Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

Metabolomics: The Key to Unraveling the Role of the Microbiome in Visceral Pain Neurotransmission

Inflammatory bowel disease (IBD), comprising Crohn’s disease and Ulcerative colitis, is a relapsing and remitting disease of the gastrointestinal tract, presenting with chronic inflammation, ulceration, gastrointestinal bleeding, and abdominal pain. Up to 80% of patients suffering from IBD experience acute pain, which dissipates when the underlying inflammation and tissue damage resolves. However, despite achieving endoscopic remission with no signs of ongoing intestinal inflammation or damage, 30–50% of IBD patients in remission experience chronic abdominal pain, suggesting altered sensory neuronal processing in this disorder. Furthermore, effective treatment for chronic pain is limited such that 5–25% of IBD outpatients are treated with narcotics, with associated morbidity and mortality. IBD patients commonly present with substantial alterations to the microbial community structure within the gastrointestinal tract, known as dysbiosis. The same is also true in irritable bowel syndrome (IBS), a chronic disorder characterized by altered bowel habits and abdominal pain, in the absence of inflammation. An emerging body of literature suggests that the gut microbiome plays an important role in visceral hypersensitivity. Specific microbial metabolites have an intimate relationship with host receptors that are highly expressed on host cell and neurons, suggesting that microbial metabolites play a key role in visceral hypersensitivity. In this review, we will discuss the techniques used to analysis the metabolome, current potential metabolite targets for visceral hypersensitivity, and discuss the current literature that evaluates the role of the post-inflammatory microbiota and metabolites in visceral hypersensitivity.

Where Do We Stand in the Behavioral Pathogenesis of Inflammatory Bowel Disease? The Western Dietary Pattern and Microbiota-A Narrative Review

Despite the increasing knowledge with regard to IBD (inflammatory bowel disease), including ulcerative colitis (UC) and Crohn’s disease (CD), the etiology of these conditions is still not fully understood. Apart from immunological, environmental and nutritional factors, which have already been well documented, it is worthwhile to look at the possible impact of genetic factors, as well as the composition of the microbiota in patients suffering from IBD. New technologies in biochemistry allow to obtain information that can add to the current state of knowledge in IBD etiology.

Prevention of Ulcerative Colitis by Autologous Metabolite Transfer from Colitogenic Microbiota Treated with Lipid Nanoparticles Encapsulating an Anti-Inflammatory Drug Candidate

Modulating the gut microbiota composition is a potent approach to treat various chronic diseases, including obesity, metabolic syndrome, and ulcerative colitis (UC). However, the current methods, such as fecal microbiota transplantation, carry a risk of serious infections due to the transmission of multi-drug-resistant organisms. Here, we developed an organism-free strategy in which the gut microbiota is modulated ex vivo and microbiota-secreted metabolites are transferred back to the host. Using feces collected from the interleukin-10 (IL-10) knockout mouse model of chronic UC, we found that a drug candidate (M13)-loaded natural-lipid nanoparticle (M13/nLNP) modified the composition of the ex vivo-cultured inflamed gut microbiota and its secreted metabolites. Principal coordinate analysis (PCoA) showed that M13/nLNP shifted the inflamed microbiota composition toward the non-inflamed direction. This compositional modification induced significant changes in the chemical profiles of secreted metabolites, which proved to be anti-inflammatory against in vitro-cultured NF-κβ reporter cells. Further, when these metabolites were orally administered to mice, they established strong protection against the formation of chronic inflammation. Our study demonstrates that ex vivo modulation of microbiota using M13/nLNP effectively reshaped the microbial secreted metabolites and that oral transfer of these metabolites might be an effective and safe therapeutic approach for preventing chronic UC.

