Metal Transformation by a Novel Pelosinus Isolate from a Subsurface Environment
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Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC 4.0 International license. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. -
Electronic Supplementary Information
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information Microbial community and antibiotic resistance profiles of biomass and effluent are distinctly affected by antibiotic addition to an anaerobic membrane bioreactor Ali Zarei-Baygi*, Moustapha Harb#,*, Phillip Wang*, Lauren Stadler^, and Adam L. Smith*† * Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA # Department of Civil and Environmental Engineering, Lebanese American University, 309 Bassil Building, Byblos, Lebanon ^ Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA †Corresponding author (Adam L. Smith) Phone: +1 213.740.0473 Email: [email protected] Number of pages: 15 Number of figures: 6 Number of tables: 6 S1 Quantification of antibiotics by LC-MS For antibiotics quantification, 10 mL samples were collected for each sampling time point from the influent and effluent of the AnMBR. Both collected samples and standard solutions were filtered through 0.2 µm PTFE syringe filters (Whatman) using 10 mL syringes with Luer lock tips and stored in certified 2 mL amber LC vials (Agilent) at 4 ºC refrigerator for no more than 3 days prior to analysis. Stock solutions of sulfamethoxazole and erythromycin were prepared in HPLC-grade methanol at concentrations of 20 mg/L and stored at -20 ºC. Ampicillin stock solution was prepared in HPLC-grade water at 4 mg/L due to its lack of solubility in methanol and stored at 4 ºC. For each antibiotic, a six-point standard calibration curve was constructed within the appropriate range (i.e., 0.1-30 µg/L to target effluent antibiotics and 30- 400 µg/L to target influent antibiotics). -
UC Berkeley UC Berkeley Electronic Theses and Dissertations
UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Corrinoid Cross-Feeding in the Microbial World Permalink https://escholarship.org/uc/item/2z66b95b Author Dirks, Erica Christine Publication Date 2014 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Corrinoid Cross-Feeding in the Microbial World By Erica Christine Dirks A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michiko E. Taga, Chair Professor John D. Coates Professor David Savage Professor Nicole King Fall 2014 Acknowledgements This work would not have been possible without the generous and kind support of many people over the past seven years. To all of my collaborators and mentors I’ve met along the way, especially the members of the Taga lab, a million thanks for all of the advice, discussions, and guidance. Your unselfish willingness to help continues to amaze and inspire me. Working with you has been a true gift. To Shan, I’ve learned so much from you. I wish you every happiness, and I will always think of you as my big sister in science. To Steve, it’s meant so much to me to have you on my side. Your breadth of knowledge astounds me. I hope you never stop telling stories. To Patrick, you are a true friend, and I would have never gotten through without you. To Jerome, together, you know we can defeat the zombie hordes. Thanks for all the car rides! To Mark, for pushing me to go further than I ever imagined I could. -
Electrochemical Startup Increases 1,3-Propanediol Titers in Mixed-Culture Glycerol Fermentations
G Model PRBI-10464; No. of Pages 10 ARTICLE IN PRESS Process Biochemistry xxx (2015) xxx–xxx Contents lists available at ScienceDirect Process Biochemistry jo urnal homepage: www.elsevier.com/locate/procbio Electrochemical startup increases 1,3-propanediol titers in mixed-culture glycerol fermentations a,∗ a,b a Nikolaos Xafenias , MarySandra Oluchi Anunobi , Valeria Mapelli a Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden b School of Engineering, University of Aberdeen, Aberdeen AB243 UE, United Kingdom a r a t i b s c t l e i n f o r a c t Article history: In this study we investigated the use of electric potential to bioelectrochemically ferment glycerol, a Received 13 May 2015 cheap by-product of biodiesel production, into valuable 1,3-propanediol (1,3-PDO). The 1,3-PDO pro- Received in revised form 7 June 2015 duction rates were increased up to 6 times in electrofermentations, compared