Gut Microbiome in Anesthesiology and Pain Medicine

The human microbiome is an intricate ecosystem, typically hosting hundreds to thousands of bacterial species, as well as viruses, fungi, and phages, which is constantly shaped by the host and its environment while also influencing its function, its health, and diseases.²  This section will review the conceptual model of microbiome research, dividing it into four distinct phases: association, causation, mechanisms, and clinical applications.

While the terms microbiota and microbiome are sometimes used interchangeably, they are not synonymous. Traditionally, microbiota refers to the ecological community of microorganisms hosted by a multicellular organism, while microbiome refers to the genomes of these microorganisms. More recent definitions regard the microbiome as the microbiota within its well-defined habitat, forming its theater of activity, including microbial and external structural elements such as genes, lipids, proteins, polysaccharides, and metabolites.³ 

The complexity of the human microbiome may be conceptualized by considering its size, diversity, and dynamics: the human body hosts hundreds of bacterial species, and the number of these bacterial cells is estimated at 1.3 times the number of human cells.⁴  The number of bacterial genes, however, is two to three orders of magnitude larger than that of human genes.⁵  This huge bacterial community is highly variable between individuals: while the human genome is 99.5% identical between any two individuals, the composition of their gut microbiomes differs considerably, even between identical twins^6,7  or individuals who share a common living environment.⁸  The composition of the human microbiome not only varies between individuals but also is highly variable among the different body sites of a given host, with distinct communities detected in the intestinal tract, skin, urinary tract, and respiratory tract and even within different niches of these sites.²  In addition to being variable, the composition of the microbiome is also dynamic: the relative abundance of bacterial taxa in the human host changes over time scales of years, months, and even days in response to a multitude of host- and environment-related factors, including age, diet, occupation, physical activity, and medications.^2,9,10  The rate of microbiome compositional changes is also variable between individuals.¹¹  Nevertheless, emerging evidence supports certain levels of resilience in gut microbiota composition, manifesting in its ability to recover to preperturbation baseline composition.¹² 

In recent years, gut microbiome research has directly benefited from the advent of next-generation sequencing technologies. Specifically, metagenomic studies fueled by 16S ribosomal RNA gene sequencing or whole-genome sequencing decode the gut microbiome composition, as well as community structure. Sequencing based on the 16S ribosomal RNA gene is cost-effective, albeit with a limited resolution, while whole-genome sequencing is more expensive than 16S ribosomal RNA sequencing but provides better phylogenetic resolution.¹³  Using these technologies, a rapidly growing body of evidence suggests an association between the composition of the human microbiome and various pathologies.¹  Initially directed at the gut microbiome and gastrointestinal diseases, these association studies revealed unique compositions of the gut microbiome in individuals with inflammatory bowel diseases, irritable bowel syndrome, cirrhosis, and other gastroenterological disorders.¹⁴  Studies in other fields of medicine established associations between the composition of the gut microbiome and a wide range of medical conditions, including metabolic, dermatologic, oncologic, cardiovascular, and rheumatologic disorders, to name only a few. Particularly interesting are reports on alterations of the gut microbiome in neurologic and psychiatric conditions, including Parkinson’s disease,^15,16  autism,¹⁷  and depression and anxiety.^18,19  The microbiome of other body sites, including the skin,²⁰  respiratory tract,^21,22  and genitourinary system,^23,24  was found to be altered in medical syndromes involving these organs.

However, it should be stressed that the association of specific microbiome compositions to a medical condition does not establish a causal relationship. Microbiome alterations could, in theory, be caused by the disease, or alternatively, both microbiome alterations and the disease could be driven by a third factor (e.g., diet, genetics, physical activity, among others). With the advent of gnotobiotic animal models, the potential causal relationships between specific microbiome compositions and medical conditions are explored.¹  The transplantation of whole microbiome ensembles or individual bacterial taxa from human patients to germ-free (or antibiotic-pretreated) animals, while monitoring the development of disease phenotypes, allows researchers to explore the putative causal role of the gut microbiome in the disease pathogenesis. Using such methods, Prevotella copri, a bacterial species found in increased abundance in humans with arthritis, induced joint inflammation in a mouse model.²⁵  In a study on Sod-1 transgenic mice, Akkermansia muciniphila ameliorated symptoms of amyotrophic lateral sclerosis, while Ruminococcus torques and Parabacteroides distasonis exacerbated symptoms.²⁶  Finally, Parabacteroides merdae was found to mediate the antiepileptic effects of the ketogenic diet in a mouse model of intractable seizures.²⁷  These and similar studies suggest that the gut microbiome may play a role in the pathogenesis of certain pathologies. However, their relevance to humans remains to be established.

After a causal relationship is demonstrated, the next step is typically exploring possible mechanisms that allow the microbiome to affect the host health. The microbiome is in a state of constant interaction with its host via a multitude of mechanisms, which are only beginning to unfold. These include bidirectional interactions with the immune system and the secretion of biologically active metabolites.²  Particularly interesting is the so-called gut–brain axis, a two-way biochemical communication between the gastrointestinal tract and the central nervous system.^18,28  The mechanisms allowing the gut microbiome to affect the function of the central nervous system remain largely unknown; however, several putative mechanisms have been proposed, including the secretion of neuromodulatory bacterial metabolic end product to circulation,^26,27  immune-mediated effects,^29,30  and modulation of microglia activity,³¹  to name a few. The available literature on the mechanisms mediating the effects of the gut microbiome on extra-intestinal pathologies remains largely in the realm of preclinical studies in animal models.

