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PII: S1043-1489(17)30069-6
DOI: http://dx.doi.org/10.1053/j.scrs.2017.09.001
Reference: YSCRS615
To appear in: Seminars in Colon and Rectal Surgery
Cite this article as: Connie Shao, Sara Gaines and John C Alverdy, Influence of
the intestinal microbiome on anastomotic healing in the colon and rectum,
Seminars in Colon and Rectal Surgery,
http://dx.doi.org/10.1053/j.scrs.2017.09.001
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Influence of the Intestinal Microbiome on Anastomotic Healing in the Colon and Rectum
John C Alverdy MD, Professor of Surgery, Director of Center for the Surgical Treatment of
Obesity, Director for Minimally Invasive Surgery and Surgical Treatment of Obesity Programs
From the Department of Surgery, The University of Chicago, The Pritzker School of Medicine,
Chicago, IL
Supported in part by Ruth L. Kirschstein National Research Service Award – T32 Institutional
Training Grant, awarded to Sara Gaines MD, from the Digestive Disease Research Core Center,
Correspondence address:
Sara Gaines, MD
Chicago, IL 60025
Phone: 828-234-9886
Fax: 773-834-0201
Sara.gaines@uchospitals.edu
ABSTRACT
Colonic and rectal anastomotic leak has long plagued the surgeons, without much
improvement despite decades of advances in suture technique and technology. At the intersection
of microbiotal changes in flux via a combination of environmental factors and the virulent
mechanism and thus possible solution for anastomotic failure. Through pre-operative
changing. This article explores the shifts in composition and expression of the digestive flora in
response to external factors and the effects thus far observed on anastomotic healing, as well as
anastomotic leak.
Key words: Microbiome, Anastomosis, Anastomotic Leak, Colonic Resection, Colorectal Cancer
INTRODUCTION
Although colon surgery has never been safer as a result of improvements in surgical
technique, anesthesia, and postoperative care, the possibility of an anastomotic leak (AL)
remains a real and present threat to even the most skilled and experienced surgeon. While
multiple studies suggest that leak rates are at a historical low, between 3 and 8% in high volume
centers of excellence (1-2), many if not most of such leaks are only included in the analysis when
symptomatic enough to elicit imaging. In many cases, unless therapy is required, leaks may not
be included in the final tally at all. Finally, as a result of the liberal use of a protective stoma,
many leaks in high risk patients go undetected and therefore opportunities to understand the
involving factors such as suture placement, device deployment, tension, and ischemia. When
technique cannot be ascribed as a proximate cause of leak, patient-related factors are often
invoked, such as malnutrition, exposure to radiation and chemotherapy, obesity, and use of
tobacco. Yet an overlooked and unexplained occurrence in this type of deductive reasoning is the
consistent observation that the majority of such high risk patients (i.e >80%), in fact, do not
develop the clinical manifestations of an AL. Whether this is due to the liberal use of a protective
stoma in such patients or other factors remains unknown and highly controversial.
As a result of the pervasive notion that ALs are more a function of the physics of
anastomotic construction than the biology of healing, multiple attempts continue to address
tension, configuration, etc) or stapling in an end-to-end versus end-to side fashion, using
extraluminal sealing with fibrin glue or acrylates or applying internal shields to protect
anastomotic tissues from the fecal stream. In the aggregate, none of these approaches has been
shown to be effective at preventing AL; in fact some have been shown to lead to higher leak
rates (5-6).
Although a significant body of evidence exists to suggest that the presence of the normal
microbiota actually promote anastomotic healing in animals (REF), in humans, as a result of the
use of broad spectrum antibiotics, evidence suggests that their presence is actually harmful to
anastomotic healing. For example, Cohn first proposed in 1955 that the microbial contents of the
gut plays a central role in the pathogenesis of AL. He found that when dogs undergoing
anastomotic surgery were treated with a direct intraluminal infusion of tetracycline at the
anastomotic site via an indwelling catheter, AL was prevented in the anastomotic segments that
were rendered ischemic by dividing the supplying blood vessels (7). More indirect evidence by
way of antibiotic administration became available in 1994 from both animals and humans when
prevented AL (8).
Unfortunately, the current inability to track changes in microbial environments over the
course of healing makes it difficult to ascertain which aspects of the microbiota, i.e. community
structure, membership, and/or function, should be preserved and which should be eliminated or
contained. Given that we do not know which microbiota are associated with progression to
normal healing and which cause poor healing, we continue to use a broad coverage approach to
kill most of the microbes in the gut. Yet, progress has been made with culture independent
methods, such as molecular techniques, as the majority of species within our microbiome are not
able to be cultured (9). This approach may allow us to better understand how to direct therapy
against harmful microbes while preserving the health benefits of the probiotic flora.
