The gut microbiota and gastrointestinal surgery

Journal name:
Nature Reviews Gastroenterology & Hepatology
Year published:
Published online


Surgery involving the gastrointestinal tract continues to prove challenging because of the persistence of unpredictable complications such as anastomotic leakage and life-threatening infections. Removal of diseased intestinal segments results in substantial catabolic stress and might require complex reconstructive surgery to maintain the functional continuity of the intestinal tract. As gastrointestinal surgery necessarily involves a breach of an epithelial barrier colonized by microorganisms, preoperative intestinal antisepsis is used to reduce infection-related complications. The current approach to intestinal antisepsis varies widely across institutions and countries with little understanding of its mechanism of action, effect on the gut microbiota and overall efficacy. Many of the current approaches to intestinal antisepsis before gastrointestinal surgery run counter to emerging concepts of intestinal microbiota contributing to immune function and recovery from injury. Here, we review evidence outlining the role of gut microbiota in recovery from gastrointestinal surgery, particularly in the development of infections and anastomotic leak. To make surgery safer and further reduce complications, a molecular, genetic and functional understanding of the response of the gastrointestinal tract to alterations in its microbiota is needed. Methods can then be developed to preserve the health-promoting functions of the microbiota while at the same time suppressing their harmful effects.

At a glance


  1. The effect of perioperative events on the intestinal microbiota.
    Figure 1: The effect of perioperative events on the intestinal microbiota.

    The entire process of intestinal surgery, from preoperative preparation to the recovery phase has a substantial and cumulative effect on the intestinal microbiota. a | Baseline microbiota. b | Purgative cleansing eliminates bulky intestinal content and oral antibiotics reduce the luminal bacterial load, leaving behind certain strains of mucosa-associated bacteria. c | Intravenous (IV) antibiotics exert further selective pressure on bacterial composition and function. d | Surgical stress might shift bacterial phenotypes. e | The healthy recovery phase includes refaunation of commensal bacteria; however, selective pressures during microbiota elimination might fundamentally change the subsequent microbiota. MBP, mechanical bowel preparation.

  2. Host-microorganism communication.
    Figure 2: Host–microorganism communication.

    Bacteria and their human hosts communicate and sense one another through various mechanisms. The host immune system can sense bacteria through microorganism-associated molecular patterns (MAMPs) and through bacterial functions such as bile acid conjugation. Bacteria can sense the host state through secreted hormones, opioids and inflammatory signals. Microorganisms communicate among themselves through quorum sensing and the exchange of genetic material.

  3. Altering anatomy alters the physiology and microenvironment of the intestine.
    Figure 3: Altering anatomy alters the physiology and microenvironment of the intestine.

    a | Normal anatomy. b | Roux-en-Y gastric bypass and c | pancreaticoduodenectomy.

  4. Microbial pathogenesis of anastomotic leak: context-dependent virulence expression in response to cues released by surgically injured tissues.
    Figure 4: Microbial pathogenesis of anastomotic leak: context-dependent virulence expression in response to cues released by surgically injured tissues.

    The tissue response to a surgical injury has a key and contributory role in the phenotype transformation or selection of intestinal microorganisms that cause anastomotic leak. The patient undergoes surgical resection inducing physiological stress. The pro-inflammatory reaction releases host stress signals into the local intestinal environment (1). Bacteria recognize host stress signals (2). Bacteria respond to host stress by increasing their adherence capacity and increasing collagenase production (3). Bacterial collagenase breaks down collagen I and activates local tissue matrix metalloproteinase (MMP)9, which then cleaves collagen IV (3). The net result of this process is anastomotic tissue breakdown due to colonizing pathogens that have been 'cued' to express collagenase and cleave MMP9132 (4). MMP, matrix metalloproteinase.


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Author information


  1. MC-6040, Department of Surgery, University of Chicago Medicine, 5841 South Maryland Avenue, Chicago, Illinois 60637, USA.

    • Kristina Guyton
  2. MC-6090, Department of Surgery, University of Chicago Medicine, 5841 South Maryland Avenue, Chicago, Illinois 60637, USA.

    • John C. Alverdy


Both authors contributed equally to all aspects of this manuscript.

Competing interests statement

The authors declare no competing interests.

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  • Kristina Guyton

    Kristina Guyton is a general surgery resident at the University of Chicago Hospitals, USA, and a research fellow in the laboratory of Dr John Alverdy. She completed her undergraduate and medical education at the University of Chicago, USA. Her research focuses on understanding the collagen degradation capacity of enteric bacteria and the part it plays in postsurgical complications and wound healing.

  • John C. Alverdy

    John Alverdy is the Sarah and Harold Lincoln Thompson Professor of Surgery and Executive Vice Chair of the University of Chicago Department of Surgery, USA. He has been the primary investigator for the past 15 years of a NIH-funded basic science laboratory at the University of Chicago, USA, focused on host–pathogen interactions in the gut and the role of the microbiota on inflammation, sepsis, postoperative complications and wound healing.

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