Precision Microbiome Engineering Research

PreMiEr Spring 2024 Seminar Series - Dr. Karthik Anantharaman
2024-02-15 12:00 - 13:00 (America/New_York)
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host institution The University of North Carolina at Charlotte for a talk from Dr. Karthik Anantharaman of the University of Wisconsin – Madison.
(Re)defining the roles of phage in microbiomes
Viruses that infect microbes (typically referred to as bacteriophages, or phages) are amongst the most abundant biological entities in all ecosystems. By infecting and lysing microbial populations, phages can affect community composition and function which can directly impact ecosystems, biogeochemistry, and human health and disease. Increasing use of sequencing approaches such as metagenomics has allowed the generation of massive quantities of ‘viral dark matter’ from microbiomes, which refers to viruses, viral genomes, and proteins which are poorly characterized. In this talk, I will present novel techniques developed in our laboratory including the use of machine and deep learning approaches to study phage ecology in microbiomes. Our approaches allow for the study of phage at multiple resolutions and enable prediction of phage-microbe metabolic interactions at the scale of entire communities in human and environmental systems. Overall, these approaches have diverse applications ranging from engineering viruses, microbiomes, and ecosystems, to phage therapy.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Spring 2024 Seminar Series - Dr. Nathan Crook
2024-02-01 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) for a seminar by Dr. Nathan Crook of North Carolina State University.
Accelerated Engineering of Nonmodel Microbes
Microbial communities are present in a diverse range of important habitats, including the built environment, the human gut, and the plant root. In these environments, microbial communities utilize available nutrients and produce molecules that have important impacts on their surroundings. Unfortunately, many of the mechanisms that underlie these important behaviors remain mysterious, which limits our ability to modify these communities when something goes wrong, or to enhance the performance of the environment they inhabit. Genetic modification, such as knockout, knock-down, or overexpression greatly facilitates the elucidation of these mechanisms, but this ability is absent in the majority of bacteria living in important microbial communities. In this talk, I will discuss the Crook Lab’s recent efforts to enable genetic engineering in nonmodel bacteria. I will first describe a cell-free approach to “disguise” incoming foreign DNA and its application to intractable gut commensals. Then, I will discuss the development of a genetic toolkit for engineering the maize root microbiome. Finally, I will introduce our new efforts to engineer and study built-environment-derived Enterobacter ludwigii.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Scholar Research-in-Progress Discussions - Limited to PreMiEr Members only
2024-01-25 12:00 - 13:00
PreMiEr scholars actively involved in research share their data, findings, and problems with other members of PreMiEr.

PreMiEr Scholars Leadership Council (SLC) Meeting
2024-01-19 10:00 - 11:00
All PreMiEr scholars (undergraduates, graduate students, post-docs, and research staff) are invited and encouraged to join the next meeting of the SLC.
Please check your email from an invitation from the SLC Chair, Jorden Rabasco, for the Zoom link.

PreMiEr Spring 2024 Seminar Series - Drs. Connie Syharat, Arash Zaghi, and Marisa Chrysochoou
2024-01-18 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host institution Duke University for a talk from Drs. Connie Syharat, Arash Zaghi, and Marisa Chrysochoou of the University of Connecticut.
Reframing Neurodiversity in Higher Education
A growing body of literature suggests that neurodiverse learners may possess assets that are highly desirable within STEM disciplines. Even so, despite the potential of neurodiverse individuals to contribute to innovation, neurodiverse students, such as those with attention deficit hyperactivity disorder (ADHD), autism, or dyslexia, remain highly underrepresented in STEM majors, and in higher education overall. This talk will argue that the predominant perception of neurodiversity as a disability limits the participation of neurodiverse students in higher education, ultimately impacting the diversity and creativity of the workforce. Instead, a strengths-based perspective of neurodiversity will be presented that may be integrated within STEM education in particular, as well as in higher education overall, as we present our vision for a transformative education system that moves beyond mere accommodation of learning differences and empowers all students to leverage their unique strengths.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr SLC December Meeting
2023-12-18 13:00 - 14:00
All students, post-docs, and research staff affiliated with PreMiEr are invited and encouraged to join the next meeting of the ERC’s Scholars Leadership Council. Please check your email for an invitation from Chair, Jorden Rabasco, for the link.