In this context, the gut microbiome adds a new dimension to our current understanding of the central nervous system, which is of utmost interest to anesthesiologists, intensivists, and pain physicians. Importantly, many other tissues and organs have resident microbiomes, including the lung, skin, oral cavity, and eye, which are increasingly appreciated as modulators of health and disease. While we focus on the gut microbiome in the current review, the intriguing interactions among different microbiome compartments in addition to gut microbiome–host interactions will likely provide a new frontier in our understandings of microbiome–host interactions.^32,33 

The demonstration of a causal role of the microbiome in medical disorders and the identification of potential downstream mechanisms may pave the way for translational studies, aiming to develop clinical applications with diagnostic and therapeutic aims. The specific gut microbiome compositions associated with various medical conditions raise the possibility of using these biologic signatures as diagnostic aids. Indeed, several preliminary reports demonstrated the feasibility of gut microbiome–based diagnosis of pathologies ranging from several types of cancer,³⁴  irritable bowel syndrome,^35,36  and fibromyalgia,³⁷  to name a few. Promising as these translational studies may be, to date, microbiome-based diagnostic tools are still in the realm of research use and are not yet available for clinical use. Another potential clinical utility is the manipulation of the gut microbiome to reverse dysbiosis and restore a “healthy” microbiome composition. This may be achieved by the use of dietary measures, including prebiotics, probiotics, and medications, or by means of fecal microbiome transplantation from healthy individuals.^38–41  Prebiotics are nutritional compounds providing preferential advantage to selected bacterial taxa. Probiotics are live microorganisms that, when administered to patients, provide health benefits presumably through active colonization and incorporation into the host gut microbiome. Fecal microbiome transplantation is the process of enriching or replacing the host gut microbiome with that of a donor, currently indicated for refractory Clostridium difficile–associated colitis.⁴²  Nevertheless, preliminary clinical studies have shown promising results in treating irritable bowel syndrome,⁴³  managing autism,⁴¹  and enhancing host response to anticancer treatment.^38,39,44  When rigorous donor screening is performed, fecal microbiome transplantation is considered safe, with most short-term adverse events being attributed to the mode of delivery (i.e., colonoscopy). Long-term risks have not been observed, and longitudinal follow-up studies are still ongoing, with no sign of harm reported thus far. Severe adverse events have been described rarely, mostly involving the transmission of antibiotic-resistant bacteria (in cases where appropriate screening was not carried out) and even mortality in severely ill immune-compromised recipients.^45–47  Defining a healthy gut microbiome and screening for microorganisms that could lead to adverse infectious events will likely enhance the safety profile of fecal microbiome transplantation.

In summary, a growing body of evidence demonstrates gut microbiome compositional changes in a variety of clinical conditions in humans. Still, evidence regarding the causal role of gut bacteria, the mechanisms by which they exert their pathophysiologic effects, and the clinical applications of these observations is largely limited to preclinical studies in animal models.

When considering the role of the gut microbiome in perioperative care and in chronic pain, important first steps have been undertaken in recent years. Following the methodologic steps of association, causation, mechanism, and clinical application, the role of the gut microbiome in these fields is constantly unraveling and will be reviewed in the next sections.

The gut microbiome is readily shaped by a wide spectrum of medications,⁴⁸  while at the same time affecting the host response to many medications. In humans, most drugs have been shown to affect the composition of the gut microbiome, and for many, the clinical efficacy is determined by its composition.^49,50  At this point, only preclinical literature regarding animal models is available.

Several recent animal models demonstrate that the composition of the gut microbiome is affected by exposure to anesthetics, whereby even a relatively short duration of anesthetic exposure could lead to significant changes in gut microbiota composition. For example, after 4 h of exposure to isoflurane, mice gut microbiota composition displayed significant changes at days 1 and 7 postexposure. These changes were characterized by a decrease in bacterial community α-diversity, an increase in the abundance of Proteobacteria and Actinobacteria, and a decrease in the abundance of Firmicutes and Clostridiales.⁵¹  By longitudinally examining the gut microbiota changes after a single episode of isoflurane exposure, Han et al.⁵²  showed that changes in gut microbiota lasted for more than 14 days. This strong perturbation was not unique to volatile anesthetics, as intravenous medication propofol was also able to induce gut microbiota changes.⁵³  Specifically, 3 h of propofol infusion in rats led to a decreased abundance of Prevotella and Lactobacillus at the genus level, which showed a recovery trend on day 14. In addition to changes in bacterial species, gut microbiota–related metabolites were also altered by anesthetics.⁵²  Some of the compositional changes in the gut microbiome after general anesthesia were long lasting, as neonatal (day 7) exposure to isoflurane induced gut microbiota changes that were observed at the juvenile stage (day 42). Specifically, the abundance of Firmicutes, Proteobacteria, Clostridia, Clostridiales, and Lachnospiraceae was significantly increased in exposed rats, and the abundance of Bacteroidetes, Actinobacteria, Bacteroidia, and Bacteroidaceae was significantly decreased compared to controls. All of these studies point to a potent and lasting effect of anesthetics (isoflurane and propofol) on the composition of the gut microbiome, although the clinical significance of these perturbations is still unknown.

