ABSTRACT WHITHAM, JASON MICHAEL. Identifying Genetic
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From Sporulation to Intracellular Offspring Production: Evolution
FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Alan Miller January 2012 © 2012 David Alan Miller FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM David Alan Miller, Ph. D. Cornell University 2012 Epulopiscium sp. type B is an unusually large intestinal symbiont of the surgeonfish Naso tonganus. Unlike most other bacteria, Epulopiscium sp. type B has never been observed to undergo binary fission. Instead, to reproduce, it forms multiple intracellular offspring. We believe this process is related to endospore formation, an ancient and complex developmental process performed by certain members of the Firmicutes. Endospore formation has been studied for over 50 years and is best characterized in Bacillus subtilis. To study the evolution of endospore formation in the Firmicutes and the relatedness of this process to intracellular offspring formation in Epulopiscium, we have searched for sporulation genes from the B. subtilis model in all of the completed genomes of members of the Firmicutes, in addition to Epulopiscium sp. type B and its closest relative, the spore-forming Cellulosilyticum lentocellum. By determining the presence or absence of spore genes, we see the evolution of endospore formation in closely related bacteria within the Firmicutes and begin to predict if 19 previously characterized non-spore-formers have the genetic capacity to form a spore. We can also map out sporulation-specific mechanisms likely being used by Epulopiscium for offspring formation. -
New Insights Into Clostridia Through Comparative Analyses of Their 40 Genomes
Bioenerg. Res. DOI 10.1007/s12155-014-9486-9 New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes Chuan Zhou & Qin Ma & Xizeng Mao & Bingqiang Liu & Yanbin Yin & Ying Xu # Springer Science+Business Media New York 2014 Abstract The Clostridium genus of bacteria contains the gene groups are shared by all the strains, and the strain- most widely studied biofuel-producing organisms such as specific gene pool consists of 22,668 genes, which is consis- Clostridium thermocellum and also some human pathogens, tent with the fact that these bacteria live in very diverse plus a few less characterized strains. Here, we present a environments and have evolved a very large number of comparative genomic analysis of 40 fully sequenced clostrid- strain-specific genes to adapt to different environments. ial genomes, paying a particular attention to the biomass Across the 40 genomes, 1.4–5.8 % of genes fall into the degradation ones. Our analysis indicates that some of the carbohydrate active enzyme (CAZyme) families, and 20 out Clostridium botulinum strains may have been incorrectly clas- of the 40 genomes may encode cellulosomes with each ge- sified in the current taxonomy and hence should be renamed nome having 1 to 76 genes bearing the cellulosome-related according to the 16S ribosomal RNA (rRNA) phylogeny. A modules such as dockerins and cohesins. A phylogenetic core-genome analysis suggests that only 169 orthologous footprinting analysis identified cis-regulatory motifs that are enriched in the promoters of the CAZyme genes, giving rise to 32 statistically significant motif candidates. Keywords Clostridium . Comparative genomics . -
Clostridium Amazonitimonense, Clostridium Me
ORIGINAL ARTICLE Taxonogenomic description of four new Clostridium species isolated from human gut: ‘Clostridium amazonitimonense’, ‘Clostridium merdae’, ‘Clostridium massilidielmoense’ and ‘Clostridium nigeriense’ M. T. Alou1, S. Ndongo1, L. Frégère1, N. Labas1, C. Andrieu1, M. Richez1, C. Couderc1, J.-P. Baudoin1, J. Abrahão2, S. Brah3, A. Diallo1,4, C. Sokhna1,4, N. Cassir1, B. La Scola1, F. Cadoret1 and D. Raoult1,5 1) Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France, 2) Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil, 3) Hopital National de Niamey, BP 247, Niamey, Niger, 4) Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal and 5) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia Abstract Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: ‘Clostridium amazonitimonense’ strain LF2T, ‘Clostridium massilidielmoense’ strain MT26T, ‘Clostridium nigeriense’ strain Marseille-P2414T and ‘Clostridium merdae’ strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation. © 2017 Published by Elsevier Ltd. Keywords: ‘Clostridium amazonitimonense’, ‘Clostridium massilidielmoense’, ‘Clostridium merdae’, ‘Clostridium nigeriense’, culturomics, emerging bacteria, human microbiota, taxonogenomics Original Submission: 18 August 2017; Revised Submission: 9 November 2017; Accepted: 16 November 2017 Article published online: 22 November 2017 intestine [1,4–6]. -
