 Accepted: 24 August 2017 hospitalization Published: xx xx xxxx Damien J. Cabral1, Jenna I. Wurster1, Myrto E. Flokas2, Michail Alevizakos2, Michelle Zabat1, Benjamin J. Korry1, Aislinn D. Rowan1, William H. Sano1, Nikolaos Andreatos2, R. Bobby Ducharme3, Philip A. Chan3, Eleftherios Mylonakis2, Beth Burgwyn Fuchs2 & Peter Belenky1 In recent years, a growing amount of research has begun to focus on the oral microbiome due to its links with health and systemic disease. The oral microbiome has numerous advantages that make it particularly useful for clinical studies, including non-invasive collection, temporal stability, and lower complexity relative to other niches, such as the gut. Despite recent discoveries made in this area, it is unknown how the oral microbiome responds to short-term hospitalization. Previous studies have demonstrated that the gut microbiome is extremely sensitive to short-term hospitalization and that these changes are associated with signifcant morbidity and mortality. Here, we present a comprehensive pipeline for reliable bedside collection, sequencing, and analysis of the human salivary microbiome. We also develop a novel oral-specifc mock community for pipeline validation. Using our methodology, we analyzed the salivary microbiomes of patients before and during hospitalization or azithromycin treatment to profle impacts on this community. Our fndings indicate that azithromycin alters the diversity and taxonomic composition of the salivary microbiome; however, we also found that short-term hospitalization does not impact the richness or structure of this community, suggesting that the oral cavity may be less susceptible to dysbiosis during short-term hospitalization.
  • Identification of Bacterial Populations in Dairy Wastewaters by Use of 16S

    Identification of Bacterial Populations in Dairy Wastewaters by Use of 16S

    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, July 2004, p. 4267–4275 Vol. 70, No. 7 0099-2240/04/$08.00ϩ0 DOI: 10.1128/AEM.70.7.4267–4275.2004 Copyright © 2004, American Society for Microbiology. All Rights Reserved. Identification of Bacterial Populations in Dairy Wastewaters by Use of 16S rRNA Gene Sequences and Other Genetic Markers Jeffery A. McGarvey,1* William G. Miller,2 Susan Sanchez,3 and Larry Stanker1 Foodborne Contaminants Research Unit1 and Produce Safety and Microbiology Research Unit,2 Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710, and Department of Medical Microbiology and Parasitology and Athens Diagnostic Laboratory, The University of Georgia, Athens, Georgia 306023 Received 1 December 2003/Accepted 5 April 2004 Hydraulic flush waste removal systems coupled to solid/liquid separators and circulated treatment lagoons are commonly utilized to manage the large amounts of animal waste produced on high-intensity dairy farms. Although these systems are common, little is known about the microbial populations that inhabit them or how they change as they traverse the system. Using culture-based and non-culture-based methods, we characterized the microbial community structure of manure, water from the separator pit, and water from the circulated treatment lagoon from a large dairy in the San Joaquin Valley of California. Our results show that both total bacterial numbers and bacterial diversity are highest in manure, followed by the separator pit water and the -lagoon water. The most prevalent phylum in all locations was the Firmicutes (low-G؉C, gram-positive bacte ria). The most commonly occurring operational taxonomic unit (OTU) had a 16S rRNA gene (rDNA) sequence 96 to 99% similar to that of Clostridium lituseburense and represented approximately 6% of the manure derived sequences, 14% of the separator pit-derived sequences and 20% of the lagoon-derived sequences.
  • Characteristics of the Gut Microbiome of Healthy Young Male Soldiers in South Korea: the Effects of Smoking

    Characteristics of the Gut Microbiome of Healthy Young Male Soldiers in South Korea: the Effects of Smoking

    Gut and Liver https://doi.org/10.5009/gnl19354 pISSN 1976-2283 eISSN 2005-1212 Original Article Characteristics of the Gut Microbiome of Healthy Young Male Soldiers in South Korea: The Effects of Smoking Hyuk Yoon1, Dong Ho Lee1, Je Hee Lee2, Ji Eun Kwon3, Cheol Min Shin1, Seung-Jo Yang2, Seung-Hwan Park4, Ju Huck Lee4, Se Won Kang4, Jung-Sook Lee4, and Byung-Yong Kim2 1Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, 2ChunLab Inc., Seoul, 3Armed Forces Capital Hospital, Seongnam, and 4Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Korea Article Info Background/Aims: South Korean soldiers are exposed to similar environmental factors. In this Received October 14, 2019 study, we sought to evaluate the gut microbiome of healthy young male soldiers (HYMS) and to Revised January 6, 2020 identify the primary factors influencing the microbiome composition. January 17, 2020 Accepted Methods: We prospectively collected stool from 100 HYMS and performed next-generation se- Published online May 13, 2020 quencing of the 16S rRNA genes of fecal bacteria. Clinical data, including data relating to the diet, smoking, drinking, and exercise, were collected. Corresponding Author Results: The relative abundances of the bacterial phyla Firmicutes, Actinobacteria, Bacteroide- Dong Ho Lee tes, and Proteobacteria were 72.3%, 14.5%, 8.9%, and 4.0%, respectively. Fifteen species, most ORCID https://orcid.org/0000-0002-6376-410X of which belonged to Firmicutes (87%), were detected in all examined subjects. Using cluster E-mail [email protected] analysis, we found that the subjects could be divided into the two enterotypes based on the gut Byung-Yong Kim microbiome bacterial composition.
  • Species Level Description of the Human Ileal Bacterial Microbiota