Early evidence suggests that the gut microbiome affects sensitivity to anesthetics in animals. For example, when specific pathogen–free mice and germ-free mice were exposed to pentobarbital anesthesia, the germ-free mice displayed much faster recovery, as determined by righting reflex, when compared with specific pathogen–free mice.¹⁷  Interestingly, conventionalization of germ-free mice did not reverse their resistance to pentobarbital. As pentobarbital undergoes xenobiotic metabolism, the differential effect of pentobarbital between germ-free and specific pathogen–free mice is likely related to liver metabolism. A microarray of 60-mer RNA from germ-free and specific pathogen–free mouse livers revealed 112 genes differentially regulated in the germ-free mice versus specific pathogen–free mice, many of which belong to the endobiotic and xenobiotic groups, which were potentially linked to pentobarbital pharmacokinetics.⁵⁴  It is unknown why germ-free mouse conventionalization did not reverse their resistance to pentobarbital. However, from gene microarray data, it is possible that some of the liver metabolic changes induced by germ-free status were long lasting and not readily reversible.⁵⁴ 

Evidence is mounting that the gut microbiome may affect the response to pain medications—specifically opioids. The interactions between opioids, opioid receptors, and the microbiome are bidirectional, whereby opioids modulate the composition of the gut microbiome, and the gut microbiome in turn affects the host response to opioids.

The administration of morphine to mice resulted in significant changes in the composition of the gut microbiome, evident as early as 1 day after treatment initiation.⁵⁵  These changes, which are regimen-dependent,⁵⁶  were also associated with metabolomic changes and specifically with altered serum concentrations of secondary bile acids, phosphatidylethanolamines, and fatty acids. Alterations in the composition and function of the gut microbiome were partially reversible by the coadministration of the µ-receptor antagonist naltrexone. Similar results have been reported that the compromised gut barrier, associated with the administration of morphine to mice, resulted in systemic inflammation that could be reversed by fecal microbiome transplantation from placebo-treated mice.⁵⁷  Moreover, after chronic treatment with oxycodone, the changes in the intestinal microbiome of mice persisted even after treatment was discontinued.⁵⁸ 

Interestingly, the host response to morphine is dependent on the gut microbiome: in a mouse model of morphine tolerance, germ-free mice and antibiotic-treated mice were less prone to developing opioid tolerance than were naïve mice.⁵⁹  Opioid tolerance was associated with the depletion of two bacterial groups: bifidobacteria and Lactobacillaeae. Microbiome reconstitution using either fecal microbiome transplantation from naïve mice or specific enrichment with bifidobacteria and Lactobacillaeae recapitulated opioid tolerance in this model. In a similar mouse model, antibiotic treatment prevented the development of tolerance but did not affect naloxone-induced withdrawal.⁶⁰  Finally, the gut microbiome and particularly the cecal microbiome have long been recognized to hydrolyze glucuronide conjugates, including morphine 3-glucuronide.⁶¹  It thus seems that while opioids shape the composition of the gut microbiome, the latter has an important role in the development of opioid tolerance in the host.

In conclusion, preclinical studies suggest that the composition of the gut microbiome is readily affected by host exposure to anesthetics and opioids. Moreover, gut bacteria play a role in host sensitivity to pentobarbital, the rate of recovery after exposure to the medication, and the development of tolerance to opioids. Notably, these preclinical findings need to be verified in clinical studies.

Recent studies shed light on the intricate role of the microbiome in the perioperative care of the patient. Animal studies suggest that these bidirectional interactions include alterations in the composition of the gut microbiota after general anesthesia, as well as the effects of gut bacteria on postoperative outcomes including postoperative pain and postoperative cognitive dysfunction. Early human studies show an association of the gut microbiome composition and postoperative outcomes including pain and delirium.

The term “perioperative neurocognitive disorders” refers to cognitive impairments identified in the preoperative or postoperative period, ranging from acute transient events (postoperative delirium) to delayed neurocognitive recovery (postoperative cognitive dysfunction). The pathogenesis of perioperative neurocognitive disorders is an area of active research with significant public health relevance. In animal models, the gut microbiome has increasingly been recognized as a key player in perioperative neurocognitive disorders.

