Exploring the gut microbiome: probiotics, prebiotics, synbiotics, and postbiotics as key players in human health and disease improvement

Abstract

The human gut microbiome accompanies us from birth, and it is developed and matured by diet, lifestyle, and environmental factors. During aging, the bacterial composition evolves in reciprocal communication with the host’s physiological properties. Many diseases are closely related to the gut microbiome, which means the modulation of the gut microbiome can promote the disease targeting remote organs. This review explores the intricate interaction between the gut microbiome and other organs, and their improvement from disease by prebiotics, probiotics, synbiotics, and postbiotics. Each section of the review is supported by clinical trials that substantiate the benefits of modulation the gut microbiome through dietary intervention for improving primary health outcomes across various axes with the gut. In conclusion, the review underscores the significant potential of targeting the gut microbiome for therapeutic and preventative interventions in a wide range of diseases, calling for further research to fully unlock the microbiome's capabilities in enhancing human health.

Introduction

The gut microbiome refers to the trillions of bacteria, viruses, fungi, and other microbes colonizing in gastrointestinal tract. This aggregate microbial population plays a leading role in maintaining our overall health (Leonard and Toro, 2023) notably assisting in human development, immunity, digestion, and nutrition absorption. The gut microbiome contributes to metabolite host independent nutrients, maintains the permeability of the host gut barrier, modulates the host immune response, protects against pathogens, and even has effects on improvement of other organs (Ogunrinola et al., 2020). In healthy hosts, these individual bacteria make communities operating together in a favorable balance. Imbalance in the composition of favorable microbial communities, known as dysbiosis, may result in disruption of interactions with the host. Such changes in microbiome composition and function can contribute to disease susceptibility (Lee et al., 2022). Therefore, gut microbiome modulation is necessary to introduce re-balance of the microbial community for human health and disease prevention.

To control the gut microbiome, probiotics, prebiotics, synbiotics, and postbiotics have emerged as potential tools in maintaining a healthy gut microbiome and promoting overall human health. The term of “probiotic” was defined by the Food and Agriculture Organization (FAO) and World Health Organization (WHO) as “live microorganisms which when administered in adequate, amounts confer a health benefit on the host” in the “Guidelines for the Evaluation of Probiotics in Food” (Hill et al., 2014). The use of probiotics has been associated with many human health benefits (although there are concerns). In particular, probiotics mainly work in the gastrointestinal tract and interact with the host. Correlation between gut microbiota and human host contributes to the maintenance of health and well-being in many ways, such as gut recovery, bowel movement, immunomodulation, and anti-carcinogenesis (Guarner and Malagelada, 2003).

The definition of the term of “prebiotic” has shifted over the past 20 years via clarifications on specificity, mechanisms of effect, health attributes, and relevance. The current definition of a prebiotic is “a substrate that is selectively utilized by host microorganisms conferring a health benefit” (Gibson et al., 2017). For instance, human milk oligosaccharides (HMOs) are the major carbohydrate component of human milk other than with lactose (Chen, 2015). Among them, the specific fucosylated and sialylated HMOs are degraded by intestinal bacteria, such as Bifidobacterium longum subsp. infantis (Sela et al., 2008), resulting in the health benefit. Some other prebiotics contain certain energy sources of gut bacteria such as galacto-oligosaccharides (GOS), fructo-oligosaccharides (FOS), arabinoxylooligosaccharides (AXOS), xylooligosaccharides (XOS) and inulin for bifidobacteria or lactobacilli (van den Broek et al., 2008). Not only carbohydrate-based prebiotics, but dietary polyphenols are considered potentially prebiotic and possess chemopreventive and therapeutic characteristics. Resveratrol, a natural polyphenolic compound in grapes and red wine, is utilized by Lactiplantibacillus plantarum (Reverón et al., 2018) and showed a therapeutic effect on chronic kidney disease with mediation of the gut microbiota (Hsu et al., 2020).

The term of “synbiotic” was defined as “a mixture comprising live microorganisms and substrate(s) selectively utilized by host microorganisms that confers a health benefit on the host”. Moreover, two subsets of synbiotics were defined: complementary and synergistic. A complementary synbiotic is a synbiotic combination of a probiotic with a prebiotic which chosen to act individually for the health benefit. A synergistic synbiotic is a synbiotic in which the prebiotics selectively enrich a supplemented probiotic in the gut (Swanson et al., 2020). The reason is that a sole probiotic needs specific nutrients and not all commensal bacteria can use prebiotics, to make a synergetic effect in the living system. The interest in synbiotics has consistently increased and there are numerous combinations of probiotics and prebiotics, or putative prebiotics, to examine. In recent study, synbiotics of fermentation with Lactobacillus gasseri 505 and Cudrania tricuspidata leaf extract showed anti-cancer effects rather than sole probiotics and prebiotics. By comparison to individual probiotics and prebiotics, synergistic synbiotics showed more effective in anti-oxidant activity, beneficial modulation of tight junctions, and downregulation of proliferation and upregulation of apoptosis of tumors (Oh et al., 2020).

The term of “postbiotic” was recently defined as “preparation of inanimate microorganisms and/or their components that confers a health benefit on the host” (Salminen et al., 2021). Thus, postbiotics might comprise both the cells and the fermentation broth in which they are made including short chain fatty acids (SCFAs), vitamins, organic acids, peptides, oligosaccharides, and other cell constituents. These are produced via fermentation and processing of beneficial bacteria and such products have been shown to improve host anti-microbial activity, gut barrier function, and intestinal immunity (Wegh et al., 2019). From this concept, a novel peptide metabolite from a postbiotic derived from L. rhamnosus GG showed beneficial increases of zonula occludens-1 and MUC2 linked to membrane integrity (Gao et al., 2019). Moreover, a metabolite from fermentation of L. gasseri with Cudrania tricuspidata leaf extract in milk identified the peptide from β-casein and this showed anti-oxidant activity (Oh et al., 2016). In addition to metabolites, heat-killed bacteria also showed beneficial effects implying that cell constituents are drivers of postbiotic mechanistic function. Heat-killed L. reuteri GMNL-263 reduced fibrosis via TGF-β suppression (Ting et al., 2015). In addition, pasteurized Akkermansia muciniphila and dried yeast fermentate are easily found in commercial markets as postbiotics to regulate gut microbiota (Abot et al., 2023; Pinheiro et al., 2017).

