The New Science of Metagenomics and the Challenges of Its Use in Both Developed and Developing Countries
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The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet Is Available from the National Academies Press, 500 Fifth Street, NW, Washington, D.C
THE NATIONALA REPORTIN BRIEF C The New Science of Metagenomics Revealing the Secrets of Our Microbial Planet ADEMIES Although we can’t see them, microbes are essential for every part of human life— indeed all life on Earth. The emerging field of metagenomics provides a new way of viewing the microbial world that will not only transform modern microbiology, but also may revolu- tionize understanding of the entire living world. very part of the biosphere is impacted Eby the seemingly endless ability of microorganisms to transform the world around them. It is microorganisms, or microbes, that convert the key elements of life—carbon, nitrogen, oxygen, and sulfur—into forms accessible to other living things. They also make necessary nutrients, minerals, and vitamins available to plants and animals. The billions of microbes living in the human gut help humans digest food, break down toxins, and fight off disease-causing pathogens. Microbes also clean up pollutants in the environment, such as oil and Bacteria in human saliva. Trillions of chemical spills. All of these activities are carried bacteria make up the normal microbial com- out not by individual microbes but by complex munity found in and on the human body. microbial communities—intricate, balanced, and The new science of metagenomics can help integrated entities that have a remarkable ability to us understand the role of microbial commu- adapt swiftly to environmental change. nities in human health and the environment. Historically, microbiology has focused on (Image courtesy of Michael Abbey) single species in pure laboratory culture, and thus understanding of microbial communities has lagged behind understanding of their individual mem- bers. -
Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
microorganisms Review Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens Edoardo Piombo 1,2 , Ahmed Abdelfattah 3,4 , Samir Droby 5, Michael Wisniewski 6,7, Davide Spadaro 1,8,* and Leonardo Schena 9 1 Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; [email protected] 2 Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden 3 Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; [email protected] 4 Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, 11418 Stockholm, Sweden 5 Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel; [email protected] 6 U.S. Department of Agriculture—Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA; [email protected] 7 Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA 8 AGROINNOVA—Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy 9 Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-0116708942 Abstract: Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegeta- bles, with a corresponding increase in economic losses caused by the introduction of transboundary Citation: Piombo, E.; Abdelfattah, A.; plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance Droby, S.; Wisniewski, M.; Spadaro, protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding D.; Schena, L. -
Genomics and Its Impact on Science and Society: the Human Genome Project and Beyond
DOE/SC-0083 Genomics and Its Impact on Science and Society The Human Genome Project and Beyond U.S. Department of Energy Genome Research Programs: genomics.energy.gov A Primer ells are the fundamental working units of every living system. All the instructions Cneeded to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instruc- tions required to create a particular organism with protein complex its own unique traits. The genome is an organism’s complete set of DNA. Genomes vary widely in size: The smallest known genome for a free-living organism (a bac- terium) contains about 600,000 DNA base pairs, while human and mouse genomes have some From Genes to Proteins 3 billion (see p. 3). Except for mature red blood cells, all human cells contain a complete genome. Although genes get a lot of attention, the proteins DNA in each human cell is packaged into 46 chro- perform most life functions and even comprise the mosomes arranged into 23 pairs. Each chromosome is majority of cellular structures. Proteins are large, complex a physically separate molecule of DNA that ranges in molecules made up of chains of small chemical com- length from about 50 million to 250 million base pairs. pounds called amino acids. Chemical properties that A few types of major chromosomal abnormalities, distinguish the 20 different amino acids cause the including missing or extra copies or gross breaks and protein chains to fold up into specific three-dimensional rejoinings (translocations), can be detected by micro- structures that define their particular functions in the cell. -
Pharmacogenomics and Nutrigenomics: Synergies and Differences
