How Gut Bacteria and Their Short-Chain Fatty Acids Relate to Health and Disease

Over 100 years ago, Nobel laureate Elie Metchnikoff proposed the idea that lactic acid bacteria are beneficial to human health.¹ Since then, research into the human gut microbiome has grown exponentially. Nowadays, bacterial constituents of a microbial population can be identified by 16S rRNA-encoding gene sequencing.² Additionally, “omics” methodologies such as transcriptomics, proteomics and metabolomics can provide information at successive levels of microbial physiology.³ Despite substantial advancements in our understanding of the bacterial portion of the normal microbiome, there are still a significant number of unknowns, including mechanistic relationships, unclassified gut bacterial species, and specific roles these bacteria may play in disease pathogenesis.

The European Metagenomics of the Human Intestinal Tract (MetaHIT)⁴ and the Human Microbiome Project (HMP)⁵ have provided a tremendous expansion of information and data in an effort to characterize the human microbiome. Characterization of bacteria that comprise a healthy human microbiome is an important initial step in understanding and determining the role of microbiome contribution to health and disease state. Despite significant efforts and research in this area, results support the idea that the gut microbiome is quite diverse compared to other body sites, and that there exists a considerable level of variation in the constituents of the gut microbiome in healthy individuals.⁶ While no true agreement has been reached, researchers and recent studies support the idea that roughly 70% of fecal bacterial species within an individual are stable for over 1 year, and few additional changes are observed out to 5 years.⁷ Calculations show that species are likely stable over decades, and potentially over an individual’s lifetime.⁷

Numerous studies have found an association between alterations in gut microbiome composition and a variety of diseases,^8-10 although the mechanisms by which these associations occur is still largely unknown. It is often difficult to differentiate between cause and effect when studying the microbiome and disease. Evidence supports that diseased states alter gut microbiome composition and function through various mechanisms,¹¹ but can the bacterial portion of the gut microbiome be a causative agent in human disease? It is important to properly elucidate relationships between gut microbiome alterations and human cell processes to determine true cause versus effect. Identification of bacterial gut microbiome constituents responsible for causing disease could allow for improvement in not only diagnostics but prevention and disease intervention.

Recently, bacterial production of short-chain fatty acids (SCFAs), specifically acetate, propionate, and butyrate, have gained a lot of attention in the research literature as they are shown to play a role in regulation of several physiologic systems in the human host including neuroinflammation within the nervous system,¹² gluconeogenesis and appetite within the liver and pancreas,¹³ as well as blood pressure and coagulation within the cardiovascular system.¹⁴ By focusing on SCFA production and their interactions within the gastrointestinal tract and immune system, new hypotheses on functional relationships and interactions can be proposed to further elucidate their role in maintaining proper health. Previous primary research and large-scale reviews have broadly focused on gut microbiome produced SCFAs as a group, with little distinction between acetate, propionate, and butyrate as individual agents. In this review, we comprehensively delineate the roles of three individual SCFAs including butyrate, acetate and propionate, with emphasis on receptor affinity, involvement with signaling pathways, as well as net physiologic effects on the host. Once specific roles are delineated it is possible to look at external factors that may positively or negatively impact SCFA production and in turn, host health.

Gut microbiota or the gut microbiome (GM) refers to the diverse microbial community that colonizes the human gastrointestinal (GI) tract. While termed gut microbiome, it does not only contain bacterial species but also fungi, viruses, and helminths.^15–17 Bacteria comprise a significant portion of the gut microbiome and are well-characterized compared to the other “dark horses” that contribute to the overall microbiome. These other biomes; virome (viruses), mycobiome (fungi) and archaeome (archaea), and helminths are far less characterized and remain incompletely elucidated.¹⁵ Even less understood yet is the relationship and interactions between the various gut biomes. A study by García-Gamboa et al. found alteration in both the gut bacterial and fungal populations in healthy patients compared to those patients with obesity.¹⁶ While changes in composition have been observed in disease states, the relationship between those imbalances and the functional implications at the gut level are yet to be fully understood.¹⁶ The gut microbiome has been estimated to contain roughly 40 trillion bacterial cells, significantly outnumbering human cells in the body.¹⁸ The GM performs many functions vital to human physiology and survival, and many refer to it as “the forgotten organ”.¹⁸