Supplementation of probiotics, prebiotics, synbiotics, and postbiotics can modulate the host gut microbiome and promote gut health along with other organ functions outside of the gut. (Ahlawat et al., 2021). The gut microbiome metabolizes various substrates to produce functional metabolites, such as SCFA, that are utilized as key signals to connect the intestine and the remote organs associated with the modulation of functions (Ahlawat et al., 2021). Although gut and the organs are not adjacent in the human body, the gut microbiome stimulates epithelial cells or immune cells to send signals to stimulate the organ. These biochemical signals travel through the bloodstream or nerve pathway to remote tissue (Cani and Knauf, 2016). These linkages of the multidirectional communication system support the impact of the gut microbiome on human physiology. Below we summarize the functional efficiency of probiotics, prebiotics, synbiotics, and postbiotics on disease from experimental and clinical studies with a focus on gut-organ interactions.

Development and aging of gut microbiota

The human gut microbiota undergoes a complex journey from birth, with numerous factors influencing this process. The fetal gut microbiota is mostly sterile before birth, and the mother’s vaginal and fecal microbiota transfer into the baby’s gut as the initiation of the infant’s gut microbiota (Arrieta et al., 2014). During the first few months, the gut microbiota is established with rapid changes in both diversity and composition. Breastfeeding is one of the major contributors to the establishment of gut microbiota both by providing microbes but also human milk contains various bioactive factors (e.g. oligosaccharides, immunoglobulins, bioactive enzymes) that support the development of the infant microbiome and immune system (Arrieta et al., 2014). During weaning, solid foods are introduced into the infant’s diet, and the gut microbiota changes to metabolize a wider range of food substrates. Throughout childhood and adolescence, the composition of the gut microbiota is influenced by factors such as diet (including complex fiber intake), use of antibiotics, stress levels, and exposure to pathogens (Carson et al., 2023). In adulthood, the gut microbiota tends to be relatively stable, with commensal bacteria that persisting over time, however, aging and age-related changes in physiology can impact the diversity and composition of the gut microbiota (Crovesy et al., 2020). Age-related diseases, such as mental disorders, chronic liver disease, chronic kidney disease, and osteoporosis, can influence the composition and function of the gut microbiota. On the contrary, alteration in the gut microbiota may result in the development or progression of these diseases based on inflammation (Xu et al., 2021). Therefore, it has been investigated whether manipulation of gut microbiota can play a role in preventing or resolving human diseases related to specific organs.

Gut-brain axis: gut microbiota as a second brain

The gut-brain axis refers to bi-directional communication between the gastrointestinal (GI) tract and the central nervous system (CNS) through the enteric nervous system (ENS) (Mayer et al., 2014). The ENS is located within the GI tract and facilitates gut motility, intestinal permeability, enteroendocrine signaling and mucosal immune activity, which are closely related to gut functions independently of the CNS (Carabotti et al., 2015). These nerve systems can be activated by signal compounds or neurotransmitters produced by gut microbiota to communicate with the brain. Also, hormones such as ghrelin and leptin stimulated by gut microbiota are indirectly involved in the communication (van de Wouw et al., 2017). In the immune pathway, microbial lipopolysaccharide (LPS) or peptidoglycan from gut microbiota stimulates immune cells to produce cytokines, furthering an immune response (Kho and Lal, 2018). These are accomplished via chemosensitive primary afferent neurons, enteroendocrine cells, and immune cells stimulated by gut microbes or their metabolites.

Recent research suggests that dysbiosis of the patient’s gut microbiota of neurodegenerative diseases, including Parkinson’s Disease and Alzheimer’s Disease, results in the production of detrimental gut metabolites (Irvine et al., 2008). In the gut of Alzheimer’s Disease patients, the butyrate producers such as Bacteroidaceae, Veillonellaceae, and Lachnospiraceae were decreased and potential pathogenic bacteria including Escherichia coli, Klebsiella, Salmonella, and Staphylococcus produced amyloid proteins inducing the misfolding of human gut endogenous proteins (Friedland and Chapman, 2017). In a mouse model for Alzheimer’s disease the diversity of gut microbiota and neuroinflammation showed a correlation (Peterson, 2020). Similarly, the gut microbiota of Parkinson’s disease showed the reduction of SCFA producing microbes and increases of pathogenic bacteria and the levels of carbohydrate metabolizers. The misfolding of gut endogenous proteins by gut microbiota, such as amyloid beta and alpha-synuclein, can be detected in the brain of the patients’ neurodegenerative disease, suggesting that microbial community may affect the brain (Jin et al., 2023; McFleder et al., 2023).

Several clinical studies have figured out the psychophysiological effects of supplementation of prebiotics, probiotics, synbiotics, or postbiotics (Table 1). Treatments of galacto-oligosaccharides or fructo-oligosaccharides improved emotional appraisal (Schmidt et al., 2015). Oligofructose-enriched inulin-treated healthy subjects showed an improvement in acute effects on mood and cognition (Smith et al., 2015). Another study where subjects took the combination of L. helveticus R0052 and B. longum R0175 reported a reduction of negative mood and distress and decreased urinary cortisol (Messaoudi et al., 2011). Treatment with probiotics containing L. acidophilus, Lacticaseibacillus casei, Limosilactobacillus fermentum and B. bifidum improved cognition and metabolic parameters in Alzheimer’s disease patients (Akbari et al., 2016). Synbiotic combination of a cocktail of probiotics and a GOS/FOS mixture was correlated with a decrease in the Beck-Anxiety-Index and Beck-Depression-Index among hemodialysis patients (Haghighat et al., 2021). Scores on positive mood states were improved by the treatment of heat-inactivated L. helveticus MCC1848 powder as a postbiotic (Mutoh et al., 2023). In addition, heat-killed L. gasseri CP2305 treatment improved sleep quality measures (Nishida et al., 2019). Many clinical studies about gut-brain axis with dietary intervention have been investigated for decades but the questions related to the clinical treatment remain. The larger scale of the samples with longitudinal study may help for understanding the mechanisms and therapeutic opportunity.

