Microbiota medicine: towards clinical revolution

The human microbiome is in a constant and dynamic interaction with the surrounding environment. It is affected by many factors involved in the daily routine of individuals such as the location, dietary intake, pollution and others. Indeed, people in urban life spend most of their time in enclosed buildings designed, built and managed by humans. For instance, in industrialized countries people spend up to 90% of their lifetime indoors, i.e. inside the built environment (BE) [12, 13]. The BE can be defined as “man-made structures, features, and facilities viewed collectively as an environment in which people live, work, recreate and travel” [13]. It comprises all structures built by humans including residential houses, public buildings, industry facilities, transportation vehicles, open spaces, but also very extreme environments, such as submarines and space stations [14]. Like in every ecosystem on the surface of the earth, different microbial communities have been found in every part of the BE and have been known as the “built environment microbiome”.

The BE microbiome and its interactions with human occupants represent a relatively new area of study and a highly interdisciplinary research field. The BE is characterized by a great microbial diversity, as well as a very fluctuating environmental conditions and sharp gradients of physicochemical parameters, which significantly shape the resident microbiomes [12]. Indeed, the composition and function of microbial communities found in the BE as well as their interaction with humans are extraordinarily complex, dynamic, and highly interconnected. Notably, such microbial’s communities’ microbes and their metabolites have been linked to the cause, exacerbation, or prevention of inflammation and other human diseases.

Due to a significant exchange between the human microbiome, in particular the skin and intestinal tract, and the BE microbiome, the essential role of the BE microbiome is evident but far from fully understood [14]. A depletion of microbial diversity in the BE is supposed to be partly responsible for an increasing prevalence of allergy and asthma in industrialized countries. In addition, there is mounting evidence that the man-made environmental conditions inside the BE, such as the extensive use of antimicrobial cleaning agents, may favor polyextremophilic microorganisms that pose a threat to the human inhabitants [15]. Nevertheless, the control of pathogenic microorganisms in the BE clearly requires antimicrobial measures to prevent infections [13].

Similarly, considerable efforts have been made to understand the effect of the BE and its microbiome on the human mental health [16, 17]. Indeed, with the increased trendy urbanization, people exhibit limited exposure to the so-called immunoregulatory microbes, referred to as the “old” friends. Such a decrease in exposure has led to an epidemic of chronic low-grade inflammatory states associated with an increased risk of stress-related psychiatric disorders [18].

Probably, a successful management of the BE microbiome for the sake of human health will require a well-balanced mixture of, among others, antimicrobial and “probiotic” measures [13, 19, 20].

The digestive tract constitutes the largest interface between the sterile part of the human body and environmental factors and pathogens. It is the most important site for colonization by thousands of microorganisms such as viruses, eukaryote, and more than 1000 types of bacteria. These microbes, named collectively "gut microbiota", are well-known to have different beneficial roles in maintaining the human homeostasis such as strengthening gut integrity, harvesting energy, protecting against pathogens, and regulating host immunity [21].

In fact, humans first encounter microorganisms in their early life, specifically at birth when different bacteria succeed to colonize the baby’s body during the first months of life. In details, microorganism start to develop in the oral and nasopharyngeal membranes as well as the skin. Gradually, the microbiota will start to increase steadily within the gastrointestinal tract, with a developed oral and salivary microbiome, less bacteria in the stomach, but with a very high concentration of bacteria inhabiting the colon [22].

A tremendous amount of extensive research work has been done in the last decades, and has revealed that the gut microbiota dysbiosis can be associated with many pathologies within the human body [21], such as periodontitis and caries [23, 24], various metabolic disorders [25‐27], chronic inflammatory bowel syndromes [28], cardiovascular diseases (CVD) [29, 30], cancer [31, 32], as well as chronic kidney diseases (CKD) [33, 34]. The extent to which gut microbiota dysbiosis may exert this systemic control and cause the induction of a given pathology depends on the functionality of gut barrier and the maturity of the immune system of the recipient [35].