The GM and its products are directly adjacent to the epithelial cells within the GI tract and alterations in its composition or metabolism may lead to changes in gut permeability and intestinal barrier function.¹⁹ This affects GI epithelial cells, immune cells, and the closely associated enteric nervous system.²⁰ Research supports a bidirectional communication system between the gut microbiota and the brain, recognized as the “microbiota-gut-brain axis”.^21,22 Additionally, gut bacteria may activate the immune system through a defective gut barrier, thus causing a systemic inflammatory response that can promote disease states, such as the increased blood–brain permeability seen in neuroinflammation.²³

Gut microbes perform key functions for human health including energy extraction, biosynthesis of vitamins, protection against pathogen overgrowth, and education of the immune system.¹⁸ Microbial colonization of the gut occurs during birth, is highly dynamic through infancy, and resembles adult structure by about 3 years of age.²⁴ Thereafter, the composition of the microbiome within an individual remains generally stable but is highly variable between individuals. Bacteria from the phylum Firmicutes and Bacteroidetes form a significant proportion (~90%) of the adult gut microbiota, while Actinobacteria composes the remaining.²⁵

Sex, age, exercise, lifestyle, drugs, and diet can all affect the composition and functionality of the gut microbiome.²⁶ Diet has been shown to promote the growth of specific microbiota patterns referred to as enterotypes, and long-term diet was shown to be strongly associated with enterotype partitioning.^27,28 Enterotype 1, seen in industrialized countries, shows Bacteroides abundance and is typically associated with high fat, low fiber diets, with large quantities of refined foods, red meats, and dairy products. Enterotype 2 has Prevotella abundance and is typically associated with high fiber diets with less meat and dairy products. Some perspectives include enterotype 3, a makeup with Ruminococcus and co-occurring Akkermansia abundance, however, many classify this profile within enterotypes 1 for simplicity.^26,29,30 Enterotype 2 is shown to produce higher SCFA compositions compared to Bacteroides dominant microbiota, due to more efficient fiber utilizing capacity.^31,32 However, more research is needed to better understand the specific impact of enterotypes on health and disease states.

Much of the GM’s effects on host physiology and homeostasis are due to production of metabolites derived from bacterial fermentation.³³ SCFAs, formic acid (C1), acetate (C2), propionate (C3), butyrate (C4), isobutyric acid (C4), isovaleric acid (C5), and valeric acid (C5) are produced through bacterial anaerobic fermentation of fibers or nondigestible carbohydrates such as resistant starch, simple sugars, and polysaccharides that cannot be digested or absorbed in the small intestine.^34,35 Fermentation reactions can generate SCFAs as well as some gases, such as hydrogen gas, carbon dioxide and methane.³⁶ SCFAs can exert both detrimental and beneficial effects on the GI tract and in distant sites throughout the body, such as the liver,³⁷ pancreas,³⁸ and brain.¹⁶ Acetate, propionate, and butyrate typically account for 95% of human production of SCFAs; this being roughly 60% acetate, and 15–25% both butyrate and propionate.^39,40 Therefore, acetate, propionate, and butyrate will be the focus of this review, although we urge other researchers to continue examining the impact of the other SCFAs on host function.

Prior to discussing the physiologic role of SCFAs, it is important to understand the variable expression of the SCFA receptors. Table 2 shows the receptor, preferred ligand, mRNA expression, and protein expression.

