DOCSLIB.ORG

Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

American University in Cairo AUC Knowledge Fountain Theses and Dissertations Student Research Summer 8-25-2021 Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments Sarah Sonbol [email protected] Follow this and additional works at: https://fount.aucegypt.edu/etds Part of the Bacteriology Commons, Biochemistry Commons, Biodiversity Commons, Bioinformatics Commons, Biotechnology Commons, Environmental Microbiology and Microbial Ecology Commons, Genomics Commons, Marine Biology Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation APA Citation Sonbol, S. (2021).Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments [Doctoral Dissertation, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/1673 MLA Citation Sonbol, Sarah. Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments. 2021. American University in Cairo, Doctoral Dissertation. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/1673 This Doctoral Dissertation is brought to you for free and open access by the Student Research at AUC Knowledge Fountain. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of AUC Knowledge Fountain. For more information, please contact [email protected]. Insights into halophilic microbial adaptation: Analysis of integrons and associated genomic structures and characterization of a nitrilase in hypersaline environments School of Sciences and Engineering A Thesis Submitted by Sarah Ali Ahmed Sonbol. MSc to the Applied Sciences Graduate Program Spring, 2021 In partial fulfillment of the requirements for the degree of Doctorate in Applied Sciences (Biotechnology) Under the supervision of: Prof. Rania Siam American University in Cairo May / 2021 Insights into halophilic microbial adaptation: Analysis of integrons and associated genomic structures and characterization of a nitrilase in hypersaline environments A Thesis Submitted by Sarah Ali Ahmed Sonbol to the Applied Sciences Graduate Program (Biotechnology) Has been approved by Dr. Rania Siam (Thesis committee Chair/Advisor) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/Internal Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/Internal Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/External Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/External Examiner) ____________________ Affiliation ____________________ Dr. ____________________ (Moderator) ____________________ Affiliation Graduate Program Director Date School Dean Date ii Dedication To my beloved family Words cannot express how grateful I am for your presence in my life, your endless support and your continuous encouragements iii Acknowledgements I am really thankful to Dr. Rania Siam for her support, guidance and supervision of this thesis. I am also grateful to Dr. Karim Seddik the Associate Dean of graduate studies for his support and help throughout many logistics. My appreciation towards Dr. Ari Ferreira for his critical revision and participation in writing the nitrilase manuscript. My deep thanks to Mr. Amged Oaf for his great efforts and help throughout my PhD especially in my lab work. Thanks to Mr. Ahmed El Hosseiny for his help in my bioinformatics work. I am also deeply indeted to Dr. Nahla Hussein and Dr. Laila Ziko for their great help and support, fruitful lab discussions, revising manuscripts, providing suggestions and feeedback and for their continuous encouragement. I would also like to express my thanks towards Dr. Rehab Abdullah for her support and help in the lab and in providing some of the used reagents. Mr. Saifullah Soliman was a great assistant in LCL library screening, thus I owe him my thanks. Moreover, E. coli B548 and C319 were kindly provided from Dr. D. Mazel lab at Pasteur’s Institute, Paris, France. Special Thanks to Dr. Céline Loot in Dr. Mazel’s lab for the useful insights and tips concerning integron recombination assays. I acknowledge Dr. H. El Saied and his lab members for providing the Aghormy Lake filtered water sample, guidance through PCR screening of metagenomic DNA, and providing 16S rRNA sequencing results. Acknowledgments to Dr. T. Soliman for performing the Qiime analysis on the 16S rRNA sequences. Special thanks to Mr. Osama Ali for his help in ordering needed reagents. I am really thankful to Dr. Ghada Moustafa, Dr. Ali El Behery, Dr. Emanbellah Ramadan and Dr. Mohamed Maged for their help, advice and useful discussions at the beginning of my PhD. I am also indeted to Salma El Shafie, Shaimaa Farag and Marina Nabil for their help, support and