European Journal of Clinical Nutrition (2007) 61, 567–574 & 2007 Nature Publishing Group All rights reserved 0954-3007/07 $30.00 www.nature.com/ejcn REVIEW Pharmacogenomics and nutrigenomics: synergies and differences D Ghosh, MA Skinner and WA Laing The Horticulture and Food Research Institute of New Zealand Ltd, Auckland, New Zealand The success of the Human Genome Project and the spectacular development of broad genomics tools have catalyzed a new era in both medicine and nutrition. The terms pharmacogenomics and nutrigenomics are relatively new. Both have grown out of their genetic forbears as large-scale genomics technologies have been developed in the last decade. The aim of both disciplines is to individualize or personalize medicine and food and nutrition, and ultimately health, by tailoring the drug or the food to the individual genotype. This review article provides an overview of synergies and differences between these two potentially powerful science areas. Individual genetic variation is the common factor on which both pharmacogenomics and nutrigenomics are based. Each human is genetically (including epigenetics) unique and phenotypically distinct. One of the expectations of both technologies is that a wide range of gene variants and related single-nucleotide polymorphism will be identified as to their importance in health status, validated and incorporated into genotype based strategies for the optimization of health and the prevention of disease. Pharmacogenomics requires rigorous genomic testing that will be regulated and analyzed by professionals and acted on by medical practitioners. As further information is obtained on the importance of the interaction of food and the human genotype in disease prevention and health, pharmacogenomics can provide an opportunity driver for nutrigenomics. -
The Human Genome Project Focus of the Human Genome Project
TOOLS OF GENETIC RESEARCH THE HUMAN GENOME PROJECT FOCUS OF THE HUMAN GENOME PROJECT The primary work of the Human Genome Project has been to Francis S. Collins, M.D., Ph.D.; produce three main research tools that will allow investigators to and Leslie Fink identify genes involved in normal biology as well as in both rare and common diseases. These tools are known as positional cloning The Human Genome Project is an ambitious research effort aimed at deciphering the chemical makeup of the entire human (Collins 1992). These advanced techniques enable researchers to ge ne tic cod e (i.e. , the g enome). The primary wor k of the search for diseaselinked genes directly in the genome without first having to identify the gene’s protein product or function. (See p ro j e c t i s t o d ev e lop t h r e e r e s e a r c h tool s t h a t w i ll a ll o w the article by Goate, pp. 217–220.) Since 1986, when researchers scientists to identify genes involved in both rare and common 2 diseases. Another project priority is to examine the ethical, first found the gene for chronic granulomatous disease through legal, and social implications of new genetic technologies and positional cloning, this technique has led to the isolation of consid to educate the public about these issues. Although it has been erably more than 40 diseaselinked genes and will allow the identi in existence for less than 6 years, the Human Genome Project fication of many more genes in the future (table 1). -
From the Human Genome Project to Genomic Medicine a Journey to Advance Human Health
From the Human Genome Project to Genomic Medicine A Journey to Advance Human Health Eric Green, M.D., Ph.D. Director, NHGRI The Origin of “Genomics”: 1987 Genomics (1987) “For the newly developing discipline of [genome] mapping/sequencing (including the analysis of the information), we have adopted the term GENOMICS… ‘The Genome Institute’ Office for Human Genome Research 1988-1989 National Center for Human Genome Research 1989-1997 National Human Genome Research Institute 1997-present NHGRI: Circa 1990-2003 Human Genome Project NHGRI Today: Characteristic Features . Relatively young (~28 years) . Relatively small (~1.7% of NIH) . Unusual historical origins (think ‘Human Genome Project’) . Emphasis on ‘Team Science’ (think managed ‘consortia’) . Rapidly disseminating footprint (think ‘genomics’) . Novel societal/bioethics research component (think ‘ELSI’) . Over-achievers for trans-NIH initiatives (think ‘Common Fund’) . Vibrant (and large) Intramural Research Program A Quarter Century of Genomics Human Genome Sequenced for First Time by the Human Genome Project Genomic Medicine An emerging medical discipline that involves using genomic information about an individual as part of their clinical care (e.g., for diagnostic or therapeutic decision- making) and the other implications of that clinical use The Path to Genomic Medicine ? Human Realization of Genome Genomic Project Medicine Nature Nature Base Pairs to Bedside 2003 Heli201x to 1Health A Quarter Century of Genomics Human Genome Sequenced for First Time by the Human Genome Project -
Comparative Genome Evolution Working Group
