Numerous Uncharacterized and Highly Divergent Microbes Which Colonize Humans Are Revealed by Circulating Cell-Free DNA
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Genome Signature-Based Dissection of Human Gut Metagenomes to Extract Subliminal Viral Sequences
ARTICLE Received 16 Apr 2013 | Accepted 8 Aug 2013 | Published 16 Sep 2013 DOI: 10.1038/ncomms3420 OPEN Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences Lesley A. Ogilvie1, Lucas D. Bowler1, Jonathan Caplin2, Cinzia Dedi1, David Diston2,w, Elizabeth Cheek3, Huw Taylor2, James E. Ebdon2 & Brian V. Jones1 Bacterial viruses (bacteriophages) have a key role in shaping the development and functional outputs of host microbiomes. Although metagenomic approaches have greatly expanded our understanding of the prokaryotic virosphere, additional tools are required for the phage- oriented dissection of metagenomic data sets, and host-range affiliation of recovered sequences. Here we demonstrate the application of a genome signature-based approach to interrogate conventional whole-community metagenomes and access subliminal, phylogen- etically targeted, phage sequences present within. We describe a portion of the biological dark matter extant in the human gut virome, and bring to light a population of potentially gut- specific Bacteroidales-like phage, poorly represented in existing virus like particle-derived viral metagenomes. These predominantly temperate phage were shown to encode functions of direct relevance to human health in the form of antibiotic resistance genes, and provided evidence for the existence of putative ‘viral-enterotypes’ among this fraction of the human gut virome. 1 Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK. 2 School of Environment and Technology, University of Brighton, Brighton BN2 4GJ, UK. 3 School of Computing, Engineering and Mathematics, University of Brighton, Brighton BN2 4GJ, UK. w Present address: Mikrobiologische and Biotechnologische Risiken Bundesamt fu¨r Gesundheit BAG, 3003 Bern, Switzerland. -
Fosmid Library End Sequencing Reveals a Rarely Known Genome Structure of Marine Shrimp Penaeus Monodon
eScholarship Title Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon Permalink https://escholarship.org/uc/item/126680ch Journal BMC Genomics, 12(1) ISSN 1471-2164 Authors Huang, Shiao-Wei Lin, You-Yu You, En-Min et al. Publication Date 2011-05-17 DOI http://dx.doi.org/10.1186/1471-2164-12-242 Supplemental Material https://escholarship.org/uc/item/126680ch#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Huang et al. BMC Genomics 2011, 12:242 http://www.biomedcentral.com/1471-2164/12/242 RESEARCHARTICLE Open Access Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon Shiao-Wei Huang1, You-Yu Lin1, En-Min You1, Tze-Tze Liu2, Hung-Yu Shu2, Keh-Ming Wu3, Shih-Feng Tsai3, Chu-Fang Lo1, Guang-Hsiung Kou1, Gwo-Chin Ma4, Ming Chen1,4,5, Dongying Wu6,7, Takashi Aoki8, Ikuo Hirono8 and Hon-Tsen Yu1* Abstract Background: The black tiger shrimp (Penaeus monodon) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. -
A Field Guide to Eukaryotic Transposable Elements
GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020. -
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. -
A Zebrafish Reporter Line Reveals Immune and Neuronal Expression of Endogenous Retrovirus
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427598; this version posted January 21, 2021. 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. A zebrafish reporter line reveals immune and neuronal expression of endogenous retrovirus. Noémie Hamilton1,2*, Amy Clarke1, Hannah Isles1, Euan Carson1, Jean-Pierre Levraud3, Stephen A Renshaw1 1. The Bateson Centre, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK 2. The Institute of Neuroscience, University of Sheffield, Sheffield, UK 3. Macrophages et Développement de l’Immunité, Institut Pasteur, CNRS UMR3738, 25 rue du docteur Roux, 75015 Paris *Corresponding author: [email protected] Abstract Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences are part of every vertebrate genome and their random integrations are thought to have contributed to evolution. Although ERVs are mainly kept silenced by the host genome, they are found activated in multiple disease states such as auto-inflammatory disorders and neurological diseases. What makes defining their role in health and diseases challenging is the numerous copies in mammalian genomes and the lack of tools to study them. In this study, we identified 8 copies of the zebrafish endogenous retrovirus (zferv). We created and characterised the first in vivo ERV reporter line in any species. Using a combination of live imaging, flow cytometry and single cell RNA sequencing, we mapped zferv expression to early T cells and neurons. -
