Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes - Identifying the host taxon of a previously undescribed plasmid
Authors/Creators
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Grodner, Benjamin
(Contact person)1
-
Shi, Hao
(Project member)2, 1
- Farchione, Owen (Project member)1
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Vill, Albert
(Project member)1
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Ntekas, Ioannis
(Project member)1
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Diebold, Peter
(Project member)1
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Wu, David T.
(Project member)3
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Chen, Chia-Yu
(Project member)3
- Kim, David M. (Project member)3
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Zipfel, Warren
(Project member)1
- et al. Show all 12 authors
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Grodner, Benjamin
(Contact person)1
-
Shi, Hao
(Project member)2, 1
- Farchione, Owen (Project member)1
-
Vill, Albert
(Project member)1
-
Ntekas, Ioannis
(Project member)1
-
Diebold, Peter
(Project member)1
-
Wu, David T.
(Project member)3
-
Chen, Chia-Yu
(Project member)3
- Kim, David M. (Project member)3
-
Zipfel, Warren
(Project member)1
-
Brito, Ilana L.
(Project member)1
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De Vlaminck, Iwijn
(Project manager)1
-
1.
Cornell University
- 2. Kanvas Biosciences
- 3. Harvard School of Dental Medicine
Description
We investigated the taxonomic association of an unknown plasmid within a plaque biofilm of a patient diagnosed with stage 3 periodontitis. We combined long- and short- read sequencing to identify a complete plasmid with minimal homology to any sequence in the RefSeq database. The plasmid carried several predicted genes for mobilization and toxin-antitoxin systems. We designed MGE-FISH probes for the plasmid and combined this MGE-FISH stain with an 18-genera HiPR-FISH panel.
Images are labeled by collection time such that the laser order for a given field of view (fov) is: 488nm Lambda, 514nm Lambda, 561nm Lambda, 633nm Airyscan, 405nm Lambda. We used Flye (https://github.com/fenderglass/Flye) to assemble the plasmid using long read Nanopore sequencing only and we used OPERA-MS (https://github.com/CSB5/OPERA-MS) to do hybrid assembly with Illumina short reads and Nanopore long reads. The assemblies are in the fasta files and the reads that map to the assemblies are in the fastq files.
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