Comparative Genome Evolution Working Group COMPARATIVE GENOME EVOLUTION MODIFIED PROPOSAL Introduction Analysis of comparative genomic sequence information from a well-chosen set of organisms is, at present, one of the most effective approaches available to advance biomedical research. The following document describes rationales and plans for selecting targets for genome sequencing that will provide insight into a number of major biological questions that broadly underlie major areas of research funded by the National Institutes of Health, including studies of gene regulation, understanding animal development, and understanding gene and protein function. Genomic sequence data is a fundamental information resource that is required to address important questions about biology: What is the genomic basis for the advent of major morphogenetic or physiological innovations during evolution? How have genomes changed with the addition of new features observed in the eukaryotic lineage, for example the development of an adaptive immune system, an organized nervous system, bilateral symmetry, or multicellularity? What are the genomic correlates or bases for major evolutionary phenomena such as evolutionary rates; speciation; genome reorganization, and origins of variation? Another vital use to which genomic sequence data are applied is the development of more robust information about important non-human model systems used in biomedical research, i.e. how can we identify conserved functional regions in the existing genome sequences of important non- mammalian model systems, so that we can better understand fundamental aspects of, for example, gene regulation, replication, or interactions between genes? NHGRI established a working group to provide the Institute with well-considered scientific thought about the genomic sequences that would most effectively address these questions. -
What Is Metagenomics? - an Introduction
What is Metagenomics? - an Introduction Josef Korbinian Vogt Information Age Do you remember? DNA Sequencing Reading the order of bases in DNA fragments How? Do you remember? Sequencing timeline Do you remember? ‘53 ‘77 ‘83 ‘86 ‘90 ‘95 ‘96 ‘00 ‘03 ‘04 ‘06 2010 - Human Genome Pyro- Completion of 3rd Generation Sanger sequencing Project starts sequencing Human Genome Sequencing Project Illumina Sequencing Polymerase chain First complete reaction developed genome of free- living organisms 454 Discovery of DNA double Pyrosequencing Helix by Watson & Crick Applied Biosystems “Next Generation” markets first automated Sequencing DNA sequencing 2nd Generation sequencing Do you remember? Reading the order of bases in DNA bases From genomics to metagenomics From genomics to metagenomics Genomics E. coli, Science, 1997 Human, Nature/Science, 2001 Metagenomics Saragasso sea, Science, 2004 Human gut, Nature, 2010 Metagenomics What is Metagenomics? Metagenomics (Environmental Genomics, Ecogenomics or Community Genomics) is the study of genetic material recovered directly from environmental samples. Chen & Pachter, Metagenomics is application of modern genomic techniques to the 2005 study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and lab cultivation of individual species Environments Metagenomics • Investigate all genomic content (i.e. bacteria, phages, plasmids…) • culture/non-culturable (~99% of microbial species cannot be cultivated) • known/unknown 16S rRNA How to? How to? How to? Methods Makes analysis hard… • Lack of references (for novel metagenomes) • Assembly: shared/similar regions between genomes work as repeats, assign contigs • Varying abundance • High diversity, large datasets Genomic vs Metagenomics Genomic vs Metagenomics Genomic vs Metagenomics Why bother? • Discovery: • novel products (e.g. -
Gene Prediction Using Deep Learning
FACULDADE DE ENGENHARIA DA UNIVERSIDADE DO PORTO Gene prediction using Deep Learning Pedro Vieira Lamares Martins Mestrado Integrado em Engenharia Informática e Computação Supervisor: Rui Camacho (FEUP) Second Supervisor: Nuno Fonseca (EBI-Cambridge, UK) July 22, 2018 Gene prediction using Deep Learning Pedro Vieira Lamares Martins Mestrado Integrado em Engenharia Informática e Computação Approved in oral examination by the committee: Chair: Doctor Jorge Alves da Silva External Examiner: Doctor Carlos Manuel Abreu Gomes Ferreira Supervisor: Doctor Rui Carlos Camacho de Sousa Ferreira da Silva July 22, 2018 Abstract Every living being has in their cells complex molecules called Deoxyribonucleic Acid (or DNA) which are responsible for all their biological features. This DNA molecule is condensed into larger structures called chromosomes, which all together compose the individual’s genome. Genes are size varying DNA sequences which contain a code that are often used to synthesize proteins. Proteins are very large molecules which have a multitude of purposes within the individual’s body. Only a very small portion of the DNA has gene sequences. There is no accurate number on the total number of genes that exist in the human genome, but current estimations place that number between 20000 and 25000. Ever since the entire human genome has been sequenced, there has been an effort to consistently try to identify the gene sequences. The number was initially thought to be much higher, but it has since been furthered down following improvements in gene finding techniques. Computational prediction of genes is among these improvements, and is nowadays an area of deep interest in bioinformatics as new tools focused on the theme are developed. -