Copycontrol™ Fosmid Autoinduction Solution
CopyControl™ Fosmid Autoinduction Solution Cat. No. AIS107F Available exclusively thru Lucigen. lucigen.com/epibio www.lucigen.com MA263E CopyControl™ Fosmid Autoinduction Solution • 12/2016 1 MA263E CopyControl™ Fosmid Autoinduction Solution 1. Introduction The CopyControl™ Fosmid Autoinduction Solution is designed to induce CopyControl Fosmid clones and clones retrofitted with the EZ-Tn5™ <oriV/KAN-2> Transposon, grown in TransforMax™ EPI300™ E. coli cells, from single-copy number to a higher-copy number of approximately 50 fosmids per cell. The Fosmid Autoinduction Solution induces expression of a mutant trfA gene contained in the TransforMax EPI300 cells. Expression of trfA gene results in initiation of replication from the oriV high copy origin of replication and subsequent amplification of the CopyControl clones to high copy number. The Fosmid Autoinduction protocol improves upon the existing induction protocol by including the autoinduction supplement in the media prior to culture inoculation, removing the need for time-consuming subculturing and the 2-hour incubation required in the standard induction protocol. The Fosmid Autoinduction Solution also contains cell growth enhancers which boost cell numbers and typically provides higher DNA yields than with the standard CopyControl induction protocol. The hands-off autoinduction protocol makes CopyControl Fosmid Autoinduction solution ideal for high-throughput purification protocols in 96-well format. The autoinduction solution is also compatible with larger scale DNA purifications and can be scaled according to the amount of media used. 2. Product Specifications Storage: Store only at –20°C in a freezer without a defrost cycle. Mix thoroughly after thawing. Size and Formulation: CopyControl Fosmid Autoinduction Solution is available in a 50-ml size concentrate of 500X in sterile water. -
Protocol for Epifos™ Fosmid Library Production
EpiFOS™ Fosmid Library Production Kit Cat. No. FOS0901 Connect with Epicentre on our blog (epicentral.blogspot.com), Facebook (facebook.com/EpicentreBio), and Twitter (@EpicentreBio). www.epicentre.com Lit. # 149 • 8/2012 1 EPILIT149 Rev. A EpiFOS™ Fosmid Library Production Kit 1. Overview of the EpiFOS Fosmid Library Production Process Fosmid vectors1-3 provide an improved method for cloning and the stable maintenance of cosmid-sized (35-45 kb) libraries in E. coli. The stability of such large constructs in vivo is facilitated by the pEpiFOS™-5 vector that maintains the clones at single copy in the cell. The EpiFOS Fosmid Library Production Kit will produce a complete and unbiased primary fosmid library. The kit utilizes a novel strategy of cloning randomly sheared, end-repaired DNA. Shearing the DNA leads to the generation of highly random DNA fragments in contrast to more biased libraries that result from fragmenting the DNA by partial restriction digests. The steps involved (protocols for steps 2-7 are included in this manual): 1. Purify DNA from the desired source (the kit does not supply materials for this step). 2. Shear the DNA to approximately 40-kb fragments. 3. End-repair the sheared DNA to blunt, 5′-phosphorylated ends. 4. Size-resolve the end-repaired DNA by Low Melting Point (LMP) agarose gel electrophoresis. 5. Purify the blunt-end DNA from the LMP agarose gel. 6. Ligate the blunt-end DNA to the Cloning-Ready pEpiFOS-5 vector. 7. Package the ligated DNA and plate on EPI100™-T1R Plating Strain. Grow clones overnight. pEpiFOS-5 is a 7518 bp. -
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. -
The Bright Side of Microbial Dark Matter: Lessons Learned
Available online at www.sciencedirect.com ScienceDirect The bright side of microbial dark matter: lessons learned from the uncultivated majority 1 2 1 Lindsey Solden , Karen Lloyd and Kelly Wrighton Microorganisms are the most diverse and abundant life forms The first realizations of just how diverse and unexplored on Earth. Yet, in many environments, only 0.1–1% of them have microorganisms are came from analyzing microbial small been cultivated greatly hindering our understanding of the subunit ribosomal RNA (SSU or 16S rRNA) gene sequences microbial world. However, today cultivation is no longer a directly from environmental samples [7]. These analyses requirement for gaining access to information from the revealed that less than half of the known microbial phyla uncultivated majority. New genomic information from contained