Of the intestinal bacteria that are able to be cultured and identified, there are four main
phyla. More than 90% of the bacterial cells are composed of Firmicutes and Bacteroides, with
the rest mostly composed of Actinobacteria and Proteobacteria. (10) These are the bacteria that
constitute the complex microbiome of over 1014 microbes, consisting of 500-1500 species. It’s an
ecosystem that remains relatively stable despite the constant fluxes in external exposures and
dietary changes. The genetic material within these microorganisms is what encompasses the
Due to changes in the nutritional availability and chemical networking from the
microbiota itself, the composition of intestinal flora varies from location to location. The small
monosaccharides, disaccharides, and amino acids. Simple sugars are absorbed by host cells in the
distal small intestine, resulting in a distinct bacterial composition. The complex carbohydrates
that persist beyond the ileocecal valve are not able to be digested by the host, nor are
Proteobacteria like Escherichi coli, resulting in abundance of Bacteroides and Clostridiales that
The major function of the resident microbiota within the gut is to protect the intestinal
epithelium from colonization of disruptive pathobionts. These microbes also have profound
systemic effects on human physiology, such as culling energy and vitamins from food (13-14),
differentiation and growth of epithelial cells (15), development and homeostasis of the immune
system (12), and keeping noncommensal organisms at bay (16). However, when this
environment is disrupted, local cytokines, inflammatory, markers, and the ability to heal are
affected.
The specific species and molecular mechanisms that underpin AL are still being
elucidated, although some species have been identified that can have significant effects on
anastomotic tissues. A study in 2015 showed that the low abundance commensal Enterococcus
AL was prevented through the use of topical antibiotics applied to the intestinal tissue or
antibiotics (17).
During surgical injury, soluble products are released that can act as chemoattractants and
induce phenotypic shifts among pathogenic bacteria such as Pseudomonas aeruginosa. This shift
allows for the in vivo expression of an adhesive phenotype among colonizing pathogens, helping
explain how their presence may shift the local environment to result in injured tissue. Both from
the use of antibiotics and the antibiotics that pathogens such as Pseudomonas themselves release,
cytoprotective microbiota are lost, including Firmicutes and Bacteroidetes, allowing for the
proliferation of, and colonization of tissues by, pathogenic organisms. With germ-free and
Lifestyle choices, known risk factors for the development of AL, such as diet, exercise,
and environmental exposures like smoking or pets have been shown to have significant and
specific effects on the microbiome although overall composition may appear stable (19). Major
physiological stressors such as surgery or a major burn injury can dramatically change the gut
microbiota in as little as 6 hours (9). As such, the quantity, structure, membership, and function
of the intestinal microbiome can be significantly affected by multiple factors that may be highly
individualized in a given patient. In light of these emerging insights from the study of the
microbiome, our current approach to prepare the bowel for intestinal surgery may suffer from a
lack of fundamental science and use of next generation technology to explain what we are doing
Bowel preparation is the reduction of fecal load through either an osmotic agent (e.g.
agents can be metabolically inert, such as polyethylene glycol, or hyperosmolar, such as sodium
phosphate. Polyethylene glycol requires the ingestion of large quantities of liquid, which can
result in adverse side effects such as nausea and vomiting, risking low compliance, though has
fewer side effects than hyperosmolar solutions (20-21). Stimulants induce colonic contractions
and are usually combined with the osmotic agent magnesium citrate to retain fluid in the colonic
lumen. The electrolyte disturbances induced by stimulant agents have been shown to require the
ingestion of at least 2 liters of water to compensate for water secretion in the colon (22). The
clearing of bulky matter may also result in mucosal inflammation detectable only by histology,
most notable for loss of superficial mucus and epithelial cells as well as inflammatory changes
with lymphocytic and polymorphonuclear infiltration (23). These mucosal changes have been
suggested to influence the interactions between cells and the extracellular matrix, affecting the
electrolytic environment, fecal load, and hydration status, it seems likely that there would be
significant and potentially adverse changes in the microbiome during its preparation for surgery.