To gain mechanistic insights into the role of the gut microbiome in perioperative neurocognitive disorders, several studies have explored bacterial signatures associated with postoperative delirium and postoperative cognitive dysfunction. For postoperative delirium, when mice undergoing abdominal surgery and anesthesia were separated into non–postoperative delirium and postoperative delirium phenotypes postoperatively, major differences were observed in the composition of the gut microbiome of the two groups, at multiple taxonomic levels. For example, at the genus level, postoperative delirium mice showed significant decreases in the levels of Ruminiclostridium, Ruminococcaceae UCG 014, and Desulfovibrio compared with the non–postoperative delirium mice.⁶²  When fecal microbiome transplantation was carried out, feces from postoperative delirium mice rendered pseudo–germ-free mice (mice with largely eradicated gut microbiome using wide-spectrum antibiotics) prone to developing postoperative delirium, supporting a key role of the gut microbiome in postoperative delirium susceptibility.⁶² 

Age is a well-established risk factor for postoperative delirium, but its biologic underpinnings remain poorly understood. Liufu et al.⁶³  specifically examined age as a biologic variable in postoperative delirium development by focusing on gut microbiome changes. They found that anesthesia and surgery induced age-dependent changes in the gut microbiome, particularly a reduction in the abundance of Lactobacillus. These changes appeared to play a causal role in postoperative delirium development, as supplementation of Lactobacillus could deter postoperative delirium development in aged mice postoperatively.⁶³ 

In line with its role in postoperative delirium, the gut microbiome also plays a role in postoperative cognitive dysfunction.^64–67  Notably, a recent animal study adopted a clinical scenario: the perioperative use of antibiotics, which are unambiguously potent microbiome-modulating agents.⁶⁸  Cefazolin, commonly used in the perioperative setting, induced gut microbiome changes, as well as cognitive dysfunction, in mice not undergoing surgery. However, when cefazolin was administered once daily for 5 consecutive days, surgery-induced postoperative memory and learning impairment were ameliorated, supporting a potential implication of gut microbiome in postoperative cognitive dysfunction.^68,69  Of note, some antibiotic agents are known to exert effects beyond mere bactericidal or bacteriostatic properties, such as neurotoxicity (cephalosporins) and microglia inhibition (minocycline); hence, symptom reversal after antibiotics does not necessarily imply a bacteria-related mechanism of action. Similar to studies in postoperative delirium, most studies on gut microbiome and postoperative cognitive dysfunction utilized rodent models, calling for future translational studies to directly examine its role in humans.

Reported gut microbiome changes in postoperative delirium and postoperative cognitive dysfunction vary across studies.^62–64,66  Some of these variations are likely related to the gut microbiome’s susceptibility to host genetics, dietary intake, and housing conditions.⁷⁰ 

In animal models, manipulation of the gut microbiome has the potential to alleviate postoperative delirium and postoperative cognitive dysfunction. The use of prebiotics, probiotics, and fecal microbiome transplantation has been proposed. Prebiotics containing galacto-oligosaccharide were recently shown to ameliorate postoperative cognitive dysfunction and attenuate surgery-induced neuroinflammation in rats. This protective role was associated with a significant change in the β-diversity of the gut microbiome and the proliferation of Bifidobacterium and other taxa with putative anti-inflammatory effect.⁷¹  The probiotic Lactobacillus is a genus of Gram-positive, non–spore-forming bacteria commonly found in dairy foods such as yogurt. Supplementation of Lactobacillus alleviated age-dependent development of postoperative delirium in mice.⁶³  These studies support the therapeutic potential of gut microbiome–based therapeutics in perioperative neurocognitive disorders. Interestingly, the gut microbiome is also modulated by nondietary factors, including lifestyles with known health benefits. For example, in mice, caloric restriction stimulates the development of functional beige fat and extends the healthy lifespan. This health benefit could be partly attributed to compositional and functional changes in the gut microbiome, which in turn dampened lipopolysaccharide absorption. Gut microbiome–depleted mice derived significantly fewer health benefits with fasting compared with mice with intact gut microbiomes.⁷²  Intermittent fasting is another lifestyle that may offer protection from age-associated pathologies in animals by enhancing mitochondrial biogenesis and energy metabolism gene expression in the hippocampus, restructuring the gut microbiome, and increasing microbial metabolites that are related to cognitive function.⁷³  It is tempting to speculate that certain health-promoting lifestyles might alleviate perioperative neurocognitive disorders through modulating the gut microbiome. Indeed, in a rat model of the metabolic syndrome, exercise reduced otherwise heightened postoperative neuroinflammation and cognitive decline, which were linked to a restored and presumably healthy gut microbiome.⁷⁴ 

In a recent single-center prospective observational study, 21 patients who underwent cardiac surgery were assessed for the development of postoperative delirium, insomnia, and pseudopsia (visual hallucination) for 1 week along with gut microbiota characterization. Staphylococcus and Pseudomonas counts were significantly higher in patients with postoperative pseudopsia.⁷⁵ 

Early evidence from a translational study suggests the microbiome may impact the incidence of chronic postoperative pain. Recently, Yao et al.⁷⁶  explored the association between the composition of gut microbiome and chronic postoperative pain after surgery for breast cancer. In a nested case-control study of 132 women undergoing surgery for breast cancer, baseline gut microbiome composition was significantly different among the 66 women who developed chronic postoperative pain at 3 months, as compared to 66 patients who were pain-free. Furthermore, a potential causal role of the gut microbiota was explored using fecal microbiome tranplantation from chronic postoperative pain or pain-free patients to mice undergoing spared nerve injury. Mechanical thresholds decreased more in mice receiving fecal microbiome transplantation from chronic postoperative pain patients than from healthy controls. These changes were accompanied by significant decrease in the concentration of peroxisome proliferator-activated receptor γ, a key metabolism modulator implicated in pain,⁷⁷  and a trend toward an increase in activated microglia in the spinal cord. As such, along with surgery factors (perioperative use of antibiotics, among others), gut microbiome appears to be linked to postoperative pain. In a clinical study with a relatively modest number of participants (n = 20), acute postoperative pain was associated with gut microbiome composition and diversity.⁷⁸  These effects are in line with the role of the gut microbiome in the pathogenesis of neuropathic pain, which will be discussed in the section Neuropathic Pain.

