Niepa μBiointerface Lab

The physicochemical mechanisms that regulate microbial growth in various settings remain poorly understood for reasons linked not only to the versatility of the microorganisms but also to the challenge of designing new platforms to study or control them. The mission of the μBiointerface Lab is to develop translational-research programs that elucidate these mechanisms by designing sustainable control strategies for microbes relevant to health, industry, and the environment. Our research plan is to pursue three interrelated research thrusts to:

• Eliminate pathogenic microbial communities (biofilms) associated with implantable devices using conductive substrate interfaces
• Model pathogenic and beneficial microbial communities (microbiomes) in artificial microniches made of soft biomaterial
• Control beneficial interfacial biofilms using surface-active compounds

Faculty

Tagbo H.R. Niepa

Arthur Hamerschlag Associate Professor, Chemical Engineering and Biomedical Engineering

Tagbo H.R. Niepa is the Arthur Hamerschlag Associate Professor of Chemical Engineering and Biomedical Engineering at Carnegie Mellon University. Niepa received his bachelor's degree in biomedical engineering from Syracuse University, after transferring from the University of Dortmund, Germany. He also received his Ph.D. in chemical engineering from Syracuse University. Niepa held a Postdoctoral Fellowship for Academic Diversity in the University of Pennsylvania's department of chemical and biomolecular engineering. Most recently, he served as an assistant professor of chemical and petroleum engineering at the University of Pittsburgh.

Niepa received the prestigious National Institutes of Health Director's New Innovator Award to support unconventional approaches to major challenges in biomedical and behavioral research. He also received a Faculty Early Career Development (CAREER) Award from the National Science Foundation (NSF) and a Rising Star of Mechanical Engineering Award from the American Society of Mechanical Engineers (ASME).

Office

3111 Doherty Hall

Email

tniepa@andrew.cmu.edu

Google Scholar

Tagbo H.R. Niepa

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Projects

Electrochemical control of persister cells

The emergence of antibiotic-resistant bacteria has presented an increasing challenge to infection control. In general, bacterial populations commonly harbor phenotypic variants, known as persister cells, which are metabolically inactive and extremely tolerant to antibiotics. The persister cells are well known to survive conventional antibacterial treatments and regenerate the bacterial populations with a similar percentage of persister cells when the antibiotic treatment is stopped. The electrochemical control of persister cells (ECCP) presents a great potential for the treatment of chronic infections. We demonstrated that bacterial persister cells could be effectively eliminated by low-level direct currents (DCs) alone, and in synergy with antibiotics. The discovery showed that DC treatments could affect the surface charge and membrane integrity of P. aeruginosa and increase the intracellular interaction of metal cations and antibiotics with the nucleic acid.

Understanding the electrophysiology of bacterial persister cells

Electrochemical treatments mediated via carbon electrodes can provoke the permeabilization of the cells to extracellular materials and lead to complete eradication of the persisters. These findings, corroborated by DNA microarray analysis, reveal that DC treatments have profound effects on the physiology of persister cells, altering the regulation of genes involved in antibiotic resistance, pyocin-related functions, and SOS response. The safety and efficacy of ECCP is further tested in co-culture models with human epithelial cells and P. aeruginosa PAO1 and in rabbit model of sinus infections. Overall, the study aims to improve the understanding of the electrophysiology of bacterial persister cells, and provides new insight for designing novel systems to effectively control infections associated with biofilms and persister cells.

Biofilms and biointerfaces

Each year, massive amounts of oil are accidentally or deliberately spilled into seawaters, polluting the ecosystem. Quick remediation responses, including in-situ burning or dispersant spraying, have been insufficient to palliate the long-lasting harm caused by the spills. One avenue that might address this need is to exploit more effectively the inherent abilities of microorganisms to break down oil molecules. Because of the large interfacial tensions between oil and water, it is expected that manipulating the properties of the bacterial films could optimize the performance of bacteria in the oil field, direct microbial dynamics toward hydrocarbon degradation, and thereby ameliorate ecosystem recovery. The premise underlying this research plan consists of elucidating the mechanisms of film formation at oil-water interface and ultimately improving the designs of sustainable bioremediation solutions. This study aims to answer three major questions: (1) how does the physical interaction between bacterial films and oil-water interfaces enhance or impede hydrocarbon bioremediation; (2) how can the community behavior and interactions among marine bacteria be utilized to benefit bioremediation; and (3) how can hydrocarbon degradation be assisted and sustained by means of eco-friendly technology? This research incorporates physical and biological approaches to describe the mechanisms of film formation at the oil-water interfaces and explain its impact on oil remediation. Moreover, sustainable models of biodegradation are assessed to promote hydrocarbon bioavailability by means of functionalized nanoparticles.

Cover art: ACS Appl. Bio Mater. 2022, 5, 5, 1868–1878

Microbial nanocultures

Bacterial infection of medical and environmental surfaces is a common phenomenon encountered in various settings. On solid surfaces, for instance, a cell has to overcome physical forces or surface charges to colonize and develop into mature films. The secretion of the exopolysaccharide (EPS) matrix becomes essential to protect the embedded cells from "adverse" environments and to control the exchange of nutrients and genetic materials. Within the biofilm, bacteria become about 1000 times more tolerant to antibiotics than their planktonic counterparts. Moreover, the presence of a sub-population of slow-growing or dormant cells (known as persister cells), which are highly resistant to antibiotics, render biofilms difficult to eradicate. Under more favorable conditions, the persisters can "wake up" and repopulate the biofilms then disperse, colonizing new areas and causing chronic infection.

Unfortunately, the physiological responses of cells to environmental stress, which contributes to bacteria adopting distinctive community behaviors, are poorly understood. The goal of this research is to understand how microbial dynamics in confined environments are affected by physico-chemical stresses, such as antibiotics, electrochemical current, and osmotic pressure. Thus, bacterial cells confined in well-defined nanocultures (2-5 nL) are subjected to external stress to examine phenotypic variation associated with cell-cell communication and persister and microcolony formation. The findings of this study may contribute to the design of novel detection and control techniques for bacterial colonization and for the testing of novel antimicrobials. Such applications are significant for the food and pharmaceutical industries through the encapsulation of microorganisms in microemulsions.

Cover art: ACS Appl. Polym. Mater. 2022, 4, 5, 2999–3012

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Research team

Chao Li

Research Scientist

Research interests

Exclusive Liquid Repellency (ELR)-empowered Open Microfluidic System (UOMS) for microbial dynamics investigation

Email

chaoli3@andrew.cmu.edu

Amy Apgar

Doctorate

Research interests

Probiotic formulation and delivery using nanocultures, Clostridioides difficile infection, gnotobiotic animal studies

Email

aapgar@andrew.cmu.edu

NSF GRFP

Ann Badia

Doctorate

Research interests

Bioprospection of human-derived probiotics, Matlab-based assessment of microbiome-dynamics, bacteria-surface interactions

Email

abadia@andrew.cmu.edu

GEM Fellowship

Camila Cue

Doctorate

Research interests

Electrochemical therapy for targeted treatments, developing new approaches to combat multidrug-resistant microorganisms, improving treatments for oral healthcare such as peri-implantitis

Email

ccue@andrew.cmu.edu

NIH T32 training

Hannah Gedde

Doctorate

Research interests

Biointerfacial phenomena of lung microbes, interfacial biofilm properties and dynamics

Email

hgedde@andrew.cmu.edu

Shakira Martinez Vasquez

Doctorate

Research interests

Interfacial and metabolic properties of skin microbes, rheological properties of interfacial biofilm, living materials at oil-water interfaces

Email

shakiram@andrew.cmu.edu

Abraham Polanco

Doctorate

Research interests

Advanced materials for health applications

Email

apolanco@andrew.cmu.edu

Rales Fellow

Huda Usman

Doctorate

Research interests

Developing nanoculture system to grow microbial dark matter, magnetic microbial housing, microfluidics, multispecies interactions in sessile drops

Email

husman@andrew.cmu.edu

Eesha Kulkarni

Masters

Research interests

Machine learning, computer vision, and microfluidics

Email

eskulkar@andrew.cmu.edu

Fangyi Li

Masters

Research interests

Bioremediation using microorganisms, interfacial biofilm dynamics, and optimizing bacterial interactions at oil-water interfaces

Email

fli2@andrew.cmu.edu

Tianyi Liu

Masters

Research interests

Interfacial and metabolic properties of skin microbes, rheological properties of interfacial biofilm, living materials at oil-water interfaces

Email

tliu4@andrew.cmu.edu

Aishwarya Mohan

Masters

Research interests

Photocatalytic and antimicrobial surfaces to combat multidrug-resistant microorganisms

Email

amohan2@andrew.cmu.edu

Santhoshi Paladugu

Masters

Research interests

Electrophysiology of Candida auris

Email

spaladug@andrew.cmu.edu

Honora Armfield

Undergraduate

Research interests

Microfluidics and blood-borne pathogens

Email

harmfiel@andrew.cmu.edu

Kaitlyn Bhalla

Undergraduate

Research interests

Interfacial phenomena associated with ultra small microbes

Email

kbhalla2@andrew.cmu.edu

Nikhita Bontha

Undergraduate

Research interests

High-throughput imaging and computer-based analysis of species interactions

Email

nbontha@andrew.cmu.edu

Naomi Dibong

Undergraduate

Research interests

Bacteria-surface interactions, functional antimicrobial surfaces

Email

nid@andrew.cmu.edu

Crystal Echeverria

Undergraduate

Research interests

High-throughput imaging and computer-based analysis of species interactions

Email

crecheve@andrew.cmu.edu

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Bugs as Materials summer internship

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Donate

The Niepa μBiointerface Lab is developing technologies to better study microbes. You can help us design new materials and new interfaces to combat drug-resistant infections, clean oil spills, and anticipate solutions for future problems.

Make a gift to the Niepa μBiointerface Lab

How your gift will be used:

• Support students: Early research opportunities in the μBiointerface Lab inspire the next generation of engineers.
• Support research: Target emerging pathogens for which there is no current treatment
• Support international outreach: Build and broaden the pipeline of scientists

Every gift, no matter the size, helps. Our work would not be possible without the generous support of government funding agencies, foundations, companies, and donors like you.

Thank you!

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Publications

Refereed journal papers

Refereed journal papers

1. Siegel, H., de Ruiter, M., Niepa, T.H.R., & Haase, M.F. The effect of charge screening for cationic surfactants on the rigidity of interfacial nanoparticle assemblies. Journal of Colloid and Interface Science 678 (2025) 201–208. doi: 10.1016/j.jcis.2024.08.133.
2. Badha, V.S., Niepa, T.H.R., Gharbi, M.A. Topological defects at smectic interfaces as a potential tool for the biosensing of living microorganisms. Langmuir (2024) 40, 22754−22761.
3. Niepa, T.H.R., Locke, L.W., Corcoran, T.E., Lee, J.S. Editorial: Mechanobiology of biofilms and associated host-pathogen interactions. Frontiers in Cellular and Infection Microbiology (2024) 14:1416131. doi: 10.3389/fcimb.2024.1416131.
4. Abd, G., Sánchez Díaz, Ra., Gupta, A., Niepa, T.H.R., Ramakrishna, S., Mondal, K., Sharma, A., Lantada, A. D., Islam, M. Carbon nanomaterials-based electrically conductive scaffolds for tissue engineering and regenerative medicine. MedComm - Biomaterials and Applications 3 (2), e76. (2024) doi: 10.1002/mba2.76.
5. Balmuri, S.R., Noaman, S.^‡, Usman, H., Niepa, T.H.R. Altering the interfacial rheology of Pseudomonas aeruginosa and Staphylococcus aureus with N-acetyl cysteine and cysteamine. Frontiers in Cellular and Infection Microbiology (2024) 13, 1338477.
6. Lieber, A., Hildebrandt, D., Davidson, S., Rivero, J., Usman, H., Niepa, T.H.R., Hornbostel, K. Demonstration of Direct Ocean Carbon Capture Using Encapsulated Solvents. (2023) Chemical Engineering Journal 470 (2023) 144140.
7. Balmuri, S.R., Phandanouvong-Lozano, V., House, S.D., Yang, J.C., Niepa, T.H.R. Mucoid Switch Provides a Growth Advantage to Pseudomonas aeruginosa at Oil-Water Interfaces. ACS Applied Bio Materials 2022, 5, 5, 1868–1878. Early Career Forum – Invited Article. Featured cover art.
8. Davidson, S-L & Niepa, T.H.R. Controlling Microbial Dynamics through Selective Solute Transport Across Functional Nanocultures. ACS Applied Polymer Materials 2022, 4, 5, 2999-3012. Early Career Forum – Invited Article. Featured cover art.
9. Davidson, S-L & Niepa, T.H.R. Micro-technologies for Assessing Microbial Dynamics in Controlled Environments. Frontiers in Microbiology 12 (2022) 745835.
10. Uzoukwu, E.^‡, Phandanouvong-Lozano, V., Usman, H., Sfeir, C.S., Niepa, T.H.R. Droplet-based microfluidics as a high-throughput method to investigate the human oral microbiome. Biotechnology Advances 55 (2022) 10790.
11. Balmuri, S.R., Keck, N^‡, Niepa, T.H.R. Assessing the performance of wax-based microsorbents for oil remediation. Colloids and Surfaces A: Physicochemical and Engineering Aspects 627 (2021) 127227.
12. Usman, H., Davidson, S-L., Manimaran, N.H., Nguyen, J.T., Seth, R.^‡, Bah, A.^‡, Beckman, E., Niepa, T.H.R. Design of a Well-Defined Poly(Dimethylsiloxane)-Based Microbial Nanoculture System. Materials Today Communications 2021, 27, 102185.
13. Coenye, T., Kjellerup, B., Stoodley, P., Bjarnsholt, T., the 2019 Biofilm Bash Participants (Niepa, T.H.R.). The future of biofilm research – Report on the '2019 Biofilm Bash'. Biofilm 2020, 2, 100012.
14. Manimaran, N.H., Usman, H., Kamga, K.^‡, Davidson, S-L., Beckman, E., Niepa, T.H.R. Developing a Functional Poly(dimethylsiloxane)-Based Microbial Nanoculture System Using Dimethylallylamine. ACS Applied Materials & Interfaces 2020, 12, 45, 50581–50591. Featured cover art.
15. Balmuri, S.R., Waters, N.G.^‡, Hegemann, J., Kierfeld, J., Niepa, T.H.R. Material Properties of Films of mucoid and non-mucoid Pseudomonas aeruginosa isolates. Acta Biomaterialia 118 (2020) 129–140.
16. Parry-Nweye, E.^‡*, Onukwugha, N.^‡*, Balmuri, S.R., Shane, J.L., Kim, D., Koo, H., Niepa, T.H.R. Electrochemical Strategy for Eradicating Fluconazole-Tolerant Candida albicans using implantable Titanium. ACS Applied Materials & Interfaces 2019, 11, 40997−41008.
17. Niepa, T.H.R.*, Vaccari L*, Leheny RL, Goulian M, Lee D, and Stebe KJ. Films of bacteria at Interfaces (FBI): Remodeling of fluid interfaces by Pseudomonas aeruginosa. Scientific Reports 7 (2017) 17864.
18. Vaccari, L., Molaei, M., Niepa, T.H.R., Lee D^#, Leheny LR, and Stebe KJ^#. Films of Bacteria at Interfaces. Advances in Colloid and Interface Science 247 (2017) 561–572.
19. Kim, D., Sengupta, A., Niepa, T.H.R., Lee, B.H., Weljie, A., Freitas-Blancos, V.S., Murata, R.M., Stebe, K.J.^#, Lee, D.^#, Koo, H. Candida albicans stimulates Streptococcus mutans microcolony development via cross-kingdom biofilm-derived metabolites. Scientific Reports 7 (2017) 41332.
20. Niepa, T.H.R., Wang, H., Gilbert, J.L., and Ren, D^#. Eradication of Pseudomonas aeruginosa cells by cathodic electrochemical currents delivered with graphite electrodes. Acta Biomaterialia 50 (2017) 344-352.
21. Murphy, D., Gemmell, B., Vaccari, L., Li, C., Bacosa, H., Evans, M., Gemmell, C., Harvey, T., Jalali, M., Niepa, T.H.R. An in-depth survey of the oil spill literature since 1968: Long term trends and changes since Deepwater Horizon. Marine Pollution Bulletin 113 (1-2) (2016) 371–379.
22. Hann, D.S., Niepa, T.H.R., Stebe, K.J.^#, Lee, D.^#. One-step generation of cell-viable compartments via polyelectrolyte complexation in an aqueous two-phase system. ACS Applied Materials & Interfaces 8 (38) (2016) 25603–25611.
23. Niepa, T.H.R., Hou, L., Jiang, H., Goulian, M., Koo, H., Stebe, K.J.^#, and Lee, D.^#. Microbial Nanoculture as an Artificial Microniche. Scientific Reports 6 (2016) 30578.
24. Niepa, T.H.R., Wang, H., Dabrowiak, J.C., Gilbert, J.L., Ren, D. Synergy between tobramycin and trivalent chromium ion in electrochemical control of Pseudomonas aeruginosa. Acta Biomaterialia 36 (2016) 286–295.
25. Niepa, T.H.R., Snepenger, L.M., Wang, H., Sivan, S., Gilbert, J.L., Jones, M.B., Ren, D. Sensitizing Pseudomonas aeruginosa cells to antibiotics by electrochemical disruption of membrane functions. Biomaterials 74 (2016) 267-279.
26. Niepa, T.H.R., Gilbert, J.L, and Ren, D^#. Controlling Pseudomonas aeruginosa persister cells by weak electrochemical currents and synergistic effects with tobramycin. Biomaterials 33(30) (2012) 7356-7365.
27. Szkotak, R., Niepa, T.H.R., Jawrani, N., Gilbert, J.L., Jones, M.B., Ren, D. Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis. AMB Express 1 (2011) 39.