Table 1.

Clinical trials with prebiotics, probiotics, synbiotics, and postbiotics for investigation of Gut-brain axis

Supplements	Subjects	Doses	Effects and mechanisms	Ref.
Prebiotics
Oligofructose-enriched inulin	Healthy males and females (n = 45, age 19–30)	5 g of sachet in a drink (tea or coffee) in a day	Prebiotic treatment improved mood, recognition memory, and recall	Smith et al. (2015)
GOS	Healthy males and females (n = 47, age 18–45)	5.5 g per day for 3 weeks in powder form	GOS intake group showed lower salivary cortisol awakening response Decreased attentional vigilance in a dot-probe task	Schmidt et al. (2015)
Probiotics
L. helveticus R0052 and B. longum R0175	Healthy males and females (n = 55, age 30–55)	1.5 g (3 × 109 CFU) per day for 30 days in powder form	Somatization, depression, and anger–hostility subscales were improved HADS and HADS-A scores were higher in probiotics group	Messaoudi et al. (2011)
L. acidophilus, L. casei, L. fermentum, and B. bifidum	Alzheimer’s disease patients (n = 23, age 60–95)	1 g (2 × 109 CFU) per day for 12 weeks in milk	Improvement of MMSE score Plasma malondialdehyde, serum high-sensitivity C-reactive protein, homeostasis model of assessment-estimated insulin resistance, and quantitative insulin sensitivity check index were significantly varied	Akbari et al. (2016)
Synbiotics
FOS, GOS, inulin, L. acidophilus, B. bifidum, B. lactis, and B. longum	Patients undergoing Hemodialysis (n = 23, age 30-65)	5 g of each prebiotics and 5 g of probiotics (2.7 × 107 CFU/g) for 12 weeks in powder form	Significant decrease in Beck-Anxiety-Index and Beck-Depression-Index score	Haghighat et al. (2021)
FOS, Bacillus coagulans, L. rhamnosus, and L. helveticus	Female with polycystic ovary syndrome (n = 28, age 18–45)	2 g of synbiotics sachets (1011 spores of Bacillus coagulans, 1010 CFU of L. rhamnosus, 1010 CFU of L. helveticus, 500 mg of FOS) for 12 weeks in powder form	Improved the scores of emotional and infertility	Hariri et al. (2024)
Postbiotics
Heat-killed L. helveticus MCC1848	Healthy young adults (n = 29, age 20–64)	One stick heat-killed L. helveticus MCC1848 (5 × 109 CFU/stick) for 4 weeks in powder form	Improved profile of Mood States 2 scores on positive mood states	Mutoh et al. (2023)
Heat-inactivated L. gasseri CP2305	Healthy young students (n = 74, age 24–26)	One tablet of Heat-inactivated L. gasseri CP2305 (5 × 109 CFU/tablet) per day for 24 weeks	Significantly reduced anxiety and sleep disturbance Shortened sleep latency and wake time after sleep onset Mitigated the reduction in Bifidobacterium and prevented the elevation of Streptococcus	Nishida et al. (2019)

GOS galacto-oligosaccharide, CFU colony forming unit, HADS hospital anxiety and depression scale, HADS-A HADS-anxiety, MMSE mini-mental state examination, FOS fructo-oligosaccharide

Gut-liver axis: the first organ before spreading to the whole body

The gut-liver axis refers to the bi-directional relationship between the GI tract and the liver connected with the portal vein, which transports absorbed materials from the gut to the liver (Albillos et al., 2020). The liver traffics almost 70% of the blood supply for the body's reticuloendothelial system from the outflow of the intestine, which means it is exposed to the metabolites from gut bacteria (and perhaps gut bacteria themselves) via the portal vein (Son et al., 2010). The bacterial products or the response signal molecules from gut epithelial or immune cells can transfer to the gut vascular barrier directly linked with the liver. The liver secretes bile, and it can be absorbed from the intestine and recirculated in the liver (Kakiyama et al., 2013). IgA produced by plasma cells in the intestine is released into the intestinal lumen as secretory IgA, which leads to metabolic alteration in the gut, and the liver is involved in transporting IgA to maintain its stability and clearing of IgA immune complexes from the circulation (Moro-Sibilot et al., 2016). In addition, gut bacteria or toxic derivatives such as LPS and endotoxin can transfer to the lymphatic vascular system in the intestinal lacteals and flow through the lymph node and thoracic duct, merging with the liver lymphatics (Bernier-Latmani and Petrova, 2017). Due to the weakened intestinal barrier by gut microbiota, therefore, toxic substances or bacteria can infiltrate the systemic circulation, leading to liver disease (Albillos et al., 2020).

