: The intestinal tract is home to a densely populated microbial community whose members have varying sensitivities to oxygen, ranging from aerobes to facultative anaerobes to obligate anaerobes. It is widely thought that the colonic environment is anaerobic. The complexity of bacterial communities along with the dramatic alterations in community structure observed in pathologic states, such as inflammatory bowel disease (IBD), suggests that resident gut microbes may be responsive to alterations in luminal oxygen. Unfortunately, very little data currently exists on the oxygen (O2) content in the colon due to the lack of appropriate methods for quantifying oxygen levels. More critically, evidence elucidating the fundamental mechanism(s) by which the colonic environment is maintained in an anaerobic state is lacking. In Preliminary Data, we show that both colonic tissue and luminal oxygen levels can be measured in vivo non- invasively by the phosphorescence quenching method, making use of non-toxic water- soluble oxygen-sensitive dyes - a technical advance that has led to the following two observations: 1) Partial pressure of oxygen (pO2) in the cecal lumen is remarkably lower than pO2 in the adjacent tissue;2) Inspiration of pure O2 leads to a rapid increase in the cecal tissue pO2 and a more gradual increase in the luminal pO2. Based on these findings, we hypothesize that a dynamic equilibrium is maintained whereby oxygen released by colonic tissue is consumed by the gut microbiota thus maintaining an anaerobic environment. In support of this notion, we also provide data showing that the microbiota adherent to the human colonic mucosa is enriched for aerobic and facultative anaerobes relative to the feces where obligate anaerobes predominate. We further hypothesize that the well-described """"""""dysbiotic"""""""" composition of the gut microbiome observed in IBD, with the bloom of aerobic Proteobacteria and Actinobacteria, is a response of the gut microbiota to higher pO2 levels and subsequent oxidative stress.

Public Health Relevance

: Growing evidence suggests that the composition of bacterial populations in the gut, collectively known as the gut microbiota, is associated with a number of important human disease processes. Using a novel approach that permits the measurement of oxygen levels in the intestinal tract, we show that the host and gut microbiota to interact to maintain a dynamic oxygen equilibrium in the gut. Ultimately, the ability to measure intestinal oxygen levels and/or alter the gut microbiota by noninvasively altering host tissue oxygenation may lead to the development of innovative therapeutic approaches in the management of disease states associated with the gut microbiota such as IBD and Clostdrium difficile colitis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZGM1-GDB-2 (MC))
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Sledjeski, Darren D
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University of Pennsylvania
Internal Medicine/Medicine
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United States
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Friedman, Elliot S; Bittinger, Kyle; Esipova, Tatiana V et al. (2018) Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proc Natl Acad Sci U S A 115:4170-4175
Ni, Josephine; Shen, Ting-Chin David; Chen, Eric Z et al. (2017) A role for bacterial urease in gut dysbiosis and Crohn's disease. Sci Transl Med 9:
Lin, Huiyun; Zhang, Rongxiao; Gunn, Jason R et al. (2016) Comparison of Cherenkov excited fluorescence and phosphorescence molecular sensing from tissue with external beam irradiation. Phys Med Biol 61:3955-68
Wu, Gary D; Compher, Charlene; Chen, Eric Z et al. (2016) Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 65:63-72
Shen, Ting-Chin David; Chehoud, Christel; Ni, Josephine et al. (2016) Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium. PLoS One 11:e0155620
Lewis, James D; Chen, Eric Z; Baldassano, Robert N et al. (2015) Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host Microbe 18:489-500
Zhang, Rongxiao; D'souza, Alisha V; Gunn, Jason R et al. (2015) Cherenkov-excited luminescence scanned imaging. Opt Lett 40:827-30
Chehoud, Christel; Albenberg, Lindsey G; Judge, Colleen et al. (2015) Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Inflamm Bowel Dis 21:1948-56
Esipova, Tatiana V; Vinogradov, Sergei A (2014) Synthesis of phosphorescent asymmetrically ?-extended porphyrins for two-photon applications. J Org Chem 79:8812-25
Wu, Gary D (2014) Diet, the gut microbiome and the metabolome in IBD. Nestle Nutr Inst Workshop Ser 79:73-82

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