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Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. Nucleic Acids Res 2021; 50:e17. [PMID: 34871418 PMCID: PMC8860608 DOI: 10.1093/nar/gkab1115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.
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Affiliation(s)
- William B Andreopoulos
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA.,Department of Computer Science, San Jose State University, CA, USA
| | - Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Miriam Lucke
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jan Balewski
- National Energy Research Scientific Computing Center (NERSC), Berkeley, CA, USA
| | - Alicia Clum
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA
| | - Natalia N Ivanova
- Joint Genome Institute, US Department of Energy, LBNL Berkeley, CA, USA
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Geller AM, Pollin I, Zlotkin D, Danov A, Nachmias N, Andreopoulos WB, Shemesh K, Levy A. The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. Nat Commun 2021; 12:3743. [PMID: 34145238 PMCID: PMC8213781 DOI: 10.1038/s41467-021-23777-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that evolved from a bacteriophage tail. Four eCISs have previously been shown to mediate interactions between bacteria and their invertebrate hosts. Here, we identify eCIS loci in 1,249 bacterial and archaeal genomes and reveal an enrichment of these loci in environmental microbes and their apparent absence from mammalian pathogens. We show that 13 eCIS-associated toxin genes from diverse microbes can inhibit the growth of bacteria and/or yeast. We identify immunity genes that protect bacteria from self-intoxication, further supporting an antibacterial role for some eCISs. We also identify previously undescribed eCIS core genes, including a conserved eCIS transcriptional regulator. Finally, we present our data through an extensive eCIS repository, termed eCIStem. Our findings support eCIS as a toxin-delivery system that is widespread among environmental prokaryotes and likely mediates antagonistic interactions with eukaryotes and other prokaryotes.
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Affiliation(s)
- Alexander Martin Geller
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Inbal Pollin
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Aleks Danov
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Nimrod Nachmias
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Keren Shemesh
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel.
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Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, Barry K, Copeland A, Singer SW, Woyke T, Grigoriev IV, James TY, Cheng JF. A single-cell genomics pipeline for environmental microbial eukaryotes. iScience 2021; 24:102290. [PMID: 33870123 PMCID: PMC8042348 DOI: 10.1016/j.isci.2021.102290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 12/05/2022] Open
Abstract
Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes. We optimized single-cell methodology using a broad sample range, for EME We combined bioinformatic and bench protocols into a concise workflow We benchmarked the pipeline and used it on environmental samples We selected a set of QC criteria for best genome quality prediction
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Affiliation(s)
- Doina Ciobanu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Steven Ahrendt
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Sandy Chan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - C Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian Foster
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Jan P Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Yung Tsu Tang
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Patrick Schwientek
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Gerald L Benny
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Shweta Deshpande
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Alex Copeland
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | | | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
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