Name: Microbes and Metagenomics
Brand: Arbor Biosciences

myBaits Custom — Predesigned Community Panels

Microbes and Metagenomics

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NGS Community Panels for bacteria and viruses.

myBaits Custom — Predesigned Community Panels – Microbes and Metagenomics

Over the last decade, researchers working in metagenomics, gene expression, functional genomics, evolutionary biology, and more have relied on myBaits Custom kits for enhancing the efficiency of their bacterial and viral targeted NGS research.

For bacteria, myBaits Custom kits have been used for genome sequencing, gene family sequencing, metagenomics, and gene expression studies on pathogens, commensal, and environmental strains, from fresh samples as well as highly degraded ancient specimens such as archaeological remains. For viruses, myBaits kits have been used in similar applications, including panels that target highly diverse groups of related viruses for discovery, surveillance, and evolutionary biology applications.

Overview
Services
Publications

Overview

myBaits Custom Community Panels for Microbes & Metagenomics

Listed below are a curated set of bacterial and viral research panels that are of broad interest to the research community, and are available for quick delivery. Daicel Arbor Biosciences extends our thanks to the authors and designers of these panels for granting permission to include them on this list for accelerating discovery of the research community.

Note about attribution: If you use one of these Community Panels (in full or modified form) in your research, please ensure that you properly cite the appropriate publication(s) in any resulting manuscripts. Where applicable, we have indicated the most appropriate current reference(s) that should be cited for each panel.

Bacteria

Resistome – Antimicrobial Resistance Genes (ARG) enrichment panel

In Guitor et al. (2019), researchers introduced a novel myBaits NGS hybridization capture panel targeting the “resistome” of antimicrobial resistance genes (ARGs), and favorably evaluated the panel’s performance for both control mock community samples as well as biological samples. This myBaits panel was demonstrated to be an effective discovery tool not only enabling comprehensive ARG profiling but also detecting novel content at considerably lower read depths compared to shotgun sequencing. Learn more at https://card.mcmaster.ca/.

Reference: Guitor, A.K., A.R. Raphenya, J. Klunk, M. Kuch, B. Alcock, M.G. Surette, A.G. McArthur, H.N. Poinar, G.D. Wright. (2019). Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy 64(1): e01324-19

Design ID: D10024agAMR

AMR-Cap - Antimicrobial Resistance Gene enrichment panel

In Beaudry et al. (2021), researchers introduced a novel myBaits NGS target enrichment panel “AMR-Cap” targeting antimicrobial resistance genes (ARGs) and pathogenicity islands, designed to enrich these targets from complex environmental DNA sources. This myBaits panel was demonstrated to be an effective discovery tool in mock and real complex samples, with >200-fold enrichment increase in the amount of target regions versus shotgun sequencing.

Reference: Beaudry, M.S., J.C. Thomas, R.P. Baptista, A.H. Sullivan, W. Norfolk, A. Devault, J. Enk, T.J. Kieran, O.E. Rhodes, Jr., K.A. Perry-Dow, L.J. Rose, N.J. Bayona-Vásquez, A. Oladeinde, E.K. Lipp, S. Sanchez, T.C. Glenn. (2021). Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environmental Microbiology, 23: 7523-7537

Design ID: D10091Rsstm

Mycobacterium leprae – Leprosy

Full genome enrichment panel designed from the Br4923 (NC_011896) M. leprae reference genome and demonstrated suitable for enriching even degraded or ancient DNA samples. In direct comparison to on-array or array-derived DIY in-solution probes, this myBaits panel was shown to meet or exceed overall performance and value for enriching both ancient and modern samples (Furtwängler et al. 2020).

Reference: Furtwängler, A., J. Neukamm, L. Böhme, E. Reiter, M. Vollstedt, N. Arora, P. Singh, S.T. Cole, S. Knauf, S. Calvignac-Spencer, B. Krause-Kyora, J. Krause, V.J. Schuenemann, A. Herbig. (2020). Comparison of target enrichment strategies for ancient pathogen DNA. BioTechniques 2020 69:6, 455-459

Design ID: D10227MLPRA

Treponema pallidum – Syphilis/Yaws

Full genome NGS enrichment panel designed from the T. pallidum ssp. pertenue strain Fribourg-Blanc reference genome (Knauf et al. 2018) and demonstrated suitable for enriching even degraded or ancient DNA samples. In direct comparison to on-array or array-derived DIY in-solution probes, this myBaits panel was shown to meet or exceed overall performance and value for enriching both ancient and modern samples (Furtwängler et al. 2020).

