A Molecular Phylogenetic Framework for Bacillus Subtilis Using Genome
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Molecular Characterization of Local Strains of Bacillus Thuringiensis in the North of Algeria
Vol. 10(45), pp. 1880-1887, 7 December, 2016 DOI: 10.5897/AJMR2016.7946 Article Number: AEEEB8A61917 ISSN 1996-0808 African Journal of Microbiology Research Copyright © 2016 Author(s) retain the copyright of this article http://www.academicjournals.org/AJMR Full Length Research Paper Molecular characterization of local strains of Bacillus thuringiensis in the North of Algeria Kebdani M.1*, Mahdjoubi M.2, Cherif A.2, Gaouar B. N.1 and Rebiahi S. A.3 1Laboratory of Ecology and Management of Naturals Ecosystems, Ecology and Environment Department, Abu Bakr Belkaid University, Imama, Tlemcen, Algeria. 2Laboratory of Biotechnology and Bio-Geo Resources Valorization, Higher Institute for Biotechnology, University of Manouba Biotechpole of Sidi Thabet Sidi Thabet, Ariana, Tunisia. 3Laboratory of Applied Microbiology and Environment, Biology Department, Abu Bakr Belkaid University, Imama, Tlemcen, Algeria. Received 1 February, 2016, Accepted 19 September, 2016. The analysis of soil samples taken from orange groves located in four cities of Northern Algeria allowed the isolation and identification of 24 strains belonging to the group Bacillus cereus, based on their physiological, biochemical and molecular characters investigated. They were divided as follow: 12 strains of Bacillus thuringiensis, 1 strain of Bacillus pumilis, 4 strains of Bacillus cereus, 5 strains of Bacillus subtilis and 2 Bacillus mycoides strains. After the molecular characterization performed with the aid of polymerase chain reaction (PCR) analysis, it was confirmed from the parasporal bodies using a scanning electron microscope that the strains of the identified collection belong to the species, B. thuringiensis. Key words: Bacillus cereus, Bacillus thuringiensis, Bacillus pumilis, Bacillus subtilis, Bacillus mycoides, polymerase chain reaction, scanning EM. -
Food Waste Composting and Microbial Community Structure Profiling
processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. -
Mai Muun Muntant Un an to the Man Uniti
MAIMUUN MUNTANTUS009855303B2 UN AN TO THEMAN UNITI (12 ) United States Patent ( 10 ) Patent No. : US 9 , 855 ,303 B2 McKenzie et al. (45 ) Date of Patent: * Jan . 2 , 2018 ( 54 ) COMPOSITIONS AND METHODS (58 ) Field of Classification Search ??? . A61K 35 / 742 (71 ) Applicant : SERES THERAPEUTICS , INC . , See application file for complete search history . Cambridge, MA (US ) (72 ) Inventors : Gregory McKenzie , Arlington , MA ( 56 ) References Cited (US ) ; Mary - Jane Lombardo McKenzie , Arlington , MA (US ) ; David U . S . PATENT DOCUMENTS N . Cook , Brooklyn , NY (US ) ; Marin 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al. Vulic , Boston , MA (US ) ; Geoffrey von 3 ,228 , 838 A 1 / 1966 Rinfret Maltzahn , Boston , MA (US ) ; Brian 3 ,608 ,030 A 9 / 1971 Tint Goodman , Boston , MA (US ) ; John 4 ,077 , 227 A 3 / 1978 Larson Grant Aunins , Doylestown , PA (US ) ; 4 , 205 , 132 A 5 / 1980 Sandine Matthew R . Henn , Somerville , MA 4 ,655 ,047 A 4 / 1987 Temple (US ) ; David Arthur Berry , Brookline , 4 ,689 , 226 A 8 / 1987 Nurmi MA (US ) ; Jonathan Winkler , Boston , 4 ,839 , 281 A 6 / 1989 Gorbach et al . 5 , 196 , 205 A 3 / 1993 Borody MA (US ) 5 , 425 , 951 A 6 / 1995 Goodrich 5 ,436 ,002 A 7 / 1995 Payne ( 73 ) Assignee : Seres Therapeutics , Inc ., Cambridge , 5 ,443 ,826 A 8 / 1995 Borody MA (US ) 5 , 599 , 795 A 2 / 1997 McCann 5 ,648 ,206 A 7 / 1997 Goodrich ( * ) Notice : Subject to any disclaimer , the term of this 5 , 951 , 977 A 9 / 1999 Nisbet et al. patent is extended or adjusted under 35 5 , 965 , 128 A 10 / 1999 Doyle et al . -
Polyhydroxyalkanoate Biosynthesis by Oxalotrophic Bacteria from High Andean Soil
