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Bioscience

Microbial measurements

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Displaying 1 - 25 of 68

Beyond Sequence Similarity: The Case for Function-Based Screening of Nucleic Acid Synthesis

May 13, 2026
Author(s)
Gary Able, Tessa Alexanian, Jacob Beal, James Diggans, Kevin Flyangolts, Gene D. Godbold, Eric Horvitz, Bin Hu, Caitlin Jagla, Rassin Lababidi, Brittany Rife Magalis, Sebastian Rivera, Bruce Wittmann, Samuel Forry, David Ross, Sheng Lin-Gibson, Samuel Curtis
Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm identifies sequences of concern (SoCs) through sequence

The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples

April 16, 2026
Author(s)
Sandra Da Silva, Nancy Lin, Kirsten Parratt, Hariharan Iyer, Guilherme Pinheiro, Holly Hack, Ian Hines, Stephanie Servetas
Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial

A mathematical framework to correct for compositionality in microbiome datasets

January 6, 2026
Author(s)
Samuel Forry, Stephanie Servetas, Jason Kralj, Monique Hunter, Jennifer Dootz
The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease

NIST 2025 Rapid Microbial Testing Methods Workshop Report

September 26, 2025
Author(s)
Jason Kralj, Kirsten Parratt, Tyler Laird, Stephanie Servetas, Nancy Lin, Dawn Henke, Scott Jackson
In 2020, the National Institute of Standards and Technology (NIST)-led Rapid Microbial Testing Methods (RMTM) Consortium was established to develop standards and measurement-based solutions to facilitate the adoption of RMTMs in advanced therapy products

Report from the 2023 NIST-Hosted Workshop on Collaborative Efforts to Enable Adoption of Rapid Microbial Testing Methods for Advanced Therapy Products

September 26, 2025
Author(s)
Stephanie Servetas, Dawn Henke, Jason Kralj, Kirsten Parratt, Scott Jackson, Nancy Lin
On April 25, 2023, the National Institute of Standards and Technology (NIST) hosted a one-day hybrid workshop focused on bringing together organizations and working groups with the common goal of enabling validation and implementation of rapid microbial

NIST 2024 Rapid Microbial Testing Methods Workshop Report

September 25, 2025
Author(s)
Jason Kralj, Nancy Lin, Kirsten Parratt, Stephanie Servetas, Dawn Henke, Scott Jackson
The NIST-led Rapid Microbial Testing Methods (RMTM) Consortium launched in 2020 to develop standards and measurement-based solutions to advance the use of RMTMs in advanced therapy products. NIST hosted 4th annual workshop on RMTMs to update the community

Measurement quality metrics to improve absolute microbial cell counting

August 18, 2025
Author(s)
Kirsten Parratt, David Newton, Joy Dunkers, Jennifer Dootz, Monique Hunter, Alshae Logan, Laura Pierce, Sumona Sarkar, Stephanie Servetas, Nancy Lin
Total and viable microbial cell counts are increasingly important for applications including live biotherapeutic products, food safety, and probiotics. In microbiology, cells are quantified using methods such as colony forming unit (CFU), flow cytometry

A Sensitivity Analysis of Methodological Variables Associated with Microbiome Measurements

January 14, 2025
Author(s)
Samuel Forry, Stephanie Servetas, Jennifer Dootz, Monique Hunter, Jason Kralj, James Filliben, Scott Jackson
The particular experimental methods employed during metagenomic sequencing analyses of microbiome samples can significantly impact the resulting data but typically vary substantially between laboratories. In this study, a full factorial experimental design

The Application of Digital PCR as a Reference Measurement Procedure to Support the Accuracy of Quality Assurance for Infectious Disease Molecular Diagnostic Testing

December 26, 2024
Author(s)
Samreen Falak, Denise O'Sullivan, Megan Cleveland, Simon Cowen, Eloise Busby, Alison Devonshire, Esmeralda Valiente, Gerwyn Jones, Martin Kammel, Mojca Milavec, Laura Vierbaum, Ingo Schellenberg, Heinz Zeichhardt, Andreas Kummrow, Peter Vallone, Rainer Macdonald, Jim Huggett
Background Nucleic Acid Amplification Tests (NAATs) are used to diagnose many infectious diseases. They are typically sensitive and specific and can be quickly developed and adapted. It is more challenging to develop standards to ensure NAATs perform

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

November 8, 2024
Author(s)
Mak Saito, Jaclyn Saunders, Matthew McIlvin, Erin Bertrand, John Breier, Margaret Brisbin, Sophie Colston, Jaimee Compton, Tim Griffin, Judson Harvey, Robert Hettich, Pratik Jagtap, Michael Janech, Rod Johnson, Rick Keil, Hugo Kleikamp, Dasha Leary, Scott McCain, Eli Moore, Subina Mehta, Dawn Moran, Jacqui Neibauer, Benjamin Neely, Michael Jakuba, Jim Johnson, Megan Duffy, Gerhard Herndl, Richard Giannone, Ryan Mueller, Brook Nunn, Martin Pabst, Samantha Peters, Andrew Rajczewski, Elden Rowland, Brian Searle, Tim Van Den Bossche, Gary Vora, Jacob Waldbauer, Haiyan Zheng, Zihao Zhao
Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory

Optimizing Wastewater Surveillance: The Necessity of Standardized Reporting and Proficiency for Public Health

August 7, 2024
Author(s)
Ishi Keenum, Nancy Lin, Alshae Logan, Adam Gushgari, Nishita D'Souza4, Joshua Steele, Devrim Kaya, Lydia Gushgari
Wastewater-based surveillance (WBS) has emerged as a valuable tool for public health, allowing a greater understanding of disease prevalence in communities. With historical significance in monitoring polio transmission,1 WBS gained further prominence in

The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)

August 7, 2023
Author(s)
Pratik Jagtap, Michael Hoopmann, Ben Neely, Anthony Harvey, Lukas Kall, Yasset Perez-Riverol, Milky Abajorga, Julie Thomas, Susan Weintraub, Magnus Palmblad
Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation

Report from the NIST Workshop: Launch of the Rapid Microbial Testing Methods Consortium

September 27, 2022
Author(s)
Nancy Lin, Scott Jackson, Stephanie Servetas, Kirsten Parratt, Joy Dunkers, Tara Eskandari, Sheng Lin-Gibson
On September 17, 2020, NIST hosted a virtual workshop to launch the Rapid Microbial Testing Methods (RMTM) Consortium. The RMTM Consortium aims to address the need for measurements and standards to increase confidence in the use of rapid testing for

Enhancing untargeted metabolomics using metadata-based source annotation

July 7, 2022
Author(s)
Scott Jackson, Paulina Piotrowski, Nancy Lin, Sandra M. Da Silva, Katrice Lippa, Christina Jones, Stephanie Servetas, Julia Gauglitz, Kiana West, Wout Bittremieux, Candace Williams, Kelly Weldon, Morgan Panitchpakdi, Francesca Ottavio, Christine Aceves, Elizabeth Brown, Nicole Sikora, Alan Jarmusch, Cameron Martino, Pieter Dorrestein, Rob Knight, Rachel Dutton, Austin Swafford, Monica Guma, Norberto Peporine Lopes, Brigid Boland, Michelli Oliveira, Mark Manary, Maria Gloria Dominguez-Bello, Kenneth Wright, Julia Beauchamp-Walters, Kyung Rhee, Jae Kim, Megan Doty, Robert Terkeltaub, David Gonzalez, Curt Wittenberg, Tatyana Kalashnikova, Parambir Dulai, Douglas Galasko, Rima Kaddurah Daouk, Robert Mills, Paulo Louzada-Junior, Rene Donizeti Ribeiro Oliveira, Thaigo Mattar Cunha, Flavio Protaso Veras, Rodrigo Moreira Silva, Juliano Geraldo Amaral, Lucas Maciel Mauriz Marques, Barry Bradford, Lourdes Herrera, Gail Ackermann, Dana Withrow, Daniela Vargas Robles, Kate Sprecher, Clarisse Marotz, Mingxun Wang, Emmanuel Elijah, Dominic Nguyen, Qiyun Zhu, Daniel McDonald, Edgar Diaz, Pedro Belda-Ferre, Katharina Spengler, Abigail Johnson, Gregory Humphrey, MacKenzie Bryant, Tara Schwartz, Lindsay Goldasich, Fernando Vargas, Roxana Coras, Justin Schaffer, Erfan Sayyari, Kathleen Dorrestein, Michael Meehan, Anupriya Tripathi
Human untargeted metabolomics studies annotate only 10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference

Reference Material 8376 Microbial Pathogen DNA Standards for Detection and Identification

June 1, 2022
Author(s)
Jason Kralj, Dieter Tourlousse, Monique Hunter, Erica Romsos, Blaza Toman, Peter Vallone, Scott Jackson
Reference Material (RM) 8376 is intended for NGS-based measurements quantitative to the chromosome. A unit of RM 8376 consists of 20 components (A-T, 19 bacteria and 1 human) each containing well-characterized DNA in 10 mmol/L Tris-HCl, 1 mmol/L EDTA pH 8

Federal Research Priorities to Support Wastewater Surveillance for SARS-CoV-2

March 30, 2022
Author(s)

Sally Gutierrez, Nancy Lin, Jessica Sweeney

Almost immediately after the start of the COVID-19 pandemic in 2020, researchers and wastewater utilities around the world began analyzing untreated wastewater for the SARS-CoV-2 RNA. These efforts were largely based on prior experience analyzing
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