Genome Signature-Based Dissection of Human Gut Metagenomes to Extract Subliminal Viral Sequences
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The Contribution of Mitochondrial Metagenomics to Large-Scale Data
Molecular Phylogenetics and Evolution 128 (2018) 1–11 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera T ⁎ Benjamin Linarda,i,j, , Alex Crampton-Platta,b,k, Jerome Morinierec, Martijn J.T.N. Timmermansa,d, Carmelo Andújara,b,l, Paula Arribasa,b,l, Kirsten E. Millera,b,m, Julia Lipeckia,n, Emeline Favreaua,o, Amie Huntera, Carola Gómez-Rodrígueze, Christopher Bartona,p, Ruie Niea,f, Conrad P.D.T. Gilletta,q, Thijmen Breeschotena,g,r, Ladislav Bocakh, Alfried P. Voglera,b a Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom b Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL5 7PY, United Kingdom c Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstrasse 21, 81247 München, Germany d Department of Natural Sciences, Hendon Campus, Middlesex University, London NW4 4BT, United Kingdom e Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, c/ Lope Gómez de Marzoa s/n, 15782 Santiago de Compostela, Spain f Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China g Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands h Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic i LIRMM, Univ. Montpellier, -
Numerous Uncharacterized and Highly Divergent Microbes Which Colonize Humans Are Revealed by Circulating Cell-Free DNA
Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA Mark Kowarskya, Joan Camunas-Solerb, Michael Kerteszb,1, Iwijn De Vlaminckb, Winston Kohb, Wenying Panb, Lance Martinb, Norma F. Neffb,c, Jennifer Okamotob,c, Ronald J. Wongd, Sandhya Kharbandae, Yasser El-Sayedf, Yair Blumenfeldf, David K. Stevensond, Gary M. Shawd, Nathan D. Wolfeg,h, and Stephen R. Quakeb,c,i,2 aDepartment of Physics, Stanford University, Stanford, CA 94305; bDepartment of Bioengineering, Stanford University, Stanford, CA 94305; cChan Zuckerberg Biohub, San Francisco, CA 94158; dDepartment of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305; ePediatric Stem Cell Transplantation, Lucille Packard Children’s Hospital, Stanford University, Stanford, CA 94305; fDivision of Maternal–Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305; gMetabiota, San Francisco, CA 94104; hGlobal Viral, San Francisco, CA 94104; and iDepartment of Applied Physics, Stanford University, Stanford, CA 94305 Contributed by Stephen R. Quake, July 12, 2017 (sent for review April 28, 2017; reviewed by Søren Brunak and Eran Segal) Blood circulates throughout the human body and contains mole- the body (18, 19); combining this observation with the average cules drawn from virtually every tissue, including the microbes and genome sizes of a human, bacterium, and virus (Gb, Mb, and viruses which colonize the body. Through massive shotgun sequenc- kb, respectively) suggests that approximately 1% of DNA by ing of circulating cell-free DNA from the blood, we identified mass in a human is derived from nonhost origins. Previous hundreds of new bacteria and viruses which represent previously studies by us and others have shown that indeed approximately unidentified members of the human microbiome. -
What Would You Do If You Could Sequence Everything?
