DOCSLIB.ORG

Paenibacillus Aquistagni Sp. Nov., Isolated from an Artificial Lake Accumulating Industrial Wastewater

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Paenibacillus Aquistagni Sp. Nov., Isolated from an Artificial Lake Accumulating Industrial Wastewater Lawrence Berkeley National Laboratory Recent Work Title Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater. Permalink https://escholarship.org/uc/item/54d1d62s Journal Antonie van Leeuwenhoek, 110(9) ISSN 0003-6072 Authors Simon, Lučka Škraban, Jure Kyrpides, Nikos C et al. Publication Date 2017-09-01 DOI 10.1007/s10482-017-0891-x Peer reviewed eScholarship.org Powered by the California Digital Library University of California Antonie van Leeuwenhoek DOI 10.1007/s10482-017-0891-x ORIGINAL PAPER Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater Lucˇka Simon . Jure Sˇkraban . Nikos C. Kyrpides . Tanja Woyke . Nicole Shapiro . Ilse Cleenwerck . Peter Vandamme . William B. Whitman . Janja Trcˇek Received: 15 May 2017 / Accepted: 22 May 2017 Ó Springer International Publishing Switzerland 2017 T Abstract Strain 11 was isolated from water of an 7 and the major fatty acid as anteiso-C15:0. The artificial lake accumulating industrial wastewater on peptidoglycan was found to contain meso-di- the outskirts of Celje, Slovenia. Phenotypic charac- aminopimelic acid. In contrast to its close relatives terisation showed strain 11T to be a Gram-stain P. alvei DSM 29T, Paenibacillus apiarius DSM 5581T positive, spore forming bacterium. The 16S rRNA and Paenibacillus profundus NRIC 0885T, strain 11T T gene sequence identified strain 11 as a member of the was found to be able to ferment D-fructose, D-mannose T genus Paenibacillus, closely related to Paenibacillus and D-xylose. A draft genome of strain 11 contains a alvei (96.2%). Genomic similarity with P. alvei 29T cluster of genes associated with type IV pilin synthesis was 73.1% (gANI), 70.2% (ANIb), 86.7% (ANIm) usually found in clostridia, and only sporadically in and 21.7 ± 2.3% (GGDC). The DNA G?C content of other Gram-positive bacteria. Genotypic, chemotaxo- strain 11T was determined to be 47.5%. The predom- nomic, physiological and biochemical characteristics inant menaquinone of strain 11T was identified as MK- of strain 11T presented in this study support the creation of a novel species within the genus Paeni- bacillus, for which the name Paenibacillus aquistagni T T L. Simon Á J. Sˇkraban Á J. Trcˇek sp. nov. is proposed, with strain 11 (=ZIM B1027 Department of Biology, Faculty of Natural Sciences and =LMG 29561T =CCM 8679T ) as the type strain. Mathematics, University of Maribor, Maribor, Slovenia N. C. Kyrpides Á T. Woyke Á N. Shapiro Keywords Paenibacillus aquistagni sp. nov. Á DOE Joint Genome Institute, Walnut Creek, CA, USA Polyphasic taxonomy Á Draft genome Á Type IV pilin Á KMG-III I. Cleenwerck Á P. Vandamme BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium Introduction W. B. Whitman Department of Microbiology, University of Georgia, Athens, GA, USA The genus Paenibacillus was proposed by Ash et al. (1993) for the members of Bacillus group 3; later, its J. Trcˇek (&) description was emended by Shida et al. (1997). Department of Biology, Faculty of Chemistry and Presently, Paenibacillus spp. are classified into over Chemical Engineering, University of Maribor, Korosˇka cesta 160, 2000 Maribor, Slovenia 200 validly named species (http://www.bacterio.net/ e-mail: [email protected] paenibacillus.html) with Paenibacillus polymyxa as 123 Antonie van Leeuwenhoek the type species (Ash et al. 1993). Most Paenibacillus type strain Paenibacillus profundus NRIC 0885T from species consist of strains that are motile, Gram-stain the Nodai Culture Collection (NRIC, Japan). All positive (some are Gram-stain variable, such as reference strains were cultured on NA medium for Paenibacillus taiwanensis and Paenibacillus comparative analyses. assamensis), spore forming, facultatively anaerobic or strictly aerobic. Most species are catalase positive and Morphological, physiological and biochemical show optimal growth at 28–40 °C and pH 7.0, with analysis some species being alkaliphilic. The major fatty acid of Paenibacillus spp. is anteiso-C15:0. The DNA G?C Colonial morphology and size were described and content of Paenibacillus spp. ranges from 40 to measured visually after cultivation on NA medium. 