a single cultivated representative. Phyla com- metagenomics and single cell genomics has provided insights posed exclusively of uncultured representatives are referred into microbial metabolic cooperation and dependence, to as Candidate Phyla (CP). Borrowing language from generating new avenues for cultivation efforts. Here we astronomy, microbiologists operationally define these CP summarize recent advances from uncultivated phyla and as microbial dark matter, because these organisms likely discuss how this knowledge has influenced our understanding account for a large portion of the Earth’s biomass and of the topology of the tree of life and metabolic diversity. biodiversity, yet their basic metabolic and ecological prop- erties are not known. This uncultivated majority represents Addresses 1 a grand challenge to the scientific community and until we Department of Microbiology, The Ohio State University, Columbus, OH solve the mysteries of the CP, our knowledge of the micro- 43210, USA 2 Department of Microbiology, University of Tennessee, Knoxville, TN bial world around us is profoundly skewed by what we have 37996, USA cultivated in the laboratory [8 ]. -
Unexpected Features of the Dark Proteome
Unexpected features of the dark proteome Nelson Perdigãoa,b, Julian Heinrichc, Christian Stoltec, Kenneth S. Sabird,e, Michael J. Buckleyc, Bruce Taborc, Beth Signald, Brian S. Glossd, Christopher J. Hammangd, Burkhard Rostf, Andrea Schafferhansf, and Seán I. O’Donoghuec,d,g,1 aInstituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal; bInstituto de Sistemas e Robótica, 1049-001 Lisbon, Portugal; cCommonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW 1670, Australia; dGenomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; eSchool of Information Technology, The University of Sydney, Sydney, NSW 2006, Australia; fDepartment for Bioinformatics and Computational Biology, Technische Universität München, 80333 Munich, Germany; and gSchool of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia Edited by Alan R. Fersht, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom, and approved October 13, 2015 (received for review April 29, 2015) We surveyed the “dark” proteome–that is, regions of proteins never In fact, discoveries have already resulted from studying regions observed by experimental structure determination and inaccessible of unknown structure, namely, intrinsically disordered regions. to homology modeling. For 546,000 Swiss-Prot proteins, we found Long known to confound structure determination (15)—thus that 44–54% of the proteome in eukaryotes and viruses was dark, forming part of the dark proteome—disorder was largely ignored ∼ compared with only 14% in archaea and bacteria. Surprisingly, until recently (16) and yet is now known to play key functional most of the dark proteome could not be accounted for by conven- roles, especially in eukaryotes (17). -
Identification of an Unusual Glycosyltransferase from a Non
Identification of an unusual glycosyltransferase from a non-cultivated microorganism and the construction of an improved Escherichia coli strain harboring the rpoD gene from Clostridium cellulolyticum for metagenome searches Dissertation Zur Erlangung der Würde des Doktors der Naturwissenschaften des Fachbereichs Biologie, der Fakultät für Mathematik, Informatik und Naturwissenschaften, der Universität Hamburg vorgelegt von Julia Jürgensen aus Henstedt-Ulzburg Hamburg 2015 Table of contents I Table of contents 1 Introduction ...................................................................................................... 1 1.1 Flavonoids................................................................................................... 1 1.2 Glycosyltransferases ................................................................................... 3 1.3 Biotechnology ............................................................................................. 4 1.3.1 Biotechnological relevance of glycosyltranferases....................................... 5 1.4 Metagenomics ............................................................................................. 5 1.5 Transcription ............................................................................................... 7 1.6 Phyla ........................................................................................................... 8 1.6.1 Proteobacteria ............................................................................................. 8 1.6.2 Firmicutes ..................................................................................................