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Structure and Dynamics of the Microbial Communities Underlying the Carboxylate Platform for Biofuel Production
Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production E.B. Hollister 1, A.K. Forrest 2, H.H. Wilkinson 3, D.J. Ebbole 3, S.A. Malfatti 4, S.G. Tringe 4, M.T. Holtzapple 2, T.J. Gentry 1 1 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA 77843-2474 2 Department of Chemical Engineering, Texas A&M University, College Station, TX, USA 77843-3122 3 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX USA 77843-2132 4 DOE Joint Genome Institute, Walnut Creek, CA, USA 94598 July 31, 2010 ACKNOWLEDGMENT The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. -
Supplementary Materials
SUPPLEMENTARY MATERIALS Table S1. Chemical characteristics of the two digestate forms (SD and WD). Values quoted are expressed as % of air-dry digestate (means followed by standard error in brackets). References for the employed methods used for determination of each chemical characteristic is also reported. SD WD Reference Org C % 44.4 (0.33) 1.1 (0.01) [81] Tot N % 1.4 (0.01) 0.4 (0.01) [82] C/N 31.4 (0.17) 3.1 (0.04) NH4-N % n.d 0.2 (0.00) [83] K % 1.7 (0.00) n.d. [84] P % 0.9 (0.01) n.d. [84] S % 0.23 (0.02) n.d. [85] SD = solid digestate; WD = whole digestate. Table S2. Soil physical and chemical characteristics at the beginning of trial (t0) (means from 9 observations followed by standard errors in brackets). Clay (%) 41.9 (1.22) Silt (%) 47.8 (2.13) Moisture (%) 24.46 (1.24) Bulk density (g cm-3) 1.39 (0.04) pH 8.3 (0) CaCO3 (%) 11.4 (0.7) TOC (g kg-1) 12.8 (0.3) TN (g kg-1) 1.4 (0) C/N 9.4 (0.3) CEC (cmol(+) kg-1) 21.0 (0.7) Exchangeable Bases (mg kg-1) K 278.7 (8.0) Na 22.0 (3.0) Mg 201.7 (25.6) Ca 3718.6 (176.3) Available Microelements (mg kg-1) Cu 28.0 (5.0) Zn 1.7 (0.2) Fe 15.4 (0.5) Mn 16.3 (0.5) TOC = total organic C; TN = total N; CEC = cation exchange capacity Table S3. -
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. -
Dissertationstefanschauer.Pdf (11.35Mb)
Institut für Biologie Biofilmbildung bei Pflanzen-assoziierten Bakterien der Gattung Methylobacterium und molekulargenetisch-physiologische Charakterisierung eines neuen Marchantia-Isolats (Mtb. sp. JT1) Inaugural‐Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt im Fachbereich Naturwissenschaften der Universität Kassel von Dipl.‐Biol. Stefan Schauer Dekan: Prof. Dr. F. Herberg Gutachter: 1. Prof. Dr. U. Kutschera 2. Prof. Dr. H. Follmann eingereicht: 12. Januar 2009 Datum der Disputation: 6. Februar 2009 Inhaltsverzeichnis Inhaltsverzeichnis Inhaltsverzeichnis............................................................................................................... 2 Abkürzungsverzeichnis..................................................................................................... 7 1 Einleitung................................................................................................................... 10 1.1 Biofilme .............................................................................................................. 10 1.1.1 Vorteile von Biofilmen ............................................................................. 11 1.1.2 Matrixkomponenten bakterieller Biofilme............................................ 11 1.1.3 Biofilme auf Pflanzenoberflächen .......................................................... 12 1.2 Die Gattung Methylobacterium......................................................................... 13 1.2.1 Assoziation -
Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles Received: 10 January 2017 Angela B
www.nature.com/scientificreports OPEN Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles Received: 10 January 2017 Angela B. Javurek1, Dhananjay Suresh 2, William G. Spollen3,4, Marcia L. Hart5, Sarah Accepted: 19 April 2017 A. Hansen6, Mark R. Ellersieck7, Nathan J. Bivens 8, Scott A. Givan 3,4,9, Anandhi Published: xx xx xxxx Upendran10,11, Raghuraman Kannan11,12 & Cheryl S. Rosenfeld 4,13,14,15 Due to their antimicrobial properties, silver nanoparticles (AgNPs) are being used in non-edible and edible consumer products. It is not clear though if exposure to these chemicals can exert toxic effects on the host and gut microbiome. Conflicting studies have been reported on whether AgNPs result in gut dysbiosis and other changes within the host. We sought to examine whether exposure of Sprague- Dawley male rats for two weeks to different shapes of AgNPs, cube (AgNC) and sphere (AgNS) affects gut microbiota, select behaviors, and induces histopathological changes in the gastrointestinal system and brain. In the elevated plus maze (EPM), AgNS-exposed rats showed greater number of entries into closed arms and center compared to controls and those exposed to AgNC. AgNS and AgNC treated groups had select reductions in gut microbiota relative to controls. Clostridium spp., Bacteroides uniformis, Christensenellaceae, and Coprococcus eutactus were decreased in AgNC exposed group, whereas, Oscillospira spp., Dehalobacterium spp., Peptococcaeceae, Corynebacterium spp., Aggregatibacter pneumotropica were reduced in AgNS exposed group. Bacterial reductions correlated with select behavioral changes measured in the EPM. No significant histopathological changes were evident in the gastrointestinal system or brain. Findings suggest short-term exposure to AgNS or AgNC can lead to behavioral and gut microbiome changes. -
