Effect of Proton Pump Inhibitor on Microbial Community, Function, and Kinetics in Anaerobic Digestion with Ammonia Stress
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Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment. -
WO 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T
(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 2014/121298 A2 7 August 2014 (07.08.2014) P O P C T (51) International Patent Classification: VULIC, Marin; c/o Seres Health, Inc., 161 First Street, A61K 39/02 (2006.01) Suite 1A, Cambridge, MA 02142 (US). (21) International Application Number: (74) Agents: HUBL, Susan, T. et al; Fenwick & West LLP, PCT/US2014/014738 Silicon Valley Center, 801 California Street, Mountain View, CA 94041 (US). (22) International Filing Date: 4 February 2014 (04.02.2014) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, English (25) Filing Language: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (26) Publication Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (30) Priority Data: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 61/760,584 4 February 2013 (04.02.2013) US KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/760,585 4 February 2013 (04.02.2013) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/760,574 4 February 2013 (04.02.2013) us OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 61/760,606 4 February 2013 (04.02.2013) 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. -
( 12 ) United States Patent
US010398154B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 398 , 154 B2 Embree et al. ( 45 ) Date of Patent: * Sep . 3 , 2019 (54 ) MICROBIAL COMPOSITIONS AND ( 58 ) Field of Classification Search METHODS OF USE FOR IMPROVING MILK None PRODUCTION See application file for complete search history . (71 ) Applicant: ASCUS BIOSCIENCES , INC ., San Diego , CA (US ) (56 ) References Cited ( 72 ) Inventors: Mallory Embree, San Diego , CA (US ) ; U . S . PATENT DOCUMENTS Luke Picking , San Diego , CA ( US ) ; 3 , 484 , 243 A 12 / 1969 Anderson et al . Grant Gogul , Cardiff , CA (US ) ; Janna 4 ,559 , 298 A 12 / 1985 Fahy Tarasova , San Diego , CA (US ) (Continued ) (73 ) Assignee : Ascus Biosciences , Inc. , San Diego , FOREIGN PATENT DOCUMENTS CA (US ) CN 104814278 A 8 / 2015 ( * ) Notice : Subject to any disclaimer , the term of this EP 0553444 B1 3 / 1998 patent is extended or adjusted under 35 U .S . C . 154 (b ) by 0 days. (Continued ) This patent is subject to a terminal dis OTHER PUBLICATIONS claimer . Borling , J , Master' s thesis, 2010 . * (21 ) Appl. No .: 16 / 029, 398 ( Continued ) ( 22 ) Filed : Jul. 6 , 2018 Primary Examiner - David W Berke- Schlessel (65 ) Prior Publication Data ( 74 ) Attorney , Agent, or Firm — Cooley LLP US 2018 /0325966 A1 Nov . 15 , 2018 ( 57 ) ABSTRACT Related U . S . Application Data The disclosure relates to isolated microorganisms — includ (63 ) Continuation of application No. ing novel strains of the microorganisms - microbial consor PCT/ US2014 /012573 , filed on Jan . 6 , 2017 . tia , and compositions comprising the same . Furthermore , the disclosure teaches methods of utilizing the described micro (Continued ) organisms, microbial consortia , and compositions compris (51 ) Int. -
CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations. -
Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food. -
Characterization of an Anaerobic Population Digesting a Model Substrate for Maize in the Presence of Trace Metals
Chemosphere 80 (2010) 829–836 Contents lists available at ScienceDirect Chemosphere journal homepage: www.elsevier.com/locate/chemosphere Characterization of an anaerobic population digesting a model substrate for maize in the presence of trace metals Herbert Pobeheim, Bernhard Munk, Henry Müller, Gabriele Berg, Georg M. Guebitz * Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria article info abstract Article history: The influence of a defined trace metal solution and additionally Ni2+ on anaerobic digestion of biomass Received 1 December 2009 was investigated. A novel synthetic model substrate was designed consisting of cellulose, starch and urea Received in revised form 6 June 2010 as carbon and nitrogen source in a ratio mimicking the basic composition of maize silage. Two indepen- Accepted 7 June 2010 dent batch fermentations were carried out over 21 d with the synthetic model substrate in the presence Available online 7 July 2010 of the trace metal solution. Particularly an increase in nickel concentrations (17 and 34 lM) enhanced methane formation by up to 20%. This increased activity was also corroborated by fluorescence micros- Keywords: copy measurements based on cofactor F . The eubacterial and methanogenic population was character- Anaerobic digestion 420 ized with the single strand conformational polymorphism analysis and the amplified 16S rDNA Biogas Cellulose restriction analysis of 16S rRNA genes amplified by different primer systems. Nearly the half of the ana- Nickel lyzed bacteria were identified as Firmicutes while 70% in this phylum belonged to the class of Clostridiales SSCP and 30% to the class of Bacilli. Bacteroides and uncultured bacteria represented each a quarter of the ana- lyzed community. -
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 . -
Investigation and Subsequent Manipulation of The
Investigation and subsequent manipulation of the intestinal microbiota of pigs, with a view to optimising feed efficiency By Ursula Mary McCormack (B.Ag.Sc) A thesis submitted for the degree of Doctor of Philosophy Waterford Institute of Technology Research Supervisors Dr. Gillian E. Gardiner Dr. Peadar G. Lawlor Submitted to Waterford Institute of Technology September 2017 Declaration No element of the work described in this thesis has been previously submitted for a degree at this or any other institution. The work in this thesis has been performed entirely by the author. Signature: ____________________________ Date: ___________________________ i Table of Contents Declaration ..................................................................................................................... i Table of Tables ............................................................................................................. xi Table of Figures .......................................................................................................... xiii List of abbreviations ................................................................................................... xvi Abstract ............................................................................................................................. 1 1. Literature Review .......................................................................................................... 2 1.1 Introduction ............................................................................................................ -