Various liver diseases are directly related to the gut-liver axis. Non-alcoholic fatty liver disease (NAFLD), caused by high-fat or low-fiber diet, results in in a reduction of SCFA production and lowering of mucus production leading to gut microbial dysbiosis and increased bacterial penetrability. Several studies of NAFLD patients showed a high abundance of Eubacterium rectale and Lactobacillus sp. along with increased inflammatory cytokines such as tumor necrosis factor (TNF)-α, Interferon-γ, and Interleukin (IL)-6 (Jiang et al., 2015; Loomba et al., 2017; Yan et al., 2017). For alcoholic liver disease (ALD), addictive alcohol consumption drives alcohol and acetaldehyde, which cause liver damage and disruption of the epithelial cells, creating a leaky gut. This results in the entry of bacteria and their metabolites or LPS into the liver via the portal vein. These initiate activation of toll-like receptors (TLRs) of the Kupper cells to increase pro-inflammatory cytokines and dysbiosis of gut microbiota (Minemura and Shimizu, 2015; Usami et al., 2015). Cholesterol is transformed into bile acids, such as cholic or chenodeoxycholic acid, in the liver by cholesterol 7 alpha-hydroxylase (CYP7A1). They are secreted into the gut lumen as primary bile acids. In cirrhosis, microbial dysbiosis in the gut results from low levels of primary bile acids by 7-α-dehydroxylating bacteria. They lead to an increment of secondary bile acids and subsequently disruption of the farnesoid X receptor (FXR) activation pathway, which is the key intestinal signaling for control of hepatic CYP7A1 expression and antimicrobial peptide synthesis (Hartmann et al., 2018; Minemura and Shimizu, 2015).

Supplementation of prebiotics, probiotics, synbiotics, or postbiotics also showed physiological effects on liver diseases (Table 2). The oligofructose as a prebiotic was fed to patients with non-alcoholic steatohepatitis (NASH), and it improved overall non-alcoholic fatty liver activity score (NAS) with up-regulation of Bifidobacterium and down-regulation of Clostridium cluster I and XI (Bomhof et al., 2019). Inulin-treated NAFLD patients showed a reduction in their mean body mass index and alanine aminotransferase (ALT) with a significantly lowered ratio of Firmicutes/Bacteroidetes (Chong et al., 2020). Supplementation of probiotic cocktail reduced fatty liver index (FLI) and serum aspartate transaminase (AST) and gamma glutamyl transferase (GGT) in NAFLD patients (Kobyliak et al., 2018). Another study showed that a supplemented probiotic mixture resulted in the improvement of the Child–Pugh score and modulated the composition of gut microbiota (Gupta et al., 2022). The synbiotic combination of B. longum and FOS treatment reduced the NASH activity index, steatosis, and serum AST levels in NASH patients (Malaguarnera et al., 2012). Bakhshimoghaddam and colleagues reported that a synbiotic yogurt (containing B. animalis and inulin) decreased liver steatosis in patients with NFLD (Bakhshimoghaddam et al., 2018). A clinical study of patients with metabolic syndrome showed that supplementation with pasteurized Akkermansia muciniphila resulted in a reduction of blood markers for liver dysfunction and inflammation (Depommier et al., 2019). While such data suggests postbiotics have potential efficacy toward liver health, more clinical study is needed to confirm their benefits (Mosca et al., 2022).

Table 2.

Clinical trials with prebiotics, probiotics, synbiotics, and postbiotics for investigation of gut-liver axis

Supplements	Subjects	Doses	Effects and mechanisms	Ref.
Prebiotics
FOS	NASH patients (n = 14, age > 18, NAS score ≥ 5)	8 g per day for 12 weeks and then 16 g per day for 24 weeks in powder form	Improvement of overall NAS score Increased Bifidobacterium Decreased Clostridium cluster I and XI Positive correlation with delta NAS and delta ALT	Bomhof et al. (2019)
Inulin	NAFLD patients (n = 20, age 19 – 71, ALT range 30–141 U/L)	4 g twice daily for 12 weeks	Reduction of ALT and AST	Chong et al. (2020)
Oligofructose	Patients with NAFLD (n = 40, age 29–48, ALT > 1.5)	8 g twice daily for 12 weeks	Decreased in triglyceride, ALT, AST, and GGT	Behrouz et al. (2020)
Resistant dextrin	Patients with NAFLD (n = 60, overweight and obesity, age 20–50)	10 g daily for 12 weeks	Decreased in WHR, AST, ALP, triglyceride, and hs-CRP Increased in HDL-c	Farhangi et al. (2022)
Probiotics
14 probiotic bacteria (Bifidobacterium, Lactobacillus, Lactococcus, Propionibacterium, Acetobacter)	Type 2 diabetic patients (n = 30, age 43–63)	10 g (Lactobacillus  + Lactococcus (6 × 1010 CFU/g), Bifidobacterium (1 × 1010/g), Propionibacterium (3 × 1010/g), Acetobacter (1 × 106/g)) per day	FLI decreased TNF-α and IL-6 reduced	Kobyliak et al. (2018)
5 probiotic bacteria (Lacticaseibacillus casei, Lacticaseibacillus rhamnosus, Lactobacillus acidophilus, B. longum, B. breve)	Patients with NAFLD (n = 36, age 31–46, ALT > 1.5)	Total 5 × 109 CFU per capsule daily for 12 weeks	Decreased in triglyceride, ALT, AST, GGT, and alkaline phosphatase	Behrouz et al. (2020)
L. rhamnosus R0011 and L. helveticus R0052	ALD patients (n = 44, age > 20, ALT > 50, alcohol-drinking (40 g/day/week))	120 mg per day for 7 days	Reduction of ALT and GGT Increased Bacteroidetes Decreased Proteobacteria and Fusobacteria	Gupta et al. (2022)
Synbiotics
FOS and B. longum	NASH patients (n = 34, age 40–52)	2.5 g per day for 24 weeks	Reduction of ALT, LDL-c, CRP, TNF-α, HOMA-IR, serum endotoxin, steatosis, and NASH activity index	Malaguarnera et al. (2012)
Inulin and B. animalis subsps. lactis BB-12	Patients with NAFLD (n = 32, age 29–48)	Synbiotic yogurt (108 CFU/ml of B. animalis subsp. lactis BB-12 and 1.5 g of inulin) per day for 24 weeks	The grades of NAFLD decreased Reduction of ALT, AST, ALP, GGT	Bakhshimoghaddam et al. (2018)
FOS and B. animalis subsps. lactis BB-12	Patients with NAFLD (n = 24, ≥ 2 fibrosis, age 21–77)	4 g of FOS twice a day and 1010 CFU per day for 12 months	Increased in adipose tissue dysfunction, SAT gene expression, and HOMA-IR	Bilson et al. (2024)
Postbiotics
Pasteurized Akkermansia muciniphila	Patients with metabolic syndrome (n = 32, BMI > 25, age 18–70)	1010 CFU/g of A. muciniphila per day for 3 months	Improved insulin sensitivity Reduced insulinemia, plasma total cholesterol, blood markers of liver dysfunction and inflammation	Depommier et al. (2019)