Para-Cresol Production by Clostridium Difficile Affects Microbial Diversity and Membrane Integrity of Gram-Negative Bacteria
RESEARCH ARTICLE Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria Ian J. Passmore1, Marine P. M. Letertre2, Mark D. Preston3, Irene Bianconi4, Mark A. Harrison1, Fauzy Nasher1, Harparkash Kaur1, Huynh A. Hong4, Simon D. Baines5, Simon M. Cutting4, Jonathan R. Swann2, Brendan W. Wren1, Lisa F. Dawson1* 1 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom, 2 Department of Surgery & Cancer, Imperial College London, London, United Kingdom, a1111111111 3 Bioinformatics and Next Generation sequencing core facility, National Institute for Biological Standards and a1111111111 Control South Mimms, Potters Bar, United Kingdom, 4 Department of Biomedical Sciences, Royal Holloway a1111111111 University of London, Egham, United Kingdom, 5 Department of Biological and Environmental Sciences, a1111111111 University of Hertfordshire, Hatfield, United Kingdom a1111111111 * [email protected] Abstract OPEN ACCESS Clostridium difficile is a Gram-positive spore-forming anaerobe and a major cause of antibi- Citation: Passmore IJ, Letertre MPM, Preston MD, otic-associated diarrhoea. Disruption of the commensal microbiota, such as through treat- Bianconi I, Harrison MA, Nasher F, et al. (2018) ment with broad-spectrum antibiotics, is a critical precursor for colonisation by C. difficile Para-cresol production by Clostridium difficile and subsequent disease. Furthermore, failure of the gut microbiota to recover colonisation affects microbial diversity and membrane integrity of Gram-negative bacteria. PLoS Pathog 14(9): resistance can result in recurrence of infection. An unusual characteristic of C. difficile e1007191. https://doi.org/10.1371/journal. among gut bacteria is its ability to produce the bacteriostatic compound para-cresol (p-cre- ppat.1007191 sol) through fermentation of tyrosine. -
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 -
Development of a Metabolic Pathway Transfer and Genomic Integration
Philipps et al. Biotechnol Biofuels (2019) 12:112 https://doi.org/10.1186/s13068-019-1448-1 Biotechnology for Biofuels RESEARCH Open Access Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii Gabriele Philipps1, Sebastian de Vries1,2 and Stefan Jennewein1* Abstract Background: Clostridium spp. can synthesize valuable chemicals and fuels by utilizing diverse waste-stream sub- strates, including starchy biomass, lignocellulose, and industrial waste gases. However, metabolic engineering in Clostridium spp. is challenging due to the low efciency of gene transfer and genomic integration of entire biosyn- thetic pathways. Results: We have developed a reliable gene transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii based on the conjugal transfer of donor plasmids containing large transgene cas- settes (> 5 kb) followed by the inducible activation of Himar1 transposase to promote integration. We established a conjugation protocol for the efcient generation of transconjugants using the Gram-positive origins of replica- tion repL and repH. We also investigated the impact of DNA methylation on conjugation efciency by testing donor constructs with all possible combinations of Dam and Dcm methylation patterns, and used bisulfte conversion and PacBio sequencing to determine the DNA methylation profle of the C. ljungdahlii genome, resulting in the detection of four sequence motifs with N6-methyladenosine. As proof of concept, we demonstrated the transfer and genomic integration of a heterologous acetone biosynthesis pathway using a Himar1 transposase system regulated by a xylose-inducible promoter. The functionality of the integrated pathway was confrmed by detecting enzyme proteo- typic peptides and the formation of acetone and isopropanol by C. -