In summary, preclinical and clinical studies demonstrate significant effects of the gut microbiome on postoperative outcomes, including an association between the composition of the gut microbiome and the risk of postoperative delirium and pain in both animal models and humans. In animal models, manipulation of gut bacteria by antibiotics, probiotics, or fecal microbiome transplantation positively affected the incidence of postoperative delirium and pain.

Critically ill patients show significant gut microbiome alterations, which are associated with disease severity as well as their clinical outcomes. The full extent of the implications of gut microbiome composition in the intensive care setting is beyond the scope of this review and has been thoroughly discussed elsewhere.^79–81  Nevertheless, several examples will be reviewed here.

Several studies explored changes in the composition of the gut microbiome in intensive care unit (ICU) patients and their prognostic significance in the disease outcome. In a prospective cohort of 61 patients admitted to the ICU, the composition of the gut microbiome was studied and correlated with clinical indices and outcomes.⁸²  The abundance of the genus Bifidobacterium was significantly higher in patients who survived as compared to the patients who died during the hospitalization. Furthermore, when added to the clinical scores, the composition of the microbiome improved the prediction of in-hospital death as compared to Acute Physiology and Chronic Health Evaluation (APACHE) II or Sequential Organ Failure Assessment (SOFA) alone.

Sepsis is a leading cause of mortality in critically ill patients, which has been strongly associated with the gut microbiome in several studies. In a recent prospective study of 10 patients admitted to the ICU with sepsis, 10 patients admitted to the ICU without sepsis, and 10 healthy controls, the composition of the gut microbiome was significantly altered in ICU patients of both groups as compared to healthy controls.⁸³  ICU patients demonstrated reduced α-diversity (indicating reduced microbiome species richness), increased abundance of Firmicutes, and decreased proportions of Bacteroidetes, Prevotella, and Lachnospira. Furthermore, significant differences were observed between sepsis and nonsepsis ICU patients, with increased abundance of Enterococcus. In a prospective study exploring the gut microbiome of 64 sepsis patients admitted to the ICU, two distinct clusters were detected.⁸⁴  One of these clusters, characterized by increased abundance of Bacteroides and an unclassified genus of Enterobacteriaceae, was associated with elevated levels of serum lactate dehydrogenase and an increased risk of developing septic shock. In line with these observations, some authors have suggested a pivotal role for the gut microbiome in the development of multiorgan failure in critically ill sepsis patients.^80,85 

Gut microbiota have recently been recognized as an important factor influencing the pulmonary system, hence, the term “gut–lung axis.”⁸⁶  In a prospective study of 21 chronic obstructive pulmonary disease patients who were intubated and admitted to the ICU, sequential endotracheal sampling revealed that an increase in the relative abundance of the Acinetobacter genus and Acinetobacter baumannii complex species was associated with decreased chances of successful weaning.⁸⁷  In another study, among patients admitted to the ICU and maintained on supplementary oxygen, exposure to hyperoxia independently predicted subsequent bacterial growth from lung specimens, with notable species-specific effects. Specifically, rates of Staphylococcus aureus isolation were not affected by early exposure to hyperoxia, whereas rates of Pseudomonas aeruginosa isolation decreased among patients receiving high concentrations of fractional inspired oxygen tension.³³  Using an animal model, the same authors found experimental evidence supporting that gut bacterial communities were altered by hyperoxia and correlated with lung inflammation. More recently, Liu et al.³²  examined human fresh lung tissue and found that short-chain fatty acids were present with interindividual variability. As short-chain fatty acids are dependent on the gut microbiome,^32,88  these findings suggest a mechanistic linkage of gut microbiome, lung microbiome, and host health.

In summary, critically ill patients admitted to the ICU demonstrate significant gut and lung dysbiosis, which is associated with various clinical outcome measures. However, the role of potential microbiome-targeted therapeutic measures has yet to be established in this setting.

A growing body of evidence suggests that the composition of the gut microbiome is altered in humans with a variety of chronic pain conditions, including visceral pain, nociplastic pain, headache, and neuropathic pain. Meanwhile, animal studies provide evidence that the gut microbiome may have a causal role in some animal pain models. The evidence for the role of the gut microbiome in experimental and clinical pain will be reviewed here.