CFCI/PreMiEr Accelerator Pitch Day - Final Presentations
2023-12-07 16:00 - 17:30
PreMiEr Members are invited to join Innovation Ecosystem director Dr. Ibrahim Mohedas and the Christensen Family Center for Innovation at Duke University for the final presentation of the participants of the inaugural CFCI/PreMiEr Accelerator Workshop.
Five teams of scholars and faculty mentors have been working to develop an idea into a product and this event is their final presentation. All members of the ERC are invited and encouraged to attend. Please see your email or PreMiEr Weekly Newsletter for details of the Zoom meeting.

PreMiEr DEI Book Club: Racism, Not Race | Ch. 11 - Conclusions
2023-11-28 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, November 28th, we will discuss Chapter 11 & Conclusions.

PreMiEr Seminar Series: Drs. Cynthia Gibas and Jessica Schlueter
2023-11-16 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Charlotte.
Speakers: Drs. Cynthia Gibas, Professor, and Jessica Schlueter, Associate Professor of Bioinformatics and Genomics
Adventures in Wastewater Monitoring
Wastewater surveillance has become an established part of US public health infrastructure via the National Wastewater Surveillance System and its network of collection sites in all 50 states. Wastewater based epidemiology has become a powerful tool for public health to monitor circulating and emerging viral variants. As a medium, wastewater is a complex mixed matrix, making the deconvolution of wastewater samples more difficult as there is a scarcity of benchmarked tools for metagenomic samples. We have created a gold-standard dataset constructed from synthetic viral controls spiked into a wastewater RNA matrix and sequenced on the Oxford Nanopore Technologies platform. We compare the performance of seven of the most commonly used deconvolution tools in identifying SARS-CoV-2 variants present in these mixtures. But there’s more to find in wastewater than just viruses and bacteria. Protein biomarkers of exposure and infection are accessible via fecal samples, and we have recently demonstrated that specific human antibodies can be detected in community wastewater. This assay has the potential to provide population-level data about the susceptibility component of the epidemiological SEIR model at a much lower cost than traditional serology.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 11 - Conclusions
2023-11-14 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, November 14th, we will discuss Chapter 11 & Conclusions.

PreMiEr Seminar Series: Andrew Hardwick
2023-11-09 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina State University.
Speaker: Andrew Hardwick, Graduate Student and PreMiEr Scholar
Ghosts in The Built Environment – Evaluating the Use of Socially Defined Variables in Microbiome Research
Halloween may have passed, but ghosts still linger. Ghost variables are cases where socially defined variables like race and sex/gender are improperly used to study and create narratives about socially defined groups. The narratives people use matter with stories having the power to shape the development of future healthcare policy and scientific funding. This research project evaluates the use of different socially defined variables correctly and incorrectly in the context of the built environment to map out their prevalence in a network that spans academia, funding agencies, and the news. This talk will focus on the methods developed to systematically study the use of ghost variables in the built environment and some preliminary results so far.
Click here to register!

PreMiEr Seminar Series: Dr. Nicole Rockey
2023-11-02 12:00 - 13:00
PreMiEr-sponsored seminar hosted by Duke University.
Speaker: Nicole Rockey, Assistant Professor, Pratt School of Engineering
Virus persistence and treatment – implications for infectious disease transmission in the built environment
Infectious diseases from emerging and endemic pathogens continue to cause significant morbidity and mortality worldwide. Recent global changes, including urbanization, climate change, and population growth, have altered the infectious disease landscape. These changes increase disease spread and risk of viral emergence. My research seeks to better understand risks from viral pathogens and identify effective strategies to limit their spread in the built environment. In this talk, I will discuss work investigating alternative molecular and predictive modeling approaches for estimating virus fate through disinfection and developing virus monitoring strategies in water treatment settings. I will also highlight research employing animal models to assess influenza virus transmission and controlled bench-scale approaches to study the persistence and spread of respiratory viruses. This work ultimately assesses the impact of engineering interventions (e.g., ventilation) on influenza virus transmission in close-contact scenarios. Overarching aims of our work are focused on establishing transmission risks in the built environment and informing engineering interventions that will aid in building robust, sustainable responses to microbial threats.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 9 - 10
2023-10-31 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 31st, we will discuss Chapters 9 & 10.