Refereed education conference papers (published)

Refereed education conference papers (published)

1. Hornbostel, K., Lieber, A., Riveroa, J., Hildebrandt, D., Snodgrass, C., Gamble, W., Neal, Z., Davidson, S., Usman, H., Niepa, T.H.R. Direct ocean carbon capture using membrane contactors (November 14, 2022). Proceedings of the 16th Greenhouse Gas Control Technologies Conference (GHGT-16) October 23-24, 2022.
2. Yin, S., Wosu, S., Niepa, T.H.R., Trahan, K.W. Diversifying the Advanced Engineering Workforce: Why Low-Income Students Pursue Master's Degrees. 53^rd Annual Conference of the Northeast Educational Research Association – October 19-21, 2022.
3. Yin, S., Wosu, S., Niepa, T.H.R., Trahan, K.W. Graduate Engineering Education Scholarship: funding and supporting low-income students' advanced degrees for industry. 52^nd Annual Meeting of the Northeastern Educational Research Association – Virtual Meeting October 13-15, 2021.
4. House, S.D.*, Balmuri, S.R.*, Yang, J.C., Niepa, T.H.R. Investigating the Mucoid Switch of Pseudomonas aeruginosa at Oil-Water Interfaces. Proceedings of Microscopy & Microanalysis 25 (Suppl 2) 2019 1128.