Univ. Sci. 23 (1): 35-59, 2018. doi: 10.11144/Javeriana.SC23-1.pbb0 Bogotá ORIGINAL ARTICLE Polyhydroxyalkanoate biosynthesis by oxalotrophic bacteria from high Andean soil Roger David Castillo Arteaga1, *, Edith Mariela Burbano Rosero2, Iván Darío Otero Ramírez3, Juan Camilo Roncallo1, Sandra Patricia Hidalgo Bonilla4 and Pablo Fernández Izquierdo2 Edited by Juan Carlos Salcedo-Reyes Abstract ([email protected]) 1. Universidade de São Paulo, Oxalate is a highly oxidized organic acid anion used as a carbon and energy Instituto de Ciências Biomédicas, Laboratório de Bioprodutos, source by oxalotrophic bacteria. Oxalogenic plants convert atmospheric CO2 Av. Prof. Lineu Prestes, 1374, São Paulo, into oxalic acid and oxalic salts. Oxalate-salt formation acts as a carbon sink in SP, Brasil, CEP 05508-900. terrestrial ecosystems via the oxalate-carbonate pathway (OCP). Oxalotrophic 2. Universidad de Nariño, bacteria might be implicated in other carbon-storage processes, including Departamento de Biología. the synthesis of polyhydroxyalkanoates (PHAs). More recently, a variety Grupo de Investigación de Biotecnología of bacteria from the Andean region of Colombia in Nariño have been Microbiana. Torobajo, Cl 18 - Cra 50. reported for their PHA-producing abilities. These species can degrade oxalate San Juan de Pasto, Colombia. and participate in the oxalate-carbonate pathway. The aim of this study 3. Universidad del Cauca, was to isolate and characterize oxalotrophic bacteria with the capacity to Facultad de Ciencias Agrarias, Grupo de Investigación en accumulate PHA biopolymers. Plants of the genus Oxalis were collected Aprovechamiento de Subproductos and bacteria were isolated from the soil adhering to the roots. The isolated Agroindustriales, Cl 5 No. -
Genome Snapshot of Paenibacillus Polymyxa ATCC 842T
J. Microbiol. Biotechnol. (2006), 16(10), 1650–1655 Genome Snapshot of Paenibacillus polymyxa ATCC 842T JEONG, HAEYOUNG, JIHYUN F. KIM, YON-KYOUNG PARK, SEONG-BIN KIM, CHANGHOON KIM†, AND SEUNG-HWAN PARK* Laboratory of Microbial Genomics, Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), P.O. Box 115, Yuseong, Daejeon 305-600, Korea Received: May 11, 2006 Accepted: June 22, 2006 Abstract Bacteria belonging to the genus Paenibacillus are rhizosphere and soil, and their useful traits have been facultatively anaerobic endospore formers and are attracting analyzed [3, 6-8, 10, 15, 22, 26]. At present, the genus growing ecological and agricultural interest, yet their genome Paenibacillus consists of 84 species (NCBI Taxonomy information is very limited. The present study surveyed the Homepage at http://www.ncbi.nlm.nih.gov/Taxonomy/ genomic features of P. polymyxa ATCC 842 T using pulse-field taxonomyhome.html, February 2006). gel electrophoresis of restriction fragments and sample genome Nonetheless, despite the growing interest in Paenibacillus, sequencing of 1,747 reads (approximately 17.5% coverage of its genomic information is very scarce. Most of the completely the genome). Putative functions were assigned to more than sequenced organisms currently belong to the Bacillaceae 60% of the sequences. Functional classification of the sequences family, in particular to the Bacillus genus, whereas data on showed a similar pattern to that of B. subtilis. Sequence Paenibacillaceae sequences is limited even at the draft analysis suggests nitrogen fixation and antibiotic production level. P. polymyxa, the type species of the genus Paenibacillus, by P. polymyxa ATCC 842 T, which may explain its plant is also of great ecological and agricultural importance, owing growth-promoting effects. -
Paenibacillus Konkukensis Sp. Nov., Isolated from Animal Feed