encouragement. I would like to thank all biology department and biotechnology graduate program professors those whom I have TAed with or have taken courses with because I have learned a lot from them all. In addition, I am really thankful to the the biology department technical lab aides Mr. Zien and Mohamed El-Bagoury for their help during lab work. Finally, this work could have never been done without th generous PhD fellowship that I have received from Youssef Jameel foundation. Thank you very much. I would also like to thank the AUC for funding my practical lab work by the AUC student research grant and for the AUC conference grant which allowed me to participate in ISME17 in Leipzig, Germany. iv Abstract Hypersaline environments are unique habitats in which residing microorganisms show distinctive adaptive measures that allow their survival under these stress conditions. Hence, halophiles are considered a unique resource of enzymes and gene cassettes with characteristics that could be exploited in different biotechnological applications. Here, due to the attention directed towards finding more stable nitrilases that has a great potential in green bioremediation processes and in different industries; we have biochemically characterized a nitrilase (NitraS-ATII) that we have previously isolated from the hypersaline and thermophilic Atlantis II Deep brine pool lower convective layer (LCL). Nitrilases can hydrolyze nitriles in a one-step reaction into their corresponding carboxylic acid and ammonia. NitraS-ATII showed higher thermal stability compared to a closely related nitrilase, and tolerance towards high concentrations of some heavy metals. We have also focused on analyzing integrons and their associated genetic structures in hypersaline environments because of their presumed adaptive role. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes within the integron at specific recombination sites. We constructed a fosmid library from the metagenome of hypersaline Aghormy Lake in Siwa Oasis. This library and the library of the Atlantis II Deep brine pool lower convective layer (LCL) were screened using pre-designed degenerate primers to amplify intI genes. However, we only detected two positive clones in the Aghormy lake library from which one (AGH-1G10) was further sequenced and analyzed and its integron components were all detected. The AGH-1G10 intI in addition to another identified IntI from Kebrit Deep brine pool Upper interface (KD UIN360) were synthesised and expressed in pBAD18 plasmid to test their in vivo excision activity. However, no activity was observed for both proteins. This could be attributed to using a deletion assay in which the used recombination sites cannot be identified by newly identified IntIs. In addition, we used IntegronFinder software to analyze 80 halophilic bacterial genomes and 141 halophilic archaeal genomes. Our results revealed the presence of 19 new complete integrons and 44 clusters of attC sites lacking a neighboring integron-integrase (CALINs) in bacterial genomes and 1 complete integron in an archaeal genome. We also analyzed 28 hypersaline metagenomic assemblies in which we have identified eight complete integrons, 18 solitary integron integrases and 92 CALINs. Toxin-antitoxin (TA) gene cassettes were abundant in most detected integrons and CALINs, regardless of the length of the gene cassette array. Moreover, as expected, we have found different classes of insertion sequences (ISs) within and nearby integrons and CALINs. Surprisingly, this was only observed within analyzed genomes rather than assembled metagenomes which could be due to frequent concurrence of transposable elements’ repetitive sequences with the peripheries of contigs. Some IS types were v more frequent than others such as IS1182 elements and different ISs that are presumably able to mobilize adjacent genetic structures in presence of one copy of the IS element. Mining for group II introns revealed the presence of not only group IIC-attC, previously found embedded within different studied integrons, but also full and truncated group IIB introns (UHB.I2, H.ha.F1 and H.ha.F2) in CALINs within the extreme halophile Halorhodospira halochloris and a hypersaline metagenome. In addition, we have observed a relative abundance in arginine repressor (ArgR) binding sites within or overlapping with IntI promoters (PintI) raising questions
Recommended publications
  • Bran Serine Hydrolases Achintya Kumar Dolui1,2, Arun Kumar Vijayakumar2,3, Ram Rajasekharan1,2,4 & Panneerselvam Vijayaraj1,2*

