DOCSLIB.ORG

University of Groningen Heat Resistance of Bacillus Spores

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Groningen Heat Resistance of Bacillus Spores University of Groningen Heat resistance of Bacillus spores Berendsen, Erwin Mathijs IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2016 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Berendsen, E. M. (2016). Heat resistance of Bacillus spores: Natural variation and genomic adaptation. Rijksuniversiteit Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 24-09-2021 Heat resistance of Bacillus spores Natural variation and genomic adaptation Erwin Mathijs Berendsen The research presented in this thesis was funded by TI Food and Nutrition (Wageningen, the Netherlands), a public-private partnership on pre- competitive research in food and nutrition. The research was conducted at NIZO Food Research BV (Ede, the Netherlands) and was embedded within the Molecular Genetics Group of the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen (Groningen, the Netherlands). Science (University of Groningen), TIFN, Danone, NIZO, and TNO. Printing of this thesis was financially supported by the Graduate School of Cover Design: Sven Menschel & Erwin Berendsen Layout: Eirlys Pijpers & Erwin Berendsen Printed by: Ipskamp Drukkers B.V. ISBN (print): 978-90-367-8802-1 ISBN (electronic): 978-90-367-8801-4 Copyright © Erwin M. Berendsen, 2016. Heat resistance of Bacillus spores Natural variation and genomic adaptation Proefschrift ter verkrijging van de graad van doctor aan de Rijksuniversiteit Groningen op gezag van de rector magnificus prof. dr. E. Sterken en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op vrijdag 3 juni 2016 om 16.15 uur door Erwin Mathijs Berendsen geboren op 5 juli 1986 te Kampen Promotor Prof. dr. O.P. Kuipers Copromotor Dr. M.H.J. Wells-Bennik Beoordelingscommissie Prof. dr. J.W. Veening Prof. dr. S. Brul Prof. dr. M. Kleerebezem Contents Chapter 1 7 General introduction Chapter 2 29 Two distinct groups within the Bacillus subtilis different spore heat resistance properties group display significantly Chapter 3 47 A mobile genetic element profoundly increases heat resistance of bacterial spores Chapter 4 81 High-level heat resistance of spores of Bacillus amyloliquefaciens and Bacillus licheniformis results from the presence of a spoVA operon in a Tn1546 transposon Chapter 5 97 Spores of Bacillus thermoamylovorans with very high heat resistances germinate poorly in rich media despite the presence of ger clusters, but efficiently upon non-nutrient Ca-DPA exposure Chapter 6 123 General discussion Addenda 143 Nederlandse samenvatting About the author List of publications Acknowledgements Chapter 1 General introduction Erwin M. Berendsen Partly based on the review published as: Wells-Bennik MHJ, Eijlander RT, den Besten HMW, Berendsen EM, Warda AK, Krawczyk AO, Nierop Groot MN, Xiao Y, Zwietering MH, Kuipers OP, Abee T (2016). Bacterial spores in food: survival, emergence, and outgrowth. Annual Review of Food Science and Technology 7:457-482. Chapter 1 Endospores Bacterial spores are widely present in nature. The resistance properties of spores allow for survival against environmental insults. A very important property of spores is their ability to withstand high temperatures. The level of resistance of spores to heating can vary between different spore forming species, but can also vary between strains. The well understood. Understanding which factors have a major impact on heat resistance mechanisms underlying strain specific variation in heat resistance of spores are not of spores can have important implications for their control in food and in applications to improve health. The focus of this thesis is on establishing variation in heat resistance that underlie this variation. of spores that exists between strains, and on the identification of genomic determinants Spore formers from the Clostridiales and Bacillales to enter sporulation as an adaptive strategy to survive conditions encountered in their orders have the extraordinary ability natural habitat, for instance in soil, aquatic environments or in the gut of insects and cell into a dormant endospore (3, 38, 50, 51, 108), a state in which it can reside for animals (23, 49, 69, 77). This complex regulatory process transforms the bacterial Bacillus sphaericus from 25 to 40 million year old Dominican amber (22), and a Bacillus undefined periods of time. The isolation of spores have been reported for a strain of sp. 2-9-3 from a salt crystal of 250 million years old (118). Although these reports were met with scepticism about potential external contamination, they illustrate the potential extent of longevity of spores. Dormant endospores are resistant to environmental stress low availability of nutrients (71, 77, 103). conditions including heat, salinity, acidity, radiation, oxygen and/or water depletion or The sporulation process is induced by high cell densities and nutrient limitation, and Bacillus subtilis strain 168, which is a gram positive model organism (38, 51). The availability of the genome sequence of B. subtilis 168 and has been extensively studies in the ability to genetically amend this strain greatly facilitated the progress to understand sporulation and spore resistance mechanisms (11, 55). The sporulation process is a and involves differentiation, intercellular signaling and programmed cell death among unique developmental