Initial studies associating the composition of the gut microbiome with human diseases focused on the gastrointestinal tract. Nociplastic gastrointestinal diseases, including irritable bowel syndrome, are among the pathologies in which the role of the gut microbiome is best established,^36,89  whereby all four research milestones—association, causation, mechanisms, and clinical applications—have been reached.⁴⁰  The association of the gut microbiome composition and irritable bowel syndrome has been demonstrated in several recent studies. While the overall composition of the gut microbiome of individuals with irritable bowel syndrome is largely similar to that of healthy controls in terms of α- and β-diversity, specific bacterial taxa are differentially abundant in these patients. These include a decreased relative abundance of the genera Bifidobacterium and Faecalibacterium and the species Faecalibacterium prausnitzii, and an increased relative abundance of Lactobacillaceae, Bacteroides, and Enterobacteriaceae. Of note, the composition of the gut microbiome was associated not only with the diagnosis of irritable bowel syndrome but also with its phenotypic subtypes (diarrhea vs. constipation predominant), as well as with syndrome severity³⁵  and with irritable bowel syndrome flares.⁹⁰  Specific gut microbiome alterations not only are associated with irritable bowel syndrome but also have been shown to be sufficient to cause the phenotype: fecal microbiome transplantation from humans with irritable bowel syndrome, but not from healthy controls, was shown to cause faster transit time, intestinal barrier dysfunction, and anxiety in germ-free recipient mice.⁹¹  Recently, in a model of chemically induced colitis in mice, the gut microbiome was implicated in visceral hypersensitivity. Fecal microbiome transplantation from viscerally hypersensitive mice, but not healthy controls, to antibiotic-treated rats resulted in long-lasting visceral hypersensitivity and alterations in luminal short-chain fatty acid concentration.⁹²  The mechanisms underlying the role of the gut microbiome in irritable bowel syndrome are still being explored, but several pathways have been suggested. Metabolomic and transcriptomic analyses revealed alterations in the gut microbiome function, including decreased levels of short-chain fatty acids (butyrate, propionate, acetate), alterations in luminal bile acids, and dysregulation of the purine salvage pathway.⁹⁰  Finally, the utility of gut microbiome manipulation by means of dietary measures,⁹³  probiotics, and fecal microbiome transplantation^43,94  have been explored, and some have demonstrated clinical efficacy in irritable bowel syndrome.

Chronic pelvic pain, another common syndrome of functional visceral pain, has also been associated with microbiome alterations. Several studies have demonstrated alterations in the gut and urinary microbiomes of individuals with chronic pelvic pain, chronic prostatitis, and interstitial cystitis.^95–98  These associations are not as well detailed at the taxonomic level as compared to irritable bowel syndrome, and the causal and mechanistic relationships have not yet been established.

Fibromyalgia, a prevalent syndrome of chronic widespread pain, fatigue, sleep disorders, and other somatic symptoms,⁹⁹  is considered a hallmark of somatic nociplastic pain. Several recent studies have demonstrated an association of the gut microbiome composition and fibromyalgia. In a study comparing the composition and function of the gut microbiome in a cohort of 77 women with fibromyalgia and 79 healthy controls, the overall composition of the gut microbiome was similar in the two groups; however, higher-resolution analysis revealed several bacterial species that were differentially abundant in fibromyalgia patients.³⁷  These patients appeared to have increased relative abundance of P. merdae and decreased abundance of P. copri and A. muciniphila (which was also decreased in a mouse model of chemotherapy-induced neuropathic pain¹⁰⁰  but increased in irritable bowel syndrome). The relative abundance of several bacterial species correlated with syndrome severity, similar to the observation in irritable bowel syndrome.³⁵  Furthermore, in line with changes observed in visceral nociplastic pain, significant changes were observed in the plasma concentration of short-chain fatty acids including butyrate and propionate. The composition of the gut microbiome, when fed to a trained machine learning algorithm, accurately classified fibromyalgia patients and controls.

In a second study comparing the composition of the gut microbiome of 105 individuals with fibromyalgia and 54 matched healthy controls, the overall composition of the gut microbiome was similar in the two groups; however, specific bacterial genera were differentially abundant in patients, as well as the serum concentration of metabolites, including amino acids and neurotransmitters.¹⁰¹  The enrichment of several bacterial genera and of certain metabolites correlated with disease severity. Of note, an earlier study investigating the gut microbiome of individuals with fibromyalgia failed to detect changes when compared to rheumatoid arthritis patients.¹⁰²  However, this study was significantly lower powered and used culture, rather than sequencing, to detect the composition of the gut microbiome.

In contrast to the changes observed in fibromyalgia, a study in patients with chronic widespread pain and two studies in patients with myalgic-encephalomyelitis/chronic fatigue syndrome demonstrated different alterations in the gut microbiome. In a study of 113 individuals with chronic widespread pain and 1,623 controls, the main outcome was decreased α-diversity and a depletion of Coprococcus comes.¹⁰³  However, participants in this study were not clinically evaluated, and their pain diagnoses were based on self-report. In two studies exploring the gut microbiome of patients with myalgic-encephalomyelitis/chronic fatigue syndrome, evidence of increased plasma lipopolysaccharide and lipopolysaccharide-binding protein was found. Taxonomic analysis showed several differentially abundant taxa, including increased abundance of Clostridium scindens (also increased in fibromyalgia) and decreased abundance of Haemophilus parainfluenza and P. merdae; in contrast, in fibromyalgia, P. merdae was increased, and H. parainfluenza depleted.^37,104–106  It would thus seem that in nociplastic somatic pain, the association of gut microbiome composition with certain syndromes seems robust, but evidence for causal and mechanistic associations is still missing, as are clinical applications.