PERspECTIVE What would you do if you could sequence everything? Avak Kahvejian1, John Quackenbush2 & John F Thompson1 It could be argued that the greatest transformative aspect ing technologies, be leveraged with insightful approaches to biology and of the Human Genome Project has been not the sequencing medicine to maximize the benefits to all? DNA sequence is no longer just of the genome itself, but the resultant development of new an end in itself, but it is rapidly becoming the digital substrate replac- technologies. A host of new approaches has fundamentally ing analog chip-based hybridization signals; it is the barcode tracking of changed the way we approach problems in basic and enormous numbers of samples; and it is the readout indicating a host of translational research. Now, a new generation of high-throughput chemical modifications and intermolecular interactions. Sequence data sequencing technologies promises to again transform the allow one to count mRNAs or other species of nucleic acids precisely, to scientific enterprise, potentially supplanting array-based determine sharp boundaries for interactions with proteins or positions technologies and opening up many new possibilities. By allowing of translocations and to identify novel variants and splice sites, all in one http://www.nature.com/naturebiotechnology DNA/RNA to be assayed more rapidly than previously possible, experiment with digital accuracy. these next-generation platforms promise a deeper understanding The brief history of molecular biology and genomic technologies has of genome regulation and biology. Significantly enhancing been marked by the introduction of new technologies, their rapid uptake sequencing throughput will allow us to follow the evolution and then a steady state or slow decline in use as newer techniques are of viral and bacterial resistance in real time, to uncover the developed that supersede them. -
Discovering Viral Genomes in Human Metagenomic Data by Predicting
www.nature.com/scientificreports OPEN Discovering viral genomes in human metagenomic data by predicting unknown protein Received: 10 May 2017 Accepted: 28 November 2017 families Published online: 08 January 2018 Mauricio Barrientos-Somarribas1, David N. Messina 2, Christian Pou1, Fredrik Lysholm1,3, Annelie Bjerkner4, Tobias Allander4, Björn Andersson 1 & Erik L. L. Sonnhammer2 Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identifcation is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of flters to extract bona fde protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fuid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM. Characterization of the human virome is crucial for our understanding of the role of the microbiome in health and disease. Te shif from culture-based methods to metagenomics in recent years, combined with the devel- opment of virus particle enrichment protocols, has made it possible to efciently study the entire fora of human viruses and bacteriophages associated with the human microbiome. -
Genome-Contric Metagenomic Investigation of 134 Samples
GENOME-CONTRIC METAGENOMIC INVESTIGATION OF 134 SAMPLES COLLECTED FROM BIOGAS REACTORS REVEALED IMPORTANT FUNCTIONAL ROLES FOR MICROBIAL SPECIES BELONGING TO UNDEREXPLORED TAXA Campanaro, S.1, Luo, G.2, Treu, L.3 Kougias, P.G.4, Zhu X.3, Angelidaki, I.3 1 University of Padova, Department of Biology, Via U. Bassi, 58b, 35131 Padova (PD), Italy 2 Fudan University, Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), 200433, Shanghai, China 3 Technical University of Denmark, Department of Environmental Engineering, Kgs. Lyngby DK-2800, Denmark 4 Institute of Animal Science, Hellenic Agricultural Organization DEMETER, Paralimni, Greece e-mail of the corresponding author: [email protected] Keywords: anaerobic digestion; metagenomics; metagenome-assembled genomes; taxonomy. INTRODUCTION In the past four years many samples collected from full-scale biogas plants and lab-scale reactors have been investigated using Illumina shotgun sequencing approaches and deposited in NCBI Sequence Read Archive database. In all these reactors, the Anaerobic Digestion (AD) process is performed by a plethora of different microorganisms organized in a complex functional network where different species have distinct roles in degradation of organic matter. Difficulties associated to cultivation of many prokaryotes present in natural and engineered ecosystems strongly limits the possibility to expand our knowledge regarding their physiology, genetics and function (Tringe and Rubin, 2005). Thanks to the bioinformatics approaches recently developed, which allow the reconstruction of microbial genomes starting from shotgun DNA sequences obtained from mixed cultures (Campanaro et al., 2016), it is now becoming possible to reveal the functional roles of microbial species resisting cultivation in axenic cultures. -
Molecular Complexity of Successive Bacterial Epidemics Deconvoluted by Comparative Pathogenomics
Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics Stephen B. Beresa,b, Ronan K. Carrolla,b, Patrick R. Sheaa,b, Izabela Sitkiewicza,b, Juan Carlos Martinez-Gutierreza,b, Donald E. Lowc, Allison McGeerd, Barbara M. Willeyd, Karen Greend, Gregory J. Tyrrelld, Thomas D. Goldmanf, Michael Feldgardeng, Bruce W. Birreng, Yuriy Fofanovh, John Boosi, William D. Wheatoni, Christiane Honischf, and James M. Mussera,b,1 aCenter for Molecular and Translational Human Infectious Diseases Research, The Methodist Hospital Research Institute, and bDepartment of Pathology, The Methodist Hospital, Houston, TX 77030; cOntario Agency for Health Protection and Promotion, and University of Toronto, Toronto, ON M5G 1X5, Canada; dDepartment of Microbiology, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; eDepartment of Laboratory medicine and Pathology, University of Alberta, Edmonton, AB T6G 2J2, Canada; fSequenom, Inc., San Diego, CA 92121; gBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142; hDepartment of Computer Science and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204; and iRTI International, Research Triangle Park, NC 27709 Edited* by Charles R. Cantor, Sequenom Inc., San Diego, CA, and approved December 14, 2009 (received for review September 30, 2009) Understanding the fine-structure molecular architecture of bacterial century that GAS has the capacity to cause epidemics charac- epidemics has been a long-sought goal of infectious disease research. terized by rapid increase in disease frequency and severity. For We used short-read-length DNA sequencing coupled with mass example, Weech (6) described an epidemic of septic scarlet fever spectroscopy analysis of SNPs to study the molecular pathogenomics in Yunnanfu, China, that killed 50,000 people, fully 25% of the of three successive epidemics of invasive infections involving 344 population of the province. -
View: Latest Perspectives on Antiinflammatory Actions of Glucocorticoids
Fleuren et al. BioData Mining 2013, 6:2 http://www.biodatamining.org/content/6/1/2 BioData Mining RESEARCH Open Access Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining Wilco WM Fleuren1,2, Erik JM Toonen3, Stefan Verhoeven4, Raoul Frijters1,6, Tim Hulsen1,7, Ton Rullmann5, René van Schaik4, Jacob de Vlieg1,4 and Wynand Alkema1,8* * Correspondence: [email protected] Abstract 1Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud Background: Glucocorticoids are potent anti-inflammatory agents used for the University Nijmegen Medical Centre, treatment of diseases such as rheumatoid arthritis, asthma, inflammatory bowel P.O. Box 91016500 HB, Nijmegen, disease and psoriasis. Unfortunately, usage is limited because of metabolic side- The Netherlands 8Present address: NIZO Food effects, e.g. insulin resistance, glucose intolerance and diabetes. To gain more insight Research BV, Ede, The Netherlands into the mechanisms behind glucocorticoid induced insulin resistance, it is important Full list of author information is to understand which genes play a role in the development of insulin resistance and available at the end of the article which genes are affected by glucocorticoids. Medline abstracts contain many studies about insulin resistance and the molecular effects of glucocorticoids and thus are a good resource to study these effects. Results: We developed CoPubGene a method to automatically identify gene-disease associations in Medline abstracts. We used this method to create a literature network of genes related to insulin resistance and to evaluate the importance of the genes in this network for glucocorticoid induced metabolic side effects and anti-inflammatory processes. -
Swabs to Genomes: a Comprehensive Workflow
UC Davis UC Davis Previously Published Works Title Swabs to genomes: a comprehensive workflow. Permalink https://escholarship.org/uc/item/3817d8gj Journal PeerJ, 3(5) ISSN 2167-8359 Authors Dunitz, Madison I Lang, Jenna M Jospin, Guillaume et al. Publication Date 2015 DOI 10.7717/peerj.960 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Swabs to genomes: a comprehensive workflow Madison I. Dunitz1,3 , Jenna M. Lang1,3 , Guillaume Jospin1, Aaron E. Darling2, Jonathan A. Eisen1 and David A. Coil1 1 UC Davis, Genome Center, USA 2 ithree institute, University of Technology Sydney, Australia 3 These authors contributed equally to this work. ABSTRACT The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it. Subjects Bioinformatics, Genomics, Microbiology Keywords Workflow, Microbial genomics, Genome sequencing, Genome assembly, Bioinformatics INTRODUCTION Thanks to decreases in cost and diYculty, sequencing the genome of a microorganism is becoming a relatively common activity in many research and educational institutions. -
Uncovering the Role of Genomic “Dark Matter” in Human Disease
Uncovering the role of genomic “dark matter” in human disease Lance Martin, Howard Y. Chang J Clin Invest. 2012;122(5):1589-1595. https://doi.org/10.1172/JCI60020. Science in Medicine The human genome encodes thousands of long noncoding RNAs (lncRNAs). Although most remain functionally uncharacterized biological “dark matter,” lncRNAs have garnered considerable attention for their diverse roles in human biology, including developmental programs and tumor suppressor gene networks. As the number of lncRNAs associated with human disease grows, ongoing research efforts are focusing on their regulatory mechanisms. New technologies that enable enumeration of lncRNA interaction partners and determination of lncRNA structure are well positioned to drive deeper understanding of their functions and involvement in pathogenesis. In turn, lncRNAs may become targets for therapeutic intervention or new tools for biotechnology. Find the latest version: https://jci.me/60020/pdf Science in medicine Uncovering the role of genomic “dark matter” in human disease Lance Martin1,2 and Howard Y. Chang1 1Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA. 2Department of Bioengineering, Stanford University, Stanford, California, USA. The human genome encodes thousands of long noncoding RNAs (lncRNAs). Although most remain functionally uncharacterized biological “dark matter,” lncRNAs have garnered considerable atten- tion for their diverse roles in human biology, including developmental programs and tumor sup- pressor gene networks. As the number of lncRNAs associated with human disease grows, ongoing research efforts are focusing on their regulatory mechanisms. New technologies that enable enu- meration of lncRNA interaction partners and determination of lncRNA structure are well posi- tioned to drive deeper understanding of their functions and involvement in pathogenesis. -