    Species Level Description of the Human Ileal Bacterial Microbiota

    www.nature.com/scientificreports OPEN Species Level Description of the Human Ileal Bacterial Microbiota Heidi Cecilie Villmones1, Erik Skaaheim Haug2, Elling Ulvestad3,4, Nils Grude1, Tore Stenstad5, Adrian Halland2 & Øyvind Kommedal3 Received: 28 November 2017 The small bowel is responsible for most of the body’s nutritional uptake and for the development of Accepted: 6 March 2018 intestinal and systemic tolerance towards microbes. Nevertheless, the human small bowel microbiota Published: xx xx xxxx has remained poorly characterized, mainly owing to sampling difculties. Sample collection directly from the distal ileum was performed during radical cystectomy with urinary diversion. Material from the ileal mucosa were analysed using massive parallel sequencing of the 16S rRNA gene. Samples from 27 Caucasian patients were included. In total 280 unique Operational Taxonomic Units were identifed, whereof 229 could be assigned to a species or a species group. The most frequently detected bacteria belonged to the genera Streptococcus, Granulicatella, Actinomyces, Solobacterium, Rothia, Gemella and TM7(G-1). Among these, the most abundant species were typically streptococci within the mitis and sanguinis groups, Streptococcus salivarius, Rothia mucilaginosa and Actinomyces from the A. meyeri/ odontolyticus group. The amounts of Proteobacteria and strict anaerobes were low. The microbiota of the distal part of the human ileum is oral-like and strikingly diferent from the colonic microbiota. Although our patient population is elderly and hospitalized with a high prevalence of chronic conditions, our results provide new and valuable insights into a lesser explored part of the human intestinal ecosystem. Te human gut microbiota has been extensively investigated in recent years owing to its impacts on human health and disease1–3.
  • Anaerobe 2016, the 13Th Biennial Congress of the Anaerobe 2016 NASHVILLE Nashville, TN, USA Society of the Americas (ASA)

    Anaerobe 2016, the 13Th Biennial Congress of the Anaerobe 2016 NASHVILLE Nashville, TN, USA Society of the Americas (ASA)

    PROGRAM & ABSTRACT BOOK 2016 NASHVILLE ANAEROBE JULY 11-14, 2016 2016 NASHVILLE ANAEROBE JULY 11-14, 2016 The 13th Biennial Congress of the Anaerobe Society of the Americas Sheraton Nashville Downtown Hotel Nashville, Tennessee PROGRAM & ABSTRACT BOOK 2016 NASHVILLE ANAEROBE JULY 11-14, 2016 CONTENTS Course Directors ii Welcome Letter iii 2016About the SocietiesNASHVILLE iv Patrons JULY 11-14,v 2016 ANAEROBEExhibitors v Keynote Speaker vi Lifetime Achievement Award vii Accreditation viii Curricular Goals & Objectives viii Presenters & Faculty ix Disclosure Information xii Congress Program xv Abstract Table of Contents 1 Abstracts 3 Poster Index 237 Author Index 249 The 13th Biennial Congress of the Anaerobe Society of the Americas Sheraton Nashville Downtown Hotel • Nashville, Tennessee 2016 NASHVILLE 2016 NASHVILLE ANAEROBE JULY 11-14, 2016 Welcome Letter ANAEROBE JULY 11-14, 2016 COURSE DIRECTOR David M. Aronoff, M.D. ASA President Vanderbilt University Medical Center Welcome to ANAEROBE 2016, the 13th biennial Congress of the Anaerobe 2016 NASHVILLE Nashville, TN, USA Society of the Americas (ASA). This forum brings2016 together cliniciansNASHVILLE and Y 11-14, 2016 Y 11-14, 2016 ANAEROBE JUL scientists from around the world to engage in presentations,ANAEROBE dialogues,JUL and ORGANIZING COMMITTEE interactions related to the clinical and microbiological aspects of anaerobic Emma Allen-Vercoe, Ph.D. Brandi Limbago, Ph.D. bacteriology. The Congress will explore the role of anaerobes in both health University of Guelph Centers for Disease Control and disease, while addressing both traditional and emerging technologies Guelph, Canada Atlanta, GA USA for identification and diagnosis. Karen Carroll, M.D. Leandro Araujo Lobo, Ph.D.
  • Arrhythmic Gut Microbiome Signatures for Risk Profiling of Type-2 Diabetes