FOS fructo-oligosaccharide, NASH non-alcoholic steatohepatitis, NFLD nonalcoholic fatty liver disease, NAS NFLD activity score, ALT alanine transaminase, AST aspartate transferase, GGT gamma-glutamyl transferase, WHR waist/hip ratio, ALP alkaline phosphatase, hs-CRP high-sensitivity C-reactive protein, HDL-c high-density lipoprotein cholesterol, CFU colony forming unit, FLI fatty liver index, TNF-α tumor necrosis factor alpha, IL interleukin, ALD alcoholic liver disease, LDL-c low-density lipoprotein cholesterol, CRP C- reactive protein, HOMA-IR homeostasis model assessment of insulin resistance, NASH non-alcoholic steatohepatitis, SAT subcutaneous adipose tissue

Gut-kidney axis: disposal system from gut microbiota

The gut-kidney axis refers to the bi-directional communication between the gut microbiota and the kidney through blood circulation, similar to the gut and the liver. This communication can be negatively influenced by uremic toxins such as trimethylamine (TMA) N-oxide (TMAO) (Maksymiuk et al., 2022), p-cresyl sulfate, and indoxyl sulfate (Lin et al., 2022) which leads to various complications (Nigam and Bush, 2019). In the gut, TMA is directly obtained from foods (such as seafood) or bacterial metabolism of betaine or l-carnitine. It transfers to the liver and is oxidized to TMAO by flavin-dependent monooxygenase. TMAO is usually excreted in urine but high concentration in plasma leads to impaired kidney function with declining glomerular filtration rate (GFR) (Zeisel and Warrier, 2017). p-Cresol and indole are derived from tyrosine and tryptophan metabolism by gut bacterial enzymes, respectively. They are further metabolized into p-cresyl sulfate and indoxyl sulfate in the liver and are mainly present as protein-bound forms in the circulatory system. They are also normally excreted in urine but the dialysis removal efficiency is low in patients undergoing hemodialysis (Lin et al., 2022). In uremia, the high level of urea in the bloodstream diffuses into the gut lumen and causes disruption of the bacterial composition. Urease-producing gut bacteria metabolize urea to produce ammonia that is hydrolyzed into ammonium hydroxide. This can interfere with the tight junction proteins, which disrupts the epithelial barrier (Kang, 1993). The leaky gut allows uremic toxins or bacterial translocation from the lumen to the circulatory system, which contributes the local systemic inflammation (Balzan et al., 2007).

In patients with chronic kidney disease (CKD), microbial dysbiosis is associated with the release of uremic toxins and enhances the progression of CKD (Lin et al., 2022; Maksymiuk et al., 2022). A high number of indole- and p-cresol-producing bacteria, including Clostridiaceae and Enterobacteriaceae, are found in patients with end-stage renal disease (ESRD) (Wong et al., 2014). Enterobacteriaceae was also relatively higher in peritoneal dialysis patients’ gut, but bifidobacteria was shown to be low level compared to healthy control (Crespo-Salgado et al., 2016). Furthermore, uremic toxins and inflammatory biomarkers, including IL-6 and monocyte chemoattractant protein-1, were higher in hemodialysis patients. Notably, dialysis patients have low levels of SCFAs and butyrate compared to healthy controls, likely due to intestinal dysbiosis (Borges et al., 2016). These suggest that uremic toxins are key factors linking the gut microbiota and the deterioration of renal function. In patients with immunoglobulin A (IgA) nephropathy (IgAN), dysbiosis of gut microbiota is also related to the pathogenesis of IgAN because it plays a role in the gut mucosal immune system. IgAN pathology leads to the elevation of free amino acids in serum, and it results in the lowering absorption of protein from the gut lumen. This causes the change of microbial composition along with the elevation of fecal p-cresol level and lowering SCFA-producing bacteria (Wong et al., 2014).

Several studies showed an improvement in renal disease using prebiotics, probiotics, synbiotics, and postbiotics (Table 3). Resistant starch treatment of patients on hemodialysis reduced free plasma levels of indoxyl sulfate and p-cresol sulfate (Sirich et al., 2014). Another study with amylose resistant starch supplementation decreased serum urea, IL-6, and TNF-α in ESRD patients (Laffin et al., 2019). The patients undergoing hemodialysis received probiotic L. rhamnosus for 4 weeks, which showed a reduction of uremic toxins (Eidi et al., 2018). Rather than prebiotics or probiotics, many clinical trials have been studied with synbiotics. The combination of probiotics (a mixture of 9 strains of Bifidobacterium, Lactobacillus and Streptococcus) and prebiotics (a mixture of GOS, FOS, inulin) was supplemented for patients with CKD and the serum p-cresol sulfate was significantly reduced combined with an alternation of microbiome (Rossi et al., 2016). A synbiotic meal containing B. longum and sorghum flakes reduced serum p-cresol- and indole-sulfate, and urea in hemodialysis patients (Lopes et al., 2019). Nevertheless, the supplementation of prebiotics, probiotics, or postbiotics for CKD patients still needs to be studied for further understanding of the links between gut microbiota and kidney diseases. While animal studies of dietary intervention have shown the molecular mechanisms of kidney disease markers with germ-free mice (Mishima et al., 2020), human studies still remain unexplored for detailed mechanisms. These results may come from the difference in physiological conditions between animal disease models and human CKD patients (Wehedy et al., 2021).