TAXONOMIC DESCRIPTION Im et al., Int J Syst Evol Microbiol 2017;67:2343–2348 DOI 10.1099/ijsem.0.001955 Paenibacillus konkukensis sp. nov., isolated from animal feed Wan-Taek Im,1 Kwon-Jung Yi,2 Sang-Suk Lee,3 Hyung In Moon,4 Che Ok Jeon,5 Dong-Woon Kim6 and Soo-Ki Kim2,* Abstract A Gram-stain-positive, oxidase- and catalase-positive, aerobic, rod-shaped bacterium, designated strain SK-3146T, was isolated from animal feed. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that the strain formed a distinct lineage within the genus Paenibacillus that was closely related to Paenibacillus yunnanensis JCM 30953T (98.6 %), Paenibacillus vulneris CCUG 53270T (98.0 %) and Paenibacillus chinjuensis DSM 15045T (96.9 %). Cells were non- motile, endospore-forming and formed milky colonies on NA and R2A agar media. Growth of strain SK-3146T occurred at temperatures of 18–45 C, at pH 6.0–9.5 and between 0.5–3.0 % NaCl (w/v). The major menaquinone was MK-7, with lesser amounts of MK-6 present. The cell wall peptidoglycan of strain SK-3146T contained meso-diaminopimelic acid. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 53.8 mol% and the DNA–DNA hybridization relatedness values between strain SK-3146T and P. yunnanensis JCM 30953T and P. vulneris CCUG 53270T were 26.13±0.8 % and 38.7±0.6 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that strain SK-3146T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus konkukensis sp. -
Operational Group B. Amyloliquefaciens” Within the B
ORIGINAL RESEARCH published: 20 January 2017 doi: 10.3389/fmicb.2017.00022 Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex Ben Fan 1, Jochen Blom 2, Hans-Peter Klenk 3 and Rainer Borriss 4, 5* 1 Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China, 2 Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, Germany, 3 School of Biology, Newcastle University, Newcastle upon Tyne, UK, 4 Fachgebiet Phytomedizin, Institut für Agrar- und Gartenbauwissenschaften, Humboldt Universität zu Berlin, Berlin, Germany, 5 Nord Reet UG, Greifswald, Germany Edited by: Rakesh Sharma, The plant growth promoting model bacterium FZB42T was proposed as the type strain Institute of Genomics and Integrative Biology (CSIR), India of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been Reviewed by: recently recognized as being synonymous to Bacillus velezensis due to phylogenomic Prabhu B. Patil, analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider Institute of Microbial Technology plant-associated close relatives of FZB42 still as “B. amyloliquefaciens.” Here, we (CSIR), India Bo Liu, reinvestigated the taxonomic status of FZB42 and related strains in its context to Fujian Academy of Agaricultural the free-living soil bacterium DSM7T, the type strain of B. amyloliquefaciens. We Sciences, China identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7T. *Correspondence: Rainer Borriss Dendrograms based on complete rpoB nucleotide sequences and on core genome [email protected] sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) B. -
Polycyclic Aromatic Hydrocarbon Degrading Bacteria from the Indonesian Marine Environment
BIODIVERSITAS ISSN: 1412-033X Volume 17, Number 2, October 2016 E-ISSN: 2085-4722 Pages: 857-864 DOI: 10.13057/biodiv/d170263 Polycyclic aromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment ELVI YETTI♥, AHMAD THONTOWI, YOPI Laboratory of Biocatalyst and Fermentation, Research Centre for Biotechnology, Indonesian Institute of Sciences. Cibinong Science Center, Jl. Raya Bogor Km 46 Cibinong-Bogor 16911, West Java, Indonesia. Tel. +62-21-8754587, Fax. +62-21-8754588, ♥email: [email protected] Manuscript received: 20 April 2016. Revision accepted: 20 October 2016. Abstract. Yetti E, Thontowi A, Yopi. 2016. Polyaromatic hydrocarbon degrading bacteria from the Indonesian Marine Environment. Biodiversitas 17: 857-864. Oil spills are one of the main causes of pollution in marine environments. Oil degrading bacteria play an important role for bioremediation of oil spill in