phd research in bacterial

College of Liberal Arts & Sciences

School of Molecular & Cellular Biology

• Meet the MCB Community
• Instruction & Advising
• MCB Academic Departments
• Supporting Offices & Resources
• Health & Wellbeing Resources
• Job Opportunities in MCB
• Undergraduate Admissions
• Master's Program Admissions
• PhD Program Admissions
• Major in MCB
• Major in Neuroscience
• Major in Biochemistry
• Pre-med & pre-health guide
• Master's Program
• Prospective students
• Current students
• School of MCB Convocation
• Biochemistry
• Cell & Developmental Biology
• Microbiology
• Molecular & Integrative Physiology
• Explore Research in MCB
• Research Collaborations & Partners
• Undergraduate Research
• Research Facilities & Resources
• In the News
• Seminars and Events
• Graduate Research Retreat
• Awards and Honors
• In Memoriam
• Media contacts in MCB
• MCB Convocation
• Diversity, Equity & Inclusion in MCB
• MCB DEI Committee
• Campus Diversity Offices and Resources
• Alumni & Friends Community
• Mentorship Program
• Share Your News & Update Contact Info
• Giving opportunities
• Make an Online Gift
• School Leadership & Support Staff
• Advising & Instruction Team
• All MCB Faculty

Department of Microbiology

Pursue a PhD in Microbiology

Microbes are the dominant organisms on the planet and drive all aspects of life. The Department of Microbiology is a close-knit group of creative, bold, and passionate scientists who are addressing some of the toughest challenges facing our world through discoveries in bacterial and archaeal biology and physiology, bacterial and viral pathogenesis, antibiotic discovery, and microbial ecology and evolution. We are a collaborative, supportive, and active community with many opportunities for connecting with other scholars in the department, school, and across campus.

With a PhD in Microbiology, you can launch a career in academia, industry, or government.   Our graduates can be found around the world, leading research programs at companies such as Abbvie and Eli Lilly and directing labs at top universities, research institutes, and government agencies.

Request information   Program overview   Apply   Current PhD students

Title Hear more from our students

Stefanie Eben, a PhD candidate in the Department of Microbiology, shares how she fell in love with microbiology and how her graduate studies at UIUC have offered the perfect mixture of academic and personal fulfillment.

The PhD Program

Graduate degrees are earned through a combination of graded courses, oral and written examinations, and independent research. We empower students to design a program, in consultation with their advisors, that aligns with their academic background and scientific (or career) goals. Because the department is part of an umbrella PhD program in MCB, students admitted into any of these departmental graduate programs can select faculty thesis advisors from over 65 research laboratories in the school. Close ties are also maintained with the School of Integrative Biology, the School of Chemical Sciences, the Carle Illinois College of Medicine, the College of Veterinary Medicine, and the Microbial Systems Initiative.

Our department provides a comprehensive training program in microbiology and molecular biology. During your first semester, you will take two core courses designed to provide a strong background in cell physiology, biochemistry (MCB 501), and genetics (MCB 502). Subsequent course work is selected to complement your interests and area of research.

First-year students rotate through three research labs to become acquainted with several labs and to learn new experimental techniques. Each rotation is five weeks long. You can choose rotation laboratories from any department in the School of MCB. Near the end of the fall semester, you will choose a research advisor, and together propose a research project that forms the basis of a dissertation.

In the spring semester of the first year, you will write a short, NIH-style grant proposal on the proposed project and describe it to a faculty committee. The committee makes suggestions regarding project strategy and may recommend areas of basic knowledge that should be explored in greater depth to enhance your success on the project and in the preliminary exam.

At the end of the second year, you will take an oral preliminary exam to test your scientific knowledge and ability to solve research problems. After passing the preliminary exam, you will concentrate on research. It takes approximately five years to complete the PhD program.

Degree requirements ​​​​​  Departmental handbook   Courses

Financial Support

All students admitted to the Ph D program receive financial support throughout their graduate training. Support includes a tuition waiver and a stipend. After the first semester, graduate students are supported by research assistantships, training grants, or teaching assistantships. Graduate students are required to pay the university health fee to cover insurance and health benefits.

The Department of Microbiology is located in the state-of-the-art Chemical and Life Sciences Laboratories (CLSL). Central to main campus, the CLSL houses all of the major equipment and expertise necessary for research in microbiology, cell biology, molecular biology, and biochemistry. Both the School of MCB and campus house a wide array of  research facilities and support services . Faculty collaborate on reseach with partners across campus.

Title Community

The Microbial Early-career Researchers Association ( microERA ), a networking and professional development group for early-career scientists at Illinois, welcomes all undergraduate, graduate students, and postdocs conducting research broadly relevant to microbiome or microbial sciences to join.

The  MCB Graduate Student Association , also known as the MCBees, organizes professional development and social activities as well as outreach events, such as Science on Tap and visits to local schools.

How to Apply

The Department of Microbiology is a part of the School of Molecular & Cellular Biology (MCB), which includes the Departments of Biochemistry, Cell & Developmental Biology, and Molecular & Integrative Physiology.

Students interested in pursuing the PhD in Microbiology should apply directly to the MCB PhD Program  and select "Microbiology" for the field of specialization in the application.

To be considered for admission, you must:

• have a bachelor's degree from an accredited college or university with course work in biological sciences, chemistry, and physics;
• submit three letters of recommendation, including at least two from science professors (if research has been performed, letters of recommendation should include one from the research supervisor);

MCB PhD Programs

Shawna M. Smith, MCB Graduate Program Coordinator Lori Raetzman, Associate Director of MCB Graduate Program [email protected] ; 217-333-1737

Andrei Kuzminov, Professor of Microbiology; Director of Graduate Studies [email protected]

James M. Slauch, Professor and Department Head [email protected] ; 217-244-1956

Diane L. Tsevelekos, Office Support Specialist [email protected] ; 217-333-1736

Microbiology, PHD

On this page:, at a glance: program details.

• Location: Tempe campus
• Second Language Requirement: No

Program Description

Degree Awarded: PHD Microbiology

The PhD program in microbiology offers a dynamic research environment; a broad range of basic, translational and use-inspired research areas; advanced transdisciplinary training; and opportunities to work with world-class faculty and collaborative research partners committed to training scientific leaders with skills necessary for addressing significant global microbiological problems and challenges.

This program focuses on the smallest of living things and immunology. Students can tailor the program around their interests and gain skills in contemporary approaches used in microbiology, biomedicine and biotechnology. They train in a broad array of fields, including microbial ecology and evolution, geomicrobiology, bacterial physiology and genetics, bacterial pathogenesis, metabolic engineering, immunology and vaccine development, and cancer biology.

Faculty members are associated with the School of Life Sciences, The Biodesign Institute, The Translational Genomics Institute, Barrow Neurological Institute, and other area hospitals and research centers.

Interdisciplinary partners within ASU

Participating faculty members and researchers come from many departments, colleges, centers and institutes across the university.

• ASU School of Life Sciences
• ASU Ira A. Fulton Schools of Engineering
• ASU The Biodesign Institute
• ASU School of Sustainable Engineering and the Built Environment
• ASU School for Energy, Material and Transport Engineering

Interdisciplinary parters outside ASU

• St. Joseph’s Hospital and Medical Center/Barrow Neurological Institute
• Carl T. Hayden Veteran's Administration Medical Center
• Mayo Clinic in Arizona
• Translational Genomics Research Institute
• University of Arizona College of Medicine-Phoenix
• Phoenix Children’s Hospital

Program Faculty   PhD Students

Courses and electives

Elective courses (6 - 24 credit hours).

• MIC 791 Seminar: Virology Journal Club
• MIC 598  Special Topics: Immun: Molecular and Cell Foundations
• MIC 598 Special Topics: Advanced Immunology
• MCB 791  Seminar: Molecular Virology Journal Club 
• BIO 611 Topics Resp Conduct Research: Emerging Technologies Life Science
• MIC 598: Immunology: Molecular & Cellular Foundations
• MIC 598: General Virology
• MIC 598: Advanced Immunology
• MIC 598: Bacterial Diversity and Systematics
• MIC 598: Novel Models for Host-Microbe Interactions
• MIC 598: Bioinformatic Analysis of High-throughput DNA Data
• MIC 598: Bacterial Pathogenesis
• MIC 598: Geomicrobiology
• MIC 598: Microbial Ecology and Evolution
• MIC 598: Viromics 

Application and admission information

How to apply.

Applications open September 1 for admission in Fall of the following year. The application deadline is December 1. We accept applications for Fall semesters only. We cannot guarantee that applications received after the December 1 deadline will be considered for admission.

All applicants must apply by filling out ASU's Graduate Admissions application. All application materials must be submitted through the application or to Graduate Admissions directly. Please do not mail or email any documents to the School of Life Sciences. 

• Required materials and information include the following:
• 1-2 page personal statement
• An up to date CV or resume
• The names of relevant SOLS faculty you have been in touch with who you might be interested in being supervised by
• Unofficial transcripts and English proficiency test scores (if applicable)
• The names and emails of at least 3 recommenders to write you letters of recommendation

Application review process and timeline

Following the December 1 deadline, faculty will begin reviewing applications. Applicants should monitor their My ASU priority tasks to ensure there are no missing materials in their application.

Faculty will decide which applicants they would like to invite to our Graduate Recruitment Weekends (GRWs), typically held in February. Applicants will hear from the School of Life Sciences in January if they are invited to participate in the GRWs.

Admission decisions will begin after the GRWs, and applicants typically receive final decisions by April 1.

Requirements

Minimum requirements for admission include the following:

• Cumulative GPA of at least 3.0 on a 4.0 scale
• There are other ways to demonstrate English proficiency beyond the tests, so please refer to ASU's English proficiency webpage to review how you might satisfy requirements

Desired qualifications typically seen in competitive candidates:

• Research experience and a letter of recommendation from a faculty research supervisor
• English proficiency scores that meet these teaching assistant language proficiency requirements

Please note that the GRE is not required.

Students offered admission to a PhD program in the School of Life Sciences will typically receive a funding offer as well. While individual funding offers may differ to some degree, they typically include teaching assistant and/or research assistant positions each semester (summer optional) for 5 years. These positions provide financial coverage through the following:

• A standard salary stipend paid biweekly
• Tuition remission covering enrollment in 6-18 credit hours for fall and spring semesters and 1-14 credit hours for summer semesters
• Health insurance coverage

To discover more, check out the ASU Graduate College's funding opportunities !