    Bran Serine Hydrolases Achintya Kumar Dolui1,2, Arun Kumar Vijayakumar2,3, Ram Rajasekharan1,2,4 & Panneerselvam Vijayaraj1,2*

    www.nature.com/scientificreports OPEN Activity‑based protein profling of rice (Oryza sativa L.) bran serine hydrolases Achintya Kumar Dolui1,2, Arun Kumar Vijayakumar2,3, Ram Rajasekharan1,2,4 & Panneerselvam Vijayaraj1,2* Rice bran is an underutilized agricultural by‑product with economic importance. The unique phytochemicals and fatty acid compositions of bran have been targeted for nutraceutical development. The endogenous lipases and hydrolases are responsible for the rapid deterioration of rice bran. Hence, we attempted to provide the frst comprehensive profling of active serine hydrolases (SHs) present in rice bran proteome by activity‑based protein profling (ABPP) strategy. The active site‑directed fuorophosphonate probe (rhodamine and biotin‑conjugated) was used for the detection and identifcation of active SHs. ABPP revealed 55 uncharacterized active‑SHs and are representing fve diferent known enzyme families. Based on motif and domain analyses, one of the uncharacterized and miss annotated SHs (Os12Ssp, storage protein) was selected for biochemical characterization by overexpressing in yeast. The purifed recombinant protein authenticated the serine protease activity in time and protein‑dependent studies. Os12Ssp exhibited the maximum activity at a pH between 7.0 and 8.0. The protease activity was inhibited by the covalent serine protease inhibitor, which suggests that the ABPP approach is indeed reliable than the sequence‑based annotations. Collectively, the comprehensive knowledge generated from this study would be useful in expanding the current understanding of rice bran SHs and paves the way for better utilization/ stabilization of rice bran. Rice (Oryza sativa) is one of the major staple foods for almost half the world’s population, especially in Asia 1.
  • Lentibacillus Salicampi Gen. Nov., Sp. Nov., a Moderately Halophilic

    Lentibacillus Salicampi Gen. Nov., Sp. Nov., a Moderately Halophilic

    International Journal of Systematic and Evolutionary Microbiology (2002), 52, 2043–2048 DOI: 10.1099/ijs.0.02335-0 Lentibacillus salicampi gen. nov., sp. nov., a NOTE moderately halophilic bacterium isolated from a salt field in Korea 1 Microbial Genomics Jung-Hoon Yoon,1 Kook Hee Kang2 and Yong-Ha Park1,3 Laboratory, Korea Research Institute of Bioscience and Author for correspondence: Biotechnology (KRIBB), Yong-Ha Park. Tel: j82 42 860 4620. Fax: j82 42 862 1315. PO Box 115, Yusong, e-mail: yhpark!mail.kribb.re.kr Taejon, Korea 2 Department of Food and A Gram-variable, aerobic, endospore-forming, rod-shaped bacterial strain, SF- Life Science, 20T, which was isolated from a salt field in Korea, was subjected to a Sungkyunkwan University, Chunchun-dong 300, polyphasic taxonomic study. Cells of this organism were motile by means of Jangan-gu, Suwon, Korea single flagella. Strain SF-20T grew optimally in the presence of 4–8% NaCl. The 3 National Research cell wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic Laboratory of Molecular diamino acid. The predominant menaquinone is MK-7. Strain SF-20T has a Ecosystematics, Institute of cellular fatty acid profile containing major amounts of branched fatty acids. Probionics, Probionic Corporation, Bio-venture The major fatty acids are anteiso-C15:0 and iso-C16:0. The cellular phospholipids Centre, KRIBB, Yusong, are phosphatidylglycerol and diphosphatidylglycerol. The GMC content of the Taejon, Korea DNA is 44 mol%. Strain SF-20T is phylogenetically closely related to the genus Bacillus and some related genera and, particularly, formed a coherent cluster with the genera Salibacillus and Virgibacillus.
  • An ER Stress/Defective Unfolded Protein Response Model Richard T