Bifidobacterium BLa80 mitigates colitis by altering gut microbiota and alleviating inflammation

This study was conducted to explore the therapeutic effect of the probiotic Bifidobacterium animalis subsp. lactis BLa80 on inflammatory bowel disease. A model of ulcerative colitis (UC) was induced in C57BL/6 mice by administering of 2.5% dextran sulphate sodium (DSS) for 8 days. After developing UC, some mice were treated via intragastric administration of BLa80 at a dose of 10⁹ colony-forming units to assess the preventive effects of BLa80 on DSS-induced UC. Compared with non-treated UC model mice, BLa80-treated mice had reduced colon shortening and improvements in colonic tissue structure. Treatment with BLa80 also decreased the serum concentrations of the proinflammatory cytokines tumor necrosis factor-alpha (TNF-α), interleukin (IL) 6 and IL-17 in mice. 16S rRNA gene sequencing revealed that BLa80 increased gut microbial diversity in mice and modulated UC-associated imbalances in the gut microbiota. BLa80 selectively promoted the growth of beneficial bacteria, including Romboutsia and Adlercreutzia, the abundances of which were negatively correlated with concentration of cellular inflammatory factors. In summary, the study results demonstrated that pretreatment with B. lactis BLa80 reduced intestinal inflammation and altered the gut microbiota, implying that BLa80 is a promising probiotic strain with potential therapeutic function in UC.

Enterococcus faecium and Pediococcus acidilactici deteriorate Enterobacteriaceae-induced depression and colitis in mice

Gut dysbiosis is closely associated with the outbreak of inflammatory bowel disease (IBD) and psychiatric disorder. The Enterobacteriaceae population was higher in the feces of patients with inflammatory bowel disease (IBD-F) than in those of healthy control volunteers (HC-F). The Enterococcaceae and Lactobacillaceae populations were higher in the feces of IBD patients with depression (IBD/D+-F) vs. the feces of IBD patients without depression (IBD/D--F). Therefore, we examined the effects of Klebsiella oxytoca, Escherichia coli, Cronobacter sakazakii, Enterococcus faecium, and Pediococcus acidolactici overpopulated in IBD/D+-F and their byproducts LPS and exopolysaccharide (EPS) on the occurrence of depression and colitis in mice. Oral gavages of Klebsiella oxytoca, Escherichia coli, and Cronobacter sakazakii belonging to Enterobacteriaceae, singly or together, caused dose-dependently colitis and depression-like behaviors in germ-free and specific-pathogen-free mice. Although Enterococcus faecium and Pediococcus acidolactici did not significantly cause colitis and depression-like behaviors, they significantly deteriorated Klebsiella oxytoca- or Escherichia coli-induced colitis, neuroinflammation, and anxiety/depression-like behaviors and increased blood LPS, corticosterone, and IL-6 levels. The EPSs from Enterococcus faecium and Pediococcus acidolactici also worsened Klebsiella oxytoca LPS-induced colitis, neuroinflammation, and depression-like behaviors in mice and increased the translocation of fluorescein isothiocyanate-conjugated LPS into the hippocampus. However, Bifidobacterium longum, which was lower in IBD/D+-F vs. IBD/D--F, or its EPS suppressed them. In conclusion, Enterococcus faecium and Pediococcus acidolactici, known as a probiotic strain, and their EPSs may be a risk factor for the outbreak of depression and IBD.

An Open-Label Trial Study of Quality-of-Life Assessment in Irritable Bowel Syndrome and Their Treatment

Background and objectives: Irritable bowel syndrome (IBS) does not only have a complex pathophysiological evolution with central and peripheral mechanisms. This study aimed to monitor the neuropsychiatric part of IBS and its management, following the quality of life of patients with IBS. Materials and Methods: Participants numbering 145 were investigated in this study for 6 months and were divided into four groups, namely the control group with a symptomatic period of less than 6 months (n = 34), the group with irritable bowel syndrome (IBS; n = 58), IBS and neuropsychiatric treatment (n = 32), and IBS with probiotic treatment (n = 22). Clinical and paraclinical analyses as well as quality of life were monitored by domestic and international psychological questionnaires. Results: It was observed that, in patients with pro-longed symptoms, neuropsychiatric impairment occurred more frequently, and both clinical and paraclinical analyses improved significantly (p < 0.05) more so in those with complex allopathic treatment and in those with probiotic treatment. There were no significant differences between the two research groups. Conclusions: It has been shown that the neuropsychological component of IBS plays an important role in its treatment, and modern probation therapy can achieve similar results to those of neuropsychiatry. This also requires further studies to ensure the best combination in the approach to IBS.