Degree Requirements

84 credit hours, a written comprehensive exam, an oral comprehensive exam, a prospectus and a dissertation

Required Core (4 credit hours) BIO 610 Introduction to Responsible Conduct of Research in Life Sciences (1) MIC 501 Foundations in Microbiology (3)

Electives or Research (68 credit hours)

Culminating Experience (12 credit hours) MIC 799 Dissertation (12)

Admission Requirements

Applicants must fulfill the requirements of both the Graduate College and The College of Liberal Arts and Sciences.

Applicants are eligible to apply to the program if they have earned a bachelor's or master's degree in the biological sciences, biochemistry or a closely related field from a regionally accredited institution.

Applicants must have a minimum cumulative GPA of 3.00 (scale is 4.00 = "A") in the last 60 hours of their first bachelor's degree program, or a minimum cumulative GPA of 3.00 (scale is 4.00 = "A") in an applicable master's degree program.

Applicants must submit the following:

• graduate admission application and application fee
• official transcripts
• academic record form
• personal statement
• curriculum vitae or resume
• three letters of recommendation
• proof of English proficiency

Additional Application Information An applicant whose native language is not English must provide proof of English proficiency regardless of their current residency.

Prior research experience is a desired qualification for admission.

Next Steps to attend ASU

Learn about our programs, apply to a program, visit our campus, learning outcomes.

• Able to review the scholarly literature associated with research questions in microbiology.
• Able to design and execute a research plan in an area of microbiology under advisement of their mentors.
• Able to communicate science effectively, both orally and in writing.

Career Opportunities

Graduates of this program's intense and interactive educational and research training are prepared for advanced careers in research and education, specifically in bacteriology, virology, mycology, immunology and oncology.

Career possibilities are diverse, with opportunities in academic organizations, research and development industries, government service and other professional organizations. Examples include:

• instructors in universities and colleges
• principal investigators in government labs and nonprofit organizations
• professors in universities and colleges
• research associates in universities
• research scientists in industry

Program Contact Information

If you have questions related to admission, please click here to request information and an admission specialist will reach out to you directly. For questions regarding faculty or courses, please use the contact information below.

• [email protected]
• 480/965-1768

Course Catalog

Microbiology, PhD

for the degree of Doctor of Philosophy in Microbiology

The requirements for a PhD from the Department of Microbiology include successful completion of course work, teaching, one to two first-author manuscripts in peer-reviewed journals, passing a preliminary examination, and writing and depositing a research thesis.

Graduate Degree Program in Microbiology

The Department of Microbiology at Illinois offers unique opportunities for graduate students to become skilled and creative microbiologists. Our graduate program of study leads to the doctor of philosophy degree (PhD.) We have outstanding resources in our internationally recognized faculty, graduate students, and research facilities. This exposes our students to the latest research techniques and fosters their development as independent scientists. The program has particular strengths in the areas of microbial physiology, metabolism, genetics, evolution, and pathogenesis. For an application and departmental materials that provide greater detail on programs, offerings, admission, degree requirements, and financial aid, visit our website .

Graduates from the Department of Microbiology are employed in colleges and universities, industry, and government. Scientific advances in genetic engineering and biotechnology provide many opportunities in pharmaceutical, chemical, and genetic engineering companies.

The Department of Microbiology is a part of the School of Molecular and Cellular Biology (MCB), which also includes the Departments of Biochemistry, Cell and Developmental Biology, and Molecular and Integrative Physiology. The Department is part of an umbrella program in MCB that encompasses over 70 different research laboratories. Students admitted into any of these departmental graduate programs can select faculty thesis advisors from these active research laboratories in the School. Close ties are also maintained with the School of Integrative Biology, the School of Chemical Sciences, the Carle Illinois College of Medicine, and the College of Veterinary Medicine.

Admission Applicants interested in the Microbiology PhD program will need to apply directly to the School of Molecular and Cellular Biology (MCB) PhD program .  The MCB PhD program is an umbrella program that requires admitted students to spend their first semester rotating among three different labs to explore their interests before joining one of our four departments.

MCB Admission requirements include a bachelor’s degree in biological or physical sciences, a grade point average of a 3.0 or higher (A = 4.0), prior research experience and three letters of recommendation from individuals who can attest to the applicant’s academic and research background. The Graduate Record Examination (GRE) is not required. Applicants interested in pursuing a PhD in Microbiology should have a total of at least 15 credit hours of physical or biology sciences, including general biology, or microbiology, chemistry through organic chemistry and biochemistry, and mathematics through calculus. In addition to these requirements, non-native English speaking applicants must attain a minimum Test of English as a Foreign Language (TOEFL) overall score of 96, with at least a score of 22 on the speaking section. MCB does not accept the International English Language Testing System (IELTS) to show English proficiency. Graduate College requirements also apply.

Graduate Teaching Experience Experience in teaching is considered to be a vital part of the graduate program and is required as part of the academic work of all PhD degree candidates.  For the Department of Microbiology, a minimum of two semesters of teaching experience is a degree requirement.

Faculty Research Interests Major areas of research interest include gene expression and regulation in bacteria, archaea, and eukaryotes; virus pathogenesis and host-cell interactions; viruses of bacteria and archaea; membrane biogenesis; lipid and polysaccharide synthesis in bacteria and yeast; cell wall biogenesis; bacterial pathogenesis and bacteria-host interactions; immunology; DNA replication, recombination, and repair; anaerobic microbiology; the biochemistry and physiology of methane formation; mechanisms of oxygen toxicity; bacterial and archaeal genomics, ecology, and evolution. For further details, please consult the Department of Microbiology's website .

Facilities and Resources The Microbiology Department is located in the modern Chemical and Life Sciences Laboratory (CLSL). Central to main campus, the CLSL houses all of the major equipment and expertise necessary for research in microbiology, cell biology, molecular biology, genomics, and biochemistry.

The University of Illinois has excellent core facilities to aid in scientific research, many of which are located in buildings adjacent to CLSL. Each core facility has full-time salaried support staff for training and support. The Roy J. Carver Biotechnology Center includes core research facilities supporting genomics, proteomics, metabolomics, flow cytometry, bioinformatics and translational medical research.  The Center for Microscopic Imaging is a campus-wide service center for electron, confocal, and light microscopy

Several services are available to graduate students for support outside of the classroom and laboratory. The University of Illinois library is the nation's third largest university library, allowing access to reference books and on-line scientific journals. The Writers Workshop offers free, personal writing assistance for class assignments, scientific manuscripts, and theses. Please visit the School of Molecular and Cellular Biology   to learn about these and other resources available to graduate students.

Financial Aid All students admitted into the PhD program receive financial support throughout their graduate training. Incoming graduate students are supported by the School of Molecular and Cellular Biology. Several University Fellowships are awarded to outstanding applicants on a competitive basis. Financial support is usually in the form of a research assistantship, teaching assistantship, and/or fellowship. In addition to this stipend, we offer a tuition and service fee waiver. A health insurance fee and other miscellaneous fees, must be paid by the student.

The requirements for a PhD from the Department of Microbiology include successful completion of course work, teaching, two first-author manuscripts in peer-reviewed journals, passing a preliminary examination and annual assessments of progress thereafter, and writing and depositing a research thesis.

For specific information, visit the Department's Graduate Student Handbook and the  Graduate College Handbook . 

Other Requirements

Students graduating with a PhD in Microbiology will have:

• Effective oral communication skills that are developed via one or more of the following tasks: group discussions in courses; presentations in departmental seminar courses; discussion of scientific topics in courses; defending their work in a preliminary exam; acting as a teaching assistant for at least 2 semesters; giving yearly student seminars.
• Effective written communication skills that are developed via one or more of the following tasks: writing at least one original, full-length manuscript that has been accepted for publication in a refereed journal; writing a dissertation; writing an NIH-style grant for the preliminary exam.
• A level of competency and research independence commensurate with the degree, such that they can obtain an initial science-related placement in a job that uses critical thinking components.
• Demonstrated ability to organize and execute a research project that uses critical-thinking components and problem-solving expertise, hypothesis-driven, and fills a gap in knowledge.
• Knowledge of the discipline and acquired technical skills in general Microbiology and in their specialized Microbiology research area.

Department of Microbiology Head of Department: James Slauch Directors of Graduate Studies: Andrei Kuzminov, Cari Vanderpool, and Rachel Whitaker Microbiology Department website B103 Chemical and Life Sciences Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801 (217) 333-1736 MCB Graduate Admissions email

College of Liberal Arts & Sciences College of Liberal Arts & Sciences website

School of Molecular & Cellular Biology School of Molecular & Cellular Biology website

Admissions Overview of MCB Admissions Requirements Graduate College Admissions & Requirements

Print Options

Send Page to Printer

Print this page.

Download Page (PDF)

The PDF will include all information unique to this page.

2023-2024 Catalog (PDF)

A copy of the full 2023-2024 catalog.

• Seeking Patient Care?
• Graduate Studies
• Doctoral Programs
• Microbiology and Immunology (Ph.D.)

Microbiology and Immunology

Application process.

Microbiology and Immunology is particularly productive in pre-clinical research and discovery. We are focused on pathogenic bacteria, viruses, and immunology. Our main research themes also focus on developing more effective cancer immunotherapy, an HIV vaccine, creating antigen-specific immune tolerance, and overcoming the antibiotic resistance of bacteria.

Key Areas of Research

• Antibiotic Resistance of Bacteria
• Antigen-specific Immune Tolerance
• Cancer Immunotherapy
• Cellular & Molecular Immunology
• Microbial Genetics
• Pathogenic Bacteriology

Microbiology & Immunology Department

Miami, unfortunately, has a high rate of disease-afflicted individuals, but this gives us the opportunity to study the root causes of these diseases up-close and develop new therapies for the people that most need them. Miami is the right fit for me because of the interdisciplinary culture at many levels: collaborations between labs, other disciplines, and clinicians.  

Engineering Bacteria to Monitor and Treat Disease with Arthur Prindle, PhD

Thanks to advancements in synthetic biology, scientists are now engineering bacterial communities with the goal of using these cells to monitor and treat diseases. In this episode, Arthur Prindle, PhD, explains how his lab is reprogramming bacteria that may be used in the future to detect disease and deliver therapeutics for many different conditions, including cancer, diabetes and inflammatory bowel disease.

“We hope to not only understand bacterial community biology, including the microbiome, but then even potentially re-engineer it or change it in a beneficial way to mitigate human disease or environmental pollution or toxin production.”  