PreMiEr Seminar Series: Dr. Alex McCumber
2023-10-26 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Chapel Hill.
Speaker: Alex McCumber, Postdoctoral Research Associate
Abstract: Evaluation of Sink Bioaerosols
Sinks are ubiquitous in modern buildings and serve an important role in reducing the transmission of diseases via hand washing. In settings where someone may encounter at risk individuals, such as hospitals, sinks are placed in nearly every room to ensure proper hand hygiene adherence. However, the p-traps beneath sinks are well documented to harbor multidrug resistant pathogens and operate as a source of bioaerosol emissions and exposure to a highly vulnerable patient population. In 2023, the Centers for Disease Control and Prevention published a weekly report describing an outbreak of Carbapenemase-Producing Carbapenem-Resistant Pseudomonas aeruginosa infections that were traced to the p-trap in the hospital room. Due to the continued risk between sink bioaerosols and infections in high-risk settings, factors that affect bioaerosol generation, fate, and transport warrant further exploration. This project is designed to take initial steps towards answering these questions and provide standardized techniques for future projects within the Center. The overarching goal of this project is to quantify the risk associated with sink bioaerosols and identify engineering or microbiological based controls that ameliorate or eliminate bioaerosol threats. Experiments are accompanied by modeling to aid prediction and identification of engineering solutions to manage p-trap bioaerosol generation. Possibilities include changes to the geometry of the sink or trap, as well as microbiological-based controls such as p-trap probiotics that mitigate the proliferation of harmful p-trap bacteria.
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PreMiEr DEI Book Club: Racism, Not Race | Ch. 7 - 8
2023-10-17 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 17th, we will discuss Chapters 7 & 8.

PreMiEr Seminar Series: Dr. Dongyang (Sunny) Deng
2023-10-12 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina North Carolina Agricultural and Technical State University.
Speaker: Dongyang (Sunny) Deng, Associate Professor, College of Science and Technology
Assessment of Health and Safety Hazards in African American Low-Income Communities of Greensboro
The research project, based in low-income areas of Greensboro, presents a detailed protocol aimed at understanding the correlation between housing conditions and health. Through meticulous sampling procedures, the study evaluates the health status of selected housing units by measuring factors such as temperature, humidity, carbon dioxide levels, metal particulates, dust, and other air contaminants. This comprehensive approach not only seeks to provide empirical data on living conditions but also incorporates educational interventions. The ultimate goal is to enhance the living environment, ensuring it is both safer and healthier for residents.
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PreMiEr Seminar Series: Dr. Anthony Fodor
2023-10-05 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Charlotte.
Speaker: Anthony Fodor, Professor, College of Computing & Informatics, PreMiEr Associate Director
Adventures with the Poisson distribution: on simplicity and reproducibility in microbial analyses
Abstract
In this talk, we explore ways in which simple algorithms can sometimes outperform more complex ones in metagenomics pipelines. We present recent results where straight-forward classical statistical approaches to differential analysis can out-perform more recently developed negative-binomial based methods. We show that data normalizations based on simple or “naïve” proportions can have some attractive properties when compared to more sophisticated, but more complex, compositionally aware transformations. And we explore how one-parameter models based on the Poisson distribution can provide reasonable null error models for 16S-based ASVs and WGS approaches to taxonomic classification. As recent controversies highlight, analysis of metagenomic data can often get bogged down in complexity. Adopting simpler methods where possible has the potential to yield more easily interpretable results that are less likely to be the result of arbitrary choices made in data analysis pipelines.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 5 - 6
2023-10-03 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 3rd, we will discuss Chapters 5 & 6.