environment. We collected 132 isolates of marine bacteria isolated from several Indonesia marine areas, i.e. Pari Island, Jakarta, Kamal Port, East Java and Cilacap Bay, Central Java. These isolates were screened for capability to degrade polyaromatic hydrocarbons (PAHs). Selection test were carried out qualitatively using sublimation method and growth assay of the isolates on several PAHs i.e. phenanthrene, dibenzothiophene, fluorene, naphtalene, phenotiazine, and pyrene. The fifty-eight isolates indicated in having capability to degrade PAHs, consisted of 25 isolates were positive on naphthalene (nap) and 20 isolates showed ability to grow in phenanthrene (phen) containing media. Further, 38 isolates were selected for dibenzothiophene (dbt) degradation and 25 isolates were positive on fluorene (flr). On the other hand, 23 isolates presented capability to degrade in phenothiazine (ptz) and 15 isolates could grow in media with pyrene (pyr). -
Bacillus Rubiinfantis Sp. Nov. Strain Mt2t, a New Bacterial Species Isolated from Human Gut
TAXONOGENOMICS: GENOME OF A NEW ORGANISM Bacillus rubiinfantis sp. nov. strain mt2T, a new bacterial species isolated from human gut M. Tidjiani Alou1, J. Rathored1, S. Khelaifia1, C. Michelle1, S. Brah2, B. A. Diallo3, D. Raoult1,4 and J.-C. Lagier1 1) Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France, 2) Hopital National de Niamey, 3) Laboratoire de microbiologie, département de biologie, Université Abdou Moumouni de Niamey, Niamey, Niger and 4) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Bacillus rubiinfantis sp. nov. strain mt2T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes. New Microbes and New Infections © 2015 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Bacillus rubiinfantis, culturomics, genome, taxonogenomics Original Submission: 7 July 2015; Revised Submission: 1 September 2015; Accepted: 7 September 2015 Article published online: 16 September 2015 The genus Bacillus was established in 1872 by Cohn and is Corresponding author: J.-C. Lagier, Faculté de Médecine, URMITE, composed of strictly aerobic and facultatively anaerobic rod- UMR CNRS 7278, IRD 198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin, 13385 Marseille cedex 5, France shaped bacteria that form heat-resisting endospores [16–19]. -
Complete Issue
J. Fernholz and Q.E. Phelps – Influence of PIT tags on growth and survival of banded sculpin (Cottus carolinae): implications for endangered grotto sculpin (Cottus specus). Journal of Cave and Karst Studies, v. 78, no. 3, p. 139–143. DOI: 10.4311/2015LSC0145 INFLUENCE OF PIT TAGS ON GROWTH AND SURVIVAL OF BANDED SCULPIN (COTTUS CAROLINAE): IMPLICATIONS FOR ENDANGERED GROTTO SCULPIN (COTTUS SPECUS) 1 2 JACOB FERNHOLZ * AND QUINTON E. PHELPS Abstract: To make appropriate restoration decisions, fisheries scientists must be knowledgeable about life history, population dynamics, and ecological role of a species of interest. However, acquisition of such information is considerably more challenging for species with low abundance and that occupy difficult to sample habitats. One such species that inhabits areas that are difficult to sample is the recently listed endangered, cave-dwelling grotto sculpin, Cottus specus. To understand more about the grotto sculpin’s ecological function and quantify its population demographics, a mark-recapture study is warranted. However, the effects of PIT tagging on grotto sculpin are unknown, so a passive integrated transponder (PIT) tagging study was performed. Banded sculpin, Cottus carolinae, were used as a surrogate for grotto sculpin due to genetic and morphological similarities. Banded sculpin were implanted with 8.3 3 1.4 mm and 12.0 3 2.15 mm PIT tags to determine tag retention rates, growth, and mortality. Our results suggest sculpin species of the genus Cottus implanted with 8.3 3 1.4 mm tags exhibited higher growth, survival, and tag retention rates than those implanted with 12.0 3 2.15 mm tags. -
