DOCSLIB.ORG

Non-Contiguous Finished Genome Sequence and Description of Clostridium Saudii Sp

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Non-Contiguous Finished Genome Sequence and Description of Clostridium Saudii Sp Angelakis et al. Standards in Genomic Sciences 2014, 9:8 http://www.standardsingenomics.com/content/9/1/8 SHORT GENOME REPORT Open Access Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov Emmanouil Angelakis1, Fehmida Bibi2, Dhamodharan Ramasamy1, Esam I Azhar2,3, Asif A Jiman-Fatani4, Sally M Aboushoushah2, Jean-Christophe Lagier1, Catherine Robert1, Aurelia Caputo1, Muhammad Yasir2, Pierre-Edouard Fournier1 and Didier Raoult1,2* Abstract Clostridium saudii strain JCCT sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes. Keywords: Clostridium saudii, Genome, Culturomics, Taxono-genomics Introduction which integrates genomic information in the taxonomic Clostridium saudii strain JCCT (=CSUR P697 = DSM framework, combining phenotypic characteristics, including 27835) is the type strain of C. saudii sp. nov. This bac- MALDI-TOF MS spectra, and genomic analysis [8-38]. terium is a Gram-positive, anaerobic, spore-forming in- The genus Clostridium was first created in 1880 [39] dole negative bacillus that was isolated from the stool and consists of obligate anaerobic rod-shaped bacilli able sample of an obese 24 year-old Saudi individual, as a to produce endospores [39]. To date, more than 200 part of a culturomics study as previously reported [1-3]. species have been described (http://www.bacterio.cict.fr/c/ The current prokaryote species classification method, clostridium.html). Members of the genus Clostridium are known as polyphasic taxonomy, is based on a combin- mostly environmental bacteria or associated with the com- ation of genomic and phenotypic properties [4]. The mensal digestive flora of mammals. However, C. botulinum, usual parameters used to delineate a bacterial species C. difficile and C. tetani are major human pathogens [39]. include 16S rDNA sequence identity and phylogeny – [2,3], genomic G + C content diversity and DNA DNA Classification and features hybridization (DDH) [4,5]. Nevertheless, some limita- A stool sample was collected from an obese 24-year-old tions appear, notably because the cutoff values vary male Saudi volunteer patient from Jeddah. The patient dramatically between species and genera [6]. The intro- gave an informed and signed consent, and the agreement duction of high-throughput sequencing techniques has of the local Ethical Committee of the King Abdulaziz made genomic data for many bacterial species available University, King Fahd medical Research Centre, Saudi [7]. To date, more than 4,000 bacterial genomes have Arabia, and of the local ethics committee of the IFR48 been published and approximately 15,000 genomes pro- (Marseille, France) were obtained under agreement number ject are anticipated to be completed in a near future [5]. 014-CEGMR-2-ETH-P and 09–022 respectively. The fecal We recently proposed a new method (taxono-genomics), specimen was preserved at −80°C after collection and sent to Marseille. C. saudii strain JCCT (Table 1) was iso- * Correspondence: [email protected] 1Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, lated in July 2013 by anaerobic cultivation on 5% sheep UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de blood-enriched Columbia agar (BioMerieux, Marcy médecine, Aix-Marseille Université, Marseille, France l’Etoile, France) after a 5-day preincubation on blood 2Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia culture bottle with rumen fluid. This strain exhibited a Full list of author information is available at the end of the article 98.3% nucleotide sequence similarity with Clostridium © 2014 Angelakis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Angelakis et al. Standards in Genomic Sciences 2014, 9:8 Page 2 of 12 http://www.standardsingenomics.com/content/9/1/8 Table 1 Classification and general features of Clostridium saudii strain JCCT MIGS ID Property Term Evidence codea Current classification Domain Bacteria TAS [41] Phylum Firmicutes TAS [42-44] Class Clostridia TAS [45,46] Order Clostridiales TAS [47,48] Family Clostridiaceae TAS [47,49] Genus Clostridium IDA [47,50,51] Species Clostridium saudii IDA Type strain JCCT IDA Gram stain Positive IDA Cell shape Rod IDA Motility Motile IDA Sporulation Sporulating IDA Temperature range Mesophile IDA Optimum temperature 37°C IDA MIGS-6.3 Salinity Unknown IDA MIGS-22 Oxygen