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Curd EE, Gal L, Gallego R, Silliman K, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2024; 6:e489. [PMID: 38370872 PMCID: PMC10871694 DOI: 10.1002/edn3.489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/19/2023] [Indexed: 02/20/2024]
Abstract
The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of both DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa then are currently curated by professional staff. Thus there is a growing need for an easy to implement computational tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R which, like it's predecessor, relies on sequence homology and PCR primer compatibility instead of keyword-searches to avoid limitations of user-defined metadata. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire a set of sequences analogous to PCR products containing a user-defined set of primer sequences. Next, these seeds are used to iteratively blast search seed sequences against a local copy of the National Center for Biotechnology Information (NCBI) formatted nt database using a taxonomic-rank based stratified random sampling approach ( blast_seeds() ). This results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer-specific reference barcode sequences from NCBI. Databases can then be compared (compare_db()) to determine read and taxonomic overlap. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, fungal ITS, and Leray CO1 loci than CRABS, MetaCurator, RESCRIPt, and ecoPCR reference databases. We then further demonstrate the utility of rCRUX by generating 24 reference databases for 20 metabarcoding loci, many of which lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Katherine Silliman
- Northern Gulf Institute, Mississippi State University, Starkville, MS, USA
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, USA
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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Curd EE, Gal L, Gallego R, Nielsen S, Gold Z. rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543005. [PMID: 37397980 PMCID: PMC10312559 DOI: 10.1101/2023.05.31.543005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given the large and continuously growing volumes of DNA sequence data and novel reference barcode targets. Monitoring and research applications require a greater diversity of specialized gene regions and targeted taxa to meet taxonomic classification goals then are currently curated by professional staff. Thus, there is a growing need for an easy to implement tool that can generate comprehensive metabarcoding reference libraries for any bespoke locus. We address this need by reimagining CRUX from the Anacapa Toolkit and present the rCRUX package in R. The typical workflow involves searching for plausible seed amplicons (get_seeds_local() or get_seeds_remote()) by simulating in silico PCR to acquire seed sequences containing a user-defined primer set. Next these seeds are used to iteratively blast search seed sequences against a local NCBI formatted database using a taxonomic rank based stratified random sampling approach (blast_seeds()) that results in a comprehensive set of sequence matches. This database is dereplicated and cleaned (derep_and_clean_db()) by identifying identical reference sequences and collapsing the taxonomic path to the lowest taxonomic agreement across all matching reads. This results in a curated, comprehensive database of primer specific reference barcode sequences from NCBI. We demonstrate that rCRUX provides more comprehensive reference databases for the MiFish Universal Teleost 12S, Taberlet trnl, and fungal ITS locus than CRABS, METACURATOR, RESCRIPt, and ECOPCR reference databases. We then further demonstrate the utility of rCRUX by generating 16 reference databases for metabarcoding loci that lack dedicated reference database curation efforts. The rCRUX package provides a simple to use tool for the generation of curated, comprehensive reference databases for user-defined loci, facilitating accurate and effective taxonomic classification of metabarcoding and DNA sequence efforts broadly.
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Affiliation(s)
- Emily E. Curd
- Vermont Biomedical Research Network, University of Vermont, VT, USA
| | - Luna Gal
- Landmark College, VT, USA
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Ramon Gallego
- Universidad Autónoma de Madrid - Unidad de Genética, Spain
| | | | - Zachary Gold
- California Cooperative Oceanic Fisheries Investigations (CalCOFI), Scripps Institution of Oceanography, University of California San Diego (UCSD), La Jolla, CA, USA
- NOAA Pacific Marine Environmental Laboratory, Seattle, WA, USA
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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Narum S, News JK, Fountain-Jones N, Hooper Junior R, Ortiz-Barrientos D, O'Boyle B, Sibbett B. Editorial 2022. Mol Ecol Resour 2021; 22:1-8. [PMID: 34919782 DOI: 10.1111/1755-0998.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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