The receptor Olfr78 in mice, OR51E2⁵⁹ being the human equivalent, mainly binds acetate and propionate and is expressed on vascular smooth muscle cells of peripheral vasculature and the renal afferent arteriole.⁶⁰ In vascular smooth muscle cells, binding of acetate or propionate to the receptor leads to an increase in cyclic adenosine monophosphate (cAMP), a second messenger with a wide variety of possible effects.⁶¹ In renal afferent arteriole cells, binding of acetate or propionate results in an increase in renin release which can contribute to an increase in blood pressure⁶¹ (Figure 3b).

Interestingly, research has shown that butyrate can induce proliferation in normal colonocytes but also terminal differentiation and apoptosis in neoplastic cells. This dual role has been termed the “butyrate paradox”.⁶⁹ In respect to gut barrier integrity, research has shown that butyrate taken up by colonocytes can strengthen barrier integrity by increasing gene expression of tight junction proteins such as claudin-1, claudin-7, ZO-1, ZO-2, occluding, and junctional adhesion molecule A (JAMA).⁷⁰ One group of researchers showed that butyrate promotes barrier integrity through activation of genes encoding tight junction components and protein assembly through transcription factors STAT3 and SP1.⁴⁷ The activation of these various genes and upregulation of tight junction proteins results in the maintenance and/or increased transepithelial electrical resistance (TEER) in humans, even after exposure to inflammatory conditions.⁷¹ Furthermore, since butyrate is the preferred source of oxidative fuel, its uptake and metabolism by colonocytes contributes to oxygen consumption and maintenance of an anerobic environment which contributes to the stabilization of hypoxia inducible factor-1α (HIF-1α). In the gut epithelium, stabilization and transcriptional activity of HIF-1α is protective to gut barrier integrity.⁷² HIF-1α transcription factor has been shown to increase expression of mucin (MUC), antimicrobial peptides (AMP), and tight junction proteins.⁷³ Butyrate is also able to modulate mucus layer thickness via increased secretion of MUC2, a predominant mucin glycoprotein, by Goblet cells⁷⁴ (Figure 4b).

Recent research shows that SCFAs not utilized by colonocytes may impact the body’s mechanisms of energy intake and energy use through FFAR3 and FFAR2 receptor activation in intestinal enteroendocrine L-cells.⁷⁵ These cells are responsible for the production and secretion of gut-derived satiety hormones peptide YY (PYY) and glucagon-like peptide-1 (GLP-1).⁷⁶ Both GLP-1 and PYY influence appetite and satiety by activating pro-opiomelanocortin (POMC) neurons in the hypothalamic arcuate nucleus which results in the suppression of neuropeptide Y (NPY).⁷⁷ Suppression of NPY in the brain results in delayed or inhibited gastric emptying.⁷⁸ Additionally, butyrate’s inhibitory action on HDAC leads to an increased expression of PYY in human L-cells.⁷⁹ Beyond the GI tract, propionate has been shown to interact with adipose tissue causing increased mRNA expression and secretion of leptin.⁸⁰ Together, these mechanisms may influence satiety and cause decreased appetite (Figure 5b).

Information presented in Table 2 brings up interesting potential connections when analyzing receptor expression on immune system cells, specifically different subsets of monocytes, and the functional roles of these cells. Monocytes can be divided into subsets based on CD14 and CD16 expression, with different subsets exhibiting distinct functional properties.⁵² Tissue mRNA expression shows that FFAR2 receptors are more predominantly expressed on non-classical monocytes and to a lesser degree on intermediate monocytes, than on classical monocytes. Similarly, GPR109a expression has significantly higher expression on non-classical monocytes, than the other subsets, but can still be found expressed on intermediate and classical monocytes to a lesser degree.