to non-electrochemical Accepted 22 June 2015 fermentations, and high concentrations up to 42 g 1,3-PDO/l were achieved in fed-batch mode. Extensive Available online xxx growth of the well-known 1,3-PDO producers Clostridiaceae (55–57%) was observed when an appro- priate potential (−1.1 V vs. SHE) was constantly applied since the start. Potential propionate producers Keywords: (Veillonellaceae) were also among the dominant families (20–21%); however, surprisingly enough, propio- 1,3-Propanediol nate production was not observed. On the contrary, Clostridiaceae were absent, Veillonellaceae dominated Bioelectrochemical systems Bioelectrosynthesis (56–72%), and propionate was produced when electric potential was not sufficient for current produc- Fermentation tion since the beginning. -
Biodegradation Treatment of Petrochemical Wastewaters
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre Dissertação Mestrado em Microbiologia Aplicada Orientadores Doutora Sandra Sanches Professora Doutora Lélia Chambel 2015 Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre 2015 This thesis was fully performed at the Institute of Experimental and Technologic Biology (IBET) of Instituto de Tecnologia Química e Bioquímica (ITQB) under the direct supervision of Drª Sandra Sanches in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Prof. Drª Lélia Chambel was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Agradecimentos Gostaria de agradecer a todas as pessoas que estiveram directamente ou indirectamente envolvidas na execução da minha tese de mestrado, pois sem eles a sua realização não teria sido possível. Queria começar por agradecer à Doutora Sandra Sanches, que se demonstrou sempre disponível para esclarecer dúvidas quando precisei, e que fez questão de me ensinar de forma rigorosa e exigente. À Doutora Maria Teresa Crespo, que assim que lhe pedi para me orientar me disse que sim imediatamente, fez questão de me treinar em vários contextos e sempre estimulou o meu envolvimento nas rotinas do laboratório. À Professora Doutora Lélia Chambel, que sempre me esclareceu dúvidas sobre processos burocráticos, me deu conselhos quando eu mais precisei e que me apoiou durante toda a minha tese. Queria também agradecer à Doutora Dulce Brito, que sempre se mostrou disponível para ajudar quando a nossa equipa mais precisava dela, e sempre me ajudou a realizar as tarefas mais básicas do meu trabalho até eu ter ganho a minha autonomia no laboratório. -
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 -
Supplementary Figure Legends for Rands Et Al. 2019
Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018). -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
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. -
International Code of Nomenclature of Prokaryotes
2019, volume 69, issue 1A, pages S1–S111 International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision) Charles T. Parker1, Brian J. Tindall2 and George M. Garrity3 (Editors) 1NamesforLife, LLC (East Lansing, Michigan, United States) 2Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) 3Michigan State University (East Lansing, Michigan, United States) Corresponding Author: George M. Garrity ([email protected]) Table of Contents 1. Foreword to the First Edition S1–S1 2. Preface to the First Edition S2–S2 3. Preface to the 1975 Edition S3–S4 4. Preface to the 1990 Edition S5–S6 5. Preface to the Current Edition S7–S8 6. Memorial to Professor R. E. Buchanan S9–S12 7. Chapter 1. General Considerations S13–S14 8. Chapter 2. Principles S15–S16 9. Chapter 3. Rules of Nomenclature with Recommendations S17–S40 10. Chapter 4. Advisory Notes S41–S42 11. References S43–S44 12. Appendix 1. Codes of Nomenclature S45–S48 13. Appendix 2. Approved Lists of Bacterial Names S49–S49 14. Appendix 3. Published Sources for Names of Prokaryotic, Algal, Protozoal, Fungal, and Viral Taxa S50–S51 15. Appendix 4. Conserved and Rejected Names of Prokaryotic Taxa S52–S57 16. Appendix 5. Opinions Relating to the Nomenclature of Prokaryotes S58–S77 17. Appendix 6. Published Sources for Recommended Minimal Descriptions S78–S78 18. Appendix 7. Publication of a New Name S79–S80 19. Appendix 8. Preparation of a Request for an Opinion S81–S81 20. Appendix 9. Orthography S82–S89 21. Appendix 10. Infrasubspecific Subdivisions S90–S91 22. Appendix 11. The Provisional Status of Candidatus S92–S93 23. -