Complementary and Alternative Medicine in Crohn's Disease

Complementary and alternative medicine (CAM) is a growing entity within inflammatory bowel disease (IBD). CAM includes mind-based therapies, body-based therapies, supplements, vitamins, and probiotics. Limitations currently exist for health care providers as it pertains to IBD and CAM that stem from knowledge gaps, conflicting reports, limited oversight, and a lack of well-organized clinical data. Even without well-described data, patients are turning to these forms of therapy at increasing rates. It is imperative that the ongoing review of CAM therapies is performed, and future trials are performed to better understand efficacy as well as adverse effects related to these therapies.

Probiotic supplementation: A prospective approach in the treatment of COVID-19

Background: Despite strategies based on social distancing, the coronavirus disease 2019 (COVID-19) expands globally, and so far, many attempts have been made to achieve effective treatment for patients with COVID-19. This disease infects the lower respiratory tract and may lead to severe acute respiratory syndrome coronavirus (SARS-CoV). COVID-19 also can cause gastrointestinal infections. Therefore, COVID-19 patients with gastrointestinal symptoms are more likely to be complicated by SARS-CoV. In this disease, acquired immune responses are impaired, and uncontrolled inflammatory responses result in cytokine storms, leading to acute lung injury and thrombus formation. Probiotics are living microorganisms that contribute to the health of the host if administered in appropriate doses. Aim: This study aimed to provide evidence to show the importance of gut dysbiosis in viral disease, especially COVID-19. Therefore, we have focused on the impact of probiotics consumption on preventing severe symptoms of the disease. Methods: We have entirely searched SCOPUS, PubMed, and Google Scholar databases to collect evidence regarding the relationship between probiotics and viral infections to expand this relationship to the COVID-19. Results: It has been shown that probiotics directly counteract SARS-CoV in the gastrointestinal and respiratory tracts. Moreover, probiotics suppress severe immune responses and prevent cytokine storms to inhibit pathologic inflammatory conditions in the body via modulation of immune responses. Conclusion: According to available evidence based on their antiviral and respiratory activities, using probiotics might be an adjuvant therapy to reduce the burden and severity of this disease.

Dietary Eggshell Membrane Powder Improves Survival Rate and Ameliorates Gut Dysbiosis in Interleukin-10 Knockout Mice

Inflammatory bowel disease (IBD) is known to be associated with compositional and metabolic changes in the gut microbiota. The aim of this study was to investigate whether dietary eggshell membrane (ESM) improves survival rate or ameliorates gut dysbiosis in a spontaneous IBD model of interleukin-10 knockout (IL10^−/−) mice. Female C57BL/6J wild-type (WT) and IL10^−/− mice (KO) were fed an AIN-93G basal diet or an ESM diet (KOE) for 19 weeks. Gut microbiota profiles were analyzed via 16S rRNA sequencing, and short-chain fatty acids in cecal content were analyzed with high-performance liquid chromatography. The results demonstrated that ESM supplementation significantly improved the survival rate and body composition in KO mice. Alpha diversity analysis of the microbiota revealed that ESM supplementation significantly increased gut microbial diversity, which was decreased in IL10^−/− mice. The Firmicutes/Bacteroidetes ratio was recovered to a normal level by ESM supplementation, suggesting that ESM helps maintain the compositional balance of the gut microbiota. ESM increased relative abundance of commensal bacterial Ruminococcus and Bacteroidales S24-7 and reduced the abundance of the proinflammatory-related bacterium, Enterobacteriaceae. Additionally, ESM supplementation promoted the production of butyrate in cecal contents and downregulated the expression of proinflammatory genes, including interleukin-1β (Il-1β) and tumor necrosis factor-α (Tnf-α) in IL10^−/− mice colon, indicating anti-inflammatory functions. These findings suggest that ESM may be used as a beneficial dietary intervention for IBD.