It is widely accepted that classical monocytes can differentiate into monocyte-derived macrophages and DCs, likely playing an integral role in shaping inflammation and resolution of inflammation in tissues.^81,82 This subset of monocyte has been shown to contribute to chronic disease.⁸⁰ Classical monocytes were found to be primed for phagocytosis, innate sensing/immune responses and migration.⁴⁹ This subset of cells is recruited during bacterial infections to sites of inflammation and function to recognize and phagocytose pathogens, secrete proinflammatory cytokines, as well as recruit other immune cells for regulation of the inflammatory response.^82-85 Classical monocytes migrate to CCL2 and CCL3 gradients and are more efficient than intermediate monocytes at producing reactive oxygen species (ROS) and containing fungi.^86-88 In humans, classical monocytes express higher levels of chemokine receptors such as CCR1, CCR2, CCR5, CXCR1, and CXCR2.^87,89 This finding highlights their potential to migrate to areas of injured or inflamed tissues. Additionally, this subset is also characterized by their ability to secrete pro-inflammatory molecules such as IL-6, IL-8, CCL2, CCL3, and CCL5.^89,90

Intermediate monocytes have comparable ROS production and phagocytosis potential to classical monocytes.⁵² However, intermediate monocytes showed lower adhesion to surfaces and higher class II molecule expression and IL-12 production than classical monocytes.⁵² Additionally, this subset of monocytes expresses the highest levels of antigen presentation-related molecules and are shown to secrete TNF-α, IL-1β, IL-6, and CCL3 upon TLR stimulation.^89–92 Intermediate monocytes are the only subset expressing CCR5 and thus well-suited for antigen presentation, cytokine secretion, apoptosis regulation, and differentiation.⁵⁰ This increased expression of CCR5 also likely accounts for their increased susceptibility to HIV-1 infections.^87–94 Higher levels of intermediate monocytes are found in the blood of patients with systemic infections, suggesting they may play a role in the rapid defense against pathogens.^95,96 However, another report found that this subset of monocytes are the main producers of IL-10 upon TLR stimulation.⁹⁷ These conflicting results contribute to the unclear nature of their exact role in immunity and inflammation.

Non-classical monocytes also have antigen processing capabilities but are distinguished from other subsets by their association with the wound healing process.⁹⁸ They are involved in complement and Fc-mediated phagocytosis and adhesion.⁵² Non-classical monocytes have been widely viewed as anti-inflammatory, as they maintain vascular homeostasis.⁸² These cells have an antagonizing function to the classical monocytes and promote neutrophil adhesion at the endothelial interface via the secretion of TNF-α and do not reach the same production level of pro-inflammatory cytokines as classical monocytes.^99,100 Non-classical monocytes are referred to as “patrolling monocytes” because the cells show a distinct motility and crawling pattern along vasculature and function to survey the luminal side of vascular endothelium in an LFA-1- and integrin-α₄-dependent manner.¹⁰¹ Additionally, this subset of monocytes recognizes and clears dying endothelial cells in a TLR7-dependent manner to maintain vascular homeostasis.^102,103

Human monocyte differentiation and function in the gut is influenced by dietary components, host metabolites and bacterial-derived products.^104–106 Bacterial-derived butyrate imprints a host protection program via epigenetic remodeling during differentiation of monocytes to macrophages in the lamina propria.¹⁰⁷ Specifically, without tissue-damaging inflammation, butyrate induces macrophages to upregulate antimicrobial proteins in the gut such as calprotectin.¹⁰⁷ Thus, in states of depleted butyrate and excess acetate, it is possible that activation of monocytes and binding via FFAR2 is more prominent than via GPR109a. A study by Ang et al. showed treatment of monocyte subsets with the SCFA acetate resulted in human monocytes with elevated p38 phosphorylation¹⁰⁸ which has been shown to promote differentiation of monocytes into M1 inflammatory macrophages.¹⁰⁹ Interestingly though, acetate signaling through FFAR2 also showed attenuation of C5, CCL1, CCL2, GM-CSF, IL-1α, IL-1β, and ICAM-1 inflammatory cytokine expression.¹⁰⁸ SCFA acetate also repressed Akt and ERK2 signaling.¹⁰⁶ Activation of the PI3K/Akt pathway is critical in restricting proinflammatory and promoting anti-inflammatory responses in TLR-stimulated macrophages.¹¹⁰ MEK/ERK signaling is involved in the activation of oxidative and nitrosative bursts, endosomal trafficking, and proinflammatory macrophage polarization.¹¹¹ Taken together, suppression of these pathways could help potentiate a dysregulated immune response and potentially a proinflammatory-biased environment.