Reference: Knauf, S., J.F. Gogarten, V.J. Schuenemann, H.M. De Nys, A. Düx, M. Strouhal, L. Mikalová, K.I. Bos, R. Armstrong, E.K. Batamuzi, I.S. Chuma, B. Davoust, G. Diatta, R.D. Fyumagwa, R.R. Kazwala, J.D. Keyyu, I.A.V. Lejora, A. Levasseur, H. Liu, M.A. Mayhew, O. Mediannikov, D. Raoult, R.M. Wittig, C. Roos, F.H. Leendertz, D. Šmajs, K. Nieselt, J. Krause, S. Calvignac-Spencer. (2018.) Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue. Emerging Microbes & Infections 7:1, 1-4

Design ID: D10230TPAL1

Viruses

ASFV – African Swine Fever Virus

Full genome enrichment panel for ASFV designed from Georgia 2007/1 (FR682468.1) and Ken06.bus (KM111295) genome reference sequences, suitable for enriched even degraded DNA samples. This panel was used in Forth et al. (2019) for ASFV genome enrichment directly from NGS libraries built from infected organ tissue samples, enabling construction of high-coverage genome sequence, which was not possible to do with shotgun sequencing alone due to very low viral levels.

Reference: Forth, J.H., L.F. Forth, J. King, O. Groza, A. Hübner, A.S. Olesen, D. Höper, L.K. Dixon, C.L. Netherton, T.B. Rasmussen, S. Blome, A. Pohlmann, M. Beer. (2019). A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses. 2019; 11(9):846

Design ID: D10228ASFV1

HBV – Hepatitis B

Full genome enrichment panel for HBV designed from 5,230 diverse reference genome sequences covering all major viral subtyptes, demonstrated suitable for enriching even degraded ancient samples. This panel was used in Ross et al. (2018) for nearly complete genome reconstruction of a 16th century HBV strain from an ancient mummy.

Reference: Ross, Z.P., J. Klunk, G. Fornaciari, V. Giuffra, S. Duchêne, A.T. Duggan, D. Poinar, M.W. Douglas, J-S. Eden, E.C. Holmes, H.N. Poinar. (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLOS Pathogens 14(1): e1006750

Design ID: D10186hpHBV

HIV – Human Immunodeficiency Virus

Full genome enrichment panel for HIV designed from various genome reference sequences. This panel was used in Colson et al. (2020) to enrich a biologically-incomplete integrated HIV genome from a patient’s clinical sample (the result of hypothesized spontaneous post-infection viral genome mutations and degradation).

Reference: Colson, P., C. Dhiver, C. Tamalet, J. Delerce, O.O. Glazunova, M. Gaudin, A. Levasseur, D. Raoult. (2020). Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection. Scientific Reports 10, 2548

Design ID: D10231cpHIV

HSV-1 and HSV-2 – Herpesvirus

Genome enrichment panel designing for herpesvirus HSV-1 and HSV-2.

Reference: Shipley, M.M., M.M. Rathbun, M.L. Szpara. (2020). Oligonucleotide Enrichment of HSV-1 Genomic DNA from Clinical Specimens for Use in High-Throughput Sequencing. Herpes Simplex Virus – Methods in Molecular Biology Book Series.

Design ID: D10229HSV12

To order, please reach out to our team today to get started quickly with one of these demonstrated peer-reviewed options.

If you are interested in learning more about how myBaits enables highly efficient targeted pathogen or microbe sequencing, please visit our Microbial Targeted Sequencing application page for more information.

Have a suggestion to add a new panel to our list? Contact us today!

Daicel Arbor Biosciences offers both custom probes and full NGS services to meet your project needs. If you do not see a suitable option among these or our predesigned myBaits Expert panels, our scientists would be happy to design a fully custom targeted NGS panel and kit that will exactly meet your research needs. Please contact us today, and visit our myBaits Custom DNA-Seq, myBaits Custom RNA-Seq, or myBaits Custom Methyl-Seq product pages to learn more. And if you’d like to outsource your targeted NGS project, our myReads lab services experts are always available to perform library preparations, target capture, sequencing, and analysis for any application.