-Arthur Prindle, PhD  

• Assistant Professor of Biochemistry and Molecular Genetics, McCormick School of Engineering    
• Assistant Professor Microbiology-Immunology

Episode Notes 

Through investigative work into biofilm communities, the Prindle Lab at Northwestern is researching the potential of engineered probiotics to detect inflammation in those with Inflammatory Bowel Disease (IBD). It is possible that similar technology could one day deliver therapeutics to these sites of inflammation, and even detect the presence of tumors, as IBD patients are at higher risk for colorectal cancer.   

• Communities of bacteria that live together are often termed biofilms. They exhibit altered behavior compared to free living bacteria, including possible changes in gene expression, metabolism, in the proteins they produce, or the signals they communicate.  
• One of the main biomedical challenges for biofilms is their high degree of antibiotic resistance, a topic of Prindle’s research. His team is also investigating the prospect of engineering probiotic bacteria to sense biomarkers of disease in the human microbiome.  
• IBD is marked by the production of the protein calprotectin, a primary clinical biomarker of IBD. An engineered probiotic could potentially sense the presence of calprotectin as a way of monitoring IBD flares, rather than current clinical procedures which are complex and time-consuming.   
• In current animal models, administered probiotics are monitored by luminescence (where bacteria produce enzymes that emit light). This will likely not work in humans, and instead, would require the use of MRI or ultrasound, which Prindle is investigating.   
• Prindle is also investigating the possibility that, in addition to detecting the presence of inflammation in IBD, could probiotics – already at the site of the flare – also deliver therapeutics.   
• IBD is associated with an increased risk of colorectal cancer. It is possible that probiotics could be engineered to survey for tumor DNA as well.   
• Now approaching the 15 to 20 year anniversary of the start of the field, synthetic biology is thriving at Northwestern, a field enabled by a combination of technologies and a variety of fields not limited to biology alone.   

 Recorded on November 9, 2023. 

Additional Reading  

• Explore Prindle’s lab  
• Read about Prindle’s paper published in the Proceedings of the National Academy of Sciences about an engineered probiotic capable of detecting inflammatory bowel disease.  
• Find out more about Prindle’s Faculty Early Career Development Program award from the National Science Foundation.  

Continuing Medical Education Credit

Physicians who listen to this podcast may claim continuing medical education credit after listening to an episode of this program..

Target Audience

Academic/Research, Multiple specialties

Learning Objectives

At the conclusion of this activity, participants will be able to:

• Identify the research interests and initiatives of Feinberg faculty.
• Discuss new updates in clinical and translational research.

Accreditation Statement

The Northwestern University Feinberg School of Medicine is accredited by the Accreditation Council for Continuing Medical Education (ACCME) to provide continuing medical education for physicians.

Credit Designation Statement

The Northwestern University Feinberg School of Medicine designates this Enduring Material for a maximum of 0.50  AMA PRA Category 1 Credit(s)™.  Physicians should claim only the credit commensurate with the extent of their participation in the activity.

American Board of Surgery Continuous Certification Program

Successful completion of this CME activity enables the learner to earn credit toward the CME requirement(s) of the American Board of Surgery’s Continuous Certification program. It is the CME activity provider's responsibility to submit learner completion information to ACCME for the purpose of granting ABS credit.

All the relevant financial relationships for these individuals have been mitigated.

Disclosure Statement

Arthur Prindle, PhD, has nothing to disclose.  Course director, Robert Rosa, MD, has nothing to disclose. Planning committee member, Erin Spain, has nothing to disclose.  FSM’s CME Leadership, Review Committee, and Staff have no relevant financial relationships with ineligible companies to disclose.

Read the Full Transcript

[00:00:00] Erin Spain, MS: This is Breakthroughs , a podcast from Northwestern University Feinberg School of Medicine. I'm Erin Spain, host of the show. The human body is full of bacterial species, collectively called the microbiome. A healthy microbiome not only supports digestion and strengthens the immune system, it can also reduce the risk of obesity, heart disease, diabetes, and even cancer. New advances in synthetic biology at Northwestern are paving the way for an even deeper understanding of these bacteria. Dr. Arthur Prindle and a team of investigators are developing ways to actually engineer bacterial communities in order to both monitor and treat disease. Dr. Prindle is an assistant professor of biochemistry and molecular genetics and of chemical and biological engineering at Northwestern University. He joins me to discuss his latest research, including a study on an engineered probiotic capable of detecting inflammatory bowel disease. Welcome to the show, Dr. Prindle.  

[00:01:17] Arthur Prindle, PhD: Oh, thanks so much. Happy to be here.  

[00:01:19] Erin Spain, MS: Let's talk a little bit about microbiome communities in your research. These are called biofilms in your research. How do they fit in with the larger context of the microbiome and disease?  

[00:01:31] Arthur Prindle, PhD: So bacteria are one of the oldest model organisms studied in biology. And we know that they exist all over planet earth and many different environmental niches, such as soil, water, like rivers and streams. And more recently, we've appreciated that bacteria exist within the human body, and that's termed the human microbiome. And while these bacteria, of course, are single celled organisms, as distinguished from a multicellular organism, you know, like a person or an animal, much more commonly in those different niches in the environment, they exist in the context of many other species of bacteria or many copies of bacteria living together. So communities of bacteria that live together are often termed biofilms, and those biofilm communities exhibit altered behavior, compared to free living bacteria, and that can mean that their gene expression has changed, their metabolism has changed, and the proteins they produce and the signals they communicate with are all changed when the bacteria are growing and living together. And so the hope is to better understand how bacteria live. We need to study how they live in communities. And by doing that,   to not only understand bacterial community biology, including the microbiome, but then even potentially re-engineer it or change it in a beneficial way to mitigate, you know, human disease or environmental pollution or toxin production.  

[00:03:02] Erin Spain, MS: How is it that you got involved with this work?  

[00:03:05] Arthur Prindle, PhD: So back in undergraduate, I was a chemical engineer. I always wanted to be an engineer and build things, sort of, in my DNA. And I didn't envision myself at that time of being a biologist or even a research scientist until I had a really excellent undergraduate research experience as a junior, where I discovered the field of synthetic biology. And the concept there, which is really sounded like a sci-fi kind of concept at the time, was reprogramming cells. So we know about building machines, we know about programming computers, but the cell, it always seemed, you know, too mysterious, too much of a black box. We don't know enough about it that we could actually reprogram a cell, but as an undergrad, I heard that people were trying, and I wanted to be one of those people. So I kind of jumped all in and I started with bacteria because there are some of the simplest cells that you could work with. So if we're going to be able to reprogram a cell, we'd probably start with bacteria.  

[00:04:02] Erin Spain, MS: You've actually said and you've been quoted saying if we understand the cell as a machine, we can seek to rearrange the parts of the cell to do a new function. So that's what you mean by this actually reprogramming of a cell?  

[00:04:15] Arthur Prindle, PhD: Exactly. So the cell, you know, as a living machine, it has parts, it has enzymes, it has proteins, it has DNA. Those are parts that are all working together to serve the function of a cell, which is usually to grow and survive. If we as a synthetic biologist or a research scientist can understand those parts well enough, we can envision new ways of rearranging those parts to do functions that are beyond survival for the cell. So we can have them produce a reporter molecule of interest that would signal the presence of a pollutant or a biomarker of a disease. We could have them produce a new enzyme from a different organism that could actually break down that pollutant, or it could actually potentially produce a therapeutic molecule in response to a disease. And so those are all functions that exist in different organisms in biology. They're not all found in the same cell. And so we can look around in different cells that people have studied and then bring those parts together to produce a new function. And we like to do that in bacteria because they're very simple or comparatively simple compared to higher organisms. But then bacteria are found, as we mentioned earlier, everywhere on planet earth. And so why can't we co-opt where those bacteria are naturally living to sense disease or pollution and then mitigate those effects.  

[00:05:36] Erin Spain, MS: So tell me about some of the diseases that you've been focused on, especially looking for therapeutics, finding a way to kind of solve some of these problems through biomedical engineering.  

[00:05:47] Arthur Prindle, PhD: So one of the main biomedical challenges related to biofilms is their high degree of antibiotic resistance. And so it's known that when these communities grow together, they produce structural changes like an extracellular matrix that can prevent antibiotics from getting to cells. But they can also have ways of keeping large numbers of bacteria alive in a nondividing state. It's sort of a mystery how this happens, but what it means is that many of the antibiotics we've developed that are effective on actively growing bacteria are now ineffective on these non-growing cells in biofilms. And so by doing sort of basic science studies of biofilms to answer the question of how do they keep these non-dividing cells alive, even though they're far away from nutrients being delivered to the biofilm. If we can answer that, it might give us new approaches to overcome that antibiotic resistance. Beyond antibiotic resistance in biofilms, we're also doing applied work in the microbiome where we're trying to re-engineer probiotic bacteria to sense biomarkers of disease in the human microbiome. And so there are a few examples that you could focus on, but one that we've had a recent study on is called inflammatory bowel disease, which is sort of a disease where you get recurrent patterns of gut inflammation, where this inflammation is manageable if detected and monitored, but it's often difficult to measure that biomarker in a timely manner, in a non invasive manner. And so the idea here is, if bacteria are already living in the environment where the disease is occurring, like the human gut, why can't we co-opt those bacteria to sense those biomarkers and then report that information out to us in a potentially less invasive and less, technically challenging manner than current methods?  

[00:07:45] Erin Spain, MS: And you mentioned this study with inflammatory bowel disease, which does affect roughly 3 million Americans. And you recently published results in the Proceedings of the National Academy of Sciences . Tell me a little bit about the results of this study and what you were able to prove.  

[00:08:02] Arthur Prindle, PhD: So, inflammatory bowel disease, or IBD, is a disease in humans that's characterized by recurrent gut inflammation. These inflammatory flares that come and go are intermittent, but whenever they arise, they are always associated with the production of calprotectin. Calprotectin is a protein produced by the human host that is the current clinical gold standard biomarker of IBD. And so, if we were going into the hospital today to get a send out lab test for IBD, that is what would be measured is calprotectin. Calprotectin itself has different functions that have been proposed. Some of them involve potentially mitigating unwanted bacteria that might be growing in the gut. But one of those functions that we took advantage of is that calprotectin can chelate or bind up metal ions, including zinc. And so we wondered whether we could find a very strong transcriptional response to that zinc binding activity of calprotectin that would allow us to engineer the probiotics to report out when they're encountering calprotectin. And so the idea would be, as a way of accurately monitoring calprotectin flares, we engineer the probiotic bacteria to sense calprotectin and then convert that to a luminescent or fluorescent output from the bacteria.  

[00:09:25] Erin Spain, MS: And this approach could be so different than what the current gold standard is right now, which involves a lot of time consuming and invasive monitoring. Can you tell me about that?  

[00:09:36] Arthur Prindle, PhD: Yeah, so current approaches to monitoring IBD, they all range in effectiveness. There's sort of trade-offs. The absolute gold standard diagnosis method for IBD would be an endoscopy or colonoscopy, which would accurately report what's going on, but it's of course invasive. There are non-invasive biomarkers that are either in blood. CRP is one. However, it's not very specific to IBD. So you would probably, if you saw a CRP up, you would then follow it up with an endoscopy or some other assay to confirm. There's a stool biomarker of IBD, which is calprotectin. So that's what we're trying to measure here with the bacteria. But the current method for measuring calprotectin is a send out lab test, which is a sort of an ELISA based lab test. So you'd go in, you'd be having symptoms, talk to the doctor. They would order that test. So, you'd provide the sample, it'd be sent off to another lab, and then, you know, seven to ten days, you'd get the result back. But the doctor needs to decide how to proceed at that time without those results. So, they usually kind of take their best guess. They might ask you to report your symptoms. How are you feeling today? How are you feeling last week? So, they will use a combination of patient reported symptoms together with the send out lab test. The send out lab test takes time and has a cost, and then the patient reported symptoms are going to be subjective, and you might not remember accurately. So what we're hoping to achieve here is something that's potentially faster and cheaper, but still highly accurate, and less invasive than the endoscopy approach.  

[00:11:13] Erin Spain, MS: So how would you be tracking? You would be using imaging?  

[00:11:16] Arthur Prindle, PhD: Yeah, so in our current study, which is a proof of principle, so we're clear this is sort of the first step towards, you know, developing this technology in humans. We show in animal models that when we orally deliver the probiotics to mice that have inflammation, that's sort of a model of IBD. We see those probiotics lighting up within the gut as they pass through the gut following oral administration. We don't see them lighting up when the mouse is healthy. And, of course, we don't see them lighting up when we just deliver probiotics that lack the engineered detection for calprotectin. That lighting up, I mean, it's called luminescence. So the bacteria are producing enzymes that emit light and then we detect the light using a camera. That works fine in mice, that likely will not work in humans. Mice, there's less tissue in the way basically to get the light out from the bacteria. To modify our diagnostic to work in humans for imaging, there are a few options that we're looking into. These would be things like MRI or ultrasound. So there are currently bacteria that can produce basically contrast agents or reporter molecules that show up in both MRI and ultrasound. So it would be the same gene expression response to calprotectin that we have in our current study, but instead of producing the luminescent output, they'd produce an MRI or an ultrasound reporter. Currently what we do have in the study is ex vivo samples. So the stool sample from the patient where they're measuring calprotectin. We test our probiotic on those same samples, and we show that we're able to get a signal that correlates very well with the lab test results for calprotectin. So the healthy patients that have low calprotectin, according to the sendout lab test, they also have low signal with our probiotic. Those patients in remission that have a low to an intermediate level, they have a still low signal, but slightly higher. And then patients with active IBD that are undergoing an inflammatory flare that had high calprotectin measurements also were very bright in our probiotic diagnostic. So, you know, it's sort of projecting forward a little bit, but if I combine in the animal, I can get in vivo bacteria lighting up as they pass through the gut. And then on the human patient samples ex vivo, my signal correlates with the calprotectin measurement. So the hope then would be that if you could try this in a person, maybe the bacteria would be able to produce a reporter molecule. That involves a lot more work, clinical trials, you know, that would be done together with, you know, a physician, appropriate study design. But a few people here have emailed me after the study came out and are interested in doing those kinds of phase one safety trials to start with.  

[00:14:04] Erin Spain, MS: I am curious, you know, you're talking about a probiotic. We think about yogurt. We think about how people consume probiotics. Would you potentially deliver this probiotic through a spoonful of yogurt, or would it be a pill?  

[00:14:17] Arthur Prindle, PhD: Exactly. Yeah. We eat food that has bacteria in it all the time, as you mentioned yogurt. This probiotic that we use, it's currently over the counter in the United States, generally regarded as safe by the FDA. You can buy it on Amazon. I believe you can buy it in Whole Foods. You know, we started with something that's totally innocuous and has proven safety in human trials. So this could be delivered either through a pill or yogurt. And then maybe, you know, wait an hour, wait 30 minutes and then go get the imaging done. There are things like this done today, not cell based as much. But that's sort of the vision there.  

[00:14:55] Erin Spain, MS: So you've mentioned you've already had some interest from clinicians who are interested in doing clinical trials. Where do you see this going? What could be next?  

[00:15:04] Arthur Prindle, PhD: So we're very excited to show safety and proof of principle in human patients. That's potentially a longer term goal that would be done with a GI physician here in sort of a phase one trial. Even before that, we're still working on improving our diagnostic in the lab. So I mentioned the different imaging readouts, such as MRI and ultrasound, that'd be one. Another capability that I always am asked about is can you not only detect the inflammatory flare, but can you actually produce and deliver a therapeutic molecule in response to that flare? You already have those probiotics at the site of disease. They can already respond to the flare. Couldn't they then secrete or release a therapeutic molecule directly in response. So we're pursuing what are called anti TNF antibodies or nanobodies. So these are molecules that are used today as therapeutics for IBD. They're usually administered in blood, I believe, although they're being developed now for oral delivery as well. And some of these are produced commercially in bacteria today. And so we have a belief that our bacteria will be able to produce them as well. And so the idea there would be that these probiotics have internal therapeutics that they're producing as they're growing in the gut. Then when they sense that inflammatory flare, they induce secretion or release of those molecules into the gut in that neighboring environment.  

[00:16:36] Erin Spain, MS: And of course, in this study, we're talking about inflammatory bowel disease, but there are many other conditions that could also be helped with this approach. Just tell me about some of those and maybe even diseases such as cancer or diabetes. Could there be a way to not only detect but deliver therapeutics?  

[00:16:54] Arthur Prindle, PhD: So we're very interested in a number of those other diseases that you mentioned. So, IBD in particular has been associated with an increased risk for colorectal cancer if left untreated. So, of course, one benefit of our diagnostic as it is today is that if IBD symptoms can be better detected and managed, that would decrease the longer term risk of colorectal cancer. But beyond that, you know, we have the goal of detecting other diseases as well. So, it's possible that you could have probiotics engineered to survey for tumor DNA in the environment. So if you had a colorectal cancer or a tumor growing, that would potentially be releasing mutant DNA, like KRAS, to the local environment, could our probiotics be collecting that DNA, and then they'd report out the presence of a mutant DNA versus an unmodified DNA. There's definitely some technical challenges there, but I think it's possible in principle. We know that bacteria can take up DNA. We know that they can incorporate that DNA into their genome, but they can also, in a sequence specific manner, using CRISPR or other things like that, look for different versions of DNA that would potentially allow a different response between healthy and tumor sequences for a given gene. So we would have our probiotics always collecting small fragments of DNA from the environment. And then in the event that they encounter a mutant DNA, like a KRAS, we'd have them produce an output that would tell us.   

[00:18:29] Erin Spain, MS: I mean, that does sound like science fiction, but so exciting.   

[00:18:33] Arthur Prindle, PhD: It is, you know, yeah, I should be honest. This is a forward looking goal. So, you know, there's many challenges here. A lot of the probiotics people take today, one of the knocks on those is they usually just pass through. They don't colonize. There's already bacteria in the microbiome. There's no room, so it's actually not that easy to get probiotics to colonize and remain persistent in the gut. But there's approaches where you could maybe re-engineer native bacteria rather than a sort of foreign probiotic. You don't always want them to colonize either, just from a safety perspective. Sometimes knowing the dynamics of when you deliver to when they're cleared is actually important. And so there's different applications you can envision. Just on the other diseases too looking for things like C. diff. So if you have pathogens or problematic bacteria that might be growing in the gut, many of those bacteria, they're always there, but they're not in a problematic or virulent state all the time. So being able to distinguish between active virulent bacteria and just sort of benign is important and can't be done just by sequencing the bacteria themselves. So you know, today, if you get a stool sample, you sequence to look for which bacteria are present. You will often find a range of bacteria, some of which could cause problems, they might not. So what you really want are activity based measurements where you say not just who's there in the microbiome, but what is their metabolic activity? Are they producing virulence genes? Are they producing toxins? So, you know, you might want to adapt this probiotic to sense C. diff toxin or sort of other pathogenic toxins that you could then report the presence of.  

[00:20:18] Erin Spain, MS: As you've mentioned, this field it is relatively young, synthetic biology, but it's thriving here at Northwestern and as a research priority. You're part of the Center for Synthetic Biology here, which has been expanding. So tell me what it's like right now at Northwestern doing this type of research here.  

[00:20:37] Arthur Prindle, PhD: Yes, synthetic biology at Northwestern is absolutely exploding right now. It's a really exciting time to be working in the field. So we have a relatively recently established Center for Synthetic Biology here. We have faculty on both the Evanston and the Chicago campuses of Northwestern. And this brings together faculty that are working to engineer and reprogram cells in all different contexts. So there are a few of us working on bacteria. There are a few working on mammalian cells, you know, engineering things like CAR-T and immunotherapy. And then there's people trying to engineer cell free systems. So it's taking the enzymes and the DNA from cells that we know and love, but now removing the cell so I can just use the parts themselves. There's, you know, faculty from engineering, from biomedical engineering, pharmacology, biochemistry, where my home department is, cell and developmental biology. And so we're all in different home departments, but we have these research themes in common. And so it's a really sort of interesting way of doing interdisciplinary research and doing new and innovative work in synthetic biology. It's a relatively young field. You know, I think we're probably approaching maybe the 15 to 20 year mark here. But it's really a field that's enabled by a combination of technologies. So we have the ability to synthesize DNA, the ability to sequence DNA. And then those led to a lot of people coming into biology that weren't maybe traditionally trained as biologists. But I, what I think they all share is this fascination with the idea of the cell as a machine, you know, can we use engineering methods that we've developed and used for machines and computers, but is it really time to apply those to biology? It's hard. The cell has its own goals and there's a lot we don't know about the cell, but I think it's still sort of a good source of inspiration and very motivating and exciting.  

[00:22:40] Erin Spain, MS: And you have actually received a number of awards, most recently the National Science Foundation Award, which specifically supports early career development of individuals who exemplify the role of teacher scholar. Just tell me, how do you see your role as an educator in this breakthrough science of synthetic biology?  