In fact, the number of bacteria collected immediately after bowel cleansing has been found to be
on average 34.7 times lower than at baseline (p<0.001), but were found to return to baseline
within several weeks (25). Even the composition of bacteria was changed, with a significant
Proteobacteria after lavage can be explained by the introduction of oxygen into the normally
anaerobic environment and an increase in pH from the loss of short chain fatty acids (26-27).
Given that Proteobacteria (i.e gram negative bacteria) are often the most pathogenic of the
Statistically significant changes in gut flora are observed depending on the duration of
mechanical bowel preparation. A study in 2012 found that Bifidobacterium and Lactobacillus
were found to be decreased significantly, more so with 1 day of bowel preparation than with 3
days. E. coli and Staphylococcus sp. were found to be higher than the preoperative level, more
significantly so in patients who had 3 days of bowel preparation. Post-operative infection was
found to be significantly lower when bowel preparation was performed over 3 days than with 1
(28). While there are many confounding factors with this study, such as the procedure itself, the
differences that occur in the gut flora with variations in bowel preparation beg a more complete
A Cochrane Database of Systematic Reviews found that bowel cleansing can be safely
omitted without affecting the morbidity or mortality in colorectal patients, as it did not reduce
rates of surgical site infections unless it was combined with both oral and systemic antibiotics
(29-30). This study and others are not in line with current standard practices. In fact, this line of
inquiry is in flux and begs a more complete understanding of how to prepare the bowel through a
higher resolution genetic analysis of the microbiome. This finding suggests again that it is the
microbial changes, and not the actual bowel preparation itself, that needs to be mapped to the the
Antibiotics
The pathogenesis of Clostridium difficile best explains the narrative of how the empirical
choice and promiscuous use of antibiotics can lead to adverse outcomes. Treating a bacterial
infection with an antibiotic such as clindamycin can result in the proliferation of an otherwise
benign bacterial species, allowing it to run rampant and wreak havoc in the form of horribly
persistent watery diarrhea. Similarly, the prophylactic administration of antibiotics, either orally
or intravenously, alters the normal physiologic symbiosis of the gut microbiota, resulting in an
altered ecosystem whose normal healing abilities may be diminished. In addition to affecting the
microbial content of the gut microbiome in the form of diversity diminution, antibiotics can also
affect microbial genetic expression, protein activity, and metabolites. Such shifts have the
potential to create an entirely new and foreign source of resources from which the mucosal cells
There have been many studies elucidating the specific changes in the microbiome that
occur as a result of the use of specific antibiotics (32-33). It is most important to note that even
short term antibiotics can have a long lasting impact with reductions in both diversity and
quantity of the normal microbiota. For example, after a 5-day administration of amoxicillin, the
percentage similarity of the dominant species that presented on day 0 was only at 89% by day 60
(34). A five-day administration of ciprofloxacin was found to have taxonomic disturbances that
Among the many goals of preparing the bowel for intestinal surgery, included is the
prevention of surgical site infections, presumed to be caused by intraoperative wound
contamination. Surgical site infections (SSIs) are a devastating and common complication of
Staphylococcus aureus is the most common cause, occurring in 20% of surgical site infections
among hospitals that report to the Centers for Disease Control and Prevention (CDC) and causes
as many as 37% of SSIs that occur in community hospitals (36). While topical transmission is
the likely contributor, other mechanisms may be a play. For example, a Trojan Horse hypothesis
of MRSA wound infection has been proposed whereby gut colonization by MRSA can lead to
the pathogen traveling inside a neutrophil from the gut to the wound causing clinical wound
infection. This was demonstrated in mice where antibiotic treatment and oral labeled MRSA
gavage caused remote MRSA wound infection with gross abscess formation by a process in
which the MRSA is picked up in the gut and delivered to the wound inside a neutrophil (37).
Such interorgan pathogen transfer from gut to wound suggests that a more complete
understanding of how to prepare the bowel for surgery may be in order. This may involve
understanding which pathogens persist in the gut when a broad-based anti-microbial regimen is
used to both debulk and eliminate the microbial contents of the gut.