59 mol% (Priest 2015). Gram-stain reaction was determined by using a Gram- Paenibacillus species have been isolated from staining kit (Sigma-Aldrich, St. Louis, MO, USA), diverse habitats, such as paperboard, deep-sea surface following the instructions of the manufacturer. sediment, honeybee larva, warm springs, farmland Cytochrome c oxidase activity was determined by soil, tree bark, blood samples, sputum, human urine, oxidation of 1% (w/v) N,N,N0,N0 - tetramethyl-1,4- rhizosphere soil and necrotic wounds (Nakamura phenylendiamin dihydrochloride and catalase activity 1996; Roux and Raoult 2004; Saha et al. 2005; Lee by observing air bubble production using 3% (v/v) et al. 2007; Roux et al. 2008; Kim et al. 2010; H2O2 as described by Gerhardt et al. (1994). Oxygen Romanenko et al. 2013; Han et al. 2015; Sitdhipol demand for growth was determined by incubating et al. 2016). During an assessment of the cultivable inoculated NA medium for 7 days in a jar with microbial diversity from water of an artificial lake anaerobic atmosphere generation bags (Sigma- located on the outskirts of Celje (Slovenia) which is Aldrich). Resistance against different concentrations accumulating liquid industrial waste, strain 11T was of NaCl and the pH range for growth were analysed in isolated. In a phylogenetic tree based on the 16S rRNA nutrient broth. The growth was detected by measuring gene sequence, strain 11T formed a separate branch an increase in turbidity. The temperature range for within the genus Paenibacillus, suggesting it could growth was analysed on NA medium by incubating the represent a novel species. To clarify its taxonomic plates for 10 days at different temperatures. Motility status, further genotypic and phenotypic analyses were was determined as described by Alexander and Strete performed. The genome of strain 11T was sequenced (2001) in a tube with semisolid NA medium contain- under the umbrella of the Genomic Encyclopedia of ing 0.5% agar by incubating the tube for 4 days at Type Strains, Phase III: the genomes of soil and plant- 30 °C. Gliding motility was analysed on the same type associated and newly described type strains (Whitman of medium in a Petri dish by inoculating the surface of et al. 2015). the medium with a spot of strain 11T culture. The presence of endospores was determined according to the method of Schaeffer-Fulton as described by Materials and methods Gerhardt et al. (1994). Other biochemical characteristics were determined Strains and growth conditions using the API 50CH, API ZYM and API 20E microtest systems (bioMe´rieux, Marcy l’Etoile, France) at A lake situated on the outskirts of Celje (Slovenia) was 30 °C, following the manufacturer’s instructions. sampled in September 2013. The water sample had a pH of 7.3. Strain 11T was isolated by plating the Phylogenetic analysis sampled water on nutrient agar (NA, Sigma-Aldrich) and incubating the plates at 25 °C in an aerobic The 16S rRNA gene sequence of strain 11T (1478 nt) atmosphere for 4 days. was determined as described previously (Trcˇek et al. The reference type strains Paenibacillus alvei DSM 2000) with the following modifications: DNA was 29T and Paenibacillus apiarius DSM 5581T were isolated with a GeneJETTM Genomic DNA Purifica- obtained from the German Collection of Microorgan- tion Kit (Thermo Fisher Scientific, Waltham, MA, isms and Cell Cultures (DSMZ, Germany) and the USA) following the protocol for Gram-positive 123 Antonie van Leeuwenhoek bacteria. The 16S rRNA gene sequence was amplified Chemotaxonomic characterisation with primers fD1 (50-AGAGTTTGATCMTGGCT- CAG-30) and rH1542 (50-AAGGAGGTGATC- The whole cell