Supplemental Table 1
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Extremozymes of the Hot and Salty Halothermothrix Orenii
Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry. -
Alternative Hydrogen Uptake Pathways Suppress Methane Production In
bioRxiv preprint doi: https://doi.org/10.1101/486894; this version posted December 4, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. 1 December 4, 2018 2 Alternative hydrogen uptake pathways 3 suppress methane production in ruminants 4 Chris Greening1 * #, Renae Geier2 #, Cecilia Wang3, Laura C. Woods1, Sergio E. 5 Morales3, Michael J. McDonald1, Rowena Rushton-Green3, Xochitl C. Morgan3, 6 Satoshi Koike4, Sinead C. Leahy5, William J. Kelly6, Isaac Cann2, Graeme T. 7 Attwood5, Gregory M. Cook3, Roderick I. Mackie2 * 8 9 1 Monash University, School of Biological Sciences, Clayton, VIC 3800, Australia 10 2 University of Illinois at Urbana-Champaign, Department of Animal Sciences and 11 Institute for Genomic Biology, Urbana, IL 61801, USA 12 3 University of Otago, Department of Microbiology and Immunology, Dunedin 9016, 13 New Zealand 14 4 Hokkaido University, Research Faculty of Agriculture, Sapporo, Japan 15 5 AgResearch Ltd., Grasslands Research Centre, Palmerston North 4410, New 16 Zealand. 17 6 Donvis Ltd., Palmerston North 4410, New Zealand. 18 19 # These authors contributed equally to this work. 20 21 * Correspondence can be addressed to: 22 23 Dr Chris Greening ([email protected]), School of Biological Sciences, 24 Monash University, Clayton, VIC 3800, Australia 25 Prof Roderick Mackie ([email protected]), Department of Animal Sciences, 26 Urbana, IL 61801, USA 27 bioRxiv preprint doi: https://doi.org/10.1101/486894; this version posted December 4, 2018. -
(12) United States Patent (10) Patent No.: US 9,018,158 B2 Onsoyen Et Al
US0090181.58B2 (12) United States Patent (10) Patent No.: US 9,018,158 B2 Onsoyen et al. (45) Date of Patent: Apr. 28, 2015 (54) ALGINATE OLIGOMERS FOR USE IN 7,208,141 B2 * 4/2007 Montgomery .................. 424/45 OVERCOMING MULTIDRUG RESISTANCE 22:49 R: R388 al al W . aSOC ea. N BACTERA 7,671,102 B2 3/2010 Gaserod et al. 7,674,837 B2 3, 2010 G d et al. (75) Inventors: Edvar Onsoyen, Sandvika (NO); Rolf 7,758,856 B2 T/2010 it. Myrvold, Sandvika (NO); Arne Dessen, 7,776,839 B2 8/2010 Del Buono et al. Sandvika (NO); David Thomas, Cardiff 2006.8 R 38 8. Melist al. (GB); Timothy Rutland Walsh, Cardiff 2003/0022863 A1 1/2003 Stahlang et al. (GB) 2003/0224070 Al 12/2003 Sweazy et al. 2004/OO73964 A1 4/2004 Ellington et al. (73) Assignee: Algipharma AS, Sandvika (NO) 2004/0224922 A1 1 1/2004 King 2010.0068290 A1 3/2010 Ziegler et al. (*) Notice: Subject to any disclaimer, the term of this 2010/0305062 A1* 12/2010 Onsoyen et al. ................ 514/54 patent is extended or adjusted under 35 U.S.C. 154(b) by 184 days. FOREIGN PATENT DOCUMENTS DE 268865 A1 1, 1987 (21) Appl. No.: 13/376,164 EP O324720 A1 T, 1989 EP O 506,326 A2 9, 1992 (22) PCT Filed: Jun. 3, 2010 EP O590746 A1 4f1994 EP 1234584 A1 8, 2002 (86). PCT No.: PCT/GB2O1 O/OO1097 EP 1714660 A1 10, 2006 EP 1745705 A1 1, 2007 S371 (c)(1), FR T576 M 3/1968 (2), (4) Date: Jan. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae -
Supplemental Material S1.Pdf