Although research in the past decades showed a bidirectional crosstalk between host and microbiota, the mechanisms in this interaction are not fully described. Interestingly, recent studies demonstrate that not only the nature of the gut microbes and their diversity influence the host, but also their metabolites [86]. The gut microbiome yields a myriad of metabolites involved in the regulation of immune functions, as well as metabolic, and neuronal responses at local and distant sites [87, 88]. Indeed, the gut microbial metabolites are intimately linked with the host health and diseases. Emerging metabolite-centered research has focused on identifying different actionable microbial targets, whether intermediate metabolites or by-products, that are relevant in many host diseases such as metabolic syndrome [89], obesity [90], diabetes [90, 91], cardiovascular morbidities [92, 93], and even cancer [94‐96].

Even though these organs are anatomically distant from each other, the microbial kingdoms at the respiratory and digestive tracts have maintained a dynamic interaction that play key roles in the body homeostasis and in disease evolution [107]. From birth till death, a close relation links the microbial community in the lungs to the gut microbiota, suggesting a microbe-microbe interaction as well as a microbe-host interplay. For example, any change in the neonate’s diet is able to affect the respiratory microbiota composition [108]. Moreover, a recent study showed that fecal microbial transplant can alleviate the acute pulmonary injury in rats, by reducing the inflammatory factors’ expression [109] and possibly can reduce the risk of COVID-19 progression to the more advanced stages [110].

In fact, mounting evidence suggests that the gut-lung axis is a central element connecting microbial dysbiosis to many human diseases. Hosts either lacking gut microbiota, i.e. germ-free mice, or treated by broad spectrum antibiotics exhibited low or impaired immune responses against viral infections such as influenza Virus or respiratory syncytial virus, as demonstrated by increasing number of research [111‐113]. In the same context, many clinical issues noticed that malnutrition and microbial dysbiosis in the gut are likely to play an important role in the progression of age-related respiratory diseases in elderly. These findings suggest that restoring an eubiosis of intestinal microbial community will promote a healthy aging [114].

The perturbation of the microbial composition and function is not only behind the increased risk of pulmonary infections, but it is also associated with tissue disruption and inflammatory diseases in the gastrointestinal tract and beyond. Higher incidence of pulmonary functional changes and diseases are found in patients with IBD, as compared to normal people [115, 116]. Moreover, the impairment in the gut-lung axis was shown to be associated with increased prevalence of asthma [117, 118]. Commensal microbes are necessary especially during early life, for the induction of a balanced, tolerogenic immune system. The disturbance of such microbiota composition in the gut-lung axis appeared to be associated with the onset and severity of the inflammatory mechanisms of the atopic asthma [119]. Efforts were made in a trial to reconstitute the microbiota, mainly in the gut, either by probiotics or engineered bacteria in order to reduce asthma progression [120]. Indeed, studies showed that early supplementation by Lactobacilli can decrease the risk of asthma in childhood [121].

Nonetheless, emerging pathogenic links between the gut-lung axis and the altered microbiota suggests that such dysbiosis might be important in the development of chronic obstructive pulmonary disease (COPD) [122]. A bidirectional interaction is responsible for the development of COPD in patients with IBD (i.e. ulcerative colitis) [123], and vice versa [124]. As such, the diet of COPD patients is of great importance and can be considered as one of the factors that exacerbate the COPD. Targeted dietary intervention by increasing the fiber intake increased the production of anti-inflammatory short chain fatty acid (SCFAs), and thus reduces the lung inflammation in COPD patients [125]. Additionally, owing to its power in maintaining the lung homeostasis, any dysfunction in the lung-gut axis and its respective microbiota could be critical in tumorigenesis and induction of lung cancer. However, their exact role in cancerogenesis and the potential therapeutic strategies to alleviate the cancer remain unclear [126, 127].