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Patents and other intellectual properties

IP4.  Niepa, T.H.R., Davidson, S-L. (2020). Microcapsules and methods of using the same (U.S. Patent US11534408B2). This IP holds two inventions.

IP3.  Romo, L., Garritano, N., Niepa, T.H.R. (2013). Door Handle Sterilization System, WO Patent 2,013,025,894.

IP2.  Ren, D. ^#, Zhang M., Niepa, T.H.R., and Gilbert J. (2013). System and method for controlling bacterial cells with weak electric currents. (U.S. Patent 8,663,914).

IP1.  Ren, D. ^#, Zhang M., Niepa, T.H.R., and Gilbert J. (2014). System and method for controlling bacterial persister cells with weak electric currents. (U.S. Patent 8,569,027).

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Join our research lab

Are you looking to make a meaningful impact as a graduate or postdoctoral research fellow? Our lab focuses on cutting-edge research in three exciting areas:

1. Microfluidics technology for high-throughput assessment of microorganisms: Explore innovative ways to integrate microfluidic chips with high-throughput imaging. Analyze large amounts of visual data at the single-cell level, advancing drug discovery, diagnostics, and personalized medicine.
2. Interfacial rheology and mechanobiology of microorganisms: Dive into the fascinating world of biofilms. Investigate their properties, growth mechanisms, and impact on natural and built environments. Uncover the secrets of these microbial communities.
3. Functional and antimicrobial materials: Work with materials that exhibit antibacterial and antiviral properties. Develop functional materials that inhibit microbial adherence through physicochemical factors.

Funding opportunities: We offer funding through federal grants and diversity supplements, providing a supportive environment for your research journey.

If you're excited about scientific exploration and want to contribute to groundbreaking discoveries, contact us! Submit your CV to tniepa@andrew.cmu.edu to discuss this exciting opportunity.

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Media mentions

Niepa honored as Rising Star of Mechanical Engineering

ChemE/BME’s Tagbo Niepa received a Rising Star of Mechanical Engineering award from the American Society of Mechanical Engineers (ASME). The award honors early-career researchers recognized through prestigious awards such as the NSF CAREER and NIH New Innovator awards.

Usman earns bionanotechnology student award at AIChE

ChemE Ph.D. student Huda Usman won 2nd place in the 2024 Bionanotechnology Graduate Student Awards at the 2024 American Institute of Chemical Engineers (AIChE) Annual Meeting.

Chemical & Engineering News

Niepa comments on synthetic polymer that mimics barnacles

ChemE’s Tagbo Niepa was quoted by Chemical & Engineering News about a recent study that developed a synthetic polymer that can mimic the ways in which barnacles clean surfaces. Niepa explained the potential benefits this development could provide, explaining, “you can think about a way of cleaning a catheter, for instance, that is fully infected with bacteria.”

CMU Engineering

Engineering faculty awarded professorships

Carnegie Mellon University has awarded professorships to five exceptional faculty members in the College of Engineering.

See More Mentions

Chemical Engineering

Taking microbial research from nano to global

Tagbo Niepa presented at symposia in Colombia and Morocco to facilitate international collaboration and apply innovations from his lab to global health challenges in different contexts.

Cue and Usman earn Emerging Researchers National Conference awards

ChemE Ph.D. students Camila Cue and Huda Usman gave oral presentations at the 2024 Emerging Researchers National (ERN) Conference in STEM. Cue won 1st place in the Technology and Engineering - Biomedical Engineering track of the graduate oral presentations.

Chemical Engineering

Studying microbes in marine environments and microcapsules

Ph.D. student Huda Usman is applying her experience at the prestigious Marine Biological Laboratory to her research miniaturizing the culture system.

Chemical Engineering

Tagbo H.R. Niepa joins ChemE faculty

In fall 2023, the Department of Chemical Engineering will welcome Tagbo H.R. Niepa as an associate professor.

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