Phylogeny of Selenophosphate synthetases (SPS) Supplementary Material S1 ! SelD in prokaryotes! ! ! SelD gene finding in sequenced prokaryotes! We downloaded a total of 8263 prokaryotic genomes from NCBI (see Supplementary Material S7). We scanned them with the program selenoprofiles (Mariotti 2010, http:// big.crg.cat/services/selenoprofiles) using two SPS-family profiles, one prokaryotic (seld) and one mixed eukaryotic-prokaryotic (SPS). Selenoprofiles removes overlapping predictions from different profiles, keeping only the prediction from the profile that seems closer to the candidate sequence. As expected, the great majority of output predictions in prokaryotic genomes were from the seld profile. We will refer to the prokaryotic SPS/SelD !genes as SelD, following the most common nomenclature in literature.! To be able to inspect results by hand, and also to focus on good-quality genomes, we considered a reduced set of species. We took the prok_reference_genomes.txt list from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/, which NCBI claims to be a "small curated subset of really good and scientifically important prokaryotic genomes". We named this the prokaryotic reference set (223 species - see Supplementary Material S8). We manually curated most of the analysis in this set, while we kept automatized the !analysis on the full set.! We detected SelD proteins in 58 genomes (26.0%) in the prokaryotic reference set (figure 1 in main paper), which become 2805 (33.9%) when considering the prokaryotic full set (figure SM1.1). The difference in proportion between the two sets is due largely to the presence of genomes of very close strains in the full set, which we consider redundant. -
Characterization of an Adapted Microbial Population to the Bioconversion of Carbon Monoxide Into Butanol Using Next-Generation Sequencing Technology
Characterization of an adapted microbial population to the bioconversion of carbon monoxide into butanol using next-generation sequencing technology Guillaume Bruant Research officer, Bioengineering group Energy, Mining, Environment - National Research Council Canada Pacific Rim Summit on Industrial Biotechnology and Bioenergy December 8 -11, 2013 Butanol from residue (dry): syngas route biomass → gasification → syngas → catalysis → synfuels (CO, H2, CO2, CH4) (alcohols…) Biocatalysis vs Chemical catalysis potential for higher product specificity may be less problematic when impurities present less energy intensive (low pressure and temperature) Anaerobic undefined mixed culture vs bacterial pure culture mesophilic anaerobic sludge treating agricultural wastes (Lassonde Inc, Rougemont, QC, Canada) PRS 2013 - 2 Experimental design CO Alcohols Serum bottles incubated at Next Generation RDP Pyrosequencing mesophilic temperature Sequencing (NGS) pipeline 35°C for 2 months Ion PGMTM sequencer http://pyro.cme.msu.edu/ sequences filtered CO continuously supplied Monitoring of bacterial and to the gas phase archaeal populations RDP classifier atmosphere of 100% CO, http://rdp.cme.msu.edu/ 1 atm 16S rRNA genes Ion 314TM chip classifier VFAs & alcohol production bootstrap confidence cutoff low level of butanol of 50 % Samples taken after 1 and 2 months total genomic DNA extracted, purified, concentrated PRS 2013 - 3 NGS: bacterial results Bacterial population - Phylum level 100% 80% Other Chloroflexi 60% Synergistetes % -
Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment
INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 The INL is a U.S. Department of Energy National Laboratory operated by Battelle Energy Alliance INL/JOU-08-14091-Revision-0 Metal Transformation by a Novel Pelosinus Isolate From a Subsurface Environment Allison E. Ray, Peter P. Sheridan, Andrew L. Neal, Yoshiko Fujita, David E. Cummings, Timothy S. Magnuson August 2018 Idaho National Laboratory Idaho Falls, Idaho 83415 http://www.inl.gov Prepared for the U.S. Department of Energy Office of Nuclear Energy Under DOE Idaho Operations Office Contract DE-AC07-05ID14517 fmicb-09-01689 July 25, 2018 Time: 20:42 # 1 ORIGINAL RESEARCH published: xx July 2018 doi: 10.3389/fmicb.2018.01689 1 58 2 59 