Finally, in light of the striking COVID-19 pandemic, decreased richness and diversity of the gut microbiota was correlated with immune deregulation, prolonged diarrhea, delayed viral clearance, and even with increased mortality by exacerbating lung infections. Thus, targeted probiotics treatment may be useful in the re-establishment of the microbial communities in the mucosal compartments of both GI and respiratory tracts and could be considered as adjunctive therapy in COVID-19 patients [128, 129].

As previously discussed in the above parts, the symbiotic gut microbiota is involved in the regulation of many homeostatic mechanisms within the body. The alteration of such intestinal microbial community was indeed associated with many metabolic, immune, and neurological disorders [21]. The relationship between the intestinal microbial diversity and the brain function has recently gained the attention of the scientific and medical community. Recent and increasing body of evidence suggest the presence of “two-ways” interaction between the gut microbiota and the brain, involving multiple neurological and endocrine signaling systems. The discovery of a such bidirectional cross-talk is reflected by the term ‘brain-gut-microbiota axis’ [130]. Accumulating experimental and clinical data confirm a key role of gut dysbiosis and disturbances within the brain–gut–microbiota axis in neurodegenerative processes [131‐134] such as stress-related disorders [135], autism spectrum disorder [136], schizophrenia [137], multiple sclerosis [138], Alzheimer’s disease (AD) [139], and Parkinson’s disease (PD) [140].

For instance, an induced condition of chronic stressful period in mice has altered the gut microbiota diversity with a reduced amount of beneficial bacteria such as Lactobacillus, Eubacterium rectale, Lachnospira, along with an increase in the number of pathogenic bacteria like Clostridium, Enterobacteriaceae, and others [141].

Moreover, it is becoming increasingly evident that the gut microbiota influences the central nervous system’s function and inflammation through different pathways. Among the latter, the innate immune inflammasome signaling complexes are overactivated when the gut microbiota is altered with presence of certain infectious agents or pathogenic intestinal bacteria. This over-activation of inflammasomes in the brain has recently been associated with the development and the progression of many neuroinflammatory conditions such as multiple sclerosis, anxiety, as well as Parkinson’s and Alzheimer’s diseases [142]. Nonetheless, the two most common neurodegenerative disorders –AD and PD—are characterized by proteopathy: amyloid beta (Aβ) deposition in AD and α-synucleinopathy in PD. The formation of abnormal protein aggregates takes place both in the enteric and central nervous systems. A large amount of amyloids is also secreted by the gut microbiota. Through molecular mimicry bacterial amyloids may cross-react with human antigens and elicit cross-seeding of misfolding inducing disturbances in the adaptive immune system and microglial priming. A new term “MAPraNosis” has been even proposed to describe the process of microbiota-associated proteopathy and neuroinflammation [143]. Moreover, age-related alterations in the gut microbiota composition characterized by its decreased diversity and stability are associated with so called “inflammaging” resulting in the immune system activation in the elderly, and disruption of the intestinal barrier and the blood–brain barrier inducing neuroinflammation and neurodegeneration [144]. There is a growing interest in the prion hypothesis of neurodegenerative disorders according to which the neurodegenerative cascade may be initiated in the gut with subsequent spreading of proteopathy including Aβ and α-synuclein aggregates from the gut to the brain in a prion-like manner [131, 132]. In this context, in one of the recent studies for Pasinetti et al., it was evident that the use of ketamine, a potential therapeutic drug in neuroinflammatory disorders, is associated with an increase in the number of beneficial intestinal bacteria along with a reduction in the opportunistic pathogens. This study opens the door for understanding the long-term safety of ketamine in the treatment of AD [139]. In another work, bacterial DNA could be isolated from the human brain suggesting that a human microbiome can exist [145]. However, further studies are needed to understand the difference in the human brain microbiome among normal individuals and patients diagnosed with AD since most of the studies are done on animal models. The impact of the gut microbiota on the development of the pathogenesis in the neurological disorders is, unfortunately, not fully understood.

The gut microbiota modulation with dietary interventions, probiotics or antibiotics may create new preventive and therapeutic options in neurodegenerative diseases [146]. Indeed, we already shown that dietary polyphenols and other probiotics can be used as novel therapeutic drugs in the treatment of depression and other neurological problems [96, 147]. Actually, these symbiotics were shown to be able to attenuate the neuroinflammation by decreasing the activity of the inflammasomes mentioned previously [145].