pathway that is fundamentally different from binary fission, others (39). The composition of a spore Bacterial spores have various layered structures (Figure 1) that provide resistance against environmental insults and thus against several food processing conditions. The way in which different structures contribute to spore resistance has been extensively reviewed elsewhere (56, 103) and will be only briefly discussed here. First and foremost, 8 General introduction 1 Coat Coat Outer membrane Outer membrane Cortex ICnonreter xmembrane Inner membrane Core Core 200 nm Figure 1. Transmission electron microscopy (TEM) cross section of a spore of Bacillus subtilis 168 (E.M. Berendsen, unpublished results). The ultra- structure’s of the spore, the coat, cortex, inner membrane, and core are indicated with arrows. the spore core is strongly dehydrated, resulting in proteins present in the spore that are largely rotationally immobilized (107). A specific type of proteins present in spores is α/β-type small acid soluble proteins (SASPs) which protect the genetic material against DNA damage. In addition, the core contains the spore-specific chemical pyridine-2,6- cations (mostly Ca2+) (103). Surrounding the core is the inner membrane that provides carboxylic acid, also known as dipicolinic acid (DPA) which is chelated with divalent protection against chemicals (47, 102) and contains proteins required for germination. Outside the inner membrane lies the germ cell wall, which becomes the cell wall after germination, and the cortex, which consists of spore-specific peptidoglycan, characterized by the muramic-δ-lactam moiety and low peptide cross linking (90). The cortex is required for the development of full resistance toward wet heat (discussed in role in resistance is known [reviewed in (56)]. Finally, the outermost layers make up the more detail below). The cortex is surrounded by an outer membrane for which no clear spore coat, which contains various proteins that provide protection against lysozyme, For certain species, (e.g. Bacillus cereus, Bacillus thuringiensis, Bacillus anthracis, and toxic chemicals, and grazing protozoa, amongst others [extensively reviewed in (71)]. Clostridium in direct contact with the environment and is potentially involved in pathogenicity spp.), the spore coat is further surrounded by an exosporium, which is [reviewed in (48, 85)]. 9 Chapter 1 Sporulation and germination The spore properties, that are at the basis of resistance and dormancy, are largely germination process. Proteins that are required for germination are already produced determined by the sporulation process. To exit the dormant state, spores undergo a during the sporulation process. The sporulation and germination process will be discussed below. The sporulation process The formation of a bacterial endospore is the result of a complex regulatory process process involves a series of steps that ultimately lead to the formation of a dormant that has been extensively reviewed elsewhere (3, 38, 50, 51, 108). The sporulation spore. The point at which a vegetative cell of B. subtilis enters the sporulation process is determined by nutrient limitation and high cell densities. The key sporulation regulator is Spo0A, which requires to be phosphorylated and to form a dimer for initiation of sporulation (19, 59).
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]
  • Heat Resistant Thermophilic Endospores in Cold Estuarine Sediments
    Heat resistant thermophilic endospores in cold estuarine sediments Emma Bell Thesis submitted for the degree of Doctor of Philosophy School of Civil Engineering and Geosciences Faculty of Science, Agriculture and Engineering February 2016 Abstract Microbial biogeography explores the spatial and temporal distribution of microorganisms at multiple scales and is influenced by environmental selection and passive dispersal. Understanding the relative contribution of these factors can be challenging as their effects can be difficult to differentiate. Dormant thermophilic endospores in cold sediments offer a natural model for studies focusing on passive dispersal. Understanding distributions of these endospores is not confounded by the influence of environmental selection; rather their occurrence is due exclusively to passive transport. Sediment heating experiments were designed to investigate the dispersal histories of various thermophilic spore-forming Firmicutes in the River Tyne, a tidal estuary in North East England linking inland tributaries with the North Sea. Microcosm incubations at 50-80°C were monitored for sulfate reduction and enriched bacterial populations were characterised using denaturing gradient gel electrophoresis, functional gene clone libraries and high-throughput sequencing. The distribution of thermophilic endospores among different locations along the estuary was spatially variable, indicating that dispersal vectors originating in both warm terrestrial and marine habitats contribute to microbial diversity in estuarine and marine environments. In addition to their persistence in cold sediments, some endospores displayed a remarkable heat-resistance surviving multiple rounds of autoclaving. These extremely heat-resistant endospores are genetically similar to those detected in deep subsurface environments, including geothermal groundwater investigated from a nearby terrestrial borehole drilled to >1800 m depth with bottom temperatures in excess of 70°C.