requirement Anaerobic IDA Carbon source Unknown IDA Energy source Unknown IDA MIGS-6 Habitat Human gut IDA MIGS-15 Biotic relationship Free living IDA Pathogenicity Unknown Biosafety level 2 MIGS-14 Isolation Human feces MIGS-4 Geographic location Jeddah, Saudi Arabia IDA MIGS-5 Sample collection time July 2013 IDA MIGS-4.1 Latitude 21.422487 IDA MIGS-4.1 Longitude 39.856184 IDA MIGS-4.3 Depth surface IDA MIGS-4.4 Altitude 0 m above sea level IDA Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidencecodes are from of the Gene Ontology project [52]. If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements. disporicum (Y18176) (Figure 1). This value was lower grey. Growth of the strain was tested in the same agar than the 98.7% 16S rRNA gene sequence threshold under anaerobic and microaerophilic conditions using recommended by Stackebrandt and Ebers to delineate a GENbag anaer and GENbag microaer systems, respect- new species without carrying out DNA-DNA hybridization ively (BioMerieux), and in aerobic conditions, with or [3] and was in the 78.4 to 98.9% range of 16S rRNA identity without 5% CO2. Growth was observed only under anaer- values observed among 41 Clostridium species with validly obic conditions and no growth occurred under aerobic published names [40]. or microaerophilic conditions. Gram staining showed For the growth of C. saudii we tested four temperatures Gram-positive rods able to form spores (Figure 1) and (25, 30, 37, 45°C); growth occurred between 25 and 37°C, the motility test was positive. Cells grown on agar ex- however optimal growth occurred at 37°C, 24 hours after hibit a mean diameter of 1 μm and a mean length of inoculation. No growth occurred at 45°C. Colonies were 1.22 μm in electron microscopy (Figure 2, Figure 3). translucent on 5% sheep blood-enriched Columbia agar C. saudii did not have catalase or oxidase activity (BioMerieux). Colonies on blood-enriched Columbia agar (Table 2). On an API Rapid ID 32A strip (BioMerieux), were about 0.2 to 0.3 mm in diameter and translucent light C. saudii presented positive reactions for α-galactosidase, Angelakis et al. Standards in Genomic Sciences 2014, 9:8 Page 3 of 12 http://www.standardsingenomics.com/content/9/1/8 98 Clostridium celatum (X77844) 100 Clostridium disporicum (Y18176) 91 Clostridium saudii (HG726039) 46 Clostridium tertium (Y18174) 100 Clostridium sartagoforme (Y18175) 81 Clostridium baratii (X68174) Clostridium paraputrificum (X75907) Clostridium aurantibutyricum (X68183) 99 32 99 Clostridium chartatabidum (X71850) Clostridium butyricum (AJ458420) Clostridium roseum (Y18171) 76 99 Clostridium beijerinckii (X68179) 100 76 Clostridium diolis (AJ458418) 52 Clostridium senegalense (JF824801) 100 Clostridium acetobutylicum (AE001437) 69 Clostridium botulinum (L37585) Clostridium carboxidivorans (FR733710) 62 57 83 Clostridium ljungdahlii (FR733688) Clostridium novyi (AB045606) Clostridium acidiurici (M59084) 62 Clostridium dakarense (KC517358) 81 100 Clostridium difficile (AB075770) 100 Clostridium cellulolyticum (X71847) Clostridium thermocellum (CP000568) 99 Clostridium leptum (AJ305238) 99 Clostridium cellulosi (L09177) 100 Clostridium clostridioforme (M59089) 63 Clostridium boltei (AJ508452) Clostridium symbiosum (M59112) 100 Clostridium hathewayi (AJ311620) Clostridium cellulovorans (CP002160) 75 Clostridium perfringens (CP000246) 100 Clostridium saccharolyticum (CP002109) Clostridium ramosum (X73440) 0.02 Figure 1 A consensus phylogenetic tree highlighting the position of Clostridium saudii strain JCCT relative to other type strains within the genus Clostridium. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximum-likelihood method in the MEGA software package. Numbers at the nodes are percentages of bootstrap values from
Load more

Recommended publications
  • Structure and Dynamics of the Microbial Communities Underlying the Carboxylate Platform for Biofuel Production
    Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production E.B. Hollister 1, A.K. Forrest 2, H.H. Wilkinson 3, D.J. Ebbole 3, S.A. Malfatti 4, S.G. Tringe 4, M.T. Holtzapple 2, T.J. Gentry 1 1 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA 77843-2474 2 Department of Chemical Engineering, Texas A&M University, College Station, TX, USA 77843-3122 3 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX USA 77843-2132 4 DOE Joint Genome Institute, Walnut Creek, CA, USA 94598 July 31, 2010 ACKNOWLEDGMENT The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California.