[00:23:00] Arthur Prindle, PhD: So the NSF Career Award is very exciting. I was very honored to receive that. That award is focused on developing sort of a systems biology or a quantitative understanding of these microbial communities. So we're doing experimental measurements of bacteria, so imaging, sort of growth, metabolism, gene expression, but then also making mathematical models of how those bacteria are interacting. So, it's a very good opportunity for training students. It's also a good way of making sure our experimental work is rigorous, using these models to make new predictions that we can then test experimentally. But then get the students excited about biology, you know, maybe that hadn't been thinking about biology as a career, like I was as a chemical engineering student. If I think back to, you know, what was the initial inspiration there, it was seeing a cell, but then imagining using equations, using engineering to describe how it's behaving and modify how it's behaving. So I hope to give that opportunity to new engineering undergraduate students here at Northwestern.  

[00:24:08] Erin Spain, MS: Thank you so much, Dr. Prindle, for coming on the show and talking about your recent work and all the exciting things ahead. We appreciate your time today.  

[00:24:16] Arthur Prindle, PhD: Thanks a lot. It was a lot of fun.  

[00:24:18] Erin Spain, MS: You can listen to shows from the Northwestern Medicine Podcast Network to hear more about the latest developments in medical research, health care, and medical education. Leaders from across specialties speak to topics ranging from basic science to global health to simulation education. Learn more at feinberg. northwestern. edu slash podcasts.

• Doing a PhD in Microbiology

What Does a PhD in Microbiology Focus On?

The exact focus of a PhD in microbiology can vary greatly, reflecting the nature of the field of study as a whole. Microbiology is defined as the study of microbes. Microbes are living organisms that are too small to be visible to the naked eye, including bacteria, viruses, and fungi.

From diseases to the production of food, microorganisms such as these play a vital role in life as we know it. The role of microbiologists includes treating and preventing infections, tracking the role of microbes in climate changes, ensuring food is safe.

A microbiology PhD programme can include:

• Molecular bacteriology – which focuses on bacterial pathogens of humans. A PhD in this field could involve studying the cellular biology of bacteria and investigating how they interact with the human immune system.
• Virology – which is the study of viruses. A PhD in virology typically revolves around infectious diseases and developing our understanding of the way viruses function.
• Molecular biology – where a student could learn about the composition and processes of cells. Research into cell biology has a wide range of application such as gene therapy, and planning effective targeting for new disease treatments.
• Mycology – which is the study of fungi. Postgraduate research in mycology could see researchers looking at the genetic properties of fungi to develop new tools to monitor and control their toxicity.
• Environmental microbiology – which focuses on the role microbes play in the environment. A PhD programme in environmental microbiology could conduct research into biofuels and bioremediation of contaminated land. Alternatively, it could focus on the monitoring of diseases in algae or coral reefs.
• Biogeochemisty – which studies the chemical, geological and biological process within the natural environment. Doctoral students in this field could investigate the emission of methane from microbes and how they contribute to climate change.

These are just a few of the areas a PhD in microbiology can specialise in. There are many others with medical, agricultural, environmental and commercial applications. Research projects typically revolve around lab work, and involve coordinating with another faculty or school within the university, and working alongside microbiologists, immunologists, biologists, biomedical scientists, and chemists.

Browse PhDs in Microbiology

A next-generation genetic technology to identify biotechnologically-valuable enzymes and transporters, development of fluorescent organic molecules for application in super-resolution imaging techniques, ubiquitin-dependent signalling pathways in ageing, speciation in facultatively sexual species, energy dissipation in human soft tissue during impacts, entry requirements for a phd in microbiology.

Basic requirements are typically a strong (2:1) Master’s degree in a relevant subject from an accredited university. Due to the scope of microbiology, relevant subjects can include biology, biochemistry, biomedical science, civil engineering, geoscience, medicine, agriculture, and earth sciences .

International students will also need to meet several minimum English language requirements set by the university, usually as part of a TOEFL or IELTS exam.

It is a good idea to think about your research interest before deciding to apply for a PhD in microbiology. For example, an undergraduate degree in medicine would be a good foundation ahead of a microbiology PhD programme focusing on the interaction of microbes and the human immune system. Alternatively, a graduate student of civil engineering would be suited for a research project investigating the degradation of crude oil in petroleum reserves.

Duration and Programme Types

The typical duration for a microbiology PhD programme is 3-4 years full-time, or 6 years part-time. In addition to the microbial research, most PhD programmes also include lectures and seminars which aim to equip postgraduates with transferable research skills such as project management, academic writing and commercial awareness.

A postgraduate microbiology course involves conducting original research in this area; therefore, applicants can expect to be involved in lab work. Most universities have the facilities for you to work on-campus, however some specialist subjects may require working at dedicated research centres. However, it is important to read the details of the research programme you are interested in. Though most programmes have a focus on lab work, other courses can be computational or statistical in nature. Therefore, the exact requirements for doing a PhD in microbiology depend greatly on the specific project.

Costs and Funding

The cost of doing a PhD in microbiology will depend on the university you study with, but average tuition fee is £4000-£6000 per academic year for UK/EU students and £20,000-£28,000 per academic year for international students.

A variety of scholarship and funding support options are available for postgraduate study. For microbiology in particular the BBSRC Doctoral Training Partnerships oversee a number of PhDs, and provide tuition fees for postgraduate research students. Each university has their own funding sources, which are advertised on their websites.

Available Career Paths

A research degree in microbiology can lead to a variety of career paths and jobs, so microbiologists can be found in a wide range of industries. The lab work nature of most PhD programmes equips you with the necessary skills for the research and development industry. Options for R&D work include specialist research areas such as molecular microbiology, microbial physiology, microbial pathogenesis, molecular genetics and immunology. Generally, the typical microbiology salary is higher in R&D than in the public sector.

Many post doctorates work in clinical setting such as medical laboratories and hospitals, operating as biomedical scientists or clinical scientists. In this setting you could expect to test samples to diagnose infections or develop treatments and vaccines.

Another career path for microbiology doctorates includes environmental science. Microbes contribute greatly to global warming, and microbiologists investigate the way in which microbes affect the atmosphere. Microbes can also be used for biofuel and for land decontamination.

Some doctorates choose to pursue microbiology jobs in agriculture, investigating the role of microbes in soil, developing techniques to contain plant pests, and preventing infectious disease in cattle. Alternatively, food manufacturing factors often look for microbiologists to oversee manufacturing processes to ensure the quality and safety of their products.

Postgraduate research often leads to a career in academia. Being a lecturer at a university is a great way to share your knowledge with others, and allows you to propose research projects and supervise PhD students to continue your research.

As mentioned previously, most microbiology PhD courses include research skill modules which equip doctorates with transferable skills which can be applied outside of the career options described above. Effective communication, project management, and research skills allow PhD students to work in any field.

Due to the wide range of microbiology jobs available, microbiology doctorates can expect a generous salary. The salary of microbiologists working for the NHS is determined by a set of pay bands , which include around £40,000 upon qualification and can exceed £100,000 at the highest pay band.

Browse PhDs Now

Join thousands of students.

Join thousands of other students and stay up to date with the latest PhD programmes, funding opportunities and advice.