The skin, the largest organ of our body, is the outermost barrier of the organism. It protects us from external harm and senses danger signals. It contains a sophisticated immune system that involves armada of immune cells comprising keratinocytes, resident antigen presenting cell, innate lymphoid cells, innate-like cells, and adaptive tissue resident memory cells and molecular mediators [148]. The skin also hosts microbial communities known as skin microbiota, constituting one living response barrier to environmental factors. Those microorganisms live in complete harmony with the immune players and are involved in the epithelial barrier reinforcement. Under homeostasis, an established alliance of immunity and microbiota intermingles innate and adaptive branches of the immune system. Under various types of stress, the symbiotic relationship changes into a dysbiotic one resulting in skin and distinct organs pathologies [149]. Surprisingly, an increasing body of evidence revealed that skin pathologies are not only due to skin microbiota dysbiosis, but they are also accompanied with alterations within the gut microbiome. In fact, both the intestinal tract and skin are densely vascularized and extensively inhabited by a wide variety of microorganisms that play many roles in maintaining the homeostasis. Different studies demonstrated a bidirectional cross-talk between skin and gut microbiota, referred to as the gut-skin-microbiota axis [150‐152]. This intimate connection, if altered, was shown to be associated with many skin diseases such as psoriasis [153], atopic dermatitis [154], and other disorders including skin cancer [155].

That so-called “gut-skin axis” has been considered as a key factor in the etiology of psoriasis, which is a chronic inflammatory disease with a complex multifactorial pathogenesis. The psoriatic skin and gut microbiota are characterized by a decreased overall diversity with a high prevalence of Staphylococcus and Streptococcus species on the skin [156] as well as Bacteroidetes and Firmicutes in the gut [157]. An increasing number of studies showed that the intestinal health as well as the individual lifestyle (such as smoking, alcohol, and increased body weight) play a pivotal role in the onset and the exacerbation of the psoriatic lesions [158, 159]. These facts have opened the door to target the dysbiotic gut microbiota in psoriatic patients by the use of probiotics [160]. Moreover, the gut-skin dysbiosis in psoriasis leads to intestinal barrier damage, which if intensified by the local inflammation, will increase translocation of antigens, bacteria and their metabolites into the circulation. Indeed, psoriatic patients exhibit very high blood concentration of TMAO and other gut microbiota-derived metabolites. This condition will put the patients with psoriasis at a high risk of CVD [161]. The intestinal inflammation in such patients is combined with an increased prevalence of IBD [162].

Another skin inflammatory condition which is affected by the gut-skin microbiota dysbiosis is the acne vulgaris. Acne is characterized by the formation of inflamed sebaceous sties, and affect around 90% of teenagers. Although the exact cause of acne is not fully elucidated, alteration of the skin microbiota as well as the host immune dysregulation play a role in the progression of such disease. Moreover, it is now believed that not only the skin microbiota but also the alteration in gut microbial communities is involved in the exacerbation of acne. For instance, the reason behind stress-induced acne is explained by the effect of the stress on the gastrointestinal tract. Stress increases intestinal permeability which leads to skin inflammation. Hence, there is an axis, involving the gut-brain-skin microbiota, that connects gut microbes, oral probiotics, diet as well as emotional and hormonal imbalance and contributes to the severity of acne [163].

Prebiotics are a group of nutrients that are degraded by gut microbiota. Glenn Gibson and Marcel Roberfroid first introduced the concept of prebiotics in 1995, being “non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health” [164]. The most recent definition of prebiotics is now “a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health” [165]. They are classified into many types and the byproducts of their degradation by the gut microbiota are most of all SCFAs that can exert an anti-inflammatory effect in the regulation of many human disorders [166]. Owing to the SCFAs’ small size and ability to diffuse to the bloodstream, prebiotics could be thus an attractive treatment not only locally for the gastrointestinal tract, but also to other distant organ systems.