Additionally, SCFA binding to FFAR2 and GPR109a on intestinal epithelial cells stimulates K⁺ efflux and hyperpolarization, causing activation of inflammasome-activating protein NLRP3 and induction of IL-18 release. Research shows that IL-18 helps with maintenance of integrity, repair, and intestinal homeostasis.¹¹⁹ Additionally, butyrate-induced inhibition of HDAC leads to increased protein acetylation and a decrease of IL-8 production in intestinal epithelial cells.¹²⁰ IL-8 (CXCL8) is also known as neutrophil chemotactic factor and functions to induce chemotaxis in targets cells, primarily neutrophils but also other granulocytes, causing immune cell migration to the site.¹²¹ Another key function of the cell signaling stimulated by IL-8 is the initiation of the oxidative burst. This process allows the buildup of proteolytic enzymes and reactive oxygen species which are necessary to break down the ECM (extracellular membrane) and basement membrane.¹²²

In dendritic cells, butyrate and propionate have been shown to decrease the release of pro-inflammatory cytokine CXCL11, CXCL10, CXCL9, CCL5, CCL4, and CCL3, as well as inhibiting expression of LPS-induced cytokine IL-6 and IL-12p40.¹²³ Butyrate is known to contribute to host defense by inducing the anti-microbial protein cathelicidin LL-37 in the gut.¹²⁴ Cathelicidin LL-37 is an antimicrobial peptide synthesized and secreted by epithelial cells, neutrophils, and lymphocytes.¹²⁴ This molecule serves a triple function for chemotaxis of innate immune cells, anti-microbial activity, and interacting with negatively charged molecules, such as the LPS component of gram-negative bacteria and teichoic acid of gram-positive bacteria.¹²⁵

Macrophages and dendritic cells express GPR109a receptors, and activation of this receptor by butyrate is demonstrated to be crucial in maintaining the balance between pro-inflammatory and anti-inflammatory T-cells.¹²⁶ Studies performed in GPR109a knock-out mice show reduced IL-10 and elevated IL-17 production by T-cells, leading to increasing susceptibility to colitis.¹²⁶

Butyrate has also been proven to increase the levels of T-regulatory cells in the gut¹²⁷ and facilitate extrathymic peripheral polarization toward regulatory T-cells in vitro and in vivo.¹²⁸ Butyrate-producing Clostridia spp. have been shown to induce colonic regulatory T-cells in mice.¹²⁹ The proposed causal mechanism is currently attributed to butyrate’s inhibitory effects on HDAC, where inhibition of HDAC is proposed to cause increases in regulatory T-cells.¹²⁸ Interestingly, it has been observed that acetate does not provide the same inhibitory action of HDAC seen with butyrate.¹³⁰ Butyrate can also induce production of TGFβ1 by intestinal epithelial cells, promoting anti-inflammatory regulatory T-cells (T-regs).¹³¹

Beyond regulatory T-cells, inhibition of HDAC by butyrate can also affect polarization and activation of Th1, Th2 and Th17 T-cells.¹³² Additionally, in cytotoxic T-cells, butyrate and propionate inhibition of HDAC has been shown to modulate gene expression by promoting INF-γ expression.¹³³ Acetate is also suggested to enhance IFN-γ production, but by acting as a metabolic substrate for cytotoxic T-cells rather than directly influencing gene expression.¹³³