    [Show full text]
  • Horizontal Gene Flow Into Geobacillus Is Constrained by the Chromosomal Organization of Growth and Sporulation
    bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Horizontal gene flow into Geobacillus is constrained by the chromosomal organization of growth and sporulation Alexander Esin1,2, Tom Ellis3,4, Tobias Warnecke1,2* 1Molecular Systems Group, Medical Research Council London Institute of Medical Sciences, London, United Kingdom 2Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom 3Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom 4Department of Bioengineering, Imperial College London, London, United Kingdom *corresponding author ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/381442; this version posted August 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Horizontal gene transfer (HGT) in bacteria occurs in the context of adaptive genome architecture. As a consequence, some chromosomal neighbourhoods are likely more permissive to HGT than others. Here, we investigate the chromosomal topology of horizontal gene flow into a clade of Bacillaceae that includes Geobacillus spp. Reconstructing HGT patterns using a phylogenetic approach coupled to model-based reconciliation, we discover three large contiguous chromosomal zones of HGT enrichment.
    [Show full text]
  • 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.
    [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]
  • Temporal Dynamics and Ecophysiology of Thermophilic Composting Analyzed Through Metagenome-Assembled Genomes
    Temporal dynamics and ecophysiology of thermophilic composting analyzed through metagenome-assembled genomes João Carlos Setubal ( [email protected] ) Universidade de Sao Paulo https://orcid.org/0000-0001-9174-2816 Lucas Palma Perez Braga Universidade de Sao Paulo Roberta Verciano Pereira Universidade de Sao Paulo Layla Farage Martins Universidade de Sao Paulo Livia Maria Silva Moura Universidade de Sao Paulo Fabio Beltrame Sanchez Universidade de Sao Paulo José Salvatore Leister Patané Instituto Butantan Aline Maria da Silva Universidade de Sao Paulo Research Keywords: thermophilic composting, MAGs, metagenome-assembled genomes, Sao Paulo Zoological Park, Brazil Posted Date: April 1st, 2020 DOI: https://doi.org/10.21203/rs.3.rs-19445/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/29 Abstract Background: Thermophilic composting is a semi-engineered process carried out by diverse microbial communities. Composting is an environment friendly way of degrading biomass; its study may help uncover important biomass-degrading organisms and key enzymes. DNA sequence-based previous studies have presented a general description of the microbial-molecular features of composting, but they have lacked more specic information on the key organisms that are active during the process and their genomes. Methods: We present an analysis of metagenome-assembled genomes (MAGs) obtained from time-series samples of a thermophilic composting process in the São Paulo Zoological Park (Brazil). Our results are based on a careful analysis of MAG gene content and on metabolic modeling of their interactions. Results: We recovered 60 MAGs from sequencing datasets from two separate composting cells.
    [Show full text]
  • André Luis Alves Neves 6
    Elucidating the role of the rumen microbiome in cattle feed efficiency and its 1 potential as a reservoir for novel enzyme discovery 2 3 by 4 5 André Luis Alves Neves 6 7 8 9 10 11 12 A thesis submitted in partial fulfillment of the requirements for the degree of 13 14 15 Doctor of Philosophy 16 17 in 18 19 Animal Science 20 21 22 23 24 25 Department of Agricultural, Food and Nutritional Science 26 University of Alberta 27 28 29 30 31 32 33 34 35 36 37 © André Luis Alves Neves, 2019 38 39 40 Abstract 1 2 The rapid advances in omics technologies have led to a tremendous progress in our 3 understanding of the rumen microbiome and its influence on cattle feed efficiency. 4 However, significant gaps remain in the literature concerning the driving forces that 5 influence the relationship between the rumen microbiota and host individual variation, and 6 how their interactive effects on animal productivity contribute to the identification of cattle 7 with improved feed efficiency. Furthermore, little is known about the impact of mRNA- 8 based metatranscriptomics on the analysis of rumen taxonomic profiles, and a strategy 9 for the discovery of lignocellulolytic enzymes through the targeted functional profiling of 10 carbohydrate-active enzymes (CAZymes) remains to be developed. Study 1 investigated 11 the dynamics of rumen microorganisms in cattle raised under different feeding regimens 12 (forage vs. grain) and studied the relationship among the abundance of these 13 microorganisms, host individuality and the diet. To examine host individual variation in 14 the rumen microbial abundance following dietary switches, hosts were grouped based on 15 the magnitude of microbial population shift using log2-fold change (log2-fc) in the copy 16 numbers of bacteria, archaea, protozoa and fungi.
    [Show full text]
  • From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
    From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.
    [Show full text]
  • 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.
    [Show full text]