Bacillus Mojavensis Sp. Nov., Distinguishable from Bacillus Subtilis by Sexual Isolation, Divergence in DNA Sequence, and Differences in Fatty Acid Composition
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1994, p. 256-264 Vol. 44, No. 2 0020-7713/94/$04.00+0 Copyright 0 1994, International Union of Microbiological Societies Bacillus mojavensis sp. nov., Distinguishable from Bacillus subtilis by Sexual Isolation, Divergence in DNA Sequence, and Differences in Fatty Acid Composition MICHAEL S. ROBERTS,' L. K. NAKAMURA,* AND FREDERICK M. COW1* Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170,' and Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Sewice, U.S. Department of Agriculture, Peoria, Illinois 616042 A number of Bacillus strains isolated from desert soil samples were shown to belong to a previously unidentified species, for which we propose the name Bacillus mojavensis. The type strain is RO-H-1 (= NRRL B-14698). On the basis of restriction digest data, B. rnojavensis is most closely related to Bacillus amylolique- faciens, Bacillus atrophaeus, and Bacillus subtilis. So far, B. mojavensis can be distinguished from B. subtilis only by differences in whole-cell fatty acid composition, divergence in DNA sequence, and resistance to genetic transformation between taxa (in addition to reduced genome relatedness values). Sequence divergence and sexual isolation may prove to be more useful than metabolic characteristics for delimiting cryptic Bacillus species. Although the species most closely related to Bacillus subtilis strain is maintained in the Agricultural Research Service are easily distinguished from one another by DNA relatedness Culture Collection at the National Center for Agricultural data (14, 15), very few phenotypic criteria that distinguish Utilization Research; each NRRL designation includes the these species are known. For example, only three phenotypic prefix B-, which identifies organisms that were obtained di- traits that distinguish Bacillus amyloliquefaciens from B. -
Draft Genome Sequence of Bacillus Amyloliquefaciens Subsp
Pinto et al. Standards in Genomic Sciences (2018) 13:30 https://doi.org/10.1186/s40793-018-0327-x EXTENDED GENOME REPORT Open Access Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential Cátia Pinto1,2, Susana Sousa1, Hugo Froufe1, Conceição Egas1,3, Christophe Clément2, Florence Fontaine2 and Ana C Gomes1,3* Abstract Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain in vineyard, with the ability to colonise grapevine and which unveils a naturally antagonistic potential against phytopathogens of grapevine, including those responsible for the Botryosphaeria dieback, a GTD disease. Herein we report the draft genome sequence of B. amyloliquefaciens subsp. plantarum Fito_F321, isolated from the leaf of Vitis vinifera cv. Merlot at Bairrada appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC content of 46.54% that contains 3697 protein-coding genes, 86 tRNA coding genes and 5 rRNA genes. The draft genome of strain Fito_F321 allowed to predict a set of bioactive compounds as bacillaene, difficidin, macrolactin, surfactin and fengycin that due to their antimicrobial activity are hypothesized to be of utmost importance for biocontrol of grapevine diseases. Keywords: Genome sequencing, Bacillus amyloliquefaciens subsp. plantarum, Fito_F321 strain, Grapevine-associated microorganism, Biocontrol, Endophytic microorganism Introduction kept as singular species across their clade however, and Bacillus amyloliquefaciens is a species from the genus due to their close relationship, these species should be Bacillus, genetically and phenotypically related to B. included in the “operational group B. amyloliquefaciens” subtilis, B. vallismortis, B. mojavensis, B.