The intestinal microbiota is extremely important to human health and development. Over the last decade, there has been a tremendous surge in the number of studies analyzing the gut microbiota; however, there are still relatively few mechanistic studies aimed at understanding basic biological properties of this ecosystem and its members. In recent years, our lab has been studying how predominant gut Bacteroidales members interact with each other in both beneficial and competitive/antagonistic relationships. These studies are essential to understanding how these bacteria become established in the mammalian intestine to form stable health- promoting communities. This proposal is a continuation of our studies of antagonism among these bacteria, specifically studying secreted antimicrobial molecules produced by the gut Bacteroidales. Under the initial project, we made unexpected findings regarding the types of secreted antimicrobial molecules produced, the range of Bacteroidales species that secrete antimicrobial molecules, and the mechanisms of resistance in producing strains. The goal of this renewal project is to understand the breadth of secreted antimicrobial molecules produced by the gut Bacteroidales, their targets and mechanisms of action in sensitive cells, and their importance in mediating competition, invasion and defense in the mammalian gut microbiota.
In Aim 1, we will study a large class of proteins with membrane attack/perforin domains produced by diverse gut Bacteroidales using predictive data to determine which of these molecules have antimicrobial activity and how they target sensitive cells.
In Aim 2, we will study a eukaryotic-like ubiquitin molecule with antimicrobial activity, likely acquired by B. fragilis by inter-kingdom transfer, and determine its target and mechanism of action.
Aim 3 is designed to analyze the breadth of antimicrobial molecules produced by the gut Bacteroidales by studying diverse Bacteroidales species that produce potent secreted antimicrobial molecules of different classes.
In Aim 4, we will use a combination of analyses, including computational modeling, experimental analyses in gnotobiotic mice, and analyses of human metagenomic datasets to understand the ecological relevance of secreted antimicrobial molecules of the gut Bacteroidales and how they contribute to ecosystem invasion, defense, and stability. Currently, we are the only group studying secreted antimicrobial proteins of the gut Bacteroidales and their ecological implications. The comprehensive analyses that will be performed in this proposal are unprecedented in the field and the ecological properties that we uncover will serve as guiding principles that can be applied to numerous human health applications such as restoring a healthy microbiota to dysbiotic patients, and the creation of improved probiotics.

Public Health Relevance

Our intestines are inhabited by a dense microbial community that is essential to our health and well-being, yet we know very little about how the microbial members of this ecosystem interact with each other to form these communities. For this project, we will study secreted antimicrobial molecules produced by the most abundant order of bacteria in our intestines and investigate their relevance in shaping the mammalian gut microbiota. These studies have numerous applications and will help us better understand how to return a healthy and stable intestinal microbiota to people with imbalances in this important microbial community.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Baqar, Shahida
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Brigham and Women's Hospital
United States
Zip Code
McEneany, Valentina Laclare; Coyne, Michael J; Chatzidaki-Livanis, Maria et al. (2018) Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species. ISME J 12:2919-2928
GarcĂ­a-Bayona, Leonor; Comstock, Laurie E (2018) Bacterial antagonism in host-associated microbial communities. Science 361:
Chatzidaki-Livanis, Maria; Coyne, Michael J; Roelofs, Kevin G et al. (2017) Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism. MBio 8:
Coyne, Michael J; Comstock, Laurie E (2016) A New Pillar in Pilus Assembly. Cell 165:520-1
Coyne, Michael J; Roelofs, Kevin G; Comstock, Laurie E (2016) Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. BMC Genomics 17:58
Roelofs, Kevin G; Coyne, Michael J; Gentyala, Rahul R et al. (2016) Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo. MBio 7:
Chatzidaki-Livanis, Maria; Geva-Zatorsky, Naama; Comstock, Laurie E (2016) Bacteroides fragilis type VI secretion systems use novel effector and immunity proteins to antagonize human gut Bacteroidales species. Proc Natl Acad Sci U S A 113:3627-32
Chatzidaki-Livanis, Maria; Comstock, Laurie E (2015) Friend turned foe: a role for bacterial sulfatases in colitis. Cell Host Microbe 17:540-1
Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson et al. (2014) Evidence of extensive DNA transfer between bacteroidales species within the human gut. MBio 5:e01305-14
Chatzidaki-Livanis, Maria; Coyne, Michael J; Comstock, Laurie E (2014) An antimicrobial protein of the gut symbiont Bacteroides fragilis with a MACPF domain of host immune proteins. Mol Microbiol 94:1361-74