fatty acids of strain 11T, P. alvei DSM CAGCCGCA-30). The nucleotide sequences of both 29T, P. apiarius DSM 5581T and P. profundus NRIC strands were determined by the primer walking 0885T, all grown for 24 h at 28 °C under aerobic method using the primers described by Boesch et al. conditions on trypticase soy agar (TSA, Difco) (1998). The 16S rRNA gene sequence was compared medium, were determined by GC using an Agilent to all type strains representing the genus Paenibacil- Technologies 6890 N gas chromatograph (Santa lus. The sequences were aligned with the Clustal X 1.8 Clara, CA, USA). The peak naming table MIDI TSBA program (Thompson et al. 1997) using the default 5.0 was used. settings of the multiple alignment tool and then The isomer type of the diamino acid in the cell wall subjected to the phylogenetic analyses by applying of strain 11T was analysed by thin-layer chromatog- the neighbour-joining method in the DNADIST pro- raphy as described previously (Schumann 2011). gram from the PHYLIP package (Felsenstein 2002). Extraction of quinones was carried out according to The tree was drawn with the Treeview program (Page the two stage method described by Tindall (1990a, b). 2000). The robustness of the phylogenetic tree topol- Quinones were separated by thin layer chromatography ogy was evaluated by bootstrap analysis with 1000 on silica gel (Macherey–Nagel Art. No. 805 023), using replications using the SEQBOOT and CONSENCE hexane:tert-butylmethylether (9:1 v/v) as solvent. UV programs from the PHYLIP package. Bootstrap values absorbing bands corresponding to menaquinones were [60% were considered to be significant. further analysed using a LDC Analytical (Thermo Separation Products) HPLC fitted with a reverse phase Sequencing of the genome column (Macherey–Nagel, 2 mm 9 125 mm, 3 lm, RP18) using methanol:heptane 9:1 (v/v) as the eluant. Genomic DNA was extracted with a NucleoSpin Menaquinones were detected at 269 nm. Tissue kit (Macherey–Nagel) using the manufac- turer’s protocol. A draft genome sequence of strain 11T was generated at the DOE Joint Genome Institute Results and discussion (JGI).
Load more

Recommended publications
  • Review Pili in Gram-Negative and Gram-Positive Bacteria – Structure
    Cell. Mol. Life Sci. 66 (2009) 613 – 635 1420-682X/09/040613-23 Cellular and Molecular Life Sciences DOI 10.1007/s00018-008-8477-4 Birkhuser Verlag, Basel, 2008 Review Pili in Gram-negative and Gram-positive bacteria – structure, assembly and their role in disease T. Profta,c,* and E. N. Bakerb,c a School of Medical Sciences, Department of Molecular Medicine & Pathology, University of Auckland, Private Bag 92019, Auckland 1142 (New Zealand), Fax: +64-9-373-7492, e-mail: [email protected] b School of Biological Sciences, University of Auckland, Auckland (New Zealand) c Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland (New Zealand) Received 08 August 2008; received after revision 24 September 2008; accepted 01 October 2008 Online First 27 October 2008 Abstract. Many bacterial species possess long fila- special form of bacterial cell movement, known as mentous structures known as pili or fimbriae extend- twitching motility. In contrast, the more recently ing from their surfaces. Despite the diversity in pilus discovered pili in Gram-positive bacteria are formed structure and biogenesis, pili in Gram-negative bac- by covalent polymerization of pilin subunits in a teria are typically formed by non-covalent homopo- process that requires a dedicated sortase enzyme. lymerization of major pilus subunit proteins (pilins), Minor pilins are added to the fiber and play a major which generates the pilus shaft. Additional pilins may role in host cell colonization. be added to the fiber and often function as host cell This review gives an overview of the structure, adhesins. Some pili are also involved in biofilm assembly and function of the best-characterized pili formation, phage transduction, DNA uptake and a of both Gram-negative and Gram-positive bacteria.