Table 3.

Clinical trials with prebiotics, probiotics, synbiotics, and postbiotics for investigation of gut-kidney axis

Supplements	Subjects	Doses		Effects and mechanisms		Ref..
Prebiotics
Resistant starch	Hemodialysis patients (n = 20, age 40–68)	15 g (60% resistant starch of amylose corn starch) per day for 6 weeks		Reduction of free indoxyl and PCS in serum		Sirich et al. (2014)
Arabinoxylan oligosaccharide	CKD patients (n = 40, age 64–76, 15 < eGFR < 45 ml/min/1.73m2)	10 g twice daily (arabinoxylan oligosaccharides) for 4 weeks		No significance in serum and urinary PCS, PCG, IS, and phenylacetylglutamine No significance in urinary TMAO Significant decreased in serum TMAO		Poesen et al. (2016)
Resistant starch	CKD patients in hemodialysis (n = 31, age 49–63)	16 g of resistant starch daily for 4 weeks on alternate days through cookies on dialysis days and powder in a sachet on non-dialysis days		Reduction in serum IL-6, TBARS, and IS		Esgalhado et al. (2018)
HAM-RS2	ESRD patients (n = 9, age 42–65)	20 g per day for a month in a biscuit		Reduction of serum urea, IL-6 and TNF- α		Laffin et al. (2019)
Resistant starch	Hemodialysis patients (n = 16, age 45–65)	16 g of resistant starch daily for 4 weeks		Reduction of RANTES, platelet-derived growth factor, and IP-10		de Paiva et al. (2020)
FOS	Non-dialysis CKD patients (n = 46, age 43–72)	12 g of FOS for 3 months		Decrease in IL-6 and trend towards PCS reduction		Armani et al. (2021)
Unripe banana flour (48% resistant starch)	Patients undergoing APD (n = 26, age 43–67)	21 g of unripe banana flour for 4 weeks		Reduction in serum IS		de Andrade et al. (2021)
Mixture of inulin and FOS	Continuous ambulatory peritoneal dialysis patients (n = 16, age 26–49)	10 g of mixture daily for 12 weeks		Reduction in uric acid, fecal uric acid degradation Increased ratio of Firmicutes/Bacteroidetes		He et al. (2022)
β-Glucan	Stage 3–5 CKD patients (n = 30, age 29–51)	3 g of β-Glucan daily for 14 weeks		Reduction in uremic IS, PCS, PCG		Ebrahim et al. (2022)
Dietary fiber (galactomannan, resistant dextrin, FOS, and starch)	ESRD patients (n = 81, age 42–59)	10 g of dietary fiber daily for 8 weeks		Increased hemoglobin, serum iron, serum ferritin, and serum butyric acid Increased B. adolescentis and Lactobacillaceae		Li et al. (2022b)
Probiotics
L. rhamnosus	Hemodialysis patients (n = 21, age 20–81)	L. rhamnosus (1.6 × 107 CFU/capsule) per day for 4 weeks		Reduction of serum PCS levels		Eidi et al. (2018)
Streptococcus thermophilus KB19, L. acidophilus KB27, B. longum KB31	CKD patients on hemodialysis (n = 11, age 32–72)	Total 9 × 1013 CFU per day for 3 months		Increased in plasma betaine levels No significant change in TMAO		Borges et al. (2019)
B. bifidum BGN4, B. longum BORI	Patients in hemodialysis (n = 22, age 61–76)	Twice a day with 2.0 × 1010 CFU for 3 months		Reduction in systemic inflammatory responses and proinflammatory monocytes Increased in Treg cells		Choi et al. (2022)
B. longum DLBL Limosilactobacillus reuteri LRE02	Patients in advanced CKD (n = 29, age 18–80)	2 g (5 × 109 of B. longum DLBL, 1 × 109 Lim. reuteri LRE02) twice a day for 1 month and once a day for 2 months		No significant change in uremic toxins		De Mauri et al. (2022)
Synbiotics
Inulin, FOS, GOS 9 strains of Lactobacillus, Bifidobacterium, Streptococcus	CKD patients (n = 37, age 59–79)	7.5 g of prebiotic powder and one probiotics capsule (4.5 × 1010 CFU/capsule), twice a day for 6 weeks		Reduction of serum PCS and IS Increase Bifidobacterium Decrease Ruminococcaceae		Rossi et al. (2016)
Extruded sorghum flakes B. longum BL-G301	Hemodialysis patients (n = 29, age 52–74)	Average 8.7 × 108 CFU/100 mL of B. longum BL-G301 and 40 g of extruded sorghum flakes per day for 7 weeks		Reduction of serum PCS, IS and urea levels Higher fecal butyric acid and lower pH		Lopes et al. (2019)
L. acidophilus T16, B. bifidum BIA-6, B. animalis subsp. lactis BIA-6, B. longum LAF-5	Diabetic patients undergoing hemodialysis (n = 30, age 47–77)	5 g of probiotics (2.7 × 107 CFU/g each) and 0.8 g of inulin per day for 12 weeks		Reduction of fasting plasma glucose, insulin levels, insulin resistance, high sensitivity C-reactive protein, and malondialdehyde levels Increased quantitative insulin sensitivity check index, total antioxidant capacity, and total glutathione levels		Soleimani et al. (2019)
Soy milk Lactiplantibacillus plantarum A7	Patients with diabetic nephropathy (n = 20, age 48–65)	200 ml per day of soy milk containing L. plantarum A7 for 8 weeks		Reduction in albuminuria, serum creatinine, serum IL-18, and serum sialic acid Improvement in eGFR		Abbasi et al. (2017)
FOS L. acidophilus, B. longum, S. thermophilus	Patients in hemodialysis (n = 50, age 34–64)	Total 250 mg of bacteria and 100 mg of FOS, three times a day for 90 days		Reduction of PCS and IS Improved quality of life		Saxena et al. (2022)
FOS L. acidophilus La-14	ESRD patients in hemodialysis (n = 30, age 48–76)	2 × 1011 CFU/g and 65 mg of FOS per day for 8 weeks		Reduction of PCS and IS		Kuskunov et al. (2023)