There are multiple influences that shape the gut microbiome beginning at birth, which are
generally not accounted for when considering how to prepare the bowel for surgery. In fact, the
very age of the patient may need to be considered as the intestinal and skin microbiome
composition have been recently shown to be age-dependent (38-39). In children, for example,
this is an effect largely made significant by the development of neonatal immune systems via the
colonization of skin flora by the mother’s vaginal microbiota at birth. Differences in the mode of
delivery are definitively linked to differences in the intestinal microbiota of babies, a finding that
has been proven repeatedly (40-43). Children born vaginally are colonized predominantly by
Lactobacillus, while those delivered by cesarean section are colonized by a mixture of bacteria
found on the skin and in a nosocomial environment, including Staphylococcus and Acinetobacter
(44). While mechanisms have yet to be elucidated, there are statistically significant connections
between these different floras and the presence of specific diseases, namely atopy and
This example of a direct connection between the topical colonization of skin flora and the
consequent colonization of the gut flora by ingestion of the colonies on their hands may have
significant implications to the hospitalized patient, as has been recently demonstrated in the
hospital microbiome project (45). While it is presumed that health care providers’ hands are the
major vectors for pathogen transmission between patients, this hypothesis not only is difficult to
prove, but may actually be incorrect. Using genetic tracking of bacterial movement, studies are
emerging to suggest that most pathogens that cause serious nosocomial infections, may come
from the patients themselves (REF). Their age, previous healthcare encounters, previous use of
antibiotics, and lifestyle choices may shape their microbial flora, whose response to stressors
such surgery and ischemia may not only be unique, but unpredictable.
Ischemia
Intestinal resection both exposes the typically anaerobic bowel lumen to oxygen while
temporarily interrupting the local blood supply when the supplying blood vessels are ligated.
This can result in the depletion of health-promoting obligate anaerobes such as Bacteroides and
These changes were first observed in the colons of patients following small bowel
transplantation by comparing the colon flora before and after ileostomy closure. (46). These
finding suggest that there is a key relationship between how surgeons manipulate environmental
ischemia and had their bacterial diversity quantified at various time points found that colonic
flora changed early and differed significantly 6 hours after reperfusion, after which they started
to recover. The shifts were largely characterized by an increase of E. coli and Prevotella oralis,
with Lactobacilli proliferation occurring with epithelial healing (9). The proliferation of E. coli
resulted in more significant alteration in cellular morphology and physiology (47-48). During
major intestinal surgery, understanding the composition and behavior of pathogens that remain
on intestinal tissues (i.e anastomoses) over the course of recovery may be just as important as
knowing which are there at the beginning. As can be seen, the empiricism of the current
approach to prepare the bowel for surgery needs a mid-course correction based on emerging
Tracking the course of intestinal healing using next generation technology may provide
clues as to how the microbiota influence the healing process. At 6 hours after reperfusion, the gut
flora is observed to be at their highest level of diversity and most altered composition compared
to baseline. The peak in microbial compositional difference at 6 hours also implies that gut
ischemia/reperfusion, a regular occurrence during routine surgery, may have a significant effect
Pharmacologic effects
Besides the direct impact on the microbial environment with antibiotics, other
pharmaceuticals used as relatively benign forms of therapy throughout the course of the surgery
and during recovery can impact the microbial composition of the patient’s colon. The use of
antacids in the Dutch community, a country that has low antibiotic use, has been associated with
Opioid analgesics are commonly used to manage pain after surgery. However, their chronic use
reduces pathogen clearance and induces bacterial translocation across the gut barrier, a process
normally prevented by an intact intestinal microbiome. Many of these concepts and processes
have been addressed by the enhanced recovery after surgery (ERAS) bundle and their
For example, morphine use, a major target of the ERAS program, has been shown to
pathogens and reducing bile-deconjugating bacterial strains, resulting in decreased bile acid
levels in the gut (50). Morphine use in rats has been shown to increase the amount of high
increased rates of impaired anastomotic healing and gross leaks. In in vitro studies with E.
faecalis isolates, exposure to morphine results in increased adhesion and collagenase production,
regardless of baseline collagenase production (51). Morphine has also been found to cause a shift
resistance that is able to cause lethal sepsis. Finally, morphine can alter intestinal mucus and
destroy gut epithelial integrit. Therefore, in the aggregate, these observations suggest that its
judicious use or avoidance after surgery, as proposed by ERAS, is scientifically rational (52).