    [Show full text]
  • Engineering the Human Microbiome, a Natural Double-Barreled Approach Towards Solving Both Our Current Antibiotic Resistance and Sepsis Problems
    American Journal of www.biomedgrid.com Biomedical Science & Research ISSN: 2642-1747 --------------------------------------------------------------------------------------------------------------------------------- Opinion Copy Right@ Toleman MA Engineering the Human Microbiome, A Natural Double-Barreled Approach Towards Solving both our Current Antibiotic Resistance and Sepsis Problems Martins W1, Mathias J1, Babenko D2 and Toleman MA1* 1Cardiff University Medical school, Department of Immunology and Infection, The Heath hospital, UK 2Karaganda Medical University, Kazakhstan *Corresponding author: Toleman MA, Cardiff University Medical school, Department of Immunology and Infection, The Heath hospital, Cardiff, UK. To Cite This Article: Martins W, Mathias J, Babenko D, Toleman MA, Engineering the Human Microbiome, A Natural Double-Barreled Approach Towards Solving both our Current Antibiotic Resistance and Sepsis Problems. Am J Biomed Sci & Res. 2020 - 11(3). AJBSR.MS.ID.001632. DOI: 10.34297/AJBSR.2020.11.001632. Received: December 12, 2020; Published: December 18, 2020 Opinion resistance mechanism responsible for this rise was an enzyme Many of the bacteria that cause life-threatening infection live called CTX-M-15 that gave resistance to the penicillin, monobactam, in very close association with us. Escherichia coli, for example and cephalosporin classes of the ß-lactam family of antibiotics (c. causes 80% of common community associated urinary tract infections and is also the main cause of serious (blood-stream) in several enteric pathogens including E. coli in New Delhi, India infection throughout Europe [1,2]. However, E. coli routinely lives 50% of all antibiotics) [7]. Its gene blaCTX-M-15 was first isolated in 2000 [8]. Later publications indicated that it was widespread as a commensal organism in our gut.
    [Show full text]
  • Paenibacillus Polymyxa
    Liu et al. BMC Microbiology (2021) 21:70 https://doi.org/10.1186/s12866-021-02132-2 RESEARCH ARTICLE Open Access Interactional mechanisms of Paenibacillus polymyxa SC2 and pepper (Capsicum annuum L.) suggested by transcriptomics Hu Liu, Yufei Li, Ke Ge, Binghai Du, Kai Liu, Chengqiang Wang* and Yanqin Ding* Abstract Background: Paenibacillus polymyxa SC2, a bacterium isolated from the rhizosphere soil of pepper (Capsicum annuum L.), promotes growth and biocontrol of pepper. However, the mechanisms of interaction between P. polymyxa SC2 and pepper have not yet been elucidated. This study aimed to investigate the interactional relationship of P. polymyxa SC2 and pepper using transcriptomics. Results: P. polymyxa SC2 promotes growth of pepper stems and leaves in pot experiments in the greenhouse. Under interaction conditions, peppers stimulate the expression of genes related to quorum sensing, chemotaxis, and biofilm formation in P. polymyxa SC2. Peppers induced the expression of polymyxin and fusaricidin biosynthesis genes in P. polymyxa SC2, and these genes were up-regulated 2.93- to 6.13-fold and 2.77- to 7.88-fold, respectively. Under the stimulation of medium which has been used to culture pepper, the bacteriostatic diameter of P. polymyxa SC2 against Xanthomonas citri increased significantly. Concurrently, under the stimulation of P. polymyxa SC2, expression of transcription factor genes WRKY2 and WRKY40 in pepper was up-regulated 1.17-fold and 3.5-fold, respectively. Conclusions: Through the interaction with pepper, the ability of P. polymyxa SC2 to inhibit pathogens was enhanced. P. polymyxa SC2 also induces systemic resistance in pepper by stimulating expression of corresponding transcription regulators.