For Immediate Release. Oct. 8Th, 2010 Microbesonline.Org Enhanced for Metagenomics and Metabolism
For Immediate Release. Oct. 8th, 2010 MicrobesOnline.org Enhanced for Metagenomics and Metabolism & The Arkin lab (genomics.lbl.gov) computational biology and bioinformatics team, as part of the Joint BioEnergy Institute (JBEI, www.jbei.org) and the Virtual Institute for Microbial Stress and Survival (VIMSS, vimss.lbl.gov), has added significant new functionality to the MicrobesOnline.org web resource for comparative and functional analysis of microbial genomes. This work, led by Dylan Chivian with John Bates, Keith Keller, Morgan Price, Paramvir Dehal, under the guidance of Adam Arkin, offers the scientific community new capabilities for metagenomic and metabolic analyses. metaMicrobesOnline Figure 1. metaMicrobesOnline permits the user to select metagenomes and isolates they want to study and then perform easy searches for keywords or gene families (e.g. “amylase” or “PFAM00128”). Scanning electron microscopy image of microbial compost community courtesy Bernhard Knierim and Manfred Auer. The new meta.MicrobesOnline.org web resource, which currently contains over 1600 genomes from bacterial, archaeal, and microeukaryotic isolates, offers combined phylogenetic gene tree analysis of millions of genes from over 150 ecological and organismal metagenomes. These trees are built using our FastTree [1] program, which offers rapid highly accurate tree building, even for very large trees. Such combined analysis is superior to BLAST-based homology approaches in that trees offers the ability to place genes from environmental samples into an evolutionary context and permits more precise functional grouping within a gene family, yielding information about the key genes for a given environment. Additionally, comparison with isolate genomes gives researchers clues for which additional genes to look for to complete the components of systems, or may possess phylogenetic markers to aid in assigning the species for environmental sequence fragments, permitting the determination of which community members are responsible for which roles. -
Genome and Pangenome Analysis of Lactobacillus Hilgardii FLUB—A New Strain Isolated from Mead
International Journal of Molecular Sciences Article Genome and Pangenome Analysis of Lactobacillus hilgardii FLUB—A New Strain Isolated from Mead Klaudia Gustaw 1,* , Piotr Koper 2,* , Magdalena Polak-Berecka 1 , Kamila Rachwał 1, Katarzyna Skrzypczak 3 and Adam Wa´sko 1 1 Department of Biotechnology, Microbiology and Human Nutrition, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; [email protected] (M.P.-B.); [email protected] (K.R.); [email protected] (A.W.) 2 Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland 3 Department of Fruits, Vegetables and Mushrooms Technology, Faculty of Food Science and Biotechnology, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland; [email protected] * Correspondence: [email protected] (K.G.); [email protected] (P.K.) Abstract: The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, Citation: Gustaw, K.; Koper, P.; 79 code for RNA, and 93 are pseudogenes. -
The Genome Project–Write Issues, Enabling Inclusive Decision-Making on the Topics Mentioned Above (7)
Human chromosomes and nucleus as visualized by scanning electron microscopy. Through open and ongoing dialogue, com- mon goals can be identified. Informed consent must take local and regional val- ues into account and enable true decision- making on particularly sensitive use of cells and DNA from certain sources. Finally, the highest biosafety standards should guide project work and safety for lab workers and research participants, and ecosystems should pervade the design process. A prior- ity will be cost reduction of both genome engineering and testing tools to aid in equi- POLICY FORUM table distribution of benefits—e.g., enabling research on crop plants and infectious agents and vectors in developing nations. GENOME ENGINEERING To ensure responsible innovation and on- going consideration of ELSI, a percentage of all research funds could be dedicated to these The Genome Project–Write issues, enabling inclusive decision-making on the topics mentioned above (7). In addi- We need technology and an ethical framework tion, there should be equitable distribution of any early and future benefits in view of on July 29, 2016 for genome-scale engineering diverse and pressing needs in different global regions. The broad scope and novelty of the By Jef D. Boeke,* George Church,* large-scale synthesis and editing of genomes. project call for consideration of appropriate Andrew Hessel,* Nancy J. Kelley,* Adam To this end, we propose the Human Genome regulation alongside development of the sci- Arkin, Yizhi Cai, Rob Carlson, Aravinda Project–Write (HGP-write), named to honor ence and societal debates. National and in- Chakravarti, Virginia W. Cornish, Liam HGP-read but embracing synthesis of all ternational laws and regulations differ, and Holt, Farren J.