Single and Combined Effects of Clostridium butyricum and Coccidiosis Vaccine on Growth Performance and the Intestinal Microbiome of Broiler Chickens

Avian coccidiosis is an important intestinal protozoan disease that has caused major economic losses to the poultry industry. Clostridium butyricum can not only maintain the stability of the intestinal barrier, but can also improve the production performance of broiler chickens. We studied the effects of feeding C. butyricum alone, administration of coccidiosis vaccine alone, and the combined administration of C. butyricum and coccidiosis vaccine on body weight gain, feed consumption, and feed conversion ratio of broilers. Meanwhile, intestinal contents of 8- and 15-day-old broilers were collected, and their intestinal microbiome was characterized by high-throughput sequencing of the V3–V4 region of 16S rDNA. We analyzed the oocysts per gram values and lesion scores in the C. butyricum alone group, in a group challenged with the coccidiosis-causing parasite, Eimeria, and in groups simultaneously challenged Eimeria and pretreated with C. butyricum, the coccidiosis vaccine, or combined C. butyricum and coccidiosis vaccine. Intestinal tissue samples were collected from 32-day-old broilers for microbiome analysis. Our results showed that combination of C. butyricum with coccidiosis vaccine significantly improved the performance of broiler chickens and also significantly reduced the oocysts per gram value and intestinal lesions caused by Eimeria sp. infection. Furthermore, C. butyricum and coccidiosis vaccine administered alone or in combination significantly increased the relative abundance of the immune biomarker genus Barnesiella. The significant increase in the abundance of the Clostridia_UCG.014, Eubacterium coprostanoligenes group and Bacteroides was a key factor in controlling Eimeria sp. infection.

Next-Generation Probiotics for Inflammatory Bowel Disease

Engineered probiotics represent a cutting-edge therapy in intestinal inflammatory disease (IBD). Genetically modified bacteria have provided a new strategy to release therapeutically operative molecules in the intestine and have grown into promising new therapies for IBD. Current IBD treatments, such as corticosteroids and immunosuppressants, are associated with relevant side effects and a significant proportion of patients are dependent on these therapies, thus exposing them to the risk of relevant long-term side effects. Discovering new and effective therapeutic strategies is a worldwide goal in this research field and engineered probiotics could potentially provide a viable solution. This review aims at describing the proceeding of bacterial engineering and how genetically modified probiotics may represent a promising new biotechnological approach in IBD treatment.

Novel Models of Crohn's Disease Pathogenesis Associated with the Occurrence of Mitochondrial Dysfunction in Intestinal Cells

Crohn’s disease remains one of the challenging problems of modern medicine, and the development of new and effective and safer treatments against it is a dynamic field of research. To make such developments possible, it is important to understand the pathologic processes underlying the onset and progression of Crohn’s disease at the molecular and cellular levels. During the recent years, the involvement of mitochondrial dysfunction and associated chronic inflammation in these processes became evident. In this review, we discuss the published works on pathogenetic models of Crohn’s disease. These models make studying the role of mitochondrial dysfunction in the disease pathogenesis possible and advances the development of novel therapies.

Oral Microbiome of Crohn's Disease Patients With and Without Oral Manifestations

BACKGROUND AND AIMS

Microbiome dysbiosis is associated with inflammatory destruction in Crohn's disease [CD]. Although gut microbiome dysbiosis is well established in CD, the oral microbiome is comparatively under-studied. This study aims to characterize the oral microbiome of CD patients with/without oral manifestations.

METHODS

Patients with CD were recruited with age-, gender- and race-matched controