DOCSLIB.ORG

Genomic Analysis of a Novel Strain of Bacillus Nealsonii, Isolated from Surti Buffalo Rumen

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Advances in Bioscience and Biotechnology, 2014, 5, 235-245 ABB http://dx.doi.org/10.4236/abb.2014.53030 Published Online February 2014 (http://www.scirp.org/journal/abb/) Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen Neelam M. Nathani1*, Srinivas M. Duggirala2*, Vaibhav D. Bhatt1, Jay KaPatel1, Chaitanya G. Joshi1 1Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, India 2Department of Microbiology, Gujarat Vidyapith, Sadra, India Email: [email protected] Received 9 November 2013; revised 16 January 2014; accepted 28 January 2014 Copyright © 2014 Neelam M. Nathani et al. This is an open access article distributed under the Creative Commons Attribution Li- cense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In accordance of the Creative Commons Attribution License all Copyrights © 2014 are reserved for SCIRP and the owner of the intel- lectual property Neelam M. Nathani et al. All Copyright © 2014 are guarded by law and by SCIRP as a guardian. ABSTRACT posed. Significance and Impact of Study: The strict anaerobic conditions prevailing in the bovine rumen Aim: Whole genome sequencing and functional an- from where AAU1 was isolated may have resulted in notation of Bacillus nealsonii strain AAU1, an amylo- genetic polymorphism influencing its metabolic cha- lytic anaerobic spore forming isolate from ruminal racteristics. contents of buffalo. Methods and Results: Morpho- logically, the strain was observed as slender Gram- KEYWORDS positive rods, occurring in pairs. Optimal growth was observed at 40˚C (range: 30˚C to 45˚C) and pH 6.5 Bacillus nealsonii AAU1; Anaerobic; Phenotypic (range: 5.5 to 7.5) when cultivated in Hungate’s me- Characterization; Genomic Analysis dium supplemented with starch. The microorganism showed extracellular constitutive amylolytic activity, 1. INTRODUCTION proving to be capable of utilizing glucose, maltose, mannose, trehalose, dextrin and starch under an- The rumen harbors a large and diverse range of micro- aerobic conditions. Sequence analysis revealed a GC organisms categorized into Bacteria, Archaea (methano- content of 35.1 mol%. Comparison of housekeeping gens) and Eucarya (protozoa and fungi) [1]. Obligatory gene sequences for RNA polymerase subunit B (rpoB) anaerobes are dominated and supplemented by faculta- and gyrase A (gyrA) identified sequence similarity tive anaerobes including Streptococcus, Staphylococcus, within the Bacillus genus, confirmed by 16S rRNA Bacillus and Lactobacillus species [2]. The complex mi- gene sequence similarity which identified Bacillus ne- crobial ecosystem of the rumen functions as an efficient alsonii DSM 15077 as the closest publically available biological fermentor and provides nutrients essential for relative. Chemotaxonomic analysis provided con- the growth and productivity of the ruminant host in the flicting results with straight-chain saturated C16: form of volatile fatty acids and microbial protein. 0/C16:0 aldehyde, C16:0 DMA, C14:0 and mono- The Bacillus genus, introduced by Cohn in the year unsaturated 16:1w7c and 16:1w9c the major fatty 1872, comprises more than 200 species and is considered acids in contrast to those reported for B. nealsonii to be among the largest bacterial genera with new addi- DSM15077. Further characterization using AN-Bi- tions identified every year. The Bacilli are rod shaped olog and physiological parameters provided genotypic gram positive bacteria, and characterized by spore form- and phenotypic support for taxonomic classification ing ability and aerobic or facultative anaerobic metabol- of isolate AAU1 with published Bacillus species in- ism [3]. Single spores are formed per cell in response to cluding B. licheniformis, B. subtilis, B. circulans and B. environmental stress, such as heat, cold, radiation or de- nealsonii. Conclusion: Based on the data presented, siccation; features which support their existence in ex- isolate is likely to represent a new strain/subspecies, treme habitats include desert sands, hot springs and Arc- for which the identifier B. nealsonii AAU1 is pro- tic soils. Sequencing bacterial genomes provide insight into the genetic basis of phenotypic plasticity and their *Nathani N. M. & Duggirala S. M. equally contribute to the article. ability to tolerate environmental stresses [4]. Bacillus OPEN ACCESS 236 N. M. Nathani et al. / Advances in Bioscience and Biotechnology 5 (2014) 235-245 nealsonii species have previously been isolated from 2.4. Characterization and Substrate potentially harsh environments including a spacecraft Utilization Profile assembly, spores of which were observed to be resistant Carbon utilization by the putative Bacillus isolate was to ultraviolet (UV) light, γ-radiation, hydrogen peroxide and desiccation [5]. Hence, study of these bacteria can investigated biochemically using the AN-Biolog® mi- improve understanding of bacterial responses to envi- croplate assay to determine substrate fermenting poten- ronmental stress and inform upon their role in complex tial as per the manufacturer’s instructions. Subsequently, microbial communities, such as those found within the the OD595 was measured using a microtiter plate reader bovine rumen. after 72 h incubation. Growth, colony characteristics and The Surti buffalo (Bubalus bubalis) is a buffalo breed morphology of the isolate were monitored according to which is popular across Gujarat, India, commonly provi- methods prescribed in Bergey’s Manual. ding milk and draught power. Buffalo are notable for their feed conversion ability from rough grazing, promoting cha- 2.5. FAME Analysis racterization of their ruminal microbiota. We describe Fatty acid methyl ester (FAME) analysis was carried out here the isolation and characterization by sequencing and by gas-liquid chromatography (Sherlock Microbial Iden- biochemical analysis of a putatively new B. nealsonii tification System [MIS]; MIDI, Inc.). Chromatographic strain or isolate with relevance to the future understand- data defining the isolate were analyzed using the Sher- ing and improvement of ruminant health and nutrition. lock software version 6.0B (S/N; 160277) MIDI, with the SMOORE6 method. 2. MATERIALS AND METHOD 2.6. Genome Sequencing and Assembly 2.1. Sampling and Enrichment The whole genome sequence of the putative Bacillus Rumen fluid samples were collected aseptically from a isolate was determined by 454 GS-FLX (Roche) and Ion Surti Buffalo at the Veterinary College, Anand Agricul- Torrent PGM platform sequencing as per the manufac- tural University (AAU), Anand, India. The ruminal fluid turer’s instructions. The results were generated by the GS samples were enriched in Hungate medium containing run browser and the sequencing reads were assembled starch in roll tubes, maintained in strict anaerobic condi- using the GS De Novo Assembler V.2.6 providing con- tions by purging N :CO (80:20) and sealed with butyl 2 2 sensus contigs. rubber and aluminum seals. 2.7. Bioinformatic Analysis: 16S rRNA and 2.2. Media and Culture Conditions Housekeeping Genes Anaerobic culture techniques and incubations were per- Comparison of similarity to published bacterial se- formed as described elsewhere by Hungate and col- quences was confirmed using homology by uploading leagues [6]. Hungate medium [7], used for enrichment, the assembled contigs into the RDP-Ribosomal Database serial dilution and subsequent cultivation of bacteria Project Classifier. For 16S rRNA homology studies, lo- from ruminal fluid, contained (per 1000 ml) K2HPO4 0.5 cal BLAST of the assembled contigs was performed g, KH2PO4 0.2 g, (NH4)2SO4 0.5 g, NaCl 1.0 g, MgSO4 against a 16S rRNA gene sequence database of 7545 0.02 g, CaCl2 0.05 g, NaHCO3 5.0 g, cysteine hydrochlo- sequences downloaded from NCBI. Comparison of genes ride 0.5 g, starch 5.0 g, clarified rumen fluid 1% and agar encoding the housekeeping proteins rpoB (RNA poly- 3% at pH 7.2. The medium was pre gassed with N2:H2 merase open promoter) and gyrase A was undertaken using (80:20); sterilized at 10 psi followed by post gassing with publically available sequences downloaded from NCBI. N2:CO2 (80:20) and sealed with butyl rubber and alumi- Sequences coding for 16S rRNA and gyrA of the genus nium seals. Bacillus were aligned with that of Bacillus nealsonii AAU1, using ClustalW. Subsequently, an evolutionary 2.3. Isolation distance matrix was generated from these nucleotide se- Serial dilutions were prepared in Hungate medium from quences in the dataset using Maximum Composite Like- enriched samples and 0.1 mL from each dilution was lihood method. Phylogenetic analysis was performed streaked on Hungate Agar medium containing starch in using the Neighbor Joining method by MEGA (Molecu- anaerobic bottles. The medium was post gassed with lar Evolutionary Genetics analysis) version 4.0 [8]. N2:CO2 (80:20). All plates were incubated at 40˚C ± 2˚C, after which colony morphology was recorded. Subse- 2.8. Gene Prediction and Annotation quently, three sequential transfers were sub-cultured from Whole genome gene prediction and annotation was per- well isolated colonies after dilution to purify the culture. formed by uploading the assembled contigs onto the Copyright © 2014 SciRes. OPEN ACCESS N. M. Nathani et al. / Advances in Bioscience and Biotechnology 5 (2014) 235-245 237 RAST-Rapid Annotation using Subsystem Technology Table 1. Substrate utilization profile of
Recommended publications
  • Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases

    Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases

    cells Review Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases Paulina Prorok 1 , Inga R. Grin 2,3, Bakhyt T. Matkarimov 4, Alexander A. Ishchenko 5 , Jacques Laval 5, Dmitry O. Zharkov 2,3,* and Murat Saparbaev 5,* 1 Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany; [email protected] 2 SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; [email protected] 3 Center for Advanced Biomedical Research, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia 4 National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; [email protected] 5 Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif, France; [email protected] (A.A.I.); [email protected] (J.L.) * Correspondence: [email protected] (D.O.Z.); [email protected] (M.S.); Tel.: +7-(383)-3635187 (D.O.Z.); +33-(1)-42115404 (M.S.) Abstract: It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the Citation: Prorok, P.; Grin, I.R.; major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field Matkarimov, B.T.; Ishchenko, A.A.; and alkylating metabolic radicals added to these threats.
  • Comparative Genome Analysis of Bacillus Okhensis Kh10-101T Reveals Insights Into Adaptive Mechanisms for Halo-Alkali Tolerance

    Comparative Genome Analysis of Bacillus Okhensis Kh10-101T Reveals Insights Into Adaptive Mechanisms for Halo-Alkali Tolerance

    Comparative genome analysis of Bacillus okhensis Kh10-101T reveals insights into adaptive mechanisms for halo-alkali tolerance Pilla Sankara Krishna University of Hyderabad Sarada Raghunathan University of Hyderabad Shyam Sunder Prakash Jogadhenu ( [email protected] ) University of Hyderabad School of Life Sciences Research article Keywords: Bacillus okhensis, alkaliphilic, halophilic, genome analysis, hydroxyl ion stress, sodium toxicity. Posted Date: May 7th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-25204/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract Background: Bacillus okhensis, isolated from saltpan near port of Okha, India, was initially reported to be a halo-alkali tolerant bacterium.We previously sequenced it’s 4.86 Mb genome, here we analyze its genome and physiological responses to high salt and high pH stress. Results: B. okhensis is a halo-alkaliphile with optimal growth at pH 10 and 5% NaCl. 16S rDNA phylogenetic analysis resulted in habitat based segregation of 106 Bacillus species into 3 major clades with all alkaliphiles in one clade clearly suggesting a common ancestor for alklaliphilic Bacilli. We observed that B. okhensis has been adapted to survive at halo-alkaline conditions, by acidication of surrounding medium using fermentation of glucose to organic acids. Comparative genome analysis revealed that the surface proteins which are exposed to external high pH environment of B. okhensis were evolved with relatively higher content of acidic amino acids than their orthologues of B. subtilis. It posess relatively more genes involved in the metabolism of osmolytes and sodium dependent transporters in comparison to B.
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function

    Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function

    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
  • Bacillus Clausii and Bacillus Halodurans Lack Glnr but Possess

    Bacillus Clausii and Bacillus Halodurans Lack Glnr but Possess

    ics om & B te i ro o P in f f o o Farazmand et al., J Proteomics Bioinform 2011, 4:9 r l m a Journal of a n t r i c u DOI: 10.4172/jpb.1000187 s o J ISSN: 0974-276X Proteomics & Bioinformatics Research Article Article OpenOpen Access Access Bacillus clausii and Bacillus halodurans lack GlnR but Possess Two Paralogs of glnA Abbas Farazmand1*, Bagher Yakhchali2, Parvin Shariati2 and Hamideh Ofoghi1 1Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), 15815-3538, Tehran, Iran 2Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965-161 Tehran, Iran Abstract Bacillus clausii and Bacillus halodurans lack GlnR but possess a single TnrA regulator of nitrogen assimilation and two paralogs of glnA. Bacillus clausii contains two paralogs of the gene encoding the glutamine synthetase (GS), glnA1 (ABC3940) and glnA2 (ABC2179). The glnA1 gene contains a TnrA site. This TnrA site is located downstream of the -10 region of the promoter. However, the glnA2 gene does not contain the TnrA site at its regulatory region. Bacillus halodurans possesses two paralogs of glnA, both with TnrA-binding sites. The glnA1 (BH2360) gene contains a TnrA site, which overlaps the -10 region of the glnA1 promoter, and the glnA2 (BH3867) gene contains a TnrA site downstream of the -10 region of its promoter. Also, the Bacillus subtilis dicistronic glnRA operon, which encodes GlnR and GS, contains two TnrA sites (glnRAo1 and glnRAo2) in its promoter region. The glnRAo2 site, which overlaps the -35 region of the glnRA promoter, was shown to be required for regulation by TnrA.
  • Food Waste Composting and Microbial Community Structure Profiling

    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.
  • Mining Bacterial Species Records for Phenotypic Trait Information

    Mining Bacterial Species Records for Phenotypic Trait Information

    RESEARCH ARTICLE Ecological and Evolutionary Science crossm Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information Albert Barberán,a Hildamarie Caceres Velazquez,b Stuart Jones,b Noah Fiererc,d Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, USAa; Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USAb; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USAc; Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USAd ABSTRACT Cultivation in the laboratory is essential for understanding the pheno- typic characteristics and environmental preferences of bacteria. However, basic phe- Received 23 May 2017 Accepted 17 July notypic information is not readily accessible. Here, we compiled phenotypic and en- 2017 Published 2 August 2017 Ͼ Citation Barberán A, Caceres Velazquez H, vironmental tolerance information for 5,000 bacterial strains described in the Jones S, Fierer N. 2017. Hiding in plain sight: International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all in- mining bacterial species records for formation made publicly available in an updatable database. Although the data span phenotypic trait information. mSphere 2: e00237-17. https://doi.org/10.1128/mSphere 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic .00237-17. strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Editor Steven J. Hallam, University of British Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants. Most of Columbia the routinely measured traits tended to show a significant phylogenetic signal, al- Copyright © 2017 Barberán et al. This is an though this signal was weak for environmental preferences.
  • OLE RNA Protects Extremophilic Bacteria from Alcohol Toxicity Jason G

    OLE RNA Protects Extremophilic Bacteria from Alcohol Toxicity Jason G

    6898–6907 Nucleic Acids Research, 2012, Vol. 40, No. 14 Published online 4 May 2012 doi:10.1093/nar/gks352 OLE RNA protects extremophilic bacteria from alcohol toxicity Jason G. Wallace1, Zhiyuan Zhou1 and Ronald R. Breaker1,2,3,* 1Department of Molecular, Cellular and Developmental Biology, 2Department of Molecular Biophysics and Biochemistry and 3Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA Received March 9, 2012; Revised April 2, 2012; Accepted April 7, 2012 ABSTRACT continue to improve. Intriguingly, novel classes of bacter- ial non-coding RNAs that rank among the largest and OLE (Ornate, Large, Extremophilic) RNAs represent a most complex known have been reported recently recently discovered non-coding RNA class found in (11–14), suggesting that numerous additional RNAs with extremophilic anaerobic bacteria, including certain distinct biochemical functions important for many species human pathogens. OLE RNAs exhibit several remain to be discovered. unusual characteristics that indicate a potentially The functions of most newfound classes of large novel function, including exceptionally high expres- non-coding RNAs remain to be validated. RNAs whose sion and localization to cell membranes via inter- functions were established long ago typically were dis- action with a protein partner called OLE-associated covered by investigating the molecular basis for specific protein (OAP). In the current study, new genetic and cellular processes. For example, processing of precursor phenotypic characteristics of OLE RNA from Bacillus tRNAs to yield mature tRNAs necessarily involves RNase activity. Studies revealed the existence of a large halodurans C-125 were established. OLE RNA is non-coding RNA (15) that was determined to function as transcribed at high levels from its own promoter an RNA-cleaving ribozyme called RNase P (16).
  • Identification and Classification of Known and Putative Antimicrobial Compounds Produced by a Wide Variety of Bacillales Species Xin Zhao1,2 and Oscar P

    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].
  • WO 2016/086210 Al 2 June 2016 (02.06.2016) P O P C T

    WO 2016/086210 Al 2 June 2016 (02.06.2016) P O P C T

    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/086210 Al 2 June 2016 (02.06.2016) P O P C T (51) International Patent Classification: (74) Agents: MELLO, Jill, Ann et al; McCarter & English, A61P 1/00 (2006.01) A61P 37/00 (2006.01) LLP, 265 Franklin Street, Boston, MA 021 10 (US). A61P 29/00 (2006.01) A61K 35/74 (2015.01) (81) Designated States (unless otherwise indicated, for every (21) International Application Number: kind of national protection available): AE, AG, AL, AM, PCT/US20 15/0628 10 AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (22) International Filing Date: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 25 November 2015 (25.1 1.2015) HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (25) Filing Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (26) Publication Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (30) Priority Data: SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/084,537 25 November 2014 (25. 11.2014) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 62/084,536 25 November 2014 (25.
  • Bacillus Subtilis Spore Resistance Towards Low Pressure Plasma Sterilization = Bacillus Subtilis Sporenresistenz Gegenüber Plas

    Bacillus Subtilis Spore Resistance Towards Low Pressure Plasma Sterilization = Bacillus Subtilis Sporenresistenz Gegenüber Plas

    Bacillus subtilis Spore Resistance towards Low Pressure Plasma Sterilization Dissertation to obtain the degree Doctor Rerum Naturalium (Dr. rer. nat.) at the Faculty of Biology and Biotechnology Ruhr University Bochum International Graduate School of Biosciences Ruhr University Bochum (Chair of Microbiology) Submitted by Marina Raguse from KönigsWusterhausen, Germany Bochum, April 2016 First supervisor: Prof. Dr. Franz Narberhaus Second supervisor: Prof. Dr. Peter Awakowicz Bacillus subtilis Sporenresistenz gegenüber Plasmasterilisation im Niederdruck Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) der Fakultät für Biologie und Biotechnologie der Ruhr-Universität Bochum Internationale Graduiertenschule für Biowissenschaften Ruhr-Universität Bochum (Lehrstuhl für Biologie der Mikroorganismen) Vorgelegt von Marina Raguse aus KönigsWusterhausen, Germany Bochum, April 2016 Erstbetreuer: Prof. Dr. Franz Narberhaus Zweitbetreuer: Prof. Dr. Peter Awakowicz This work was conducted externally at the German Aerospace Center, Institute for Aerospace Medicine, Department of Radiation Biology, Research Group Astrobiology/Space Microbiology, in 51147, Cologne, Germany, under the supervision of Dr. Ralf Möller from 01.12.2012 until 31.07.2016. Diese Arbeit wurde extern durchgeführt am Deutschen Zentrum für Luft- und Raumfahrt, Institut für Luft-und Raumfahrtmedizin, Abteilung Strahlenbiologie, Arbeitsgruppe Astrobiologie/Weltraummikrobiologie in 51147, Köln, unter der Betreuung von Dr. Ralf Möller im Zeitrahmen vom 01.12.2012 – 31.07.2016. Danksagung Zuerst möchte ich mich herzlich bei meinem Doktorvater Prof. Dr. Franz Narberhaus für die Unterstützung bedanken und für die Möglichkeit auch extern am Lehrstuhl für Biologie der Mikroorganismen der Ruhr-Universität Bochum zu promovieren. Mein großer Dank gilt ebenfalls meinem Korreferenten Prof. Dr. Peter Awakowicz, für sein allzeit großes Interesse an der Arbeit mit Sporen und die anregenden Diskussionen in den PlasmaDecon- Meetings.
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y

    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y

    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
  • Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus

    Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus

    life Article Effects of Heavy Ion Particle Irradiation on Spore Germination of Bacillus spp. from Extremely Hot and Cold Environments Vincenzo Zammuto 1 , Maria G. Rizzo 1,*, Laura M. De Plano 1, Domenico Franco 1 , Salvatore Guglielmino 1, Maria T. Caccamo 2 , Salvatore Magazù 2, Akira Fujimori 3, Angelina Lo Giudice 4 , Mauro Guglielmin 5, Kevin Roderick McAlpin 6,7, Ralf Moeller 6,7 and Concetta Gugliandolo 1 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Centre for Extreme Environments and Extremophiles, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; [email protected] (V.Z.); [email protected] (L.M.D.P.); [email protected] (D.F.); [email protected] (S.G.); [email protected] (C.G.) 2 Department of Mathematics, Computer Sciences, Physics and Earth Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; [email protected] (M.T.C.); [email protected] (S.M.) 3 Department of Basic Medical Sciences for Radiation Damages, Molecular and Cellular Radiation Biology Group, NIRS/QST, Chiba 263-8555, Japan; [email protected] 4 Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy; [email protected] 5 Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant, 21100 Varese, Italy; [email protected] 6 Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center, Aerospace Microbiology, DLR, Linder Höhe, D-51147 Cologne/Köln, Germany; [email protected] (R.M.); [email protected] (K.R.M.) 7 Natural Sciences Department, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), D-53359 Rheinbach, Germany * Correspondence: [email protected] Received: 13 October 2020; Accepted: 28 October 2020; Published: 30 October 2020 Abstract: Extremophiles are optimal models in experimentally addressing questions about the effects of cosmic radiation on biological systems.