3 60 4 61 5 62 6 63 7 64 8 65 9 Metal Transformation by a Novel 66 10 67 11 Pelosinus Isolate From a Subsurface 68 12 69 13 Environment 70 14 71 15 Allison E. Ray1,2, Stephanie A. Connon1,3, Andrew L. Neal4†, Yoshiko Fujita2, 72 5 2† 1 16 David E. Cummings , Jani C. Ingram and Timothy S. Magnuson * 73 17 74 1 Department of Biological Sciences, Idaho State University, Pocatello, ID, United States, 2 Bioenergy Technologies, Idaho 18 3 75 Edited by: National Laboratory, Idaho Falls, ID, United States, California Institute of Technology, Pasadena, CA, United States, 19 4 5 76 Pankaj Kumar Arora, Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States, Department of Biology, Point Loma 20 77 Babasaheb Bhimrao Ambedkar Nazarene University, San Diego, CA, United States 21 University, India 78 22 79 Reviewed by: The capability of microorganisms to alter metal speciation offers potential for 23 80 Ramprasad E.V.V., the development of new strategies for immobilization of toxic metals in the 24 University of Hyderabad, India 81 25 Bärbel Ulrike Fösel, environment. -
Ancestry and Adaptive Radiation of Bacteroidetes As Assessed by Comparative Genomics
1 Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics 2 3 Raul Munoza,b,*, Hanno Teelinga, Rudolf Amanna and Ramon Rosselló-Mórab,* 4 5 a Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 6 Bremen, Germany. 7 b Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani 8 d’Estudis Avançats (CSIC-UIB), E-07190 Esporles, Balearic Islands, Spain. 9 10 * Corresponding authors: 11 Raul Munoz, Marine Microbiology Group, Carrer Miquel Marquès 21, 07190 Esporles, Illes 12 Balears, Spain. e-mail: [email protected] 13 Ramon Rosselló-Móra, Marine Microbiology Group, Carrer Miquel Marquès 21, 07190 Esporles, 14 Illes Balears, Spain. e-mail: [email protected] 15 16 17 18 Keywords + 19 Bacteroidetes, Na -NQR, alternative complex III, caa3 cytochrome oxidase, gliding, T9SS. 20 21 Abbreviations 22 m.s.i.: median sequence identity. 23 24 25 26 27 ABSTRACT 28 As of this writing, the phylum Bacteroidetes comprises more than 1,500 described species with 29 diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits on 30 a genomic level. We compiled a representative set of 89 Bacteroidetes genomes and used pairwise 31 reciprocal best match gene comparisons and gene syntenies to identify common traits that allow to 32 trace Bacteroidetes’ evolution and adaptive radiation. Highly conserved among all studied 33 Bacteroidetes was the type IX secretion system (T9SS). Class-level comparisons furthermore 34 suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal 35 lineage, and was secondarily lost in extant anaerobic Bacteroidetes. -
November 2014, Version 6.0 This Document Was Created Under National Center for Emerging and Zoonotic Diseases/ Office of Infectious Diseases (NCEZID/OD)
November 2014, Version 6.0 This document was created under National Center for Emerging and Zoonotic Diseases/ Office of Infectious Diseases (NCEZID/OD). The printed version of CDC's Infectious Diseases Laboratory Test Directory contains information that is current as of November 18st, 2014. All information contained herein is subject to change. For the most current test information, please view the CDC's Infectious Diseases Laboratory Test Directory on: http://www.cdc.gov/laboratory/specimen-submission/list.html. Test Order Acanthamoeba Molecular Detection CDC-10471 Synonym(s) Free-living ameba, parasite Pre-Approval Needed None Supplemental Information None Required Supplemental Form None Performed on Specimens From Human Acceptable Sample/ Specimen For Acanthamoeba and Balamuthia molecular detection, tissue is the preferred Type for Testing specimen