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M. Ashfaqul Alam, PhD


Office: (859) 562-2827
Office: MS 423 Medical Science Bldg.


  • Assistant Professor

College Unit(s)

Biography and Education


Ph.D.: Department of Microbiology and Immunology, Laboratory of Dr. Michelle Dziejman, University of Rochester School of Medicine and Dentistry, Rochester, NY. Faculty and Postdoctoral training: Epithelial Biology & Microbiome Study in Gastrointestinal Diseases, Laboratory of Professor Andrew Neish, MD, Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA.


Current research in the Alam laboratory focuses on the study of host-microbiota interactions. Trillions of microorganisms are living inside every person, which are collectively known as the microbiota. Moreover, the microbiota and its genes are known as the microbiome. The mammalian intestine harbors a diverse microbial community, which profoundly influences many aspects of host biology. The intestinal epithelial cells provide a barrier function by separating the colonized microbes from the systemic tissues, and yet, it provides a gateway for the cross-talk between the host and microbiome. The epithelial barrier function is central to health. Thus, the breakdown of the barrier is involved in a wide variety of clinical conditions, including inflammatory bowel diseases and colorectal cancer. The alterations in gut microbiota, which is termed microbial dysbiosis, damage the intestinal epithelial barrier and result in intestinal inflammation and impaired repair. However, mechanistically, little is known about how the gut microbiota dampens the inflammation and restores homeostasis. Previously, we have reported that Akkermansia muciniphila (an anaerobic, mucinophilic novel enteric bacteria) stimulated proliferation and migration of enterocytes. However, we do not know how A. muciniphila ameliorates inflammation. We apply state-of-the-art computational and bioinformatics tools to perform metagenomic and metabolomic analysis to determine the intestinal microbiome and their products. At the same time, we utilize cutting-edge microbiology and molecular biology techniques to investigate the functional role of specific commensal bacteria, their genes, and metabolic products. Figure_Spatiotemporal change of microbiome.pdf…

Selected Publications

Absence of neurotensin attenuates intestinal dysbiosis and inflammation by maintaining Mmp7/α-defensin axis in diet-induced obese mice. 2020 May 2. Authors: Li J, Li X, Song J, Yan B, Rock SA, Jia J, Liu J, Wang C, Weiss T, Weiss HL, Gao T, Alam A, Evers BM. FASEB J. 2020;00:1–15

Initiation of Parkinson's disease from gut to brain by -secretase. 01/01/2020 Authors: Ahn EH; Kang SS; Liu X; Chen G; Zhang Z; Chandrasekharan B; Alam AM; Neish AS; Cao X; Ye K Cell Res. Volume: 30 Page(s): 70 - 87

Neutrophil-Derived Reactive Oxygen Orchestrates Epithelial Cell Signaling Events during Intestinal Repair. 11/01/2019 Authors: Matthews JD; Owens JA; Naudin CR; Saeedi BJ; Alam A; Reedy AR; Hinrichs BH; Sumagin R; Neish AS; Jones RM Am J Pathol. Volume: 189 Page(s): 2221 - 2232.

Interactions Between Commensal Bacteria and Enteric Neurons, via FPR1 Induction of ROS, Increase Gastrointestinal Motility inMice. 07/01/2019 Authors: Chandrasekharan B; Saeedi BJ; Alam A; Houser M; Srinivasan S; Tansey M; Jones R; Nusrat A; Neish AS Gastroenterology. Volume: 157 Page(s): 179 - 192.e2

Role of gut microbiota in intestinal wound healing and barrier function. 01/01/2018 Authors: Alam A; Neish A Tissue Barriers. Volume: 6 Page(s): 1539595

The microenvironment of injured murine gut elicits a local pro-restitutive microbiota. 01/27/2016 Authors: Alam A; Leoni G; Quiros M; Wu H; Desai C; Nishio H; Jones RM; Nusrat A; Neish AS Nature Microbiology. Volume: 1 Page(s): 15021

Neutrophil interactions with epithelial-expressed ICAM-1 enhances intestinal mucosal wound healing. 09/01/2016 Authors: Sumagin R; Brazil JC; Nava P; Nishio H; Alam A; Luissint AC; Weber DA; Neish AS; Nusrat A; Parkos CA Mucosal Immunol. Volume: 9 Page(s): 1151 - 1162.

