Hazime H, Ducasa GM, Santander AM, Brito N, Gonzalez-Horta EE, Quintero MA, Barnes S, Wilson L, Zhang Y, Yu F, Gharaibeh RZ, Jobin C, Faust KM, Damas OM, Deshpande A, Kerman DH, Proksell S, Pignac-Kobinger J, Fernández I, Burgueño JF, Abreu MT.
Wheat-based protein slows disease progression in Pkd1 knockout mice.
Gut. 2025 Apr 29:gutjnl-2024-334346. doi: 10.1136/gutjnl-2024-334346. Online ahead of print. PMID: 40301115 Free article.
DUOX2 activation drives bacterial translocation and subclinical inflammation in IBD-associated dysbiosis
Hazime H, Ducasa GM, Santander AM, Brito N, Gonzalez-Horta EE, Quintero MA, Barnes S, Wilson L, Zhang Y, Yu F, Gharaibeh RZ, Jobin C, Faust KM, Damas OM, Deshpande A, Kerman DH, Proksell S, Pignac-Kobinger J, Fernández I, Burgueño JF, Abreu MT.
DUOX2 activation drives bacterial translocation and subclinical inflammation in IBD-associated dysbiosis
Gut. 2025 Apr 29:gutjnl-2024-334346. doi: 10.1136/gutjnl-2024-334346. Online ahead of print.PMID: 40301115 Free article.
PowerTalks Seminar Series – Stephen Barnes, Ph.D. (April 18, 2025)
Metabolomics and data science: data structure, interpretation and discovery
Summery
Dr. Stephen Barnes discussed the origins and data interpretation of metabolomics, his personal journey in the field, and his role in organizing a workshop on metabolomics. He also detailed the process of analyzing samples using a column, the challenges of interpreting large amounts of data, and the use of software for data analysis. The discussion also covered the use of mass spectrometry in analyzing patient samples, the process of converting cholesterol into bile acids, and the findings of various studies on metabolomics.
MetabHole Talk: Metabolomics and Africa
Apr 18, 2025

Stephen Barnes, PhD, FASN
University of Alabama at Birmingham
Birmingham, AL, USA
MetabHole is a group headed by Olakunle Jaiyesimi, a postdoctoral fellow at Harvard, that has as its goal the education of African scientists in the techniques of metabolomics and associated data analysis. It’s an extension of “Teaching metabolomics: a UAB outreach to researchers in sub-Saharan Africa” in 2016
Metabolomics and Africa Welcome, with Professor Stephen Barnes
Apr 20, 2025
Welcome to this special MetabHole Webinar in collaboration with the Drosophila Research and Training Center, Nigeria, featuring the distinguished Professor Steven Barnes from the University of Alabama.
Metabolomics and Africa A Background Professor Stephen Barnes
Apr 20, 2025
Join us for this extraordinary MetabHole webinar, where world-renowned scientist Professor Stephen Barnes (University of Alabama at Birmingham, UAB) shares his incredible journey—from his early days working with Nobel Laureates to pioneering global training in metabolomics.
Metabolomics and Africa Why is Metabolomics important Professor Stephen Barnes
Apr 20, 2025
What makes life work? In this captivating session, Professor Stephen Barnes (UAB) explores why metabolomics is essential to understanding human biology, nutrition, and even agricultural innovation.
Metabolomics and Africa Short History of Metabolomics Professor Stephen Barnes
Apr 20, 2025
Join Professor Stephen Barnes as he delves into the transformative journey of metabolomics, highlighting pivotal advancements in analytical chemistry and data processing. This comprehensive lecture offers insights into the methodologies that have shaped modern metabolomic studies.
Metabolomics and Africa Training Options in Metabolomics Professor Stephen Barnes
Apr 20, 2025
Join renowned Professor Stephen Barnes as he shares a deeply informative and inspiring session on metabolomics education, training programs, and international collaborations—with a spotlight on Africa’s emerging metabolomics capacity.
Metabolomics and Africa Summary and Conclusions Professor Stephen Barnes
Apr 20, 2025
In this powerful closing session, Professor Stephen Barnes delivers heartfelt reflections on the evolution of metabolomics—from early chromatography experiments to cutting-edge multi-omics data integration. He shares valuable insights into the future of biological systems research, celebrates global collaborations, and honors the mentors, students, and colleagues who helped shape a lifetime of discovery.
Metabolomics and Africa – Questions and Discussions Professor Stephen Barnes
Apr 20, 2025
Join us for the engaging and enlightening Q&A and concluding session of the MetabHole webinar titled “The Importance of Metabolomics to Students, Graduates, and Universities”. Featuring global metabolomics pioneer Professor Stephen Barnes of the University of Alabama at Birmingham (UAB), this session dives deep into practical applications, challenges, and training opportunities in targeted and untargeted metabolomics, NMR, LC-MS, and biomarker discovery.
Macrophage-Specific Lactate Dehydrogenase Expression Modulates Inflammatory Function In Vitro
Lu Y, Osis G, Zmijewska AA, Traylor A, Thukral S, Wilson L, Barnes S, George JF, Agarwal A.
Macrophage-Specific Lactate Dehydrogenase Expression Modulates Inflammatory Function In Vitro
Kidney360. 2025 Feb 1;6(2):197-207. doi: 10.34067/KID.0000000630 Epub 2024 Nov 12. PMID: 39531318 Free PMC article.
COPD and BPD: Inhalation of live Lactobacilli lessens lung inflammation and improves lung function
Research & Innovation, August 21, 2024
Media contact: Jeff Hansen