Ultrastructure of the Obligately Anaerobic Bacteria Clostridium Kluyveri and Cl
ULTRASTRUCTURE OF THE OBLIGATELY ANAEROBIC BACTERIA CLOSTRIDIUM KLUYVERI AND CL. ACETOBUTYLICUM By K. Y. CHO*t and C. H. DoY* [Manuscript received 22 August 1972J Abstract The morphology of Cl. kluyveri is compared with that of CI. acetobutylicum. The multilayered cell wall of both organisms differ in the number of layers and total thickness. The plasma membrane of Cl. acetobutylicum is asymmetric in electron density and can be separated from the rest of the cell by plasmolysis. Tubular or vesicular structures are observed between the wall and the plasma membrane. In contrast, the plasma membrane of Cl. kluyveri is more symmetrical, with no structures between the cell wall and the plasma membrane. Intracytoplasmic membrane systems present in Cl. acetobutylicum are morpholo gically similar to the mesosomes of Gram-positive aerobes. The intracytoplasmic mem brane systems' of ct. kluyveri are characteristically rough in appearance, and differ in general morphology from systems usually described as mesosomes. Roughness is attributed to membrane-bound ribosomes, these being smaller than those of Escheri chia coli. Polygonal structures containing moderately electron-dense material (possibly DNA) were observed in C/. kluyveri. Cl. acetobutylicum possesses membrane-bounded inclusions containing electron-dense particles similar in dimensions to E. coli ribo somes. Rows of electron-dense bands were also observed. It is suggested that the polygonal structures and rough membranes of Cl. kluyveri are components of a system for the functional expression of genetic informa tion. I. INTRODUCTION Investigations of the ultrastructure of bacteria have been mainly with aerobic species (Salton 1967). In comparative studies of the ultrastructure of bacteria differing in oxygen requirements (Cho 1968) the obligate anaerobes Clostridium kluyveri and CI. -
Implications for Clostridium Botulinum Group I Strains
Food Microbiology 59 (2016) 205e212 Contents lists available at ScienceDirect Food Microbiology journal homepage: www.elsevier.com/locate/fm Characterization of the spore surface and exosporium proteins of Clostridium sporogenes; implications for Clostridium botulinum group I strains Thamarai K. Janganan a, b, Nic Mullin a, c, Svetomir B. Tzokov a, b, Sandra Stringer d, * Robert P. Fagan a, b, Jamie K. Hobbs a, c, Anne Moir b, Per A. Bullough a, b, a Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK b Dept. of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK c Dept. of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK d Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK article info abstract Article history: Clostridium sporogenes is a non-pathogenic close relative and surrogate for Group I (proteolytic) Received 24 March 2016 neurotoxin-producing Clostridium botulinum strains. The exosporium, the sac-like outermost layer of Received in revised form spores of these species, is likely to contribute to adhesion, dissemination, and virulence. A paracrystalline 26 May 2016 array, hairy nap, and several appendages were detected in the exosporium of C. sporogenes strain NCIMB Accepted 3 June 2016 701792 by EM and AFM. The protein composition of purified exosporium was explored by LC-MS/MS of Available online 6 June 2016 tryptic peptides from major individual SDS-PAGE-separated protein bands, and from bulk exosporium. Two high molecular weight protein bands both contained the same protein with a collagen-like repeat Keywords: Spore appendages domain, the probable constituent of the hairy nap, as well as cysteine-rich proteins CsxA and CsxB. -
Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update