Several recent studies have established the important role of the gut microbiome in the development of neuropathic pain in animal models while also shedding light on potential mechanisms of action. In an association study, the composition of the gut microbiome was significantly altered in chronic constriction injury to the sciatic nerve–treated as compared to sham-treated rats,¹⁰⁷  showing several differentially abundant taxa in the chronic constriction injury group. The relative abundance of some differentially abundant taxa correlated with the clinical phenotype, including mechanical withdrawal threshold and thermal withdrawal latency. Associated metabolomic changes were observed in both the serum and spinal cord. Specifically, decreased abundance of butyrate-producing bacteria correlated with both phenotypic indices and with serum and spinal cord levels of β-hydroxybutyric acid. Alterations in butyrate-producing bacteria and their metabolic end products were also observed in chronic pain conditions in humans.³⁷ 

A causal role of the gut microbiome in the development of neuropathic pain was demonstrated in several recent studies. In an animal model of chemotherapy-induced neuropathic pain, the development of mechanical hyperalgesia after treatment with oxaliplatin was prevented in antibiotic-treated mice and in germ-free mice,¹⁰⁸  supporting an essential role for the gut microbiome in the development of chemotherapy-induced neuropathic pain. In this study, the pronociceptive effect of the gut microbiome was associated with increased exposure of the dorsal-root ganglia to lipopolysaccharide, a cell wall component of Gram-negative bacteria. The increased concentrations of lipopolysaccharide in the dorsal root ganglia in turn led to an increased inflammatory response, manifesting as elevated concentrations of inflammatory cytokines, macrophages, and reactive oxygen species.

The important role of the microbiome in the development of chemotherapy-induced neuropathic pain was further demonstrated using fecal microbiome transplantation in germ-free mice.¹⁰⁰  Specifically, paclitaxel-associated chemotherapy-induced neuropathic pain was more pronounced in the C57BL/6 strain of mouse than in the 129SvEv strain. The reciprocal fecal microbiome transplantation from a chemotherapy-induced neuropathic pain-resistant 129SvEv strain to a chemotherapy-induced neuropathic pain-sensitive C57BL/6 strain protected C57BL/6 from chemotherapy-induced neuropathic pain, while fecal microbiome transplantation from a C57BL/6 strain to a 129SvEv strain rendered 129SvEv susceptible to chemotherapy-induced neuropathic pain.

A recent study demonstrated that neuroimmune interactions serve as a mechanism through which the gut microbiome influences pain: in a mouse chronic constriction injury model, spinal cord–infiltrating T cells were found to be different between the antibiotic-treated and the sham-treated groups,¹⁰⁹  with decreased interferon- γ–producing T helper type 1 cells and increased Foxp3⁺ regulatory T cells in the former, indicating an attenuated inflammatory infiltration in the antibiotic-treated mice. Antibiotic-induced T cell changes were linked to a protective effect on pain. Depletion of Foxp3⁺ regulatory T cells reversed the protective effect of antibiotic treatment.

Another study confirmed a causal role of the gut microbiome in chronic constriction injury–induced neuropathic pain, reproducing the protective effect of gut microbiome depletion using antibiotic pretreatment.¹¹⁰  Short-chain fatty acids were significantly increased in the intestines of chronic constriction injury–treated mice as compared to sham-treated mice and were almost depleted when mice were treated with antibiotics. Intestinal short-chain fatty acids concentrations correlated with microglia activation and inflammatory cytokine concentrations in both the spinal cord and the hippocampus. Finally, oral short-chain fatty acid administration partially reversed the protective effect of antibiotics on chronic constriction injury phenotype, as well as on spinal cord and hippocampal microglia activation and inflammatory markers.

The role of the gut microbiome was recently demonstrated in an additional model of neuropathic pain, induced by obesity.¹¹¹  Mice fed a Western diet developed mechanical and thermal sensitivity, which was reversible by fecal microbiome transplantation from lean mice. Fecal microbiome transplantation resulted in alterations of gene expression in the dorsal root ganglia and the sciatic nerve, decreased RYR2-dependent calcium release in dorsal root ganglia neurons, and altered macrophage polarization in the dorsal root ganglia and sciatic nerve and in a reversal of dermal small fiber loss. Serum butyrate, which increased after fecal microbiome transplantation, correlated with mechanical thresholds.

Recently, in a mouse model of lumbar disc herniation, the protective effect of Lactobacillus paracasei supplementation was demonstrated. Lumbar disc herniation mice receiving L. paracasei, but not sham, exhibited an attenuated behavioral pain response and decreased inflammatory response in the dorsal root ganglia.¹¹² 

In humans, association studies are scarce. One such study explored the composition of the gut microbiome in a small cohort of patients with complex regional pain syndrome.¹¹³  The composition of the gut microbiomes of 16 complex regional pain syndrome patients was altered as compared to that of 16 healthy adults, with lower diversity and a decreased Firmicutes to Bacteroidetes ratio.