In fact, prebiotics are safe and effective, having a great therapeutic effect along with minimal side effects in the maintenance of IBD [167]. For example, in one of the earliest studies, Lindsay et al. showed that the use of 15 g of fructooligosaccharides in Crohn’s Disease patients had increased the mucosal Bifidobacteria, and reduced the inflammation index [168]. Moreover, prebiotics have been shown also effective against genetically-induced obesity at doses lower than the usually used grams per days and for a limited period of only 2 weeks [169]. Despite all the efforts, there are few studies on humans, and the majority of research work has investigated the efficacy of prebiotics in IBD in vitro or in animal models [170]. Prebiotics were also shown, alone or combined with probiotics, to positively influence the cross-talk between immune system and microbiota, in the prevention of the CRC in patients with its high risk [171]. Therefore, prebiotics intake is recommended to improve the immunological response in CRC patients either in their preoperative or postoperative periods, as shown in a recent study by Xie et al., confirming that prebiotics consumption could change the abundance of four commensal microbiota [172].

At distance from the gastrointestinal tract, these non-digestible oligosaccharides are proven to be effective in the modulation of the gut-brain axis, more specifically in the regulation of the neurological disorders [173]. Several studies showed that the use of prebiotics can improve the lifestyle of patients with Huntington’s disease, and can also alleviate the severity of symptoms [174, 175]. Moreover, prebiotics showed a good preventive effect in many of neuropsychiatric disorders such as autism and depression [176]. Indeed, many studies reveal mental health benefits of prebiotics in females by reducing the stress and anxiety in a matter of days [177].

The clinical use of probiotics to modulate gut microbiota has been documented in the context of therapeutic trials of many diseases. In fact, probiotics, referred to as “live organisms that when administered in adequate doses confer a health benefit to the host” [178], are administered in food, pills, or powders, and are available in pharmacies, and even in the online shops. Probiotics have been successfully used in the prevention and treatment of obesity in infants and adults [179]. Such administration of beneficial microorganism was shown to reduce HbA1c and the insulin resistance level in T2 diabetes mellitus patients [180, 181]. The use of probiotics, whether single-strain or multi-strain, was studied in the treatment of irritable bowel syndrome [182]. In particular, the “next-generation” probiotic Faecalibacterium prausnitzii has promising effects in the gut dysbiosis diseases improvement. Lower amounts of F. prausnitzii were detected in IBD, Clostridioides (formerly Clostridium) difficile infection (CDI), and COVID-19. As this strain of bacteria is butyrate-producing, it induces immune responses and anti-inflammatory effects, as well as improved intestinal barrier function [183, 184].

The use of probiotics was not only advised in the use of gastrointestinal and metabolic diseases, but also interestingly in more distant disorders such as respiratory infections [185], and neuro-inflammatory pathologies [185] including multiple sclerosis [186] and AD [187].

Probiotics were also used to control the transmission of the nosocomial infections, referred to as healthcare–associated infections (HAIs). Major causes of HAIs include the persistent microbial contamination of the hospital environment, as well as the growing antimicrobial-resistance (AMR), due to the selective pressure exerted by the huge and extensive use of disinfectants and antibiotics in hospitals. To this aim, monocentric and multicenter studies were performed, by substituting the conventional chemical-based cleaning procedures with a probiotic-based system, and examining simultaneously the microbiome of the hospital environment, its antibiotic-resistant genes content, called ‘resistome’, the incidence of HAIs and the associated therapy costs. The results showed that probiotic-based sanitation system could induce a stable remodulation of the hospital microbiome, allowing a stable control of bioburden and AMR, and a significant reduction of HAI incidence, HAI-related antibiotic consumption and HAI-related therapy costs [188, 189].