In preclinical models, the inhalation of a mixture of living Lactobacilli bacteria attenuated pulmonary inflammation and improved lung function and structure for the chronic lung diseases bronchopulmonary dysplasia and chronic obstructive pulmonary disease.
This study, published in the journal Nature Communications, determined the mechanism of this live biotherapeutic product — a powder mixture of living Lactobacilli bacteria — to reduce neutrophilic inflammation and reduce a broad swath of inflammatory markers in BPD and COPD, says Charitharth Vivek Lal, M.D., a University of Alabama at Birmingham neonatologist who co-led the research with Amit Gaggar, M.D., Ph.D., a UAB pulmonologist.
Their findings “provide a paradigm for the progression of structural lung disease,” Lal said, because it identifies the Lactobacilli as critical to regulating lung protease activity that is linked to the destruction caused by matrikine generation, extracellular matrix turnover and chronic neutrophilic inflammation that damages air sacs in the lungs.
A possible protective role for Lactobacilli in the lung and the possible use of Lactobacilli to treat chronic lung disease had its foundation in 2016 when Lal and UAB colleagues discovered that the airways of infants with severe bronchopulmonary dysplasia had decreased numbers of Lactobacilli, increased numbers of proteobacteria and increased concentrations of proteobacterial endotoxin. In this latest study, the UAB researchers provide a mechanism of action for the Lactobacilli treatment to decrease downstream disease development and showed safety and effectiveness of the live biotherapeutic treatment in a mouse pup model for BPD and three mouse models of COPD.
Bronchopulmonary dysplasia develops in some extremely premature infants after damage induced by high oxygen tension or mechanical ventilation needed to keep them alive. COPD occurs in older people, especially smokers, and kills about 130,000 Americans a year and about 3 million more worldwide.

“Inhaled live biotherapeutic products show promise in addressing common pathways of disease progression that in the future can be targeted at a variety of lung diseases,” Lal said. “Preclinical animal data is suggestive, and safety of the potential drug in humans will be tested in a forthcoming clinical trial. Human adult safety data in COPD will help de-risk the pathway to approval for use of the drug in bronchopulmonary disease infants.”
The UAB researchers hypothesized that mouse models of BPD would show heightened levels of acetylated proline-glycine-proline, or Ac-PGP, an extracellular matrix-derived peptide, as had been seen in premature infants with BPD.
This was demonstrated in BPD mouse models, and gain- or loss-of-function studies showed the impact of Ac-PGP. Intranasal instillation of Ac-PGP increased neutrophilic inflammation and lung degradation. When an inhibitor of Ac-PGP was given with the Ac-PGP, markers of neutrophilic inflammation decreased and lung structure improved.
Researchers then showed that a proprietary Lactobacilli blend of L. planatarum, L. acidophilus and L. rhamnosus performed best in synergy to reduce the inflammatory proteinase MMP-9, which helps release the Ac-PGP from extracellular matrix. Furthermore, supernatant from Lactobacilli growth medium also reduced MMP-9 at a similar magnitude as live Lactobacilli bacteria.
A key finding was that L(+) lactic acid, which is produced in Lactobacilli growth medium supernatant, reduced MMP-9 in vitro, showing an important role for this lactic acid as an anti-inflammatory molecule. Researchers found that live Lactobacilli in the lungs provided an ongoing, sustained release of L(+) lactic acid in a controlled and well-tolerated manner.
A major technological advance reported in the study was creating the inhaled Lactobacilli powder through particle engineering — particles small enough to reach deep into the lungs while preserving viable bacteria. This live biotherapeutic product was then tested in the BPD and COPD models. In the COPD mouse models, the blend successfully reduced inflammation in the lung microenvironment whether treated concurrently or post-injury, showing anti-inflammatory effects, decrease of several pro-inflammatory markers and elevation of the anti-inflammatory marker IgA.

An interesting finding was the favorable performance of the live biotherapeutic product. It reduced MMP-9 and other pro-inflammatory cytokines as well as, or in some cases better than, fluticasone furoate, a United States Food and Drug Administration-approved inhaled corticosteroid found in COPD combination therapies.
Safety and biodistribution studies in one of the COPD mouse models showed that inhalation of the bacterial powder did not initiate adverse reactions or disease, and the Lactobacilli did not translocate to distal tissues or accumulate in the lungs.
Co-first authors of the study, “A Lactobacilli-based inhaled live biotherapeutic product attenuates pulmonary neutrophilic inflammation,” are Teodora Nicola and Nancy Wenger, UAB Department of Pediatrics, Division of Neonatology.
Other authors, along with Lal, Gaggar, Nicola and Wenger, are Xin Xu, Camilla Margaroli, Kristopher Genschmer, J. Edwin Blalock, UAB Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine; and Michael Evans, Luhua Qiao, Gabriel Rezonzew, Youfeng Yang, Tamas Jilling, Kent Willis and Namasivayam Ambalavanan, UAB Department of Pediatrics, Division of Neonatology.
Support came from National Heart, Lung and Blood Institute of the National Institutes of Health grants HL141652, HL135710, HL166433, HL156275 and HL164156.
Part of this research is patented under “Inhaled respiratory probiotics for lung diseases of infancy, childhood and adulthood,” U.S. 11,141,443 B2, held under the University of Alabama at Birmingham Research Foundation, which is part of the Bill L. Harbert Institute for Innovation and Entrepreneurship, with Lal, Gaggar and Ambalavanan as inventors. This proprietary product has been commercialized through UAB startup Alveolus Bio, Inc., based in Birmingham, Alabama, and Boston, Massachusetts.
At UAB, Pediatrics and Medicine are departments in the Marnix E. Heersink School of Medicine, and Lal is the director of Clinical Innovation at the Marnix E. Heersink Institute for Biomedical Innovation. Lal is an associate professor in the Division of Neonatology, and Gaggar is professor in the Division of Pulmonary, Allergy and Critical Care Medicine. Lal is also the founder of UAB startups Alveolus Bio, Inc., and Resbiotic Nutrition, Inc.
Faculty recognized at Endowed Chairs and Professorships Reception
May 01, 2023
Written by: Jessica Martindale

Anupam Agarwal, M.D., dean of the Heersink School of Medicine, welcomed faculty members and their families to the Endowed Chairs and Professorships Reception on April 25. Leaders from the Heersink School of Medicine joined the faculty honorees and their families to celebrate their endowed chairs and professorships.
Endowed chairs and professorships give donors the chance to link their names to an area of special interest within the university. Some choose to direct their gifts—to endow a chair or professorship in the academic discipline that inspired them, to create scholarships or fellowships for deserving students, or to support medical research of particular importance to them.
Recipients were honored and donors who have created or contributed to the endowed chairs and professorships were recognized. Following the awards, the honored faculty members stayed for group pictures and enjoyed light refreshments with the other guests.
The faculty recognized for new endowed chairs and professorships include:
Ray L. Watts, M.D.
Charles S. Ackerman Endowed Professorship in Parkinson’s Disease
Michelle Gray, Ph.D.
Jarman F. Lowder Endowed Professorship in Neuroscience
Edie R. Hapner, Ph.D.
George W. Barber, Jr., Foundation Professorship in Otolaryngology
C. Blake Simpson, M.D.
Abroms Endowed Professorship for the Department of Otolaryngology
Michael J. Mugavero, M.D.
Jeanne M. Marrazzo, M.D., M.P.H., Endowed Professorship in Innovation and Advancement through Mentorship
Bassel El-Rayes, M.D.
Albert F. LoBuglio Endowed Chair for Translational Cancer Research

Amit Gaggar, M.D., Ph.D.
William C. Bailey, M.D., Endowed Chair in Pulmonary Disease
Surya P. Bhatt, M.D., MSPH
Endowed Professorship in Airways Disease
Luciano Costa, M.D., Ph.D.
Mary and Bill Battle Endowed Professorship for Multiple Myeloma
Renee Heffron, Ph.D., MPH
Jim Straley Endowed Chair in AIDS Research
Erwin G. Van Meir, Ph.D.
David Hart White Endowed Professorship for Brain Cancer Research
Farah D. Lubin, Ph.D.
Triton Endowed Professorship in Neurobiology
David A. Schneider, Ph.D.
Louise T. Chow, Ph.D.-Heersink Endowed Chair in Biochemistry and Molecular Genetics
Suzanne E. Lapi, Ph.D.
Emmet O’Neal II Endowed Professorship in Lung Cancer Research
Karen L. Gamble, Ph.D.
E. Cleveland Kinney Endowed Chair in Geriatric Psychiatry
Karen Cropsey, Psy.D.
Kathy Ireland Endowed Chair for Psychiatric Research
Lewis Z. Shi, M.D., Ph.D.
Koikos-Petelos-Jones-Bragg ROAR Endowed Professorship for Cancer Research
Brant Wagener, M.D., Ph.D.
Simon Gelman Endowed Professorship in Anesthesiology
See photos from the event below or click here to see all reception photos.