    [Show full text]
  • Supplementary Materials
    SUPPLEMENTARY MATERIALS Table S1. Chemical characteristics of the two digestate forms (SD and WD). Values quoted are expressed as % of air-dry digestate (means followed by standard error in brackets). References for the employed methods used for determination of each chemical characteristic is also reported. SD WD Reference Org C % 44.4 (0.33) 1.1 (0.01) [81] Tot N % 1.4 (0.01) 0.4 (0.01) [82] C/N 31.4 (0.17) 3.1 (0.04) NH4-N % n.d 0.2 (0.00) [83] K % 1.7 (0.00) n.d. [84] P % 0.9 (0.01) n.d. [84] S % 0.23 (0.02) n.d. [85] SD = solid digestate; WD = whole digestate. Table S2. Soil physical and chemical characteristics at the beginning of trial (t0) (means from 9 observations followed by standard errors in brackets). Clay (%) 41.9 (1.22) Silt (%) 47.8 (2.13) Moisture (%) 24.46 (1.24) Bulk density (g cm-3) 1.39 (0.04) pH 8.3 (0) CaCO3 (%) 11.4 (0.7) TOC (g kg-1) 12.8 (0.3) TN (g kg-1) 1.4 (0) C/N 9.4 (0.3) CEC (cmol(+) kg-1) 21.0 (0.7) Exchangeable Bases (mg kg-1) K 278.7 (8.0) Na 22.0 (3.0) Mg 201.7 (25.6) Ca 3718.6 (176.3) Available Microelements (mg kg-1) Cu 28.0 (5.0) Zn 1.7 (0.2) Fe 15.4 (0.5) Mn 16.3 (0.5) TOC = total organic C; TN = total N; CEC = cation exchange capacity Table S3.
    [Show full text]
  • 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.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (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 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • 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].
    [Show full text]
  • Antibitoic Treatment for Tuberculosis Induces a Profound Dysbiosis of the Gut Microbiome That Persists Long After Therapy Is Completed
    ANTIBITOIC TREATMENT FOR TUBERCULOSIS INDUCES A PROFOUND DYSBIOSIS OF THE GUT MICROBIOME THAT PERSISTS LONG AFTER THERAPY IS COMPLETED A Thesis Presented to the Faculty of the Weill Cornell Graduate School of Medical Sciences in Partial Fulfillment of the Requirements for the Degree of Masters of Science by Matthew F. Wipperman May 2017 © 2017 Matthew F. Wipperman ABSTRACT Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world’s population and causes substantial mortality worldwide. In its shortest format, treatment of drug sensitive TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is much longer. The widespread use of this regimen worldwide makes this one the largest exposures of humans to antimicrobials, yet the effects of antimycobacterial agents on intestinal microbiome composition and long term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of Haitian TB cases during antimycobacterial treatment and following cure by 6 months of TB therapy. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The perturbation by TB therapy lasts at least 1.5 years after completion of treatment, indicating that the effects of TB treatment are long lasting and perhaps permanent. These results demonstrate that TB treatment has dramatic and durable effects on the intestinal microbiome and highlight unexpected extreme consequences of treatment for the world’s most common infection on human ecology. BIOGRAPHICAL SKETCH NAME POSITION TITLE Wipperman, Matthew Frederick Postdoctoral Researcher at eRA COMMONS USER NAME Memorial Sloan Kettering Cancer Center MFWIPPERMAN DEGREE INSTITUTION AND (if MM/YY FIELD OF STUDY LOCATION applicable) Franklin & Marshall College B.A.