All myBaits kits are for research-use only, and are not validated for diagnostic or therapeutic purposes.

Services

End-to-End Solutions for Your Next NGS Project

Daicel Arbor Biosciences operates a full-services NGS laboratory that can handle any scale project for custom targeted sequencing or whole genome or whole transcriptome sequencing. We have processed thousands of DNA and RNA samples with an extremely high success rate, even for difficult and challenging samples. We can develop a new custom kit specifically tuned to your exact research targets of interest, or utilize one of our recommended predesigned baitsets for rapid processing.

In addition, our in-house team can now work directly with you to provide cloud-based and bespoke bioinformatics solutions. With years of NGS experience across a wide variety of applications, we can develop a custom solution to fit your expertise and research needs.

Publications

Featured Publications

The featured publications listed below correspond to the collection of Community Panels highlighted in the Overview tab. For hundreds more examples of published papers that utilize myBaits Custom and Expert kits, please visit our dedicated Publications page. Daicel Arbor Biosciences thanks these authors for sharing their probe designs for the benefit of the wider research community!

Beaudry, M.S., J.C. Thomas, R.P. Baptista, A.H. Sullivan, W. Norfolk, A. Devault, J. Enk, T.J. Kieran, O.E. Rhodes, Jr., K.A. Perry-Dow, L.J. Rose, N.J. Bayona-Vásquez, A. Oladeinde, E.K. Lipp, S. Sanchez, T.C. Glenn. (2021). Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture. Environmental Microbiology, 23: 7523-7537
Colson, P., C. Dhiver, C. Tamalet, J. Delerce, O.O. Glazunova, M. Gaudin, A. Levasseur, D. Raoult. (2020). Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection. Scientific Reports 10, 2548
Forth, J.H., L.F. Forth, J. King, O. Groza, A. Hübner, A.S. Olesen, D. Höper, L.K. Dixon, C.L. Netherton, T.B. Rasmussen, S. Blome, A. Pohlmann, M. Beer. (2019). A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses. 2019; 11(9):846
Guitor, A.K., A.R. Raphenya, J. Klunk, M. Kuch, B. Alcock, M.G. Surette, A.G. McArthur, H.N. Poinar, G.D. Wright. (2019). Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy 64(1): e01324-19
Furtwängler, A., J. Neukamm, L. Böhme, E. Reiter, M. Vollstedt, N. Arora, P. Singh, S.T. Cole, S. Knauf, S. Calvignac-Spencer, B. Krause-Kyora, J. Krause, V.J. Schuenemann, A. Herbig. (2020). Comparison of target enrichment strategies for ancient pathogen DNA. BioTechniques 2020 69:6, 455-459
Knauf, S., J.F. Gogarten, V.J. Schuenemann, H.M. De Nys, A. Düx, M. Strouhal, L. Mikalová, K.I. Bos, R. Armstrong, E.K. Batamuzi, I.S. Chuma, B. Davoust, G. Diatta, R.D. Fyumagwa, R.R. Kazwala, J.D. Keyyu, I.A.V. Lejora, A. Levasseur, H. Liu, M.A. Mayhew, O. Mediannikov, D. Raoult, R.M. Wittig, C. Roos, F.H. Leendertz, D. Šmajs, K. Nieselt, J. Krause, S. Calvignac-Spencer. (2018.) Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue. Emerging Microbes & Infections 7:1, 1-4
Ross, Z.P., J. Klunk, G. Fornaciari, V. Giuffra, S. Duchêne, A.T. Duggan, D. Poinar, M.W. Douglas, J-S. Eden, E.C. Holmes, H.N. Poinar. (2018). The paradox of HBV evolution as revealed from a 16th century mummy. PLOS Pathogens 14(1): e1006750
Shipley, M.M., M.M. Rathbun, M.L. Szpara. (2020). Oligonucleotide Enrichment of HSV-1 Genomic DNA from Clinical Specimens for Use in High-Throughput Sequencing. Herpes Simplex Virus – Methods in Molecular Biology Book Series.

Contact

Daicel Arbor Biosciences
5840 Interface Dr. Suite 101,
Ann Arbor, MI 48103

1.734.998.0751