    Arrhythmic Gut Microbiome Signatures for Risk Profiling of Type-2 Diabetes

    bioRxiv preprint doi: https://doi.org/10.1101/2019.12.27.889865; this version posted December 28, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Arrhythmic gut microbiome signatures for risk profiling of Type-2 2 Diabetes 3 4 Sandra Reitmeier1,10, Silke Kießling1,10, Thomas Clavel1,2, Markus List3, Eduardo L. 5 Almeida4, Tarini S. Ghosh4, Klaus Neuhaus1, Harald Grallert5, Martina Troll5, Wolfgang 6 Rathmann5, Birgit Linkohr5, Andre Franke6, Caroline I. Le Roy7, Jordana T. Bell7, Tim 7 Spector7, Jan Baumbach3, Peter W. O’Toole4, Annette Peters5,8,9, Dirk Haller1,10 8 9 1 ZIEL Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 10 3, 85354 Freising, Germany 11 2 Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH 12 University Hospital, Pauwelsstraße 30, 52074 Aachen, Germany 13 3 Chair of Experimental Bioinformatics, Technical University of Munich, Maximus-von- 14 Imhof-Forum 3, 85354 Freising, Germany 15 4 School of Microbiology and APC Microbiome Ireland, University College Cork, Ireland 16 5 Institute of Epidemiology, Helmholtz Zentrum Munich, Ingolstädter Landstraße 1, 85764 17 Oberschleißheim 18 6 Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 19 Rosalind-Franklin-Straße 12, 24105 Kiel, Germany 20 7 Department of Twin Research & Genetic Epidemiology, King’s College London, Strand 21 London, WC2R 2LS, United Kingdom, UK 22 8 German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, 85764 23 Oberschleißheim 24 9 Chair of Epidemiology, Ludwig-Maximilians University, Marchioninistr.
  • Thi Na Utaliblat in Un Minune Talk

    Thi Na Utaliblat in Un Minune Talk

    THI NA UTALIBLATUS010064900B2 IN UN MINUNE TALK (12 ) United States Patent ( 10 ) Patent No. : US 10 , 064 ,900 B2 Von Maltzahn et al . ( 45 ) Date of Patent: * Sep . 4 , 2018 ( 54 ) METHODS OF POPULATING A (51 ) Int. CI. GASTROINTESTINAL TRACT A61K 35 / 741 (2015 . 01 ) A61K 9 / 00 ( 2006 .01 ) (71 ) Applicant: Seres Therapeutics, Inc. , Cambridge , (Continued ) MA (US ) (52 ) U . S . CI. CPC .. A61K 35 / 741 ( 2013 .01 ) ; A61K 9 /0053 ( 72 ) Inventors : Geoffrey Von Maltzahn , Boston , MA ( 2013. 01 ); A61K 9 /48 ( 2013 . 01 ) ; (US ) ; Matthew R . Henn , Somerville , (Continued ) MA (US ) ; David N . Cook , Brooklyn , (58 ) Field of Classification Search NY (US ) ; David Arthur Berry , None Brookline, MA (US ) ; Noubar B . See application file for complete search history . Afeyan , Lexington , MA (US ) ; Brian Goodman , Boston , MA (US ) ; ( 56 ) References Cited Mary - Jane Lombardo McKenzie , Arlington , MA (US ); Marin Vulic , U . S . PATENT DOCUMENTS Boston , MA (US ) 3 ,009 ,864 A 11/ 1961 Gordon - Aldterton et al. 3 ,228 ,838 A 1 / 1966 Rinfret (73 ) Assignee : Seres Therapeutics , Inc ., Cambridge , ( Continued ) MA (US ) FOREIGN PATENT DOCUMENTS ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 CN 102131928 A 7 /2011 EA 006847 B1 4 / 2006 U .S . C . 154 (b ) by 0 days. (Continued ) This patent is subject to a terminal dis claimer. OTHER PUBLICATIONS ( 21) Appl . No. : 14 / 765 , 810 Aas, J ., Gessert, C . E ., and Bakken , J. S . ( 2003) . Recurrent Clostridium difficile colitis : case series involving 18 patients treated ( 22 ) PCT Filed : Feb . 4 , 2014 with donor stool administered via a nasogastric tube .
  • Bacterial Diversity of Symptomatic Primary Endodontic Infection by Clonal Analysis