Exploring the Biosynthetic Pathways of Glutamate and Benzoate in Syntrophus Aciditrophicus
Exploring the biosynthetic pathways of glutamate and benzoate in Syntrophus aciditrophicus Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg Vorgelegt von Marie Kim aus Daegu, Republic of Korea Marburg/Lahn, Germany 2011 Die Untersuchungen zur vorliegenden Arbeit wurden von September 2007 bis Juni 2011 im Laboratorium für Mikrobiologie, Fachbereich Biologie, der Philipps-Universität Marburg unter der Leitung von Prof. Dr. W. Buckel durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation am 06. 07. 2011 angenommen. Erstgutachter: Prof. Dr. Wolfgang Buckel Zweitgutachter: Prof. Dr. Johann Heider Tag der mündlichen Prüfung am: 07. 07. 2011 Contents Abbreviations ......................................................................................................................................... 5 Zusammenfassung ................................................................................................................................. 6 Summary ................................................................................................................................................ 7 Introduction ........................................................................................................................................... 8 1. Anaerobic food chain and syntrophic metabolism .............................................................................. 8 1.1 Anaerobic food chain ............................................................................................................... -
WO 2016/086209 Al June 2016 (02.06.2016) W P O P C T
(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 2016/086209 Al June 2016 (02.06.2016) W P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill, Ann et al; Mccarter & English, A61K 35/74 (2015.01) A61P 1/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61K 35/741 (2015.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 15/062809 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 25 November 2015 (25.1 1.2015) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/084,536 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,537 25 November 2014 (25. 11.2014) US (84) Designated States (unless otherwise indicated, for every 62/084,540 25 November 2014 (25. -
Analysis of the Gut Microbiota of Walking Sticks (Phasmatodea)
UC Davis UC Davis Previously Published Works Title Analysis of the gut microbiota of walking sticks (Phasmatodea) Permalink https://escholarship.org/uc/item/4f96w24x Journal BMC Research Notes, 6(1) ISSN 1756-0500 Authors Shelomi, Matan Lo, Wen-Sui Kimsey, Lynn S et al. Publication Date 2013-09-11 DOI http://dx.doi.org/10.1186/1756-0500-6-368 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Shelomi et al. BMC Research Notes 2013, 6:368 http://www.biomedcentral.com/1756-0500/6/368 RESEARCH ARTICLE Open Access Analysis of the gut microbiota of walking sticks (Phasmatodea) Matan Shelomi1, Wen-Sui Lo2,3,4, Lynn S Kimsey1 and Chih-Horng Kuo2,3,5* Abstract Background: Little is known about the Phasmatodea gut microbial community, including whether phasmids have symbiotic bacteria aiding in their digestion. While symbionts are near ubiquitous in herbivorous insects, the Phasmatodea’s distinctively thin body shape precludes the gut enlargements needed for microbial fermentation. High-throughput sequencing was used to characterize the entire microbiota of the fat bodies, salivary glands, and anterior and posterior midguts of two species of walking stick. Results: Most bacterial sequences belonged to a strain of Spiroplasma (Tenericutes) found primarily in the posterior midgut of the parthenogenetic species Ramulus artemis (Phasmatidae). Beyond this, no significant differences were found between the R. artemis midgut sections or between that species and Peruphasma schultei (Pseudophasmatidae). Histological analysis further indicated a lack of bacteriocytes. Conclusions: Phasmids are unlikely to depend on bacteria for digestion, suggesting they produce enzymes endogenously that most other herbivorous insects obtain from symbionts. -
Investigating the Microbiology and Microbial Processes Involved During the Anaerobic Degradation of High Strength Industrial Wastewaters
This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Investigating the microbiology and microbial processes involved during the anaerobic degradation of high strength industrial wastewaters Venkatakrishnan, Harish 2016 Venkatakrishnan, H. (2016). Investigating the microbiology and microbial processes involved during the anaerobic degradation of high strength industrial wastewaters. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/144041 https://doi.org/10.32657/10356/144041 This work is licensed under a Creative Commons Attribution‑NonCommercial 4.0 International License (CC BY‑NC 4.0). Downloaded on 01 Oct 2021 22:10:49 SGT INVESTIGATING THE MICROBIOLOGY AND MICROBIAL PROCESSES INVOLVED DURING THE ANAEROBIC DEGRADATION OF HIGH STRENGTH INDUSTRIAL WASTEWATERS HARISH VENKATAKRISHNAN School of Civil and Environmental Engineering 2016 INVESTIGATING THE MICROBIOLOGY AND MICROBIAL PROCESSES INVOLVED DURING THE ANAEROBIC DEGRADATION OF HIGH STRENGTH INDUSTRIAL WASTEWATERS HARISH VENKATAKRISHNAN School of Civil and Environmental Engineering A thesis submitted to the Nanyang Technological University in partial fulfilment of the requirements for the degree of Doctor of Philosophy 2016 LIST OF PUBLICATIONS Venkatakrishnan, H., Tan, Y., Pathak, S., Sendjaja, A.Y., Li, D., Liu, J.J.L., Yan, Z., M. A. Majid, and W. J. Ng (2014) Effect of a high strength chemical industry wastewater on microbial community dynamics and mesophilic methane generation, Journal of Environmental Science, 26, 875– 884. Impact Factor - 2.002 Article as a result of experiments performed in Chapter 4 CONFERENCE ORAL PRESENTATION 1) H. Venkatakrishnan, Y. M. Tan, S. Pathak, A. Y. Sendjaja, D. Li, Yan, Z., M. A. Majid, W. J.