    An ER Stress/Defective Unfolded Protein Response Model Richard T

    ORIGINAL RESEARCH Ethanol Induced Disordering of Pancreatic Acinar Cell Endoplasmic Reticulum: An ER Stress/Defective Unfolded Protein Response Model Richard T. Waldron,1,2 Hsin-Yuan Su,1 Honit Piplani,1 Joseph Capri,3 Whitaker Cohn,3 Julian P. Whitelegge,3 Kym F. Faull,3 Sugunadevi Sakkiah,1 Ravinder Abrol,1 Wei Yang,1 Bo Zhou,1 Michael R. Freeman,1,2 Stephen J. Pandol,1,2 and Aurelia Lugea1,2 1Department of Medicine, Cedars Sinai Medical Center, Los Angeles, California; 2Department of Medicine, or 3Psychiatry and Biobehavioral Sciences, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California Pancreatic acinar cells Pancreatic acinar cells - no pathology - - Pathology - Ethanol feeding ER sXBP1 Pdi, Grp78… (adaptive UPR) aggregates Proper folding and secretion • disordered ER of proteins processed in the • impaired redox folding endoplasmic reticulum (ER) • ER protein aggregation • secretory defects SUMMARY METHODS: Wild-type and Xbp1þ/- mice were fed control and ethanol diets, then tissues were homogenized and fraction- Heavy alcohol consumption is associated with pancreas ated. ER proteins were labeled with a cysteine-reactive probe, damage, but light drinking shows the opposite effects, isotope-coded affinity tag to obtain a novel pancreatic redox ER reinforcing proteostasis through the unfolded protein proteome. Specific labeling of active serine hydrolases in ER with response orchestrated by X-box binding protein 1. Here, fluorophosphonate desthiobiotin also was characterized pro- ethanol-induced changes in endoplasmic reticulum protein teomically. Protein structural perturbation by redox changes redox and structure/function emerge from an unfolded was evaluated further in molecular dynamic simulations. protein response–deficient genetic model.
  • Catalysis by Acetylcholinesterase

    Catalysis by Acetylcholinesterase

    Proc. Nat. Acad. Sci. USA Vol. 72, No. 10, pp. 3834-38, October 1975 Biochemistry Catalysis by acetylcholinesterase: Evidence that the rate-limiting step for acylation with certain substrates precedes general acid-base catalysis (enzyme mechanism/diffusion control/induced-fit conformational change/pH dependence/deuterium oxide isotope effects) TERRONE L. ROSENBERRY Departments of Biochemistry and Neurology, College of Physicians and Surgeons, Columbia University, New York, N.Y. 10032 Communicated by David Nachmansohn, June 9,1975 ABSTRACT Inferences about the catalytic mechanism of The proposed intermediates include the initial Michaelis acetylcholinesterase (acetyicholine hydrolase, EC 3.1.1.7) are complex E-RX and the acyl enzyme ER, for which evidence frequently made on the basis of a presumed analogy with has long been obtained (5, 6, 1). The pH dependence of sub- chymotrypsin, EC 3.4.21.1. Although both enzymes are serine hydrolases, several differences in the steady-state kinetic strate hydrolysis for chymotrypsin and other serine hydro- properties of the two have been observed. In this report par- lases suggests general acid-base catalysis by a group in the ticujar attention is focused on the second-order reaction con- free enzyme with a pKai of 6 to 7. Furthermore, Hammett stant, kcat/KapD While the reported pH dependence and deu- relationships with positive rho values are found with chymo- terium oxide isotope effect associated with this parameter trypsin both for deacylation (7) and acylation (8) reactions for chymotrypsin are generally consistent with simple mod- and indicate rate-limiting general base catalysis. Deacyla- els involving rate-limiting general acid-base catalysis, this study finds a more complicated situation with acetylcholi- tion rates are typically reduced in deuterium oxide by fac- nesterase.
  • Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus Salicampi ATCC BAA-719T

    Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus Salicampi ATCC BAA-719T

    University of New Hampshire University of New Hampshire Scholars' Repository Faculty Publications 7-18-2019 Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719T Milto Simoes University of New Hampshire, Manchester Kyle S. MacLea University of New Hampshire, Manchester, [email protected] Follow this and additional works at: https://scholars.unh.edu/faculty_pubs Recommended Citation Simoes, Milto and MacLea, Kyle S., "Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719T" (2019). Microbiology Resource Announcements. 702. https://scholars.unh.edu/faculty_pubs/702 This Article is brought to you for free and open access by University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Faculty Publications by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. GENOME SEQUENCES crossm Downloaded from Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719T Milto Simoes Junior,a Kyle S. MacLeaa,b,c http://mra.asm.org/ aBiotechnology Program, University of New Hampshire, Manchester, New Hampshire, USA bBiology Program, University of New Hampshire, Manchester, New Hampshire, USA cDepartment of Life Sciences, University of New Hampshire, Manchester, New Hampshire, USA ABSTRACT Lentibacillus salicampi SF-20T (ϭATCC BAA-719T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719T genome sequence has a predicted length of 3,897,716 bp, containing on November 15, 2019 at UNIVERSITY OF NEW HAMPSHIRE LIBRARY 3,945 total genes and a CRISPR array, with a GϩC content of 43.0%.
  • Proquest Dissertations

    Proquest Dissertations

    Quantitative analysis of soil microbial diversity in the hyperarid Atacama Desert, Chile Item Type text; Dissertation-Reproduction (electronic) Authors Drees, Kevin Paul Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 28/09/2021 01:59:18 Link to Item http://hdl.handle.net/10150/284318 QUANTITATIVE ANALYSIS OF SOIL MICROBIAL DIVERSITY IN THE HYPERARID ATACAMA DESERT, CHILE by Kevin Paul Drees A Dissertation Submitted to the Faculty of the DEPARTMENT OF SOIL, WATER, AND ENVIRONMENTAL SCIENCE In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY WITH A MAJOR IN ENVIRONMENTAL MICROBIOLOGY In the Graduate College THE UNIVERSITY OF ARIZONA 2004 UMI Number: 3132214 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. UMI UMI Microform 3132214 Copyright 2004 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O.
  • The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z

    The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z

    REVIEW pubs.acs.org/CR The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z. Long* and Benjamin F. Cravatt* The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States CONTENTS 2.4. Other Phospholipases 6034 1. Introduction 6023 2.4.1. LIPG (Endothelial Lipase) 6034 2. Small-Molecule Hydrolases 6023 2.4.2. PLA1A (Phosphatidylserine-Specific 2.1. Intracellular Neutral Lipases 6023 PLA1) 6035 2.1.1. LIPE (Hormone-Sensitive Lipase) 6024 2.4.3. LIPH and LIPI (Phosphatidic Acid-Specific 2.1.2. PNPLA2 (Adipose Triglyceride Lipase) 6024 PLA1R and β) 6035 2.1.3. MGLL (Monoacylglycerol Lipase) 6025 2.4.4. PLB1 (Phospholipase B) 6035 2.1.4. DAGLA and DAGLB (Diacylglycerol Lipase 2.4.5. DDHD1 and DDHD2 (DDHD Domain R and β) 6026 Containing 1 and 2) 6035 2.1.5. CES3 (Carboxylesterase 3) 6026 2.4.6. ABHD4 (Alpha/Beta Hydrolase Domain 2.1.6. AADACL1 (Arylacetamide Deacetylase-like 1) 6026 Containing 4) 6036 2.1.7. ABHD6 (Alpha/Beta Hydrolase Domain 2.5. Small-Molecule Amidases 6036 Containing 6) 6027 2.5.1. FAAH and FAAH2 (Fatty Acid Amide 2.1.8. ABHD12 (Alpha/Beta Hydrolase Domain Hydrolase and FAAH2) 6036 Containing 12) 6027 2.5.2. AFMID (Arylformamidase) 6037 2.2. Extracellular Neutral Lipases 6027 2.6. Acyl-CoA Hydrolases 6037 2.2.1. PNLIP (Pancreatic Lipase) 6028 2.6.1. FASN (Fatty Acid Synthase) 6037 2.2.2. PNLIPRP1 and PNLIPR2 (Pancreatic 2.6.2.
  • EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By

    EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By

    EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated
  • Supplementary Figure Legends for Rands Et Al. 2019

    Supplementary Figure Legends for Rands Et Al. 2019

    Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018).
  • Assessment of Chicken Carcass Microbiome Responses During

