Phylogenomic Analysis Supports the Ancestral Presence of LPS-Outer Membranes in the Firmicutes
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Extremozymes of the Hot and Salty Halothermothrix Orenii
Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry. -
Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms. -
Localizing Transcripts to Single Cells Suggests an Important Role of Uncultured Deltaproteobacteria in the Termite Gut Hydrogen Economy
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy Adam Z. Rosenthala,1, Xinning Zhanga,1, Kaitlyn S. Luceya, Elizabeth A. Ottesena, Vikas Trivedib, Harry M. T. Choib, Niles A. Pierceb,c, and Jared R. Leadbettera,2 aRonald and Maxine Linde Center for Global Environmental Science, bDepartment of Bioengineering, and cDepartment of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved August 13, 2013 (received for review April 29, 2013) Identifying microbes responsible for particular environmental and in situ assays to address such matters directly. We interro- functions is challenging, given that most environments contain gated a tiny, yet complex environment that accommodates robust, an uncultivated microbial diversity. Here we combined approaches stable, and species-rich microbial communities—the hindgut of a to identify bacteria expressing genes relevant to catabolite flow wood-feeding lower termite, Zootermopsis nevadensis (1). and to locate these genes within their environment, in this case Termites and their gut microbiota digest lignocellulose, the the gut of a “lower,” wood-feeding termite. First, environmental most abundant natural composite material on Earth. For some time now, it has been known that a key activity in this nutritional transcriptomics revealed that 2 of the 23 formate dehydrogenase + (FDH) genes known in the system accounted for slightly more than mutualism involves the bacterial conversion of H2 CO2, gen- one-half of environmental transcripts. FDH is an essential enzyme erated during wood polysaccharide fermentation, into acetate in a process called CO -reductive acetogenesis (2, 3). -
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. -
Bacteroidota and Lachnospiraceae Integration Into the Gut Microbiome at Key Time Points in Early Life Are Critical for Neurodevelopment
Bacteroidota and Lachnospiraceae Integration Into the Gut Microbiome at Key Time Points in Early Life are Critical for Neurodevelopment Kaitlyn Oliphant University of Chicago Division of the Biological Sciences https://orcid.org/0000-0002-6921-7094 Mehneez Ali University of Chicago Division of the Biological Sciences Mark D'Souza University of Chicago Division of the Biological Sciences Patrick D. Hughes University of Chicago Comer Children's Hospital Dinanath Sulakhe University of Chicago Division of the Biological Sciences Annie Z. Wang University of Chicago Comer Children's Hospital Bingqing Xie University of Chicago Division of the Biological Sciences Rummanu Yeasin University of Chicago Division of the Biological Sciences Michael M. Msall University of Chicago Division of the Biological Sciences Bree Andrews University of Chicago Division of the Biological Sciences Erika C. Claud ( [email protected] ) Department of Pediatrics, Biological Sciences Division, University of Chicago, Chicago, IL, USA https://orcid.org/0000-0002-2408-2114 Research Keywords: Human gut microbiome, Infant microbiome succession, Infant neurodevelopment Posted Date: July 14th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-668952/v1 Page 1/40 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/40 Abstract Background: The early life microbiome plays critical roles in host development, shaping long-term outcomes including brain functioning. It is not known which initial infant colonizers elicit optimal neurodevelopment; thus, this study investigated the association between gut microbiome succession from the rst week of life and head circumference growth (HCG), the earliest validated marker for neurodevelopment. -
Sporulation Evolution and Specialization in Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. -
Expanding Diversity of Asgard Archaea and the Elusive Ancestry of Eukaryotes
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.19.343400; this version posted October 20, 2020. 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-ND 4.0 International license. 1 Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes 2 3 Yang Liu1†, Kira S. Makarova2†, Wen-Cong Huang1†, Yuri I. Wolf2, Anastasia Nikolskaya2, Xinxu 4 Zhang1, Mingwei Cai1, Cui-Jing Zhang1, Wei Xu3, Zhuhua Luo3, Lei Cheng4, Eugene V. Koonin2*, Meng 5 Li1* 6 1 Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen 7 University, Shenzhen, Guangdong, 518060, P. R. China 8 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of 9 Health, Bethesda, Maryland 20894, USA 10 3 State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic 11 Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State 12 Oceanic Administration, Xiamen 361005, P. R. China 13 4 Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of 14 Ministry of Agriculture, Chengdu 610041, P.R. China 15 † These authors contributed equally to this work. 16 *Authors for correspondence: [email protected] or [email protected] 17 18 19 Running title: Asgard archaea genomics 20 Keywords: 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.19.343400; this version posted October 20, 2020. -
Download/Issues/Mining/Reference Guide to Treatment Technologi Es for MIW.Pdf
Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water by Frank Nkansah - Boadu BSc., Kwame Nkrumah University of Science and Technology, 2003 MASc., The University of British Columbia, 2013 A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2019 © Frank Nkansah - Boadu, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water submitted by Frank Nkansah-Boadu in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Chemical and Biological Engineering Examining Committee: Susan Baldwin, Chemical and Biological Engineering Supervisor Vikramaditya Yadav, Chemical and Biological Engineering Supervisory Committee Member Troy Vassos, Adjunct Professor, Civil Engineering Supervisory Committee Member Anthony Lau, Chemical and Biological Engineering University Examiner Scott Dunbar, Mining Engineering University Examiner ii Abstract Biological treatment to remove dissolved selenium from mining-influenced water (MIW) is inhibited by co-contaminants, especially nitrate. It was hypothesized that selenium reducing microorganisms can be obtained from native mine bacteria at sites affected by MIW due to the selection pressure from elevated selenium concentrations at those sites. Enrichment of these microorganisms and testing of their capacity to remove dissolved selenium from actual coal MIW was the objective of this dissertation. Fifteen sediments were collected from eleven different vegetated or non-vegetated seepage collection ponds and one non-impacted natural wetland. -
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. -
Phylogenomic Networks Reveal Limited Phylogenetic Range of Lateral Gene Transfer by Transduction
The ISME Journal (2017) 11, 543–554 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction Ovidiu Popa1, Giddy Landan and Tal Dagan Institute of General Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage- mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. -
A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
Microorganisms 2015, 3, 500-517; doi:10.3390/microorganisms3030500 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis Violetta La Cono 1, Erika Arcadi 1, Gina La Spada 1, Davide Barreca 2, Giuseppina Laganà 2, Ersilia Bellocco 2, Maurizio Catalfamo 1, Francesco Smedile 1, Enzo Messina 1, Laura Giuliano 1,3 and Michail M. Yakimov 1,* 1 Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina 98122, Italy; E-Mails: [email protected] (V.L.C.); [email protected] (E.A.); [email protected] (G.L.S.); [email protected] (M.C.); [email protected] (F.S.); [email protected] (E.M.); [email protected] (L.G.) 2 Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, Villaggio S. Agata, Messina 98166, Italy; E-Mails: [email protected] (D.B.); [email protected] (G.L.); [email protected] (E.B.) 3 Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-090-6015-437. Academic Editors: Ricardo Amils and Elena González Toril Received: 1 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015 Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. -
Lung Microbiota Predict Invasive Pulmonary Aspergillosis and Its Outcome in Immunocompromised Patients
Respiratory infection Original research Thorax: first published as 10.1136/thoraxjnl-2020-216179 on 25 June 2021. Downloaded from Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients Anaïs Hérivaux,1,2 Jesse R Willis,3,4 Toine Mercier,5,6 Katrien Lagrou,6,7 Samuel M Gonçalves,1,2 Relber A Gonçales,1,2 Johan Maertens,5,6 Agostinho Carvalho,1,2 Toni Gabaldón,3,4,8 Cristina Cunha 1,2 ► Additional supplemental ABStract material is published online Rationale Recent studies have revealed that the lung Key messages only. To view, please visit the journal online (http:// dx. doi. microbiota of critically ill patients is altered and predicts org/ 10. 1136/ thoraxjnl- 2020- clinical outcomes. The incidence of invasive fungal What is the key question? 216179). infections, namely, invasive pulmonary aspergillosis ► Does the lung microbiota modulate (IPA), in immunocompromised patients is increasing, but susceptibility to invasive pulmonary For numbered affiliations see the clinical significance of variations in lung bacterial aspergillosis (IPA) and predict its clinical end of article. communities is unknown. outcome? Objectives To define the contribution of the lung Correspondence to What is the bottom line? microbiota to the development and course of IPA. Dr Cristina Cunha, Life and ► We show that variation in the lung microbiota Health Sciences Research Methods and measurements We performed an is associated with the development of IPA in Institute (ICVS), University observational cohort study to characterise the lung critically ill patients. Patients with IPA display of Minho, Braga 4710-057, microbiota in 104 immunocompromised patients using Portugal; a microbiota signature in the lower airways bacterial 16S ribosomal RNA gene sequencing on cristinacunha@ med.