• Mission, Facts and Figures
• Deans, Chairs and Staff
• Leadership Council
• Dean in the News
• Get Involved
• DEIB Mission
• Message from DEIB Associate Dean
• News and Media
• Reading Lists
• The Yale and Slavery Research Project
• Photo Gallery
• Winslow Medal
• Coat of Arms & Mace
• $50 Million Challenge
• For Pandemic Prevention and Global Health
• For Understanding the Health Impacts of Climate Change
• For Health Equity and Justice
• For Powering Health Solutions through Data Science
• For Future Leaders
• For Faculty Leaders
• For Transformational Efforts
• An abiding love for Yale turns into a lasting gift – in 15 minutes
• Endowed Professorship Created at Critical Time for Yale School of Public Health
• Brotherly encouragement spurs gift to support students
• Prestipino creates opportunities for YSPH students, now and later
• Alumna gives back to the school that “opened doors” in male-dominated field
• For Public Health, a Broad Mission and a Way to Amplify Impact
• Couple Endows Scholarship to Put Dreams in Reach for YSPH Students
• A Match Made at YSPH
• A HAPPY Meeting of Public Health and the Arts
• Generous Gift Bolsters Diversity & Inclusion
• Alumni Donations Aid Record Number of YSPH Students
• YSPH’s Rapid Response Fund Needs Donations – Rapidly
• Podiatric Medicine and Orthopedics as Public Health Prevention
• Investing in Future Public Health Leaders
• Support for Veterans and Midcareer Students
• Donor Eases Burden for Policy Students
• A Personal Inspiration for Support of Cancer Research
• Reducing the Burden of Student Debt
• Learning About Global Health Through Global Travel
• A Meeting in Dubai, and a Donation to the School
• Rapid Response Fund
• Planned Giving
• Testimonials
• Faculty, Postdoc Jobs
• For the Media
• Issues List
• PDF Issues for Download
• Editorial Style Guide
• Social Media
• Accreditation
• Faculty Directory by Name
• Career Achievement Awards
• Annual Research Awards
• Teaching Spotlights
• Biostatistics
• Chronic Disease Epidemiology
• Climate Change and Health Concentration
• Environmental Health Sciences
• Epidemiology of Microbial Diseases
• Global Health
• Health Policy and Management
• Maternal and Child Health Promotion Track
• Public Health Modeling Concentration
• Regulatory Affairs Track
• Social & Behavioral Sciences
• U.S. Health Justice Concentration
• Events and Contact
• What Does it Take to be a Successful YSPH Student?
• How to Apply and FAQs
• Incoming Student Gateway
• Traveling to Yale
• Meet Students and Alumni
• Past Internship Spotlights
• YSPH in Video
• Student-run Organizations
• MS and PhD Student Leaders
• Staff Spotlights
• Life in New Haven
• Libraries at Yale
• The MPH Internship Experience
• Practicum Course Offerings
• Summer Funding and Fellowships
• Downs Fellowship Committee
• Stolwijk Fellowship
• Climate Change and Health
• Career Management Center
• What You Can Do with a Yale MPH
• MPH Career Outcomes
• MS Career Outcomes
• PhD Career Outcomes
• Employer Recruiting
• Tuition and Expenses
• External Funding and Scholarships
• External Fellowships for PhD Candidates
• Alumni Spotlights
• Bulldog Perks
• Stay Involved
• Board of Directors
• Emerging Majority Affairs Committee
• Award Nomination Form
• Board Nomination Form
• Alumni Engagement Plus
• Mentorship Program
• The Mentoring Process
• For Mentors
• For Students
• Recent Graduate Program
• Transcript and Verification Requests
• Applied Practice and Student Research
• Competencies and Career Paths
• Applied Practice and Internships
• Student Research
• Seminar and Events
• Competencies and Career paths
• Why the YSPH Executive MPH
• Message from the Program Director
• Two-year Hybrid MPH Schedule
• The Faculty
• Student Profiles
• Newsletter Articles
• Approved Electives
• Physicians Associates Program
• Joint Degrees with International Partners
• MS in Biostatistics Standard Pathway
• MS Implementation and Prevention Science Methods Pathway
• MS Data Sciences Pathway
• Internships and Student Research
• Competencies
• Degree Requirements - Quantitative Specialization
• Degree Requirements - Clinical Specialization
• Degree Requirements- PhD Biostatistics Standard Pathway
• Degree Requirements- PhD Biostatistics Implementation and Prevention Science Methods Pathway
• Meet PhD Students in Biostatistics
• Meet PhD Students in CDE
• Degree Requirements and Timeline
• Meet PhD Students in EHS
• Meet PhD Students in EMD
• Meet PhD Students in HPM
• Degree Requirements - PhD in Social and Behavioral Sciences
• Degree Requirements - PhD SBS Program Maternal and Child Health Promotion
• Meet PhD Students in SBS
• Differences between MPH and MS degrees
• Academic Calendar
• Translational Alcohol Research Program
• Molecular Virology/Epidemiology Training Program (MoVE-Kaz)
• For Public Health Practitioners and Workforce Development
• Course Description
• Instructors
• Registration
• Coursera Offerings
• Non-degree Students
• International Initiatives & Partnerships
• NIH-funded Summer Research Experience in Environmental Health (SREEH)
• Summer International Program in Environmental Health Sciences (SIPEHS)
• 2022 Student Awards
• APHA Annual Meeting & Expo
• National Public Health Week (NPHW)
• Leaders in Public Health
• The Role of Data in Public Health Equity & Innovation Conference
• Innovating for the Public Good
• Practice- and community-based research and initiatives
• Practice and community-based research and initiatives
• Activist in Residence Program
• Publications
• Health Care Systems and Policy
• Heart Disease and Stroke
• SalivaDirect™
• COVID Net- Emerging Infections Program
• Panels, Seminars and Workshops (Recordings)
• Public Health Modeling Unit Projects
• Rapid Response Fund Projects
• HIV-AIDS-TB
• The Lancet 2023 Series on Breastfeeding
• 'Omics
• News in Biostatistics
• Biostatistics Overview
• Seminars and Events
• Seminar Recordings
• Statistical Genetics/Genomics, Spatial Statistics and Modeling
• Causal Inference, Observational Studies and Implementation Science Methodology
• Health Informatics, Data Science and Reproducibility
• Clinical Trials and Outcomes
• Machine Learning and High Dimensional Data Analysis
• News in CDE
• Nutrition, Diabetes, Obesity
• Maternal and Child Health
• Outcomes Research
• Health Disparities
• Women's Health
• News in EHS
• EHS Seminar Recordings
• Climate change and energy impacts on health
• Developmental origins of health and disease
• Environmental justice and health disparities
• Enviromental related health outcomes
• Green chemistry solutions
• Novel approaches to assess environmental exposures and early markers of effect
• 1,4 Dioxane
• Reproducibility
• Tissue Imaging Mass Spectrometry
• Alcohol and Cancer
• Olive Oil and Health
• News in EMD

Antimicrobial Resistance

• Applied Public Health and Implementation Science
• Emerging Infections and Climate Change
• Global Health/Tropical Diseases
• HIV and Sexually Transmitted Infections
• Marginalized Population Health & Equity
• Pathogen Genomics, Diagnostics, and Molecular Epidemiology
• Vector-borne and Zoonotic Diseases

Disease Areas

• EMD Research Day
• News in HPM
• Health Systems Reform
• Quality, Efficiency and Equity of Healthcare
• Substance Abuse and Mental Health
• Modeling: Policy, Operations and Disease
• Pharmaceuticals, Vaccines and Medical Devices
• Health and Wellbeing
• News in SBS
• Aging Health
• Community Engagement
• Health Equity
• Mental Health
• Reproductive Health
• Sexuality and Health
• Nutrition, Exercise
• Stigma Prevention
• Community Partners
• For Public Health Practitioners
• Reports and Publications
• Fellows Stipend Application
• Agency Application
• Past Fellows
• PHFP in the News
• Frequently Asked Questions
• International Activity
• Research Publications
• Grant Listings
• Modeling Analyses
• 3 Essential Questions Series

INFORMATION FOR

• Prospective Students
• Current Students

Antimicrobial resistance is one of the top global health threats. Antibiotic resistant organisms and new resistance mechanisms and are emerging and spreading across the globe, thereby threatening our ability to treat and prevent common infectious diseases. Estimates from the Centers for Disease Control (CDC) and Prevention indicate that antibiotic resistance causes more than two million illnesses and 23,000 deaths yearly in the United States. Without action, the problem of antibiotic resistance will likely get worse over time; projections indicate that deaths due to antibiotic resistance may reach 10 million per year globally and surpass cancer deaths by 2050. Reducing the overall risk of antibiotic resistance requires sustained research and public health prevention efforts that simultaneously addresses antimicrobial resistance from several different perspectives. Efforts include antimicrobial stewardship, surveillance for antibiotic resistant bacteria, development of diagnostics, and design of novel therapeutic and prevention approaches.

Through a combination of clinical epidemiologic studies, laboratory-based work, and mathematical modeling, YSPH faculty are working to address the global health threat of antimicrobial resistance.

Ted Cohen’s research focuses on how Mycobacterium tuberculosis drug-resistance and medical comorbidities impede efforts to control epidemics, with the ultimate goal of developing effective approaches to limit morbidity caused by this pathogen. He and his research team are also developing new modeling approaches that integrate data on pharmacokinetics and bacterial killing in vivo and in vitro to inform the development of new anti-tuberculosis regimens.

Melinda Pettigrew serves on the Steering Committee of the Antibiotic Resistance Leadership Group. The Antibiotic Resistance Leadership Group is a national network of scientists who develop and manage a clinical research agenda to combat antimicrobial resistance. Dr. Pettigrew’s research examines complex relationships between the microbiota, antibiotic exposure, and risk of respiratory and hospital-acquired infections.

Clostridium difficile is a leading cause of hospital-acquired infections and the incidence of community-acquired C. difficile infections is increasing. Students, faculty, and staff at the Connecticut Emerging Infections Program are conducting surveillance on C. difficile to increase understanding of the epidemiology of community- and healthcare-associated C. difficile infections and to generate hypotheses for future research .

While many projects in EMD focus on antibiotic resistance in bacterial pathogens, Sunil Parikh’s research focuses on the first-line therapies for malaria, the artemisinin-based combination therapies. His group conducts pharmacokinetic/pharmacodynamic studies in sub-Saharan Africa. Through a combination of observational and clinical trials, lab-based studies, and modeling, the group aims to understand how antimalarial PK/PD contribute to the development of resistance. The ultimate goal is to optimize treatment regimens to maximize the useful therapeutic life of current and future antimalarials.

• Respiratory Tract Infections
• Enteric Infections

Faculty of Interest

Professor of Epidemiology (Microbial Diseases)

• Drug Resistance, Microbial
• Epidemiology
• Europe, Eastern
• Models, Biological
• Public Health
• South America
• Tuberculosis
• HIV Infections
• Molecular Epidemiology
• Africa South of the Sahara
• Bordetella pertussis
• Influenza, Human
• Respiratory Syncytial Viruses

Associate Professor of Epidemiology (Microbial Diseases) and of Infectious Diseases

• Burkina Faso
• Developing Countries
• Parasitic Diseases
• Infectious Disease Medicine

Professor Adjunct; Affiliated Faculty, Yale Institute for Global Health

• Drug Resistance
• Infection Control
• Pulmonary Disease, Chronic Obstructive
• Gastrointestinal Microbiome

Associate Research Scientist in Epidemiology (Microbial Diseases); Affiliated Faculty, Yale Institute for Global Health; Lead, Antimicrobial Resistance Faculty Network

• Carrier State
• Disease Reservoirs
• Gram-Negative Bacteria
• Legionellosis
• Typhoid Fever
• Water Microbiology
• Community-Acquired Infections
• Disease Transmission, Infectious
• Gene Transfer, Horizontal
• Drug Resistance, Bacterial
• Wastewater-Based Epidemiological Monitoring

Centers and other resources

• CT Emerging Infections Program (EIP) The goals of the program are to assess the public health impact of emerging and re-emerging infections and to evaluate methods for their prevention and control.
• HPV Working Group

If you love sunshine, pristine beaches, a dazzling array of world-class attractions, and microbiology, this postdoctoral scholar position at San Diego State University might be for you.

There are TWO  postdoctoral scholar openings as of June 2023 for talented postdocs to join the Roach Lab focused on studying infectious diseases and bacteriophages.  The Roach Lab investigates several aspects of the tripartite interactions between bacteria, phages and human hosts using innovative models of disease, including those for the pre-clinical and clinical development of phage therapies. The lab has long-term academic, academic-medical and academic-industry collaborations to stimulate and strengthen research and development in phage therapy initiatives. The Roach lab is now using their ever-expanding phage library and manufacturing platform to provide phages for compassionate use phage therapy under the FDA's expanded access pathway.

In the first open role , you will have the opportunity to develop modern bioanalytics with biofilm-on-chip microfluidics research with an emphasis on influence of hydrodynamic flow and phage lytic forces on biofilms. While great advances have been made in the understanding of biofilms from the perspective of molecular biology, there is a growing need for quantitative characterization under well-defined and physiologically-relevant conditions. The in vitro evaluation of phage efficacy against biofilm infections has been mostly performed on polystyrene microtiter plates. However, the natural complexity of biofilms in human infections is not well mimicked in these ‘static’ based assays. Due to excellent control over a host of physiochemical, hydrodynamic and thermal parameters, microfluidic (MF) channels are becoming indispensable in microbiological studies. The clear planar surface and tiny dimensions of MF channels offers the opportunity to non-invasively image live biofilms, crucial for elucidating biofilm functions and expected to revolutionize the field of anti-biofilm development. One of our long-term goals will be to gain a comprehensive understanding of phage-natural-state biofilm interactions under physiologically-relevant conditions to reveal new anti-biofilm formations and structures.