PreMiEr Seminar Series: Dr. Benjamin Callahan
2023-09-28 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina State University.
Speaker: Benjamin Callahan, Associate Professor, College of Veterinary Medicine
Topic: Microbiome or not? Measuring low biomass environments in placentas, feline bile, and cancer.
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PreMiEr Seminar Series: Dr. Karis Boyd-Sinkler
2023-09-21 12:00 - 13:00
PreMiEr-sponsored seminar hosted by Duke University.
Speaker: Karis Boyd-Sinkler, Director of Diversity, Equity, & Inclusion and Adjunct Assistant Professor at Duke University’s Pratt School of Engineering
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 3 - 4
2023-09-19 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, September 19th, we will discuss Chapters 3 & 4.

PreMiEr Seminar Series: Dr. Jill Stewart
2023-09-14 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Chapel Hill.
Speaker: Jill Stewart, Philip C. Singer Distinguished Professor, Department of Environmental Sciences and Engineering
Seminar Abstract: Environmental Antimicrobial Resistance (AMR) in the Built Environment
Antimicrobial resistance is an increasing threat to public health and modern medicine. Clinical cases of antimicrobial resistance are on the rise. However, the environmental dimensions of resistance remain poorly understood. Building on previous research to understand the evolution and ecology of resistance, we aim to develop tools and recommendations for antibiotic resistance in the built environment where humans spend most their time. Specifically, we aim to (1) establish reproducible methods to identify and prioritize antibiotic resistance genes and their biological meaning in the built environment; (2) expand sampling of key indicators and signatures to study the evolutionary ecology of resistance in these systems; and (3) evaluate the critical ability of resistance to move among humans, animals, and the built environment and potential risks to human health. We seek to work collaboratively with other PreMiEr Center projects, including sharing samples and methodological insights. Together this work will advance capabilities to study environmental dimensions of antimicrobial resistance and will contribute knowledge, recommendations, and products to advance the global fight against resistant infections.
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PreMiEr Seminar Series: Dr. Misty Thomas
2023-09-07 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina Agricultural and Technical State University.
Speaker: Misty Thomas, Associate Professor of Biology
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Intro - Ch. 2
2023-09-05 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, September 5th, we will discuss the Introduction through Chapter 2.

PreMiEr Scholars Leadership Council (SLC) Monthly Meeting
2023-08-30 12:00 - 13:00
SLC leadership invites all scholars associated with PreMiEr to attend a meeting to discuss issues related to students, post-docs, and research staff, and to learn about opportunities and initiatives within the center.
Please check your emails for the Zoom meeting link

Summer Research Experiences for Undergraduates (REU) Poster Presentations
2023-07-27 10:00 - 12:30
Please join us through the Zoom link provided in emails and the PreMiEr Newsletter for the final poster presentations of our inaugural class of REU participants!

PreMiEr REU & RET Lunch & Learn
2023-07-18 12:00 - 13:00, 2023-07-11 12:00 - 13:00
All members of PreMiEr are welcome! Check your email for details.

Scholars Leadership Council Meeting
2023-07-12 14:00 - 15:00
Meeting for scholars associated with PreMiEr, including undergraduate students, graduate students, post-docs, research staff, and lab managers.
ERC-funded scholars and SLC leadership are required to attend.
Other PreMiEr-associated scholars are welcome to attend.
Please see your email invitation from the SLC Chair, Ivory Blakley, for the Zoom link.

PreMiEr Innovation Bootcamp
2023-06-01 09:00 - 17:00
William (Bill) Walker, PreMiEr’s Innovation Ecosystem Director will be leading an Innovation Bootcamp on June 1, 2023 from 9:00 AM to 5:00 PM ET.