The fecal microbiota transplantation (FMT) consists in the introduction of liquefied or encapsulated pre-processed stool from a healthy donor into a recipient’s colon. In fact, FMT (or fecal bacteriotherapy) became increasingly and rapidly accepted and medically performed because of its success in treating bacterial infections, mainly C. difficile [190], but also, intriguingly, in the treatment of other disorders like obesity and diabetes [191], as well as the metabolic syndrome [192].

Microbiota Transplantation is now recognized as an efficient therapeutic for the management of recurrent Clostridioides difficile-induced colitis, which is a major cause of nosocomial disease with increasing occurrence and mortality [193]. Such infection is usually associated with the repetitive use of antibiotics and its relapses are often seen in 20–30% of the patients after the first antibiotic treatment. The unusually high success rate of FMT (85–95%) in this setting is the reason why it is recommended by the European and North American medical professional societies in this setting [194]. However, patient access to FMT remains hampered by logistic aspects of treatment including manufacturing, storing, delivering the fecal inocula, as well as the protocols of preparation. Recent studies have reported the use of capsules of either frozen or freeze-dried stool allowing oral administration in the in- and outpatient settings, prepared by different protocols [195, 196]. Altogether, these studies represent an important step forward to improve the standardization of the stool preparation procedures and reduce the process time, thus facilitating pharmaceutical and medical practices and comfort of patients.

Nowadays, a growing interest for FMT treatment is rising, because intestinal diseases other than infection due to C. difficile may benefit from this practice [194, 197]. However, clinical trials have yielded mitigate results highlighting an important donor stool effect. The new goal is thus to refine donor’s selection beyond safety to optimize the quality and efficacy of this new treatment beyond rCDIs. In this regard, animal models still remain crucial for the development and a better understanding of how FMT works on both donor and recipient side. In fact, also the preparation of the recipient may account for the efficacy of FMT. FMT without antibiotics and laxatives preparation before the procedure in the recipient showed lower success rates [35].

Another emerging indication to perform fecal microbiota transplantation (FMT) is the gastrointestinal (GI) tract colonization by antibiotic-resistant bacteria (ARB), which is, according to the WHO, one of the biggest threats to global health, food security, and development today [197‐202]. ARB gut colonization could be detrimental to the patient when causing infections with gut-colonizing organism or, even resulting in immunologic disorders being a marker of gut dysbiosis [203, 204]. Bilinski et al. first reported the high efficacy of FMT reaching 60–100% of different ARB decolonization rate after one month from FMT [198, 205]. The microbiota composition analysis, using next-generation sequencing, showed greater bacterial richness in the donor’s fecal material given to the responders with a higher abundance of Barnesiella, Butirycimonas and Bacteroides compared with non-responders. Further studies confirmed these findings [193, 197, 199, 206, 207]. Also, Bilinski’s team have shown the promising results of FMT as an immunomodulatory agent in the treatment of acute gastrointestinal graft-versus-host disease [208, 209] what was confirmed in other groups [210].

Growing evidences show that FMT could be a promising tool for the treatment of both diabetes type 1 and type 2. Indeed, in one of the most recent studies, De Groot et al. demonstrated that FMT can induce a decline in endogenous production of insulin in recently diagnosed patients with T1D 12 months after disease onset. The residual function of beta cells was preserved, and was equally linked to many bacterial strains and microbiota-derived plasma metabolites. Finally, beneficial increase in the whole blood immune cell subsets such as CXCR3 + CD4 + T cells was reported following FMT [211]. Regarding type 2 diabetes, the use of FMT results in the improvement of pancreatic islet β-cells preservation by inhibiting the apoptosis, and in the decrease of insulin resistance. The inflammatory response in the pancreas was decreased, and a decline in the markers of inflammation was noted [212].

A refinement to the FMT, also known as the fecal virome transplantation (FVT), has also been developed. It relies on the use of bacteriophages (phages) to restore the dysbiotic gut microbiota. We previously shed the light on the importance of phages in eliminating the gastroenteritis-associated pathogenic bacteria, and in modulating the beneficial bacteria by adding new functions such as metabolites biosynthesis (SCFAs and H₂S) in the management of many metabolic and neurological disorders [213]. More recent work, achieved by Hsu et al., revealed that a programmed phage λ can be used to repress E. coli genes in the mammalian gut. This virus could be administered in the human body via an oral delivery using an adequate aqueous-based encapsulation formulation [214]. However, despite the promising advantages of FVT, the prophage-encoded virulence factors remain a safety issue, which limits the use of phages in medicine [215].