In the second open role , you will have the opportunity to 1) investigate whether phage growth parameters are impacted by facultative aerobic hosts growing under physiological oxygen conditions of the human body, and 2) develop a commercially viable technology that enables high-throughput environmental isolation and pre-characterization of phages against diverse multidrug-resistant bacteria. Phage population growth simply cannot exist without a healthy host population. Indeed, most bacteria are highly sensitive their environment’s oxygen levels, with these levels being a major predictor of cell health. The first goal will be to use an in vitro system with physiologically ‘correct’ tissue oxygen tensions to predict physiological functions of bacteria in hypoxia and thus, define phage growth parameters inside the human body. The second goal will be to further develop a proof-of-concept modular microfluidic phage filtration system with academic-industry partners. The research will focus on building a miniaturized and ruggedized system for targeted phage filtration and propagation directly from environmental samples. This work will also involve collaborating on prototype manufacturing and technology validation.

You will have the opportunity to closely collaborate with wet-lab and dry-lab students and staff. You will develop expertise in bacterial and phage genetics, molecular biology, biochemical methods, and infectious disease models. You will organize results for presentation and viewing by lab members, the wider scientific community, and prepare data for publication in scientific journals.  You will assist with grant preparation and reporting.

The successful candidate will be an independent, highly motivated problem solver who communicates well and enjoys working in a collaborative, interdisciplinary environment.

Required qualifications:

The ideal candidate will have a PhD (within the last 1-3 years) in microbiology, molecular biology, bioengineering, or a related field. 

Excellent oral and written communication skills including the ability to organize/present technical reports and provide a proven track record of recent or pending scientific publications.

Demonstrated interpersonal skills including experience collaborating with a diverse interdisciplinary research team.

Preferred qualifications:

Expertise in microbiology and molecular biology

Excellent written and oral communication skills in English

Experience with bacteriophages is desirable, but not required

Experience with biofilms is desirable, but not required (project specific)

Experience with bioinformatics is desirable, but not required

Experience in research and development, but not required

Applicant Special Instructions:

Please email your C.V. and cover letter detailing past related research  experience and why you are interested in this position to Dr. Dwayne Roach at [email protected]

Three PhD Students Awarded Three-Year Graduate Research Fellowships from the NSF

Biochemistry PhD students Violet Beaty, Porter Ellis and Celeste Marin have been awarded prestigious three-year Graduate Research Fellowships from the National Science Foundation (NSF) and join classmate, Dalal Azzam, who matriculated to Duke Biochemistry with an NSF Graduate Fellowship in 2022.  This award financially supports outstanding graduate students in NSF-supported STEM disciplines.  Past recipients have contributed to research, teaching, and innovation in their areas of expertise; whilst the fellowship recognition has helped them become successful leaders in their academic and professional careers.  Provided below are brief descriptions of the projects and potential outcomes on which each of these students is working.  

Dalal Azzam, a second-year graduate student in the laboratory of Lorena Beese: Appreciating the mechanistic underlays of protein-DNA interactions helps us understand the complex mechanisms that govern biological function.  The interdisciplinary approach combining biochemistry with structural biology provides a multi-dimensional look into the science at the core of all life.  Through this project, I am excited to expand our collective understanding of DNA-protein interactions, contribute high-resolution structures of key regulatory complexes, and elucidate how faults in these interactions promote catastrophic downstream misregulations.   

Violet Beaty, a second-year graduate student in the laboratory of Shuo Han: The human microbiota contains diverse bacterial phyla, encompassing remarkable genetic and metabolic diversity.  While the gut microbiota contributes to age-associated physiology in its host organisms, we do not yet understand which gut bacterial species within the community promote healthy aging.  Furthermore, it is unknown how these bacterial and host metabolic pathways play a role in longevity.  My work aims to understand gut bacterial signals which modulate host aging and physiology.  

Porter Ellis, a second-year graduate student in the laboratory of Maria Schumacher: In prokaryotes, i.e., bacteria, nucleoid associated proteins, or NAPs, support the compaction and organization of genomic DNA.  Emerging evidence highlights the importance of NAPs in fundamental biological processes, including gene regulation, virulence, and stress responses.  However, there is currently little information available on the mechanisms by which many NAPs interact with DNA and function in regulatory processes.  Thus, to better understand these NAP functions, my research focusses on the structural interrogation of a novel NAP and its interactions with key biological partners.  

Celeste Marin, a second-year graduate student in the laboratory of Christopher Nicchitta: Routine transcriptional and post-transcriptional processes are altered significantly under stress conditions, and how these events unfold is critical for cell survival.  However, it remains unknown how the regulatory processes coupled to mRNA export are influenced under stress.  Through my research I shall leverage optical imaging techniques to probe mRNA trafficking dynamics under stress and further our understanding of these fundamental regulatory process

Suggestions or feedback?

MIT News | Massachusetts Institute of Technology

• Machine learning
• Social justice
• Black holes
• Classes and programs

Departments

• Aeronautics and Astronautics
• Brain and Cognitive Sciences
• Architecture
• Political Science
• Mechanical Engineering

Centers, Labs, & Programs

• Abdul Latif Jameel Poverty Action Lab (J-PAL)
• Picower Institute for Learning and Memory
• Lincoln Laboratory
• School of Architecture + Planning
• School of Engineering
• School of Humanities, Arts, and Social Sciences
• Sloan School of Management
• School of Science
• MIT Schwarzman College of Computing

When an antibiotic fails: MIT scientists are using AI to target “sleeper” bacteria

Press contact :.

Previous image Next image

Since the 1970s, modern antibiotic discovery has been experiencing a lull. Now the World Health Organization has declared the antimicrobial resistance crisis as one of the top 10 global public health threats. 

When an infection is treated repeatedly, clinicians run the risk of bacteria becoming resistant to the antibiotics. But why would an infection return after proper antibiotic treatment? One well-documented possibility is that the bacteria are becoming metabolically inert, escaping detection of traditional antibiotics that only respond to metabolic activity. When the danger has passed, the bacteria return to life and the infection reappears.  

“Resistance is happening more over time, and recurring infections are due to this dormancy,” says Jackie Valeri, a former MIT-Takeda Fellow  (centered within the MIT Abdul Latif Jameel Clinic for Machine Learning in Health) who recently earned her PhD in biological engineering from the Collins Lab. Valeri is the first author of a new paper published in this month’s print issue of Cell Chemical Biology that demonstrates how machine learning could help screen compounds that are lethal to dormant bacteria. 

Tales of bacterial “sleeper-like” resilience are hardly news to the scientific community — ancient bacterial strains dating back to 100 million years ago have been discovered in recent years alive in an energy-saving state on the seafloor of the Pacific Ocean. 

MIT Jameel Clinic's Life Sciences faculty lead James J. Collins, a Termeer Professor of Medical Engineering and Science in MIT’s Institute for Medical Engineering and Science and Department of Biological Engineering, recently made headlines for using AI to discover a new class of antibiotics, which is part of the group’s larger mission to use AI to dramatically expand the existing antibiotics available. 

According to a paper published by The Lancet , in 2019, 1.27 million deaths could have been prevented had the infections been susceptible to drugs, and one of many challenges researchers are up against is finding antibiotics that are able to target metabolically dormant bacteria. 

In this case, researchers in the Collins Lab employed AI to speed up the process of finding antibiotic properties in known drug compounds. With millions of molecules, the process can take years, but researchers were able to identify a compound called semapimod over a weekend, thanks to AI's ability to perform high-throughput screening.

An anti-inflammatory drug typically used for Crohn’s disease, researchers discovered that semapimod was also effective against stationary-phase Escherichia coli and Acinetobacter baumannii . 

Another revelation was semapimod's ability to disrupt the membranes of so-called “Gram-negative” bacteria, which are known for their high intrinsic resistance to antibiotics due to their thicker, less-penetrable outer membrane. 

Examples of Gram-negative bacteria include E. coli , A. baumannii , Salmonella , and Pseudomonis , all of which are challenging to find new antibiotics for. 

“One of the ways we figured out the mechanism of sema [sic] was that its structure was really big, and it reminded us of other things that target the outer membrane,” Valeri explains. “When you start working with a lot of small molecules ... to our eyes, it’s a pretty unique structure.” 

By disrupting a component of the outer membrane, semapimod sensitizes Gram-negative bacteria to drugs that are typically only active against Gram-positive bacteria. 

Valeri recalls a quote from a 2013 paper published in Trends Biotechnology : “For Gram-positive infections, we need better drugs, but for Gram-negative infections we need any drugs.” 

Share this news article on:

Related links.

• Collins Lab
• Abdul Latif Jameel Clinic for Machine Learning in Health
• Institute for Medical Engineering and Science
• Department of Biological Engineering

Related Topics

• Biological engineering
• Institute for Medical Engineering and Science (IMES)
• Jameel Clinic
• Artificial intelligence
• Health sciences and technology
• Drug discovery
• Antibiotics

Related Articles

Using AI, MIT researchers identify a new class of antibiotic candidates

Using AI, scientists find a drug that could combat drug-resistant infections

Artificial intelligence yields new antibiotic

Previous item Next item

More MIT News

Has remote work changed how people travel in the US?

Read full story →

Physicist Netta Engelhardt is searching black holes for universal truths

MIT community members gather on campus to witness 93 percent totality

Extracting hydrogen from rocks

MIT engineers design flexible “skeletons” for soft, muscle-powered robots

This 3D printer can figure out how to print with an unknown material

• More news on MIT News homepage →

Massachusetts Institute of Technology 77 Massachusetts Avenue, Cambridge, MA, USA

• Map (opens in new window)
• Events (opens in new window)
• People (opens in new window)
• Careers (opens in new window)
• Accessibility
• Social Media Hub
• MIT on Facebook
• MIT on YouTube
• MIT on Instagram

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

• View all journals
• Explore content
• About the journal
• Publish with us
• Sign up for alerts
• CORRESPONDENCE
• 02 April 2024

How can we make PhD training fit for the modern world? Broaden its philosophical foundations

• Ganesh Alagarasan 0

Indian Institute of Science Education and Research, Tirupati, India.

You can also search for this author in PubMed   Google Scholar

You have highlighted how PhD training assessment has stagnated, despite evolving educational methodologies (see Nature 613 , 414 (2023) and Nature 627 , 244; 2024 ). In particular, you note the mismatch between the current PhD journey and the multifaceted demands of modern research and societal challenges.

Access options

Access Nature and 54 other Nature Portfolio journals

Get Nature+, our best-value online-access subscription

24,99 € / 30 days

cancel any time

Subscribe to this journal

Receive 51 print issues and online access

185,98 € per year

only 3,65 € per issue

Rent or buy this article

Prices vary by article type

Prices may be subject to local taxes which are calculated during checkout

Nature 628 , 36 (2024)

doi: https://doi.org/10.1038/d41586-024-00969-x

Competing Interests

The author declares no competing interests.

Related Articles

See more letters to the editor

• Research management
• Scientific community

Ready or not, AI is coming to science education — and students have opinions

Career Feature 08 APR 24

After the genocide: what scientists are learning from Rwanda

News Feature 05 APR 24

The neuroscientist formerly known as Prince’s audio engineer

Career Feature 14 MAR 24

Brazil’s postgraduate funding model is about rectifying past inequalities

Correspondence 09 APR 24

Declining postdoc numbers threaten the future of US life science

How we landed job interviews for professorships straight out of our PhD programmes

Career Column 08 APR 24

How two PhD students overcame the odds to snag tenure-track jobs

Adopt universal standards for study adaptation to boost health, education and social-science research

Correspondence 02 APR 24

Postdoctoral Research Associate

Qualifications: PhD degree in chemistry, radiochemistry, or nuclear medicine technology with at least 3 years of PET radiochemistry work experience i

Charlottesville, Virginia

University of Virginia Health

Postdoctoral Associate

Palm Beach, Florida

University of Florida, Scripps Institute

Laboratory Director

Houston, Texas (US)

Baylor College of Medicine (BCM)

PhD, Postdoc and Technician positions in the Cluster of Excellence "MicroPlanet"

PhD, Postdoc and Technician positions in interdisciplinary microbiome project

Austria (AT) - Vienna, and Lower Austria

University of Vienna - Centre for Microbiology and Environmental Systems Science

Assistant Professor in Integrated Photonics

We offer you the chance to design a unique and autonomous research program, networking with specialists, students and entrepreneurs.

Gothenburg (Stad), Västra Götaland (SE)

Chalmers University of Technology

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Quick links

• Explore articles by subject
• Guide to authors
• Editorial policies

• Search the site GO Please fill out this field.
• Newsletters

Research Shows Bacterium Found in the Mouth Also Present in 50% of Colorectal Cancer Tumors

• New research found that a specific subtype of a bacterium commonly found in the mouth was also present in 50% of colorectal cancer tumors that were studied by researchers.
• Previous research shows that this particular bacterium subtype, when present in a tumor, has been linked to a worse prognosis for colorectal cancer patients.
• These findings could help scientists develop new methods to screen, prevent, and treat colorectal cancer.

Researchers discovered a strain of a bacterium commonly found in the mouth in about half of colorectal tumors they tested. The subtype they identified is notable because it appears to shield tumor cells from cancer-fighting drugs.

Experts say the researchers’ findings, published in the journal Nature , could help scientists develop new ways to combat colorectal cancer .

“Most exciting is that it suggests that targeting these specific bacteria in cancer could be used as another weapon against cancer during treatment,” Christopher D. Johnston, PhD , co-lead study author and assistant professor at Fred Hutchinson Cancer Center, told Health .

The study comes at a time when colorectal cancer cases are rising at an alarming rate among people younger than 55. Between 1995 and 2019, diagnoses of people in this age group jumped from 11% to 20%. The American Cancer Society predicts that colorectal cancer will kill more than 53,000 people in 2024, making it the second-leading cause of cancer deaths in the United States.

Luis Alvarez / Getty Images

How a Mouth Bacterium Affects Colorectal Cancer

Scientists have known about the potential link between colorectal cancer and the oral bacterium  Fusobacterium nucleatum , which causes gum disease , for more than a decade. 

Previous research has found that people with higher amounts of the bacteria in their colorectal tumors have a poorer prognosis and that treating the bacteria with antibiotics reduces tumor growth in mice, suggesting that eliminating the bacteria may also improve cancer.  

Studies have also revealed certain aspects of how the bacteria function: They appear to stick with colorectal cancer as it spreads and can invade and change cancer cells in a way that may support cancer growth.

For this study, the research team wanted to drill down into the specific Fusobacterium nucleatum subtypes associated with colorectal cancer.

According to Johnston, understanding the Fusobacterium nucleatum strains linked to colorectal cancer is crucial because each one can have a unique effect on cancer. “We set out to find out what makes these tumor-homing bacteria genetically distinct or special,” he said.

To do this, Johnson and his colleagues looked for the presence of Fusobacterium nucleatum in colorectal tumors from over 200 patients.

They found that Fusbobacterium nucleatum dominates the microbiome in the tumors of some patients. They also discovered higher amounts of the subtype Fna C2 in about half of the tissue samples examined. Additionally, about 30% of stool samples collected from people with colorectal cancer showed the presence of Fna C2 .

A genetic analysis also revealed how this subtype may be able to survive so far away from the mouth. Scientists found that it has specific traits that might allow it to travel to the lower gut and to withstand stomach acid without dying.

“We have pinpointed the specific clade that is associated with [colorectal cancer], and it is important for therapeutic and preventative implications,” Johnston said.

Michael White, MD , assistant professor of colon and rectal surgery at The University of Texas MD Anderson Cancer Center, who was not involved in the study, told Health that the subspecies may even cause cancer to form. 

“This subtype of bacteria, while normal in the oral cavity, is not regularly identified in the colons of a healthy population,” he said. “This has led to the hypothesis that these bacteria may play a role in the development of colorectal cancers as these bacterial species are only regularly found in the colon in the setting of a malignancy.”

New Hope for Treatment and Prevention

White said that scientists are just beginning to figure out how this information can benefit patients. 

He and his colleagues are planning a trial that would involve the use of chemotherapy to clear Fusbacterium nucleatum in rectal cancers, he said. 

There’s also the potential for the bacterium itself to fight cancer cells. 

Researchers have shown that this subtype can enter cancer cells easily, so it might be possible to genetically modify the bacteria to carry cancer-fighting drugs directly into the tumors. The method would involve a version of the bacterium that can’t cause disease but can still invade the colorectal tumor.

The new findings may also spark new screening regimens, according to Johnston.

“Now that we pinpointed the specific bacteria type that is present in these tumors," said Johnston, "it opens up routes to screen high-risk populations for these bacteria, to design minimally invasive screening kits to detect colorectal cancers earlier."

Zepeda-Rivera M, Minot SS, Bouzek H, et al. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche . Nature . Published online March 20, 2024. doi:10.1038/s41586-024-07182-w

Siegel RL, Wagle NS, Cercek A, Smith RA, Jemal A. Colorectal cancer statistics, 2023 . CA Cancer J Clin . 2023;73(3):233-254. doi:10.3322/caac.21772

American Cancer Society. Key statistics for colorectal cancer .

Bullman S, Pedamallu CS, Sicinska E, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer .  Science (New York, NY) . 2017;358(6369):1443-1448. doi:10.1126/science.aal5240

Galeano Niño JL, Wu H, LaCourse KD, et al. Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer .  Nature . 2022;611(7937):810-817. doi:10.1038/s41586-022-05435-0

Related Articles

• Education Home
• Medical Education Technology Support
• Graduate Medical Education
• Medical Scientist Training Program
• Public Health Sciences Program
• Continuing Medical Education
• Clinical Performance Education Center
• Center for Excellence in Education
• Research Home
• Biochemistry & Molecular Genetics
• Biomedical Engineering
• Cell Biology
• Microbiology, Immunology, & Cancer Biology (MIC)
• Molecular Physiology & Biological Physics
• Neuroscience
• Pharmacology
• Public Health Sciences
• Office for Research
• Clinical Research
• Clinical Trials Office
• Funding Opportunities
• Grants & Contracts
• Research Faculty Directory
• Cancer Center
• Cardiovascular Research Center
• Carter Immunology Center
• Center for Behavioral Health & Technology
• Center for Brain Immunology & Glia
• Center for Diabetes Technology
• Center for Immunity, Inflammation & Regenerative Medicine
• Center for Public Health Genomics
• Center for Membrane & Cell Physiology
• Center for Research in Reproduction
• Myles H. Thaler Center for AIDS & Human Retrovirus Research
• Child Health Research Center (Pediatrics)
• Division of Perceptual Studies
• Research News: The Making of Medicine
• Core Facilities
• Virginia Research Resources Consortium
• Center for Advanced Vision Science
• Charles O. Strickler Transplant Center
• Keck Center for Cellular Imaging
• Institute of Law, Psychiatry & Public Policy
• Translational Health Research Institute of Virginia
• Clinical Home
• Anesthesiology
• Dermatology
• Emergency Medicine
• Family Medicine
• Neurosurgery
• Obstetrics & Gynecology
• Ophthalmology
• Orthopaedic Surgery
• Otolaryngology
• Physical Medicine & Rehabilitation
• Plastic Surgery, Maxillofacial, & Oral Health
• Psychiatry & Neurobehavioral Sciences
• Radiation Oncology
• Radiology & Medical Imaging
• UVA Health: Patient Care
• Diversity Home
• Diversity Overview
• Student Resources
• GME Trainee Resources
• Faculty Resources
• Community Resources

Mete Civelek, PhD, Receives Established Investigator Award from the American Heart Association

April 9, 2024 by [email protected]

Mete Civelek, PhD

Mete Civelek, PhD, an associate professor in the Department of Biomedical Engineering and a resident faculty of the Center for Public Health Genomics, received the Established Investigator Award from the American Heart Association.

The five-year grant supports established investigators who are in a rapid growth phase of their careers, have established records of accomplishments, and continue to show extraordinary promise. The research proposal, “Systems Genetics of Sex Differences in Cardiometabolic Disorders,” will study how the genetic makeup of individuals affects blood vessel cells and fat tissue differently in men and women. Members of the Civelek Lab will use a systems genetics approach to identify the molecular and cellular mechanism of genomic regions that show sex-specific association with coronary artery disease risk in humans. They will then expand these studies using a genome-wide approach to identify critical regulators of transcription that lead to sex differences in vascular smooth muscle cells and adipose tissue.

Filed Under: Honors & Awards , Research

• Submit News/Event
• Subscribe to News
• Call for Nominations
• Dean's Message
• Diversity, Equity & Inclusion
• Honors & Awards
• Media Highlights
• Philanthropy

April 15, 2024 – ERC Seminar – Gurumurthy Ramachandran, PhD, CIH