GBE Revisiting the Evolution and Taxonomy of Clostridia,a Phylogenomic Update Pablo Cruz-Morales1,3, Camila A. Orellana1,GeorgeMoutafis2, Glenn Moonen2, Gonzalo Rincon2, Lars K. Nielsen1, and Esteban Marcellin1,* 1Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia 2Zoetis, Parkville, Victoria, Australia 3Present address: Joint BioEnergy Institute, Emeryville, CA *Corresponding author: E-mail: [email protected]. Accepted: May 6, 2019 Abstract Clostridium is a large genus of obligate anaerobes belonging to the Firmicutes phylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined as Clostridiales, which includes the class Clostridia. Here, we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to 1) confirm that the group is composed of more than one genus, 2) detect major differences between pathogens classified as a single species within the group of authentic Clostridium spp. (sensu stricto), 3) identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains, and 4) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification of Clostridium species hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria, and highlights the importance of phylogenomics for taxonomic studies. -
3-Methylindole Production Is Regulated in Clostridium Scatologenes ATCC 25775 K.C
Letters in Applied Microbiology ISSN 0266-8254 ORIGINAL ARTICLE 3-Methylindole production is regulated in Clostridium scatologenes ATCC 25775 K.C. Doerner1, K.L. Cook2 and B.P. Mason1 1 Department of Biology, Western Kentucky University, Bowling Green, KY, USA 2 USDA-ARS, AWMRU, Bowling Green, KY, USA Keywords Abstract animal waste, emissions, malodour, skatole, tryptophan. Aims: 3-Methylindole (3-MI) is a degradation product of l-tryptophan and is both an animal waste malodorant and threat to ruminant health. Culture con- Correspondence ditions influencing 3-MI production in Clostridium scatologenes ATCC 25775 Kinchel C. Doerner, Department of Biology, were investigated. Western Kentucky University, 1906 College Methods and Results: Extracellular 3-MI levels in cells cultured in brain heart Heights Blvd.-11080, Bowling Green, KY infusion (BHI) medium (pH 7Æ0) at 33°C and 37°C for 72 h were 907 ± 38 42101-1080, USA. ) and 834 ± 121 lmol l 1, respectively. Cells cultured in tryptone-yeast (TY) E-mail: [email protected] ) extract medium at 37°C for 48 h produced 104 ± 86 lmol l 1 3-MI; however, )1 2008 ⁄ 0871: received 21 May 2008, revised addition of 1 mmol l l-tryptophan failed to increase extracellular levels ) 3 October 2008 and accepted 4 October (113 ± 50 lmol l 1 3-MI). Specific activity of indole acetic acid decarboxylase ) 2008 measured in BHI, TY and TY plus 1 mmol l 1 tryptophan-grown cells dis- played 35-, 33- and 76-fold higher levels than in semi-defined medium-grown doi:10.1111/j.1472-765X.2008.02502.x cells. -
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. -
Updates on the Sporulation Process in Clostridium Species
Updates on the sporulation process in Clostridium species Talukdar, P. K., Olguín-Araneda, V., Alnoman, M., Paredes-Sabja, D., & Sarker, M. R. (2015). Updates on the sporulation process in Clostridium species. Research in Microbiology, 166(4), 225-235. doi:10.1016/j.resmic.2014.12.001 10.1016/j.resmic.2014.12.001 Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse *Manuscript 1 Review article for publication in special issue: Genetics of toxigenic Clostridia 2 3 Updates on the sporulation process in Clostridium species 4 5 Prabhat K. Talukdar1, 2, Valeria Olguín-Araneda3, Maryam Alnoman1, 2, Daniel Paredes-Sabja1, 3, 6 Mahfuzur R. Sarker1, 2. 7 8 1Department of Biomedical Sciences, College of Veterinary Medicine and 2Department of 9 Microbiology, College of Science, Oregon State University, Corvallis, OR. U.S.A; 3Laboratorio 10 de Mecanismos de Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de 11 Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. 12 13 14 Running Title: Clostridium spore formation. 15 16 17 Key Words: Clostridium, spores, sporulation, Spo0A, sigma factors 18 19 20 Corresponding author: Dr. Mahfuzur Sarker, Department of Biomedical Sciences, College of 21 Veterinary Medicine, Oregon State University, 216 Dryden Hall, Corvallis, OR 97331. Tel: 541- 22 737-6918; Fax: 541-737-2730; e-mail: [email protected] 23 1 24 25 Abstract 26 Sporulation is an important strategy for certain bacterial species within the phylum Firmicutes to 27 survive longer periods of time in adverse conditions. All spore-forming bacteria have two phases 28 in their life; the vegetative form, where they can maintain all metabolic activities and replicate to 29 increase numbers, and the spore form, where no metabolic activities exist.