    [Show full text]
  • Current Issues of Nano-Bio-Science
    Current Issues of Nano-Bio-Science CeNS Winterschool 2003 Mauterndorf, Austria 24-28 February 2003 Current Issues of Nano-Bio-Science CeNS Winterschool 2003 Mauterndorf, Austria 24-28 February 2003 in cooperation with SFB 486 and SFB 513 Program Committee Organisation Christoph Bräuchle Monika Kaempfe Jan von Delft Evelyn Morgenroth Hermann Gaub Joachim Rädler Jörg P. Kotthaus Paul Leiderer Joachim Rädler Internal Students’ Seminar: Schedule Saturday, 22nd February 7:30 pm Meeting in front of the castle’s lower gate to go the “Skialm” together 8:00 pm Get-together at the „Skialm“ in Mauterndorf (in the Skiing center) (kitchen closes at 9:30 pm) Sunday, 23rd February 9:45 am Introduction (W. Parak, F. Simmel) 10:00 am Simon Keller (AG Rädler) 10:30 am Stefan Griessl (AG Heckl) 11:00 am Coffee break 11:30 am Christine Meyer (AG Kotthaus) 12:00 pm Michael Sindel (AG von Delft) 12:30 pm Lunch (not provided), informal discussions 5:00 pm Ferdinand Kühner (AG Gaub) 5:30 pm Stefan Beyer (NG Simmel) Teresa Pellegrino (NG Parak) 6:00 pm Stefan Kowarik (AG Feldmann) 6:30 pm Break 7:00 pm Niklolay Petkov (AG Bein) 7:30 pm Sebastian Gritschneder (AG Reichling) 8:00 pm Ralf Bausinger / Johanna Kirstein (AG Bräuchle) 8:30 pm Conclusion Program Monday, 24th February 2003 8.30 – 8.45 Opening 8.45 – 9.45 Cees Dekker, Delft University of Technology Carbon nanotubes as model systems for nanoelectronics and nanosensors 9.45 – 10.45 Ulf Diederichsen, Universität Göttingen Molecular architecture with biooligomers 10.45 – 11.15 Coffee Break 11.15 – 12.15 Wolfgang
    [Show full text]
  • Cell Structure and Function in the Bacteria and Archaea
    4 Chapter Preview and Key Concepts 4.1 1.1 DiversityThe Beginnings among theof Microbiology Bacteria and Archaea 1.1. •The BacteriaThe are discovery classified of microorganismsinto several Cell Structure wasmajor dependent phyla. on observations made with 2. theThe microscope Archaea are currently classified into two 2. •major phyla.The emergence of experimental 4.2 Cellscience Shapes provided and Arrangements a means to test long held and Function beliefs and resolve controversies 3. Many bacterial cells have a rod, spherical, or 3. MicroInquiryspiral shape and1: Experimentation are organized into and a specific Scientificellular c arrangement. Inquiry in the Bacteria 4.31.2 AnMicroorganisms Overview to Bacterialand Disease and Transmission Archaeal 4.Cell • StructureEarly epidemiology studies suggested how diseases could be spread and 4. Bacterial and archaeal cells are organized at be controlled the cellular and molecular levels. 5. • Resistance to a disease can come and Archaea 4.4 External Cell Structures from exposure to and recovery from a mild 5.form Pili allowof (or cells a very to attach similar) to surfacesdisease or other cells. 1.3 The Classical Golden Age of Microbiology 6. Flagella provide motility. Our planet has always been in the “Age of Bacteria,” ever since the first 6. (1854-1914) 7. A glycocalyx protects against desiccation, fossils—bacteria of course—were entombed in rocks more than 3 billion 7. • The germ theory was based on the attaches cells to surfaces, and helps observations that different microorganisms years ago. On any possible, reasonable criterion, bacteria are—and always pathogens evade the immune system. have been—the dominant forms of life on Earth.
    [Show full text]
  • Paenibacillaceae Cover
    The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ...........................................................................................................................
    [Show full text]
  • Identification of Bacterial Isolates Originating from the Human Hand Leisa M
    Undergraduate Research Article Identification of Bacterial Isolates Originating from the Human Hand 1 2 3 Leisa M. Rauch , Annette M. Golonka , and Eran S. Kilpatrick 1University of South Carolina Columbia, College of Nursing 2University of South Carolina Lancaster, Department of Math, Science, Nursing and Public Health 3University of South Carolina Salkehatchie, Division of Mathematics and Science The human body provides habitat for a diversity of bacterial species that are part of the normal human microbiota. Identification of various members of the normal microbiota to the species level requires a combination of biological staining procedures, biochemical tests, and molecular techniques. In this experiment, ten bacterial isolates originating from the hands of nine students and one faculty member at USC Salkehatchie were identified. Classification to a general taxonomic group was accomplished with standard staining and biochemical tests. Sequences for the 16S ribosomal RNA section of DNA for each isolate were analyzed with BLAST to generate a list of potential species identifications. Species associated with confidence levels greater than 98% were considered positive identifications. The samples were then analyzed using Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). Five isolates were identified as Bacillus megaterium (2 isolates), Bacillus thuringiensis, Paenibacillus alvei, and Micrococcus luteus. Four isolates were identified as Bacillus and Brevibacterium species. One isolate had conflicting identifications based on molecular and MALDI-TOF MS and is only listed as a Bacillus species. In addition to contributing to the study of the human normal microbiota, the diagnostic properties and identities of each isolate will be incorporated into a laboratory resource used by microbiology students at USC Salkehatchie.