    [Show full text]
  • A Report of 22 Unrecorded Bacterial Species in Korea, Isolated from Namhangang
    Journal114 of Species Research 7(2):114-122, 2018JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2 A report of 22 unrecorded bacterial species in Korea, isolated from Namhangang Chaeyun Baek1 and Hana Yi1,2,* 1Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 2School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea *Correspondent: [email protected] As part of a larger study of indigenous prokaryotic species diversity in South Korea, various samples from Namhangang were subjected to analyses. Fresh water, underwater sediment, and moss-inhabiting aerobic and anaerobic bacteria were isolated. 22 of the isolates were identified as unrecorded bacterial species in Korea that had ≥98.7% 16S rRNA gene sequence similarity with published species. The aerobic strains isolated were Kurthia gibsonii and Massilia plicata. Also identified were four facultative anaerobic strains: Bacillus hisashii, Enterococcus rotai, Paenibacillus vini, and Pediococcus pentosaceus. 16 strictly anaerobic strains were identified as Bacteroides xylanolyticus, Carnobacterium maltaromaticum, Clostridium argentinense, Clostridium beijerinckii, Clostridium butyricum, Clostridium cavendishii, Clostridium diolis, Clostridium frigidicarnis, Clostridium perfringens, Clostridium saccharoperbutylacetonicum, Clostridium sphenoides, Clostridium subterminale, Cutibacterium acnes, Paraclostridium bifermentans, Prevotella paludivivens, and Romboutsia lituseburensis. Based on the examination of morphological, cultural, physiological, and biochemical properties of the isolates, descriptive information of these previously unrecorded species is provided here. Keywords: anaerobes, Namhangang, unrecorded species Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.2.114 INTRODUCTION and Jungnyeongcheon, are freshwater rivers with 10.19 km2, 69.11 km2, 150.5 km2, and 130.19 km2 areas, respec- While molecular methods have supplanted traditional tively.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • Comparison of Sampling Techniques and Different Media for The
    Systematic and Applied Microbiology 42 (2019) 481–487 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermentersଝ a a b a,∗ Regina Rettenmaier , Carina Duerr , Klaus Neuhaus , Wolfgang Liebl , a,c,∗ Vladimir V. Zverlov a Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany b Core Facility Microbiome/NGS, ZIEL — Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany c Institute of Molecular Genetics, RAS, Kurchatov Sq. 2, 123128 Moscow, Russia a r t i c l e i n f o a b s t r a c t Article history: Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. Received 27 March 2019 This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating Received in revised form 15 May 2019 enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We Accepted 17 May 2019 compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region Keywords: of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biolog- Biogas fermenter ical triplicates, revealed an average richness of 48 different OTU’s with an average evenness of 0.3 in Cellulose degradation each sample.
    [Show full text]
  • ( 12 ) United States Patent
    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
    [Show full text]
  • Outline Release 7 7C
    Garrity, et. al., March 6, 2007 Taxonomic Outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 7 – The Bacteria: Phylum “Firmicutes”: Class “Clostridia” George M. Garrity, Timothy G. Lilburn, James R. Cole, Scott H. Harrison, Jean Euzéby, and Brian J. Tindall F Phylum Firmicutes AL N4Lid DOI: 10.1601/nm.3874 Class "Clostridia" N4Lid DOI: 10.1601/nm.3875 71 Order Clostridiales AL Prévot 1953. N4Lid DOI: 10.1601/nm.3876 Family Clostridiaceae AL Pribram 1933. N4Lid DOI: 10.1601/nm.3877 Genus Clostridium AL Prazmowski 1880. GOLD ID: Gi00163. GCAT ID: 000971_GCAT. Entrez genome id: 80. Sequenced strain: BC1 is from a non-type strain. Genome sequencing is incomplete. Number of genomes of this species sequenced 6 (GOLD) 6 (NCBI). N4Lid DOI: 10.1601/nm.3878 Clostridium butyricum AL Prazmowski 1880. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 19398. High-quality 16S rRNA sequence S000436450 (RDP), M59085 (Genbank). N4Lid DOI: 10.1601/nm.3879 Clostridium aceticum VP (ex Wieringa 1940) Gottschalk and Braun 1981. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 35044. High-quality 16S rRNA sequence S000016027 (RDP), Y18183 (Genbank). N4Lid DOI: 10.1601/nm.3881 Clostridium acetireducens VP Örlygsson et al. 1996. Source of type material recommended for DOE sponsored genome sequencing by the JGI: DSM 10703. High-quality 16S rRNA sequence S000004716 (RDP), X79862 (Genbank). N4Lid DOI: 10.1601/nm.3882 Clostridium acetobutylicum AL McCoy et al. 1926. Source of type material recommended for DOE sponsored genome sequencing by the JGI: ATCC 824.
    [Show full text]