ANASTOMOTIC COMPLICATIONS
Further research is needed to more completely elucidate the molecular mechanisms that
drive complete and uncomplicated anastomotic healing. Simply culturing expelled stool and
testing for antibiotic resistance is inadequate. Phenotype characterization is essential to
understanding how commensal bacteria transform in vivo in response to the ever-changing and
individualized environmental factors that can influence the expression of novel traits of virulence
or pathogenicity. This will require next generation technology in order to guide practice. Bacteria
are promiscuous gene-swapping organisms and through horizontal gene transfer, phenotype
switching, and bacteriophage transmission, the exact actions of different microbial organisms
cannot be understood without an in-depth molecular analysis. This approach is now becoming
cheaper, faster and more readily available. Bioinformatic analysis and graphic display are also
Current practice for preparing the bowel for surgery includes a mechanical bowel
utilization of these methods is highly variable as is the selection of antimicrobial agents. A more
complete understanding of how current practices target and alter healing in the context of
microbial community structure, membership, and function and how the environment influences
these elements can help establish interventions and methods for a more effective preparation.
for an anastomosis to heal. Probiotic supplementation with Bifidobacteria and Lactobacilli before
and after surgery have been shown to have possible therapeutic effects (53-54), Combining
probiotics with a fiber rich diet has been shown to decrease the rate of AL, due to the production
of short chain fatty acids (55). Creating a combination of probiotic species and fiber for
consumption before and after the anastomosis creation could prophylactically preserve beneficial
species and provide the sources of energy to keep low abundance pathogens from proliferating
and responding to the often hostile inflammatory environment that occurs after major resection
in a high risk patient. Understanding how surgeons can maintain a more favorable local intestinal
demonstrate that bacteria “sense” local environmental changes and “respond” with enhanced
Along this line of reasoning, pathogens such as P. aeruginosa and E. faecalis have been
implicated in the pathogenesis of ALs. They have been shown to express virulence traits, such as
collagenase, that can directly impair anastomotic healing leading to leak. Contemporaneous with
this effect, the composition and function of the indigenous microbiome present at anastomotic
tissues becomes highly disrupted and allows these pathogens not only to proliferate, but also to
become “cued” by local environmental factors released during surgery possibly as a result of
tissue manipulation, transient ischemia, and inflammation. As a result of this process, these
pathogens are then activated and equipped to amplify the tissue inflammatory response after
anastomotic surgery, which remains unbalanced as a result of the lack of opposing forces by the
normal microbiota which have been eliminated by antibiotic use. As such, a pathoadaptive
Given that bacteria can rapidly evolve within minutes to hours and subvert all attempts to
silence or eliminate them, new approaches are needed. As we have witnessed with the emerging
problem of antibiotic resistance, there are no evolution-proof drugs. Simply targeting the
pathogens and not their virulence factors would leave room for the expansion and expression of
different forms of virulence and other pathogens acquiring the collagenase phenotype either by
horizontal gene transfer or other mechanisms. While many approaches are now being proposed,
such as phage therapy, cas-CRISPR targeted gene editing, and oral antibodies to target virulence
factors, novel approaches that might suppress virulence expression at its very onset may be a
more evolutionarily stable strategy. This approach may allow the normal microbiota to
participate in healing (58). Approaches to consider include the idea that it might bacteria may be
rendered harmless without elimination. Surprisingly this idea was proposed as early as 1899,
SURGERY
Surgeons have long realized the importance of understanding how intestinal microbes
influence outcomes following colorectal surgery. As we enter the molecular era of personalized
medicine driven by advances next generation technology, many of the time-honored practices
that are associated with improved outcomes will be confirmed or rejected at the scientific level.
The bundled approach of ERAS is a great example of this as is the potential benefit of use of
hyperoxygenation during colorectal surgery (60-61). As explained by the above discussion, early
feeding, avoidance of opioids, limiting transient ischemia, and early laxation may all be working
Understanding precisely how the microbiota respond to surgery and the various
manipulations that follow will be critical to design new therapies to improve outcome. For
example, in our own work, we have shown that intestinal phosphate becomes rapidly depleted in
the gut following surgery and is a critical “public good” resource for bacteria to thrive. When
phosphate is depleted, bacteria express virulence in order to gain access to host cells where there
is abundant phosphate such as ATP. In this process, cellular harm occurs. We developed an oral
phosphate based solution that delivers phosphate to the distal gut, suppresses bacterial virulence
without affecting bacterial growth, and prevents AL in mice (62). Properly nourishing the gut
during anastomotic surgery in the future will require approaches that appeal to the viability and
survival of the normal microbiota, which seems to play an underappreciated role in intestinal
healing. Yet not allowing the “bad actors” to proliferate may require non-microbiocidal
approaches given the concern of rapidly evolving antibiotic resistance. Through ERAS and other
approaches, it is now possible for surgeons to apply next generation technology to determine
what works and why. Using this approach, science-based design will lead us forward to improve
outcomes and prevent devastating complications such as ALs and SSIs, to which no surgeon is
immune.
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