Antibitoic Treatment for Tuberculosis Induces a Profound Dysbiosis of the Gut Microbiome That Persists Long After Therapy Is Completed
ANTIBITOIC TREATMENT FOR TUBERCULOSIS INDUCES A PROFOUND DYSBIOSIS OF THE GUT MICROBIOME THAT PERSISTS LONG AFTER THERAPY IS COMPLETED A Thesis Presented to the Faculty of the Weill Cornell Graduate School of Medical Sciences in Partial Fulfillment of the Requirements for the Degree of Masters of Science by Matthew F. Wipperman May 2017 © 2017 Matthew F. Wipperman ABSTRACT Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world’s population and causes substantial mortality worldwide. In its shortest format, treatment of drug sensitive TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is much longer. The widespread use of this regimen worldwide makes this one the largest exposures of humans to antimicrobials, yet the effects of antimycobacterial agents on intestinal microbiome composition and long term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of Haitian TB cases during antimycobacterial treatment and following cure by 6 months of TB therapy. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The perturbation by TB therapy lasts at least 1.5 years after completion of treatment, indicating that the effects of TB treatment are long lasting and perhaps permanent. These results demonstrate that TB treatment has dramatic and durable effects on the intestinal microbiome and highlight unexpected extreme consequences of treatment for the world’s most common infection on human ecology. BIOGRAPHICAL SKETCH NAME POSITION TITLE Wipperman, Matthew Frederick Postdoctoral Researcher at eRA COMMONS USER NAME Memorial Sloan Kettering Cancer Center MFWIPPERMAN DEGREE INSTITUTION AND (if MM/YY FIELD OF STUDY LOCATION applicable) Franklin & Marshall College B.A. -
New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V
INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 24, No. 2 April 1974, p. 260-277 Printed in U.S.A. Copyright 0 1974 International Association of Microbiological Societies New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V. HOLDEMAN and W. E. C. MOORE Anaerobe Laboratory, Virginia Polytechnic Institute and State University, Blacksburg, Virginia24061 A new genus of anaerobic cocci, Coprococcus, and 12 new species of anaerobes, Coprococcus eutactus, C. catus, C. comes, RuminococCus callidus, R. torques, Streptococcus hansenii, Bacteroides eggerthii, Eubacterium eligens, E. formicigenerans, E. hallii, Lactobacillus rogosae, and Clostridium nexile, are described. Emended descriptions and proposed neotype strains for Strepto- coccus constellatus (Prkvot) comb. nov., S. morbillorum (Prkvot) comb. nov., S. in termedius PrCvot, and Eubacterium biiorme (Eggerth) PrCvot are presented. During quantitative and qualitative studies of The moles percent guanine plus cytosine (G+C) the human fecal flora, a large number of content of the deoxyribonucleic acid (DNA) prepara- previously undescribed bacterial species was tions was determined by the thermal melting point encountered as predominant members of the (T,) method (7) by using an automatic recording flora. Of these species, those for which we have spectrophotometer (Gilford Instrument Laboratories). DNA from Escherichia coli B was included in each set nine or more isolates from six or more persons of analyses as a standard. are described here. In addition, the taxonomic position of some species of cocci is discussed, RESULTS AND DISCUSSION and for Eubacterium biforme (Eggerth) Prbvot, an emended description is presented and a Anaerobic Cocci neotype strain is designated. -
Functional Deficits in Gut Microbiome of Young and Middle-Aged
nutrients Article Functional Deficits in Gut Microbiome of Young and Middle-Aged Adults with Prediabetes Apparent in Metabolizing Bioactive (Poly)phenols Xuhuiqun Zhang , Anqi Zhao, Amandeep K. Sandhu, Indika Edirisinghe and Britt M. Burton-Freeman * Department of Food Science and Nutrition and Center for Nutrition Research, Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60616, USA; [email protected] (X.Z.); [email protected] (A.Z.); [email protected] (A.K.S.); [email protected] (I.E.) * Correspondence: [email protected]; Tel.: +1-708-341-7078 Received: 20 October 2020; Accepted: 20 November 2020; Published: 23 November 2020 Abstract: Background: Gut microbiota metabolize select dietary (poly)phenols to absorbable metabolites that exert biological effects important in metabolic health. Microbiota composition associated with health/disease status may affect its functional capacity to yield bioactive metabolites from dietary sources. Therefore, this study assessed gut microbiome composition and its related functional capacity to metabolize fruit (poly)phenols in individuals with prediabetes and insulin resistance (PreDM-IR, n = 26) compared to a metabolically healthy Reference group (n = 10). Methods: Shotgun sequencing was used to characterize gut microbiome composition. Targeted quantitative metabolomic analyses of plasma and urine collected over 24 h were used to assess microbial-derived metabolites in response to a (poly)phenol-rich raspberry test drink. Results: PreDM-IR compared to the Reference group: (1) enriched Blautia obeum and Blautia wexlerae and depleted Bacteroides dorei and Coprococcus eutactus. Akkermansia muciniphila and Bacteroides spp. were depleted in the lean PreDM-IR subset; and (2) impaired microbial catabolism of select (poly)phenols resulting in lower 3,8-dihydroxy-urolithin (urolithin A), phenyl-γ-valerolactones and various phenolic acids concentrations (p < 0.05). -
Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V
INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 24, No. 2 April 1974, p. 260-277 Printed in U.S.A. Copyright 0 1974 International Association of Microbiological Societies New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V. HOLDEMAN and W. E. C. MOORE Anaerobe Laboratory, Virginia Polytechnic Institute and State University, Blacksburg, Virginia24061 A new genus of anaerobic cocci, Coprococcus, and 12 new species of anaerobes, Coprococcus eutactus, C. catus, C. comes, RuminococCus callidus, R. torques, Streptococcus hansenii, Bacteroides eggerthii, Eubacterium eligens, E. formicigenerans, E. hallii, Lactobacillus rogosae, and Clostridium nexile, are described. Emended descriptions and proposed neotype strains for Strepto- coccus constellatus (Prkvot) comb. nov., S. morbillorum (Prkvot) comb. nov., S. in termedius PrCvot, and Eubacterium biiorme (Eggerth) PrCvot are presented. During quantitative and qualitative studies of The moles percent guanine plus cytosine (G+C) the human fecal flora, a large number of content of the deoxyribonucleic acid (DNA) prepara- previously undescribed bacterial species was tions was determined by the thermal melting point encountered as predominant members of the (T,) method (7) by using an automatic recording flora. Of these species, those for which we have spectrophotometer (Gilford Instrument Laboratories). DNA from Escherichia coli B was included in each set nine or more isolates from six or more persons of analyses as a standard. are described here. In addition, the taxonomic position of some species of cocci is discussed, RESULTS AND DISCUSSION and for Eubacterium biforme (Eggerth) Prbvot, an emended description is presented and a Anaerobic Cocci neotype strain is designated. -
Comparison of Sampling Techniques and Different Media for The
Systematic and Applied Microbiology 42 (2019) 481–487 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermentersଝ a a b a,∗ Regina Rettenmaier , Carina Duerr , Klaus Neuhaus , Wolfgang Liebl , a,c,∗ Vladimir V. Zverlov a Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany b Core Facility Microbiome/NGS, ZIEL — Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany c Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123128 Moscow, Russia a r t i c l e i n f o a b s t r a c t Article history: Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. Received 27 March 2019 This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating Received in revised form 15 May 2019 enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We Accepted 17 May 2019 compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region Keywords: of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biolog- Biogas fermenter ical triplicates, revealed an average richness of 48 different OTU’s with an average evenness of 0.3 in Cellulose degradation each sample. -
André Luis Alves Neves 6
Elucidating the role of the rumen microbiome in cattle feed efficiency and its 1 potential as a reservoir for novel enzyme discovery 2 3 by 4 5 André Luis Alves Neves 6 7 8 9 10 11 12 A thesis submitted in partial fulfillment of the requirements for the degree of 13 14 15 Doctor of Philosophy 16 17 in 18 19 Animal Science 20 21 22 23 24 25 Department of Agricultural, Food and Nutritional Science 26 University of Alberta 27 28 29 30 31 32 33 34 35 36 37 © André Luis Alves Neves, 2019 38 39 40 Abstract 1 2 The rapid advances in omics technologies have led to a tremendous progress in our 3 understanding of the rumen microbiome and its influence on cattle feed efficiency. 4 However, significant gaps remain in the literature concerning the driving forces that 5 influence the relationship between the rumen microbiota and host individual variation, and 6 how their interactive effects on animal productivity contribute to the identification of cattle 7 with improved feed efficiency. Furthermore, little is known about the impact of mRNA- 8 based metatranscriptomics on the analysis of rumen taxonomic profiles, and a strategy 9 for the discovery of lignocellulolytic enzymes through the targeted functional profiling of 10 carbohydrate-active enzymes (CAZymes) remains to be developed. Study 1 investigated 11 the dynamics of rumen microorganisms in cattle raised under different feeding regimens 12 (forage vs. grain) and studied the relationship among the abundance of these 13 microorganisms, host individuality and the diet. To examine host individual variation in 14 the rumen microbial abundance following dietary switches, hosts were grouped based on 15 the magnitude of microbial population shift using log2-fold change (log2-fc) in the copy 16 numbers of bacteria, archaea, protozoa and fungi. -
From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.