The gut microbiota-associated metabolites have not only emerged as pivotal regulators in the development and progression of many human diseases, but also as one of the novel therapeutic strategies. Metabolites are actually used in the treatment of local inflammation and in the modulation of cardiometabolic and neurological disorders, as well as cancers. Their properties make these metabolites relevant therapeutic candidates: natural bioavailability, high concentrations, easy administration, and tissue tolerability [216].

Although the TMAO, an important gut microbe-dependent metabolite, was shown to be involved in the mechanisms of atherosclerotic CVD [217], there is still no consensus about the role of TMAO in the pathogenesis of CVD since regular consumption of TMAO-rich seafood is considered to be beneficial for the primary prevention of cardiovascular events [218]. Indeed, a recent study evidenced that the short-term administration of TMAO did not show any effect on the cardiac functionality. Furthermore, long-term TMAO administration prevented impaired mitochondrial energy metabolism with a tendency of restoring the ventricular function in mice with In-Vitro induced right ventricular dysfunction [219].

In the context of the therapeutic use of metabolites, the SCFAs have been shown to exhibit anti-inflammatory effects, as previously discussed, in modulation of many local and systemic disorders, such in the gut-brain axis [95, 220]. Indeed, the oral administration of SCFAs can alleviate the severe symptoms of brain-associated inflammatory encephalitis [221], and the auto-immune multiple sclerosis [222]. Particularly, ingestion of butyrate not only suppressed the demyelination, but also triggered the remyelination, along with facilitating oligodendrocyte differentiation in mice with induced multiple sclerosis [223]. Furthermore, colon-delivered SCFAs can attenuate hypothalamic–pituitary–adrenal axis reactivity to psychosocial stress [224], suggesting hereby that SCFA supplementation alleviates mood alterations induced by repeated psychosocial stress [225].

Recently, Piscotta et al. investigated the antiviral activity of microbiota derived metabolites on COVID-19. The team found bacterial metabolites that were able to inhibit the infection by COVID-19. These metabolites present similar structural and functional properties to synthetic drugs used for the treatment of COVID-19 patients. The discovered compounds are the nucleoside analogue N6-(Δ2-isopentenyl) adenosine (homologue of remdesivir), the 5-hydroxytryptamine receptor agonist tryptamine (homologous to fluvoxamine), and the pyrazine 2,5-bis(3-indolylmethyl)pyrazine (similar to favipiravir) [226]. Also, Bilinski et al. shown a possible correlation with fecal microbiota transplantation and COVID-19 symptoms relief when FMT administered in the beginning of symptomatic disease [110].

At last, with the advances of metabolomics’ technologies, studies profiling microbiota-derived metabolites have greatly boosted our understanding in the role of the gut-associated metabolites in the cancerogenesis of CRC [227]. Accordingly, new potential clinical applications of such metabolites have arisen in cancer treatment. Given the encouraging results in the preclinical studies, the direct metabolites supplementation has shown success in the CRC prevention and therapy. For instance, butyrate administration, in a short-term clinical study, was able to increase the SCFAs level and prevent the red meat-induced deleterious adduct formation in the rectum [228]. Moreover, butyrate was also shown to enhance the efficacy of radiotherapy in CRC patients [229], suggesting that gut microbiota-derived metabolites could be associated to modalities in the treatment of cancer.