PCS p-cresol sulfate, CKD chronic kidney disease, eGFR estimated glomerular filtration rate, PCG p-cresyl glucuronide, IS indoxyl sulfate, TMAO trimethylamine N-oxide, IL interleukin, TBARS thiobarbituric acid reactive substances plasma, HAM-RS2 high amylose maize resistant starch type 2, ESRD end-stage renal disease, TNF-α tumor necrosis factor α, RANTES regulated upon activation normal T-cell expressed and secreted, IP-10 interferon-inducible protein 10, FOS fructo-oligosaccharide, APD automated peritoneal dialysis, CFU colony forming unit

Gut-bone axis: mineral storage from gut microbiota

The gut-bone axis refers to the communications between gut microbiota and skeletal system through the absorption of nutrition and osteoimmunological metabolism. The gut microbiota significantly influences nutrient absorption, including minerals and vitamins, which are crucial for bone health regulation and bile acid metabolism (Villa et al., 2017). For example, vitamin D is the major stimulator of calcium absorption and participates in the regulation of bile acid (Rodríguez et al., 2013). Moreover, gut microbiota regulates the cytokines levels in the epithelial lumen and this can alter various immune factors and bone metabolic processes. In the bone, osteoblasts regenerate bones, and osteoclasts degrade bone for remodeling and meditation of bone loss by resorption (Boyce et al., 2009). The activities of osteoblasts and osteoclasts are balanced in bone remodeling and this balance can be regulated by cytokines. Osteoclasts are activated by proinflammatory cytokines, such as TNF-α, IL-1, and IL-6. Osteoblasts induce macrophage colony stimulating factor (M-CSF), which leads to the expression of receptor activator of nuclear factor-κB (RANK) on osteoclasts, and RANK ligand (RANKL), which binds to RANK to initiate the bone resorption of osteoclasts at the surface of the bone, leaving behind resorptive pits. During the bone forming of osteoblasts, osteoprotegerin (OPG) is expressed as a decoy receptor for RANKL to prevent the binding with RANK, inhibiting osteoclastogenesis and bone resorption for maintaining the symbiosis between bone resorption and forming. The dysregulation of immune cells in inflammatory conditions drives high levels of RANKL and low levels of OPG, leading to osteoporosis (Kitaura et al., 2020; Nanjundaiah et al., 2013).

Rheumatoid arthritis, one of the major diseases related to the bone, is still partially understood but known as a pathological response to aberrant immune activation (Dong et al., 2003). The gut microbiome is closely associated to the immune system, implying that the dysregulation of immune response by gut microbes may influence onset of rheumatoid arthritis. Prevotella copri, which was in high abundance gut bacteria in the patients with early stage of rheumatoid arthritis, showed a potential role in pathogenesis (Scher et al., 2013). Another study showed P. gingivalis harbors peptidyl arginine deiminase, which leads to autoantibodies that play a crucial role in the development of rheumatoid arthritis (Li et al., 2013). In the active period of rheumatoid arthritis, Haemophilus sp., Collinsella, and Akkermansia showed higher relative abundances in various studies (Chiang et al., 2019; Zhang et al., 2015). Based on these experiments, gut microbial change may have a crucial role at the early or activated stage of rheumatoid arthritis, but further research is needed to identify specific biomarkers from gut microbiota. For the mechanism of osteoporosis, complex factors are involved in bone remodeling, including the immune system, gut metabolites, and endocrine hormones (Lyu et al., 2023). In the immune system, RANKL is a key chemokine expressed from T cells and mesenchymal lineage cells for the connection with the skeletal system. Among T cells, only Th17 TNF-α⁺ cells selectively express M-CSF and RANKL, leading to osteoclastogenesis, while Treg cells inhibit bone resorption but promote bone formation by secretion of anti-inflammatory cytokines (Ciucci et al., 2015; Fujisaki et al., 2011). Butyrate is one of the major SCFAs from gut microbiota and is also involved in bone formation. Studies with the treatment of butyrate in the animal model showed the inhibition of osteoclastogenesis or promotion of bone formation, suggesting that the regulation of SCFAs in bone remodeling can be a potential therapeutic treatment for osteoporosis (Chen et al., 2007; Katono et al., 2008; Lucas et al., 2018; Tyagi et al., 2018).

Dietary intervention studies with prebiotics, probiotics, synbiotics, and postbiotics showed improvement in calcium absorption and skeletal systems (Table 4). The treatment of healthy young adolescents with long chain inulin-type fructans resulted in an increment of bone mineral density (BMD) (Abrams et al., 2005). Supplementation of GOS led to improvement in calcium absorption in both low- and high-dose groups, and Bifidobacterium increased in the gut (Whisner et al., 2013). In patients with postmenopausal osteoporosis supplementation of B. animalis subsp. lactis Probio-M8 improved bone metabolism, such as decreased parathyroid hormone and procalcitonin levels in serum (Zhao et al., 2023). Another study with postmenopausal women showed that supplementation of L. fermentum SRK414 maintained osteocalcin levels and increased BMD (Han et al., 2022). Up to date, there is only one clinical study with synbiotic supplementation to rheumatoid arthritis, but it showed no significant difference in disease improvement, suggesting that the treatment period needs to be extended (Esmaeili et al., 2020). Current research on postbiotics for the improvement of the skeletal system is limited to animal studies, implying that various studies are still needed to clarify the mechanisms of action.

Table 4.

Clinical trials with prebiotics, probiotics, synbiotics, and postbiotics for investigation of gut-bone axis

Supplements	Subjects	Doses	Effects and mechanisms	Ref.
Prebiotics
Long-chain inulin-type fructans	Healthy adolescents (n = 100, age 9–13)	8 g per day for 12 months with 180–240 ml of calcium-fortified orange juice	Calcium absorption, whole body bone mineral content, and whole-body bone mineral density increased	Abrams et al. (2005)
GOS	Premenarcheal girls (n = 31, age 10–13)	2.5 or 5 g, twice a day for 3 weeks in smoothie drinks	Improvement in calcium absorption in both low and high dose groups Increased Bifidobacterium	Whisner et al. (2013)
Soluble corn fiber	Healthy adolescent females (n = 28, age 11–14)	10 or 20 g per day for 4 weeks in a muffin and fruit flavored beverage	Increased calcium absorption Increased α-diversity (Chao1 and observed OUT) Significantly separated by each group in β-diversity Increased Parabacteroides	Whisner et al. (2016)
Soluble corn fiber	Postmenopausal women (n = 20, age 57- 69)	20 g (24 g of Promitor™ Soluble Fiber 85) twice per day for 2 months	No differences between groups in changes in fractional calcium absorption Significant difference in β-diversity	Wu et al. (2022)
Probiotics
B. animalis subsp. lactis Probio-M8	Patients in postmenopausal osteoporosis (n = 20, age 50–80)	2 g of B. animalis subsp. lactis Probio-M8 1.5 × 1010 CFU per day for 3 months	Increased vitamin D3 level Decreased PTH, PCT, and calcium levels in serum	Zhao et al. (2023)
L. fermentum SRK414	Patients in postmenopausal osteoporosis (n = 27, age > 55)	Two capsule of L. fermentum SRK414 per day for 6 months	Increased in femur neck BMD Maintained osteocalcin levels	Han et al. (2022)
L. reuteri ATCC PTA 6475	Women with osteopenia (n = 32, age 75–80, high BMD)	L. reuteri 6475 1 × 1010 CFU per day for 12 months	97 metabolites significantly different Increased butyrylcarnitine Decreased serum inflammation marker Decreased E. coli Increased SCFAs-producing bacterial species	Li et al. (2021, 2022a, )
L. reuteri ATCC PTA 6475	Elderly women (n = 45, age 75–77)	L. reuteri 6475 1 × 1010 CFU per day for 12 months	No significance in volumetric BMD and areal BMD	Nilsson et al. (2018)
Bacillus subtilis C-3102	Healthy postmenopausal women (n = 34, age 50–69)	3 tablets contained 3.4 × 109 CFU per day for 24 weeks	Increased hip BMD Decreased urinary type I collagen cross-linked N-telopeptide Increased Bifidobacterium Decreased Fusobacterium	Takimoto et al. (2018)
Synbiotics
FOS, L. acidophilus, L. bulgaricus, L. casei, L. rhamnosus, B. breve, B. longum, and Streptococcus thermophiles	Patients in rheumatoid arthritis (n = 186, age 17–85)	500 mg capsule (containing a prebiotic and 109 CFU/ml of each bacterium) per day for 3 months	No significant differences	Esmaeili et al. (2020)

GOS galacto-oligosaccharides, OTU operational taxonomic unit, CFU colony forming unit, PTH parathyroid hormone, PCT procalcitonin, BMD bone mineral density, SCFA short chain fatty acid, FOS fructo-oligosaccharide

Discussion and conclusion

The gut microbiota and the organs reciprocally communicate in multiple ways via the nervous system, the immune system, through host derived signals, and bacterial metabolites. A single metabolic substance or cytokine is not just confined to specific tissue cells, rather it’s interconnected throughout the body, such as cells, tissues, and organs. Research about the connection between gut microbiota and other organs in the host is continuously being investigated as well as brain, liver, kidney, and bone. The metabolic, immune, nervous, and endocrine systems are involved in the complicated communication network in the gut-skin axis (Vaughn et al., 2017). For example, atopic dermatitis, an inflammatory disease of the skin, results from disrupted Th1/Th2 ratio caused by the expression of biased cytokines (Lee et al., 2018). The mammalian target of rapamycin (mTOR) signaling pathway is also involved in gut-skin communication. It has been studied that it directly regulates the gut barrier function as well as gut bacterial metabolites influence mTOR for immune cell profiles and cytokine production (Noureldein and Eid, 2018). For the gut-heart axis, in addition, intestinal dysbiosis and gut metabolites are involved in the relationship between gut and heart failure (Desai et al., 2023).

The gut-organ axes share the gut metabolites and immune system for their communication. The gut bacteria-derived uremic acid, LPS, TMAO, p-cresyl sulfate, and indoxyl sulfate transfer to the liver, heart, and kidney, leading to dysfunction. Prebiotics, probiotics, synbiotics, or postbiotics regulate gut microbiota dysbiosis, facilitate production of beneficial SCFA, such as butyric acid, and reduce pathogenic factors. These lead to the regulation of gut microbiota to stimulate Treg cells to Th1 and Th2 balance in inflammatory status (Wu and Wu, 2012). In contrast, the metabolites from the malfunctioning organ can be transferred to the gut and lead to bacterial dysbiosis. Even though a full understanding of the interactions between the gut microbiota and diseases in organs is indeterminate, it is clear that prebiotics, probiotics, synbiotics, and postbiotics are recognized as effectors in the regulation of gut microbiota and host physiopathology. For further safe and functional food, however, clinical trials are needed to confirm the safety and efficacy of dietary interventions.

Declarations

Conflict of interest

The authors declare no conflicts of interest.