Research substantially supports that the SCFA butyrate, specifically, has anti-inflammatory properties thought to be owing to an epigenetic mechanism¹³⁴ or to the effects of SCFA receptors. It has also been shown that these receptor effects are anti-inflammatory, anti-microbial, and decrease intestinal barrier leakiness¹²⁶ by maintaining tight junctions and preventing dysbiosis-associated gut permeability.¹³⁵ Butyrate also alters the activity of enteric neurons by reversible hyperpolarization and reducing colonic contractility.^136,137 Sodium-butyrate, a histone deacetylase inhibitor (HDACi), protects dopaminergic neurons^136,138 and prevents motor impairment in a toxin-induced drosophila model of Parkinson’s Disease.¹³⁹ In critically ill patients, lower concentrations of butyrate are associated with GI dysmotility.¹⁴⁰ Colonizing germ-free mice with butyrate-producing bacteria Clostridium tyrobutyricum or oral administration of sodium butyrate upregulated tight junction protein function.¹⁴¹ Additionally, intragastric treatment of Clostridium butyricum shows improvement of neurological dysfunction, brain edema, neurodegeneration, and blood–brain barrier impairment in post-traumatic brain injury mouse models.¹⁴²

This collection of research supports the notion that butyrate plays a significant role in many different systems within the host. Unlike the other SCFAs that are routinely associated with, acetate and propionate, alterations in butyrate levels seem to have a more substantial impact on host physiology, pathophysiology, and disease processes. Thus, it is possible that alterations in gut microbiome composition and function, specifically relating to butyrate-producing bacteria, may serve as pathologic drivers in various inflammatory and colonic-associated disease, or as a route to explore as preventative treatment in a variety of conditions.

The gut microbiome does not exist within a vacuum and is susceptible to numerous internal and external factors that can alter its composition and function. The most common external perturbations to the gut microbiome are diet, environment, and medications, specifically antibiotics.^143,144 Individual microbiome response to antibiotics is highly variable and dependent upon the state of the microbiome at the time of perturbation and the strength of the perturbation.¹⁴⁵ Antibiotics have revolutionized the treatment of infectious diseases and are widely prescribed with recent studies reporting continued increased consumption of antibiotics in certain countries in the past few years.¹⁴⁶ However, researchers have recently shown the detrimental effect of broad-spectrum antibiotics, such as cephalosporins, on the gut microbiome.¹⁴⁷

Numerous studies have evaluated antibiotic use and its impacts on the microbiome, both short term and long term.^153–155 Infants appear to be the most susceptible due to lack of a well-established gut microbiome at birth and microbiome maturation in the first years of life.¹⁵⁶ The first years of life are incredibly important in developing a healthy microbiome profile.¹⁵⁷ Early antibiotic administration has been associated with many health conditions, including increased BMI,¹⁵⁸ wheezing,¹⁵⁹ infantile colic.¹⁶⁰ Even before birth an infant’s gut microbiome and future health can be affected by exposure to antibiotics in pregnancy, which has been associated with increased risk of Very Early Onset Inflammatory Bowel Disease (VEO-IBD).¹⁶¹ However, not all antibiotics are shown to impact the microbiome equally. In the example of broad-spectrum antibiotic use in neonates, which are indicated in the suspicion of early onset neonatal sepsis, researchers demonstrated amoxicillin + cefotaxime co-administration for 48 hours conveyed the largest effects on microbiome composition and antimicrobial resistance gene profile in the treatment group¹⁶² when compared to a control group of healthy, non-antibiotic treated infants. Researchers also assessed other antibiotic combinations such as penicillin + gentamicin and co-amoxicillin/clavulanate + gentamicin each with 48 hours of administration. Penicillin + gentamicin exhibited the least effects on microbial community composition and antimicrobial resistance gene profiles.¹⁶² Additionally, they found the genera Bifidobacterium to be reduced in the amoxicillin + cefotaxime group compared to the penicillin + gentamicin group.¹⁶² The study concluded that there are significant long-term side effects of broad-spectrum antibiotic use in treatment of infants with suspected early onset neonatal sepsis, despite most neonates’ antibiotics being stopped after 48 hours. They also found that the impact to microbial diversity, community composition, and antimicrobial resistance gene profiles were still measurable at 12 months of life.¹⁶²