    Bacterial Diversity of Symptomatic Primary Endodontic Infection by Clonal Analysis

    ORIGINAL RESEARCH Endodontic Therapy Bacterial diversity of symptomatic primary endodontic infection by clonal analysis Abstract: The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Letícia Maria Menezes NÓBREGA(a) Francisco MONTAGNER(b) Samples were collected from 10 patients and submitted to bacterial Adriana Costa RIBEIRO(c) DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. (c) Márcia Alves Pinto MAYER A bacterial genomic library was constructed and bacterial diversity Brenda Paula Figueiredo de Almeida GOMES(a) was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84%) were different species and 29 (38.15%) (a) Universidade Estadual de Campinas were taxa reported as yet-uncultivable or as yet-uncharacterized (UNICAMP), Piracicaba Dental School, Endodontics Division, Piracicaba, SP, Brazil. species. Prevotella spp., Fusobacterium nucleatum, Filifactor alocis, and Peptostreptococcus stomatis were the most frequently detected species, (b) Universidade Federal do Rio Grande do Sul (UFRGS), Department of Conservative followed by Dialister invisus, Phocaeicola abscessus, the uncharacterized Dentistry, Porto Alegre, RS, Brazil. Lachnospiraceae oral clone, Porphyromonas spp., and Parvimonas micra. (c) Universidade de São Paulo (USP), Institute Eight phyla were detected and the most frequently identified taxa of Biomedical Science, Department of Oral belonged to the phylum Firmicutes (43.5%), followed by Bacteroidetes Microbiology, São Paulo, SP, Brazil. (22.5%) and Proteobacteria (13.2%). No species was detected in all studied samples and some species were identified in only one case.
  • Characterisation of Early Microbial Colonisers Within the Spiral Colon of Pre- and Post-Natal Piglets

    Characterisation of Early Microbial Colonisers Within the Spiral Colon of Pre- and Post-Natal Piglets

    life Article Characterisation of Early Microbial Colonisers within the Spiral Colon of Pre- and Post-Natal Piglets Tanya L. Nowland 1,* , Roy N. Kirkwood 1, Valeria A. Torok 1,2 , Kate J. Plush 3 and Mary D. Barton 4 1 School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA 5371, Australia; [email protected] (R.N.K.); [email protected] (V.A.T.) 2 South Australian Research and Development Institute, Food Sciences, Urrbrae, SA 5064, Australia 3 SunPork Group, Murarrie, QLD 4172, Australia; [email protected] 4 School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia; [email protected] * Correspondence: [email protected]; Tel.: +61-08-8313-7786 Abstract: Initial enteric microbial colonisation influences animal health and disease, hence an under- standing of the first microbial colonisers within the piglet is important. The spiral colon of piglets that were stillborn (n = 20), born-alive (n = 10), and born alive and had sucked (n = 9) were collected from 28 sows to investigate whether initial microbial colonisation occurs pre- or post-partum and how it develops during the first 24 h post-partum. To examine this, DNA was extracted and 16S rRNA am- plicon analysis was performed to allow analysis of microbial communities. The results indicate that microbial colonisation of the spiral colon had occurred in stillborn pigs, suggesting microbial expo- sure prior to birth. Alpha diversity metrics indicated that the number of taxa and community richness were higher in piglets that sucked (p < 0.001) and community evenness was lower in stillborns in comparison to born-alive (p < 0.001) but was not affected by colostrum consumption (p < 0.001).

  • Protease Activities of Vaginal Porphyromonas Species Disrupt Coagulation and Extracellular Matrix in the Cervicovaginal Niche

    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.447795; this version posted July 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Protease activities of vaginal Porphyromonas species disrupt coagulation and 2 extracellular matrix in the cervicovaginal niche 3 4 5 Karen V. Lithgow1, Vienna C.H. Buchholz1*, Emily Ku1, Shaelen Konschuh1, Ana D’Aubeterre1†, and Laura 6 K. Sycuro1,2,3,4,# 7 8 9 1Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, 10 Canada 11 2Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada 12 3Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada 13 4International Microbiome Centre, University of Calgary, Calgary, AB, Canada 14 15 16 #Corresponding author: Laura Sycuro, [email protected] 17 *Present affiliation: 18 Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada 19 †Present affiliation: 20 Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada 21 22 Running Title: Protease activity of vaginal Porphyromonas species 23 24 Abstract: 240 words 25 Importance: 141 words 26 Main Text: 7540 words bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.447795; this version posted July 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 27 Abstract 28 Porphyromonas asaccahrolytica and Porphyromonas uenonis are frequently isolated from the human 29 vagina and are linked to bacterial vaginosis and preterm labour.