Workshop “Bridging the Gap Between Clinical and Basic Research to Understand COPD Mechanisms”
NIH, June 13 – June 14, 2023
Description
The National Heart, Lung, and Blood Institute (NHLBI) organized a two-day virtual workshop titled “Bridging the Gap Between Clinical and Basic Research to Understand Chronic Obstructive Pulmonary Disease (COPD) Mechanisms” on June 13th – 14th, 2023. More than 200 participants joined this virtual workshop from across the United States and worldwide. This workshop brought together a diverse group of experts, including clinical and basic scientists from the COPD research community. The primary objectives of the workshop were twofold: first, to evaluate the current state of COPD research, particularly focusing on the knowledge gained from major cohort studies of COPD patients, and second, to explore how this knowledge can be applied to generate relevant and testable questions that can be addressed through basic mechanistic research. The workshop also aimed to identify challenges and opportunities in COPD pathogenesis research. Over the last several decades, a number of large longitudinal clinical studies of COPD patients in the United States and elsewhere have generated a wealth of data, significantly enhancing our understanding of COPD pathophysiology, risk factors, and progression. However, there has been a notable gap in bridging the findings from clinical research to hypothesis-driven basic research. There remain significant deficits in understanding of the mechanisms that underlie the onset and progression of COPD, which is increasingly clinically complex and heterogeneous, and might be better addressed through more effective interactions between clinical and basic researchers. The strategic intent of this workshop was to define a research vision and agenda for advancing COPD pathogenesis studies. To that end, the participants worked toward developing promising and testable hypotheses and identifying appropriate experimental systems and tools. Gaining a deeper understanding of COPD pathobiology and pathogenesis will facilitate the discovery of therapeutic strategies that go beyond treating symptoms and move toward arresting progression and ultimately cure of the disease.
Program Book
View the program book at NIH website.
Barnes elevated to Distinguished Professor
UAB Reporter
July 30, 2018
The University of Alabama System Board of Trustees awarded the rank of Distinguished Professor to five faculty during its meeting June 8.

Stephen Barnes, Ph.D., was named Distinguished Professor of Pharmacology and Toxicology in the School of Medicine. Barnes came to UAB in 1977 as a mathematical gastroenterology fellow through the National Library of Medicine and joined the faculty in 1979 as an assistant professor. Now, in addition to his position in the Department of Pharmacology and Toxicology, Barnes is a senior scientist at UAB’s Center for Free Radical Biology, Nutrition Obesity Research Center, Center for Bone and Joint Disease and Nephrology Research and Training Center and he has dual appointments in the departments of Environmental Health Sciences, Genetics and Vision Sciences.
Barnes has published more than 300 peer-reviewed journal articles, reviews and book chapters and has delivered lectures at institutions such as Vanderbilt University, Johns Hopkins University and the University of Durham in in Durham, England. In 2012, Barnes was named UAB’s Distinguished Faculty Lecturer. He also is a member of the International Science Advisory Panel at Imperial College London’s National Phenome Center.
UAB School of Engineering and Medicine: Weekly Seminar
1:25 pm – 2:15 pm, Friday, October 27, 2017
Heritage Hall – Room 125

Stephen Barnes, Ph.D.
Professor of Pharmacology and Toxicology, Biochemistry and Molecular Genetics, Environmental Health Sciences, and Vision Sciences
Director, Targeted Metabolomics and Proteomics Laboratory
Senior Scientist, UAB Comprehensive Cancer Center
“Metabolomics and engineering – a two-way process”
As for many other areas of science, bioanalysis is built on the principles of physics and its application to physical processes and the engineering needed to make it better/faster/cheaper. Chromatographic separation of biological analytes is no exception – it began over a century ago in the separation of plant pigments, and has moved to concepts of phase partition (and a Nobel Prize in 1952) to GC and LC and is combined with all sorts of detection systems (another Nobel Prize in 2002). By identifying critical steps in metabolism associated with disease identified with metabolomics, geneticists are applying gene therapy as clinical treatments. The same principles can be applied to organisms that can be engineered make either unique compounds with complex chiral chemistry, or large amounts of chemicals suitable as feedstocks. Engineering and science is now catching up with yeasts and the wine industry that figured out how to this before the advent of systematic bioanalytical science.