Using S. cerevisiae as a Model System to Investigate V. cholerae VopX-Host Cell Protein Interactions and Phenotypes. 10/14/2015 Authors: Seward CH; Manzella A; Alam A; Butler JS; Dziejman M Toxins (Basel). Volume: 7 Page(s): 4099 - 4110

Annexin A1-containing extracellular vesicles and polymeric nanoparticles promote epithelial wound repair. 03/02/2015 Authors: Leoni G; Neumann P-A; Kamaly N; Quiros M; Nishio H; Jones HR; Sumagin R; Hilgarth RS; Alam A; Fredman G J Clin Invest. Volume: 125 Page(s): 1215 - 1227.

Redox signaling regulates commensal-mediated mucosal homeostasis and restitution and requires formyl peptide receptor 1. 05/01/2014 Authors: Alam A; Leoni G; Wentworth CC; Kwal JM; Wu H; Ardita CS; Swanson PA; Lambeth JD; Jones RM; Nusrat A Mucosal Immunol. Volume: 7 Page(s): 645 - 655.

Symbiotic lactobacilli stimulate gut epithelial proliferation via Nox-mediated generation of reactive oxygen species. 11/27/2013 Authors: Jones RM; Luo L; Ardita CS; Richardson AN; Kwon YM; Mercante JW; Alam A; Gates CL; Wu H; Swanson PA EMBO J. Volume: 32 Page(s): 3017 - 3028.

Annexin 1 in microparticles promotes intestinal mucosal wound repair during inflammation. 05/01/2013 Authors: Nusrat A; Leoni G; Neumann P-A; Alam A; Lambeth D; Hilgarth R; Kusters D; Reutelingsperger C; Perretti M; Parkos C J Clin Invest. Volume: 190.

Annexin A1, formyl peptide receptor, and NOX1 orchestrate epithelial repair. 01/01/2013 Authors: Leoni G; Alam A; Neumann P-A; Lambeth JD; Cheng G; McCoy J; Hilgarth RS; Kundu K; Murthy N; Kusters D J Clin Invest. Volume: 123 Page(s): 443 - 454.

Enteric commensal bacteria induce extracellular signal-regulated kinase pathway signaling via formyl peptide receptor-dependent redox modulation of dual specific phosphatase 3. 11/04/2011 Authors: Wentworth CC; Alam A; Jones RM; Nusrat A; Neish AS J Biol Chem. Volume: 286 Page(s): 38448 - 38455

Identification of Vibrio cholerae type III secretion system effector proteins. 04/01/2011 Authors: Alam A; Miller KA; Chaand M; Butler JS; Dziejman M Infect Immun. Volume: 79 Page(s): 1728 - 1740

vttRA and vttRB Encode ToxR family proteins that mediate bile-induced expression of type three secretion system genes in a non-O1/non-O139 Vibrio cholerae strain. 06/01/2010 Authors: Alam A; Tam V; Hamilton E; Dziejman M Infect Immun. Volume: 78 Page(s): 2554 - 2570

Identification of in vivo-induced bacterial protein antigens during human infection with Salmonella enterica serovar Typhi. 09/01/2006 Authors: Harris JB; Baresch-Bernal A; Rollins SM; Alam A; LaRocque RC; Bikowski M; Peppercorn AF; Handfield M; Hillman JD; Qadri F. Infect Immun. Volume: 74 Page(s): 5161 - 5168.

Application of in vivo induced antigen technology (IVIAT) to Salmonella enterica serotype typhi: Identification of pagc as a marker of S-typhi infection. 12/01/2005 Authors: Harris JB; Baresch-Bernal A; Alam A; LaRocque RC; Qadri F; Calderwood SB; Breiman RF; Brooks WA; Handfield M; Rollins S. AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE. Volume: 73 Page(s): 190 - 190

Hyperinfectivity of human-passaged Vibrio cholerae can be modeled by growth in the infant mouse. 10/01/2005 Authors: Alam A; Larocque RC; Harris JB; Vanderspurt C; Ryan ET; Qadri F; Calderwood SB Infect Immun. Volume: 73 Page(s): 6674 - 6679

Host-induced epidemic spread of the cholera bacterium. 06/06/2002 Authors: Merrell DS; Butler SM; Qadri F; Dolganov NA; Alam A; Cohen MB; Calderwood SB; Schoolnik GK; Camilli A. Nature. Volume: 417 Page(s): 642 - 645