    Assessment of Chicken Carcass Microbiome Responses During

    www.nature.com/scientificreports OPEN Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Received: 26 September 2016 Accepted: 23 January 2017 Commercial Antimicrobials Using Published: 23 February 2017 a Next Generation Sequencing Approach Sun Ae Kim1,*, Si Hong Park1,*, Sang In Lee1, Casey M. Owens2 & Steven C. Ricke1 The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality. Chickens and other poultry products are some of the most popular primary food products throughout the world1.
  • Serine Hydrolases Involved in Lipid Metabolism in P

    Serine Hydrolases Involved in Lipid Metabolism in P

    Article The Antimalarial Natural Product Salinipostin A Identifies Essential a/b Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites Graphical Abstract Authors Euna Yoo, Christopher J. Schulze, Barbara H. Stokes, ..., Eranthie Weerapana, David A. Fidock, Matthew Bogyo Correspondence [email protected] In Brief Using a probe analog of the antimalarial natural product Sal A, Yoo et al. identify its targets as multiple essential serine hydrolases, including a homolog of human monoacylglycerol lipase. Because parasites were unable to generate robust in vitro resistance to Sal A, these enzymes represent promising targets for antimalarial drugs. Highlights d Semi-synthesis of an affinity analog of the antimalarial natural product Sal A d Identification of serine hydrolases as the primary targets of Sal A in P. falciparum d Sal A covalently binds to and inhibits a MAGL-like protein in P. falciparum d Parasites are unable to generate strong in vitro resistance to Sal A Yoo et al., 2020, Cell Chemical Biology 27, 143–157 February 20, 2020 ª 2020 Elsevier Ltd. https://doi.org/10.1016/j.chembiol.2020.01.001 Cell Chemical Biology Article The Antimalarial Natural Product Salinipostin A Identifies Essential a/b Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites Euna Yoo,1,11 Christopher J. Schulze,1,11 Barbara H. Stokes,2 Ouma Onguka,1 Tomas Yeo,2 Sachel Mok,2 Nina F. Gnadig,€ 2 Yani Zhou,3 Kenji Kurita,4 Ian T. Foe,1 Stephanie M. Terrell,1,5 Michael J. Boucher,6,7 Piotr Cieplak,8 Krittikorn Kumpornsin,9 Marcus C.S. Lee,9 Roger G.
  • MT November 2011

    MT November 2011

    DECEMBER 2011% VOLUME 5, ISSUE 1 The Microbial Taxonomist A Newsletter Published by Bergey’s Manual Trust Fred A. Rainey Elected to Chair of BMT Fred A. Rainey is a native of Join BISMiS or renew your Belfast, Northern Ireland. He membership today! See forms obtained a BSc(Hons) in at end of this newsletter or Microbiology and Microbial join online at: Technology in 1988 from University www.bergeys.org/bismis.html of Warwick. Fred's doctoral studies were carried out at the Thermophile Research Laboratory at the University of Waikato, VOLUME 5 NEWS Hamilton, New Zealand. In 1991 Fred joined the group of Erko Volume 5 of Bergey’s Manual of Stackebrandt at the University of Systematic Bacteriology, which Queensland, Brisbane, Australia. In focuses on the Actinobacteria, is associate and since 2000 as a 1993, when Erko Stackebrandt in the final stages of production. trustee (and secretary). He has became the Director and CEO of contributed many chapters to This volume is the largest of the German Collection of Volumes 1–5 of the 2nd edition of the three that I have managed, Microorganisms and Cell Cultures Bergey's Manual of Systematic and will be more than 2000 (DSMZ), Fred joined the DSMZ Bacteriology and was an Associate pages in length, with 431 figures and set up the molecular Editor of Volume 3, which covered and 320 tables. Its size is such identification laboratory and the Firmicutes. Since his PhD that it will need to be bound in services. studies Fred has been involved in two separate parts. It was at the beginning of 1997 bacterial systematics and has The first round of proofs was that Fred moved to the United authored or coauthored over 200 sent out to the authors in six States and accepted his first papers in the field as well as some batches beginning in August; I academic appointment at 85 book chapters.