    [Show full text]
  • Fusaricidin Produced by Paenibacillus Polymyxa WLY78 Induces Systemic Resistance Against Fusarium Wilt of Cucumber
    International Journal of Molecular Sciences Article Fusaricidin Produced by Paenibacillus polymyxa WLY78 Induces Systemic Resistance against Fusarium Wilt of Cucumber Yunlong Li and Sanfeng Chen * State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100094, China; [email protected] * Correspondence: [email protected]; Tel.: +86-10-6273-1551 Received: 7 July 2019; Accepted: 17 October 2019; Published: 22 October 2019 Abstract: Cucumber is an important vegetable crop in China. Fusarium wilt is a soil-borne disease that can significantly reduce cucumber yields. Paenibacillus polymyxa WLY78 can strongly inhibit Fusarium oxysporum f. sp. Cucumerium, which causes Fusarium wilt disease. In this study, we screened the genome of WLY78 and found eight potential antibiotic biosynthesis gene clusters. Mutation analysis showed that among the eight clusters, the fusaricidin synthesis (fus) gene cluster is involved in inhibiting the Fusarium genus, Verticillium albo-atrum, Monilia persoon, Alternaria mali, Botrytis cinereal, and Aspergillus niger. Further mutation analysis revealed that with the exception of fusTE, the seven genes fusG, fusF, fusE, fusD, fusC, fusB, and fusA within the fus cluster were all involved in inhibiting fungi. This is the first time that demonstrated that fusTE was not essential. We first report the inhibitory mode of fusaricidin to inhibit spore germination and disrupt hyphal membranes. A biocontrol assay demonstrated that fusaricidin played a major role in controlling Fusarium wilt disease. Additionally, qRT-PCR demonstrated that fusaricidin could induce systemic resistance via salicylic acid (SA) signal against Fusarium wilt of cucumber. WLY78 is the first reported strain to both produce fusaricidin and fix nitrogen.
    [Show full text]
  • Identification and Classification of Known and Putative Antimicrobial Compounds Produced by a Wide Variety of Bacillales Species Xin Zhao1,2 and Oscar P
    Zhao and Kuipers BMC Genomics (2016) 17:882 DOI 10.1186/s12864-016-3224-y RESEARCH ARTICLE Open Access Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species Xin Zhao1,2 and Oscar P. Kuipers1* Abstract Background: Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. Results: We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. Conclusions: Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified. Keywords: Antimicrobials, Bacillales, Bacillus, Genome-mining, Lanthipeptides, Sactipeptides, Thiopeptides, NRPs, PKs Background (bacteriocins) [4], as well as non-ribosomally synthesized Most of the species of the genus Bacillus and related peptides (NRPs) and polyketides (PKs) [5].
    [Show full text]
  • Multiple Conformations Facilitate Pilt Function in the Type IV Pilus
    bioRxiv preprint doi: https://doi.org/10.1101/672212; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Multiple conformations facilitate PilT function in the type IV pilus Matthew McCallum1,2, Samir Benlekbir2, Sheryl Nguyen2, Stephanie Tammam2, John L. Rubinstein1,2,3,*, Lori L. Burrows4,*, and P. Lynne Howell1,2,* 1Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada 2Program in Molecular Structure & Function, Peter Gilgan Centre for Research and Learning, The Hospital for SicK Children, Toronto, ON M5G 0A4, Canada. 3Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1l7, Canada. 4Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada. To whom correspondence should be addressed: Dr. Lynne Howell. Phone: 416-813-5378; Email: [email protected] Dr. Lori Burrows, Phone: 905-525-9140, x22029; Email: [email protected] Dr. John Rubinstein. Phone 416-813-7255; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/672212; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Type IV pilus-like systems are protein complexes that polymerize a fibre of pilins. They are critical for virulence in many pathogens. Pilin polymerization and depolymerization are powered by motor PilT-like ATPases thought to possess C2 symmetry. However, most PilT-like ATPases crystallize with either C3 or C6 symmetry and the relevance of these conformations is unclear.