Mouse studies also consistently show significant shifts in microbiome profiles with a variety of antibiotic use, all sharing similar depletion of SCFAs butyrate, acetate, and propionate.^163–166 Mouse studies show administration of ceftriaxone significantly reduces concentrations of SCFAs following withdrawal.¹⁶⁷ Given the importance of butyrate to the intestinal barrier, as discussed above, it is no surprise that mouse models show antibiotic-induced dysbiosis with reduced levels of ZO-1, occludin, and claudin-1. Reduction of these proteins results in tight junction damage and increased intestinal permeability.¹⁶⁸ Additionally, increased intestinal permeability due to alterations in tight junction protein expression may contribute to increased food sensitivity seen following antibiotic use.¹⁶⁸ Research also supports the hypothesis that cognitive impairment secondary to antibiotic use is likely related to gut dysbiosis rather than systemic antibiotic response as demonstrated by antibiotic-induced distinct alterations in tight junction proteins and circulating metabolite levels similar to those of germ-free mouse models.¹⁶³

Given that medications are one of the most common sources of external perturbations, it can be established that oral administration of antibiotics has the potential to affect the gut microbiome composition, regardless of class or spectrum.¹⁴⁵ Antibiotic presence in the gut, regardless of if the GI tract is the source of the infection or just the method of absorption of the antibiotic, can exert toxicity to the bacteria within its spectrum.

As shown in Figure 2 and Table 2, the Butyryl-CoA: acetate-CoA transferase pathway is the preferred butyrate production pathway in human gut microbiota. Importantly, this pathway utilizes mostly gram-positive bacteria. This is important because gram-positive bacteria are historically most susceptible to commonly used antibiotics focused on disrupting cell wall synthesis, most notably amoxicillin and the 1^st generation cephalosporin cephalexin. For example, Roseburia, one of the most abundant contributors to Butyral-CoA: acetate-CoA transferase pathways, has been shown to be very susceptible to oral amoxicillin/clavulanic acid treatment.^169,170 Other major butyrate-producing bacteria have been shown to be reduced with amoxicillin including Clostridium and Ruminococcus spp.^171,172 Thus, certain antibiotic use may have a unique preference for disrupting gut barrier integrity by promoting the reduction of important butyrate specific producing bacteria.

Since treatment with certain antibiotics can ultimately lead to decreased butyrate-producing species in the proximal colon, the niche can be filled by various other organisms depending on disease state, diet, and several other external factors. This includes the potential of recolonization by primarily acetate and propionate producing species or even pathologic bacteria. Recolonization by species such as Lactobacillus or Bifidobacterium may be possible by patient co-ingestion of antibiotics and probiotics. This can be expected since the seven core genera of microbial organisms most often used in probiotic products are Lactobacillus, Bifidobacterium, Saccharomyces, Streptococcus, Enterococcus, Escherichia, and Bacillus.^172–174 It is also possible that recolonization by acetate- and propionate-producing species in the GI tract may have physiologic mechanisms that allow certain genera or species to recolonize these vacancies in a faster manner, possess mechanisms associated with accelerated doubling time, or may not be as susceptible to certain antibiotics. Regardless of method, if the vacated niche is recolonized by non-butyrate-producing species or species that prefer other SCFA production, the ability of butyrate-producing species to repopulate will be diminished, leading to the consequences observed with decreased butyrate in the GI tract.

Another potential mechanism for decreased butyrate-producing bacteria could be initiated by some form of gut microbiome dysbiosis of butyrate-producing bacteria secondary to external factors, such as a lack of prebiotics or diets high in simple sugars. Prebiotics are a source of food for the gut’s healthy bacteria, such as carbohydrates that cannot be digested by humans but instead are digested by gut microbes in the lower GI tract and act as food source for healthy commensal bacteria. Prebiotics are in foods such as whole grains, bananas, greens, onions, garlic, soybeans, and artichokes. Not consuming enough prebiotics can lead to dysbiosis, which has been linked to various GI problems such as IBS and related symptoms. Probiotics, on the other hand, are foods or supplements that contain live organisms^173,175 and may also be implicated in external factors inducing dysbiosis. If patients were to supplement with commercially available probiotics, this could result in population/colonization of the proximal colon with primarily acetate and propionate producing bacteria. This would result in a change in the pH of the proximal colon and further inability for repopulation of butyrate-producing bacteria (due to pH, space occupied by other bacteria, etc).

Thus, it may be beneficial for patients to supplement antibiotic treatment with prebiotics and butyrate-producing specific bacterial probiotics. Thus, targeted probiotic therapy with butyrate-producing bacteria, such as Roseburia, may lead to a more efficacious oral microbiome reseeding protocol following common antibiotic treatments that deplete favorable butyrate-producing pathways. This may improve gut level integrity and reduce immune system activation in cases of certain antibiotic usage or other dysbiosis. Overall, Roseburia or other butyrate-producing bacteria focused probiotic protocols should be studied as a possible mechanism to help improve gut epithelial integrity.

Additionally, due to the positive gut protective effects of butyrate, isolated butyrate supplementation may be beneficial during the use of antibiotics until butyrate-producing bacteria are properly recolonized. Butyrate supplementation has already been utilized to improve intestinal mucosa integrity and as a tool for reducing inflammation in systemic diseases.^176-177

Similar mechanisms can be seen for all other SCFA and their appropriate levels as well, but Butyrate has shown significant importance in its anti-inflammatory and immunoregulatory mechanisms. Also, due to Roseburia specific susceptibility, we argue butyrate production should be focused on further in research given the significant side effect of recurrent or excessive antibiotic use.

Microbiome research is historically complex, and consensus is continually changing. It is unknown if probiotics truly alter microbiome composition over extended use timelines, however, it has been proven that even if the composition of the gut microbiome doesn’t change, the administration of probiotics does impact the GI metabolome, conferring a positive overall effect.¹⁷⁸ Specific prebiotic supplements are even less researched, so it is largely unknown what the long-term effects on the gut microbiome are, however, diet is a major external factor that has the potential to alter GM composition, so it is plausible that prebiotics may alter GM composition. Lastly, although we discuss oral probiotics in this review, oral probiotics are significantly less effective than fecal microbiome transplants in reversing antibiotic associated dysbiosis,¹⁷⁹ thus fecal transplants of butyrate-producing bacteria may be a better strategy. However, fecal transplants are much more expensive and usually reserved for serious cases of Clostridium difficile, therefore, data would be needed to show efficacy in such cases.

Many studies discuss SCFAs as a broad category, however, we propose it is important to start delineating butyrate, propionate, and acetate due to their unique receptor interactions, physiologic functions, and associated gut microbes. Although all SCFAs have some role in colonocyte energy supply, each SCFA can activate unique pathways in specific tissue types and promote different metabolic pathways. For example, butyrate possesses the ability to improve gut health and epithelial integrity by promoting tight junction protein expression and goblet cell-dependent mucin production. Additionally, it has well documented anti-inflammatory effects owing to extensive innate and adaptive immune cell interactions and regulation. As gut microbiomes and gut dysbiosis have gained increased attention in several diseased states, it is vital for clinicians and researchers to consider the potential negative iatrogenic effects of treatment plans. As discussed, antibiotics serve as an important mechanism for eliminating and treating bacterial infection, however, treatment with certain antibiotics may also negatively impact vital butyrate-producing bacteria. Antibiotic therapy can lead to increased gut permeability, gut-associated inflammation, as well as systemic inflammation. Thus, future research and treatment protocols should emphasize the importance of prophylactic or reseeding protocols for butyrate-producing bacteria for patients prescribed antibiotics, in order to reduce negative outcomes.