In summary, a growing body of evidence substantiates a causal role for the gut microbiome in murine neuropathic pain models, including chronic constriction injury, chemotherapy-induced neuropathic pain, and obesity-induced neuropathic pain, highlighting potential mechanisms involving the levels of circulating bacterial metabolites and lipopolysaccharide, immune responses, and microglia activation. The clinical relevance of these observations has yet to be established.

Data on the role of the gut microbiome in headache disorders are scarce. Two studies reported on alterations of the gut and oral microbiomes in humans with migraine. One study compared the composition of the gut microbiome of 25 pairs of twins, of whom one sibling suffered from migraines.¹¹⁴  Several differentially abundant species were observed, including F. prausnitzii, Bifidobacterium adolescentis, and Methanobrevibacter smithii; all species were decreased in migraine patients. The other study found that the composition of the oral microbiome was altered in 26 migraine patients as compared to 29 healthy controls.¹¹⁵ 

The gut microbiome has also been implicated in many medical conditions, some of which are associated with comorbid pain. These include degenerative¹¹⁶  and inflammatory joint diseases,^117,118  neurologic conditions including Parkinson’s disease¹⁶  and multiple sclerosis,³⁰  inflammatory bowel diseases,^119,120  and others. We have limited the scope of this review to include mainly primary pain conditions; however, interested readers may find further reading in the references.^16,94–99  In summary, research on the role of gut microbiome in chronic pain is still taking its first steps, with accumulating evidence on correlations, some evidence on causation and as yet scant insight into mechanisms and clinical applications.

Evolving research on the human gut microbiome is substantially changing our understanding of pathologies in various fields of medicine. In particular, the accumulating evidence on the interactions of the gut microbiome with the central and peripheral nervous systems holds the potential to offer new mechanistic insights regarding pathologies relevant to anesthesiologists and pain physicians. Specifically, association studies demonstrate gut microbiome alterations that correlate with both chronic pain and some postoperative outcomes in humans. Animal models provide evidence that the gut microbiome may play a role in the pathogenesis of these conditions, proposing possible mechanisms mediating this effect (fig. 1).

The potential of this research field to transform our understanding of chronic pain and postoperative outcomes is exciting. Microbiome-related variability could, in theory, answer some long-lasting perplexing clinical dilemmas: Why do certain patients develop chronic pain? Why are patients’ responses to analgesic medications so variable? The variability of the human microbiome may explain some of the clinical variability we observe, in addition to established genetic and environmental factors. Nevertheless, it should be noted that research in the field is only taking its first steps and that the available data represent only a few pieces of the puzzle. Future studies are underway aiming to explore the association of gut microbiome composition and other pain conditions, attempting to identify and separate bacterial taxa that are common to chronic pain in general from those that are specific to certain diagnoses.

Other important considerations include studies demonstrating a causal role for specific bacterial taxa or ensembles in the pathogenesis of specific pain and perioperative disorders in animals. Establishing causal relationships may also allow the characterization of mechanistic pathways mediating these roles.

Finally, a more comprehensive understanding of the role of individual bacterial taxa in the pathogenesis of pain and perioperative disorders may allow for the development of personalized clinical applications. These may include (1) objective diagnostic tools allowing for a fast and accurate diagnosis of chronic pain conditions; (2) prognostic tools allowing identification of patients at risk for perioperative complications or those more likely to respond to certain analgesic classes; and (3) therapeutic tools based on the manipulation of the gut microbiome composition and gut microbiome–derived metabolites that may allow for novel treatment modalities for patients with chronic pain and those undergoing anesthesia and surgery.

Gut microbiome studies continue to benefit from powerful computational processes and machine learning–based computer algorithms to allow for integrated multiomic analyses (i.e., metagenomics, metabolomics, proteomics, lipidomics, transcriptomics, epitranscriptomics, among others). Quickly evolving technical platforms will facilitate the identification of gut microbiome compositional changes including bacterial taxa that are functionally important for clinical phenotypes, including chronic pain, transition from acute to chronic pain, and perioperative neurocognitive disorders. Additionally, fecal biobanking might provide unprecedented opportunities to capture preoperative baseline features to identify perturbations of the gut microbiome in the perioperative setting and to accelerate research in gut microbiome and perioperative medicine.

Promising and exciting as this new field may be, one must bear in mind that the available literature is mostly preclinical and that translational clinical applications are not yet available. As perioperative and pain physicians, in the not too distant future, we may witness major breakthroughs not only in our mechanistic understanding of the pathologies we treat but also the emergence of diagnostic and therapeutic tools that may be delivered to our patients.

Supported by National Institutes of Health (Bethesda, Maryland) grants No. R35 GM128692 and RF1AG070141, in addition to grants No. NS116423, AG067947, and AG065606 (to Dr. Shen).

Dr. Minerbi received speaker fees from Syqe Medical (Tel Aviv, Israel). Dr. Shen declares no competing interests.