Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies
Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.
Authors
- Se Jin Song (ORCID: https://orcid.org/0000-0003-0750-5709)
- MacKenzie Bryant (ORCID: https://orcid.org/0000-0003-0749-2995)
- Rodolfo A. Salido (ORCID: https://orcid.org/0000-0003-0631-2817)
- Daniel T. McDonald (ORCID: https://orcid.org/0000-0003-0876-9060)
- Antonio López González (ORCID: https://orcid.org/0000-0002-5801-6561)
- Celeste Allaband (ORCID: https://orcid.org/0000-0003-1832-4858)
- Rob Knight (ORCID: https://orcid.org/0000-0002-0975-9019)
- Caitriona Brennan (ORCID: https://orcid.org/0000-0003-3943-6701)
- Pedro Belda‐Ferre (ORCID: https://orcid.org/0000-0001-6532-1161)
- Gail Ackermann (ORCID: https://orcid.org/0000-0002-3901-4931)
- Pieter C. Dorrestein (ORCID: https://orcid.org/0000-0002-3003-1030)
- Vincent Charron‐Lamoureux (ORCID: https://orcid.org/0000-0001-9440-7036)
- Kalen Cantrell (ORCID: https://orcid.org/0000-0002-6262-1668)
- Simone Zuffa (ORCID: https://orcid.org/0000-0001-7237-3402)
- Gillian Wright (ORCID: https://orcid.org/0000-0003-2183-711X)
- Ipsita Mohanty (ORCID: https://orcid.org/0000-0001-9194-5795)
- Madison Ambre
- Tara Boyer
Institutions
- University of California San Diego (US)
- University of Montana (US)
Publication Details
- Journal
- mSystems
- Published
- 2024-09-16
- DOI
- https://doi.org/10.1128/msystems.00985-24
- Citations
- 15
- Primary Topic
- Ethics in Clinical Research
- Type
- article
- Field-Weighted Citation Impact
- 8.14
Funders
- National Institutes of Health