type; however, these amoebae can occasionally be detected in cerebrospinal fluid (CSF). For Naegleria fowleri molecular detection, CSF is the preferred specimen type. Minimum Volume Required 500 uL Storage & Preservation of Storage and preservation is specimen specific Specimen Prior to Shipping Transport Medium Not Applicable Specimen Labeling Test subject to CLIA regulations and requires two patient identifiers on the specimen container and the test requisition. In addition to two patient identifiers (sex, date of birth, name, etc.), provide specimen type and date of collection. Shipping Instructions which Ship Monday – Thursday, overnight to avoid weekend deliveries. Ship specimen Include -
Plesiomonas Shigelloides S000142446 Serratia Plymuthica
0.01 Plesiomonas shigelloides S000142446 Serratia plymuthica S000016955 Serratia ficaria S000010445 Serratia entomophila S000015406 Leads to highlighted edge in Supplemental Phylogeny 1 Xenorhabdus hominickii S000735562 0.904 Xenorhabdus poinarii S000413914 0.998 0.868 Xenorhabdus griffiniae S000735553 Proteus myxofaciens S000728630 0.862 Proteus vulgaris S000004373 Proteus mirabilis S000728627 0.990 0.822 Arsenophonus nasoniae S000404964 OTU from Corby-Harris (Unpublished) #seqs-1 GQ988429 OTU from Corby-Harris et al (2007) #seqs-1 DQ980880 0.838 Providencia stuartii S000001277 Providencia rettgeri S000544654 0.999 Providencia vermicola S000544657 0.980 Isolate from Juneja and Lazzaro (2009)-EU587107 Isolate from Juneja and Lazzaro (2009)-EU587113 0.605 0.928 Isolate from Juneja and Lazzaro (2009)-EU587095 0.588 Isolate from Juneja and Lazzaro (2009)-EU587101 Providencia rustigianii S000544651 0.575 Providencia alcalifaciens S000127327 0.962 OTU XDS 099-#libs(1/0)-#seqs(1/0) OTU XYM 085-#libs(13/4)-#seqs(401/23) 0.620 OTU XDY 021-#libs(1/1)-#seqs(3/1) Providencia heimbachae S000544652 Morganella psychrotolerans S000721631 0.994 Morganella morganii S000721642 OTU ICF 062-#libs(0/1)-#seqs(0/7) Morganella morganii S000129416 0.990 Biostraticola tofi S000901778 0.783 Sodalis glossinidius S000436949 Dickeya dadantii S000570097 0.869 0.907 0.526 Brenneria rubrifaciens S000022162 0.229 Brenneria salicis S000381181 0.806 OTU SEC 066-#libs(0/1)-#seqs(0/1) Brenneria quercina S000005099 0.995 Pragia fontium S000022757 Budvicia aquatica S000020702 -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Corrinoid Cross-Feeding in the Microbial World Permalink https://escholarship.org/uc/item/2z66b95b Author Dirks, Erica Christine Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Corrinoid Cross-Feeding in the Microbial World By Erica Christine Dirks A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michiko E. Taga, Chair Professor John D. Coates Professor David Savage Professor Nicole King Fall 2014 Acknowledgements This work would not have been possible without the generous and kind support of many people over the past seven years. To all of my collaborators and mentors I’ve met along the way, especially the members of the Taga lab, a million thanks for all of the advice, discussions, and guidance. Your unselfish willingness to help continues to amaze and inspire me. Working with you has been a true gift. To Shan, I’ve learned so much from you. I wish you every happiness, and I will always think of you as my big sister in science. To Steve, it’s meant so much to me to have you on my side. Your breadth of knowledge astounds me. I hope you never stop telling stories. To Patrick, you are a true friend, and I would have never gotten through without you. To Jerome, together, you know we can defeat the zombie hordes. Thanks for all the car rides! To Mark, for pushing me to go further than I ever imagined I could.