Ubin – a Manual Refining Tool for Metagenomic Bins Designed for Educational 2 Purposes 3 4 Till L.V
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.15.204776; this version posted July 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 uBin – a manual refining tool for metagenomic bins designed for educational 2 purposes 3 4 Till L.V. Bornemann1, Sarah P. Esser1, Tom L. Stach1, Tim Burg2, and Alexander J. Probst1 5 6 1: Institute for Environmental Microbiology and Biotechnology, Department of Chemistry, 7 University Duisburg-Essen, Germany 8 2: Tim Burg, Im Acker 59, 56072 Koblenz, Germany 9 10 To whom the correspondence should be addressed: 11 [email protected] 12 13 Abstract 14 15 Resolving bacterial and archaeal genomes from metagenomes has revolutionized our 16 understanding of Earth’s biomes, yet producing high quality genomes from assembled 17 fragments has been an ever-standing problem. While automated binning software and their 18 combination produce prokaryotic bins in high-throughput, their manual refinement has been 19 slow and sometimes difficult. Here, we present uBin, a GUI-based, standalone bin refiner that 20 runs on all major operating platforms and was specifically designed for educational purposes. 21 When applied to the public CAMI dataset, refinement of bins was able to improve 78.9% of 22 bins by decreasing their contamination. We also applied the bin refiner as a standalone binner 23 to public metagenomes from the International Space Station and demonstrate the recovery of 24 near-complete genomes, whose replication indices indicate active proliferation of microbes in 25 Earth’s lower orbit. -
Haemophilus Influenzae Genome Evolution During Persistence in The
Haemophilus influenzae genome evolution during PNAS PLUS persistence in the human airways in chronic obstructive pulmonary disease Melinda M. Pettigrewa, Christian P. Ahearnb,c, Janneane F. Gentd, Yong Konge,f,g, Mary C. Gallob,c, James B. Munroh,i, Adonis D’Melloh,i, Sanjay Sethic,j,k, Hervé Tettelinh,i,1, and Timothy F. Murphyb,c,l,1,2 aDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510; bDepartment of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203; cClinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203; dDepartment of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06510; eDepartment of Biostatistics, Yale School of Public Health, New Haven, CT 06510; fDepartment of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510; gW.M. Keck Foundation Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT 06510; hInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201; iDepartment of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201; jDivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203; kDepartment of Medicine, Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215; and lDivision of Infectious Diseases, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203 Edited by Rino Rappuoli, GSK Vaccines, Siena, Italy, and approved February 27, 2018 (received for review November 10, 2017) Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and adaptation cannot be accurately studied in vitro or in animal infect humans and are critical to the pathogenesis of chronic obstruc- models as a result of the unique physiological and immunological tive pulmonary disease (COPD). -
The Contribution of Mitochondrial Metagenomics to Large- Scale Data Mining and Phylogenetic Analysis of Coleoptera
bioRxiv preprint doi: https://doi.org/10.1101/280792; this version posted March 12, 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-NC-ND 4.0 International license. The contribution of mitochondrial metagenomics to large- scale data mining and phylogenetic analysis of Coleoptera Benjamin Linard1,8, Alex Crampton-Platt1,3,16, Jérome Moriniere7, Martijn J.T.N. Timmermans1,4, Carmelo Andujar1,2,14, Paula Arribas1,2,14, Kirsten E. Miller1,2,9, Julia Lipecki1,11, Emeline Favreau1,10, Amie Hunter1, Carola Gomez-Rodriguez5, Christopher Barton1, Ruie Nie1,15, Conrad P.D.T. Gillett1,12, Thijmen Breeschoten1,13, Ladislav Bocak6, Alfried P. Vogler1,2 1 Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom 2 Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom 3 Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, United Kingdom 4 Department of Natural Sciences, Hendon Campus, Middlesex University, London, NW4 4BT, United Kingdom 5 Departamento de Zoología, Facultad de Biología, Universidad de Santiago de Compostela, c/ Lope Gómez de Marzoa s/n, 15782 Santiago de Compostela, Spain 6 Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic 7 Bavarian State Collection of Zoology (SNSB – ZSM),