    [Show full text]
  • Paenibacillus All Patients Sought Treatment for Fever Ranging from 37.8°C to 39.8°C and Admitted to Continuing to Inject Illicit Larvae Bacteremia Drugs Or Methadone
    The Study Paenibacillus All patients sought treatment for fever ranging from 37.8°C to 39.8°C and admitted to continuing to inject illicit larvae Bacteremia drugs or methadone. Information about patient character- istics, clinical signs and symptoms, laboratory and mico- in Injection biologic investigations, and treatment details are summa- rized in the Table. P. larvae was identifi ed in blood cultures Drug Users (BacT/ALERT 3D-System; bioMérieux, Marcy l’Etoile, Siegbert Rieg, Tilman Martin Bauer, France) of each patient described. The clinical course of Gabriele Peyerl-Hoffmann, Jürgen Held, P. larvae bacteremia was benign in 3 patients, and com- Wolfgang Ritter, Dirk Wagner, plications developed in 2 patients. Patient 1 had relapsing Winfried Vinzenz Kern, and Annerose Serr disease and spontaneous bacterial peritonitis; patient 4 had pulmonary embolism without defi nite evidence of sep- Paenibacillus larvae causes American foulbrood in tic embolism. Patients 2 and 3 recovered without specifi c honey bees. We describe P. larvae bacteremia in 5 in- antimicrobial drug treatment; for patients 4 and 5, defer- jection drug users who had self-injected honey-prepared vescence and negative follow-up blood cultures were ob- methadone proven to contain P. larvae spores. That such preparations may be contaminated with spores of this or- served after they received treatment with β-lactam agents ganism is not well known among pharmacists, physicians, (imipenem or cefuroxime). The recurrent P. larvae infec- and addicts. tion observed in patient 1 was probably the consequence of repeated injection of contaminated methadone rather than an inadequate response to antimicrobial drug therapy. s a consequence of needle sharing and repeated par- In 2 cases, culture of the honey used to prepare metha- Aenteral administration of nonsterile material, injection done or of honey-containing ready-to-use methadone also drug users risk becoming ill from a variety of infections, yielded P.
    [Show full text]
  • Characterisation and Biofilm Screening of the Predominant Bacteria Isolated from Whey Protein Concentrate 80 Siti Norbaizura Md Zain, Steve H
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Archive Ouverte en Sciences de l'Information et de la Communication Characterisation and biofilm screening of the predominant bacteria isolated from whey protein concentrate 80 Siti Norbaizura Md Zain, Steve H. Flint, Rod Bennett, Hong-Soon Tay To cite this version: Siti Norbaizura Md Zain, Steve H. Flint, Rod Bennett, Hong-Soon Tay. Characterisation and biofilm screening of the predominant bacteria isolated from whey protein concentrate 80. Dairy Science & Technology, EDP sciences/Springer, 2016, 96 (3), pp.285-295. 10.1007/s13594-015-0264-z. hal- 01532311 HAL Id: hal-01532311 https://hal.archives-ouvertes.fr/hal-01532311 Submitted on 2 Jun 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Dairy Sci. & Technol. (2016) 96:285–295 DOI 10.1007/s13594-015-0264-z ORIGINAL PAPER Characterisation and biofilm screening of the predominant bacteria isolated from whey protein concentrate 80 Siti Norbaizura Md Zain1,2 & Steve H. Flint 1 & Rod Bennett1 & Hong-Soon Tay3 Received: 18 August 2015 / Revised: 7 October 2015 / Accepted: 8 October 2015 / Published online: 3 November 2015 # INRA and Springer-Verlag France 2015 Abstract The source of microbiological contamination of whey protein concentrate (WPC), a quality problem for the dairy industry, has not been thoroughly investigated.
    [Show full text]