Among all the striking techniques and approaches to manipulate the gut microbiome, some recent findings raise the possibility of using miRNAs as novel therapeutic tools. In fact, microRNAs (miRNA) are short non-coding RNA molecules that regulate gene expression post-transcriptionally. In the intestine, miRNAs are critical for maintenance of homeostasis, and have been known for decades for their role in the posttranscriptional regulation of gene expression at the cellular level. Recently, they have emerged as important regulators of microbiome-host interaction as their role in the inter-species communication has been proven [230]. In human intestines, miRNAs are mainly synthesized in the intestinal epithelial cells and Hopx + cells. Any deficiency in the miRNA synthesis by those cells was associated with gut microbial dysbiosis [230]. Moreover, pre-clinical studies have shown that caecal miRNA signatures depend on the presence of the microbiome, with potential implications for the regulation of the barrier function [231]. In addition, intestinal miRNA may orchestrate responses to pathogenic and probiotic bacteria. For example, colonic miRNA that are deregulated in response to Citrobacter rodentium infection are part of a regulatory network affecting apoptosis and hyperproliferation [232]. While some commonalities exist in terms of miRNA responding to different pathogens, specific signatures have been identified. In line with this, probiotic bacteria can alter intestinal miRNA in a species- and strain-specific manner [233]. As an example, Bifidobacterium bifidum affects intestinal gene expression via miRNA in a time-dependent manner [233], with implications for probiotic administration protocols. In summary, intestinal miRNAs respond to commensal, pathogenic and probiotic bacteria. Manipulation of the gut microbiome may be a strategy to sustain intestinal health via miRNA.

Hyaluronan (HA) is considered as a novel tool for the development of novel therapeutic agents for the treatment of diseases underlying dysregulation of the microbiota–immune–gut axis [234]. Indeed, in recent years, many researches suggest that HA, an unbranched glycosaminoglycan (GAG) component of the extracellular matrix, may be an effective therapeutics in several pathological conditions [235]. Exogenously administered HA, owing to its remarkable water retention and lubricant properties, has proved to be efficacious in ophthalmic surgeries [236], for the treatment of osteoarthritis [237], and for wound-dressing in ulcers trauma, and burns [238]. Recently, HA appeared to directly modulate the promotion and resolution of IBD by controlling recruitment of immune cells, through the release of inflammatory cytokines, and through balancing homeostasis [239]. The majority of studies on the role of HA in IBD have focused on the involvement of the GAG in the development of fibrotic tissue within the submucosal and muscularis propria layers and on its chemoattractant action for leukocytes in both layers. The biologic effects of HA are mediated by recruiting different receptors, such as CD44 [240], and by promoting the activation of PAMP, such as toll-like receptors, particularly, TLR2 and TLR4, present in different cell types, including fibroblasts, smooth muscle cells, epithelial cells, immune and neuronal cells [241, 242]. During experimental inflammation, HA promotes epithelial repair via TLR4 activation, suggesting the potential therapeutic action of the GAG [243, 244]. Recently, it was demonstrated that, in the rat colon, HA contributes to the formation of an extracellular matrix basal membrane enveloping the surface of myenteric ganglia and of a perineuronal net surrounding myenteric neurons [245]. An experimentally-induced colitis was associated with up-regulation of HA deposition on myenteric ganglia and loss of the HA perineuronal structure, contributing to myenteric neuron derangement during the inflammatory challenge.

Novel nanomedicine-based approaches are experimented in the manipulation of the gut microbiota for cancer prevention. Laborious studies are trying to shape nanomaterials able to alter the cancer-causing dysbiotic microorganisms as well as their metabolites found in the cancer microenvironment [246].

The extracellular vesicles, exosomes and their relation with microbiota is now a surging hot topic of interest. In fact, many research groups are now focusing on the communication between microbiota, mitochondria and the host [95]. It was found that microbiota has the ability to interact with host cells and mitochondria, when needed, through extracellular vesicles [247‐249]. This interaction could lead to the endocytosis of the extracellular vesicle and its content delivery. The prospective use of microbiota- and host- derived [250] extracellular vesicles in restoring the microbiome integrity and improving mucosal immunity is being extensively reported. Recent findings have shown that exosomal microRNA derived from mesenchymal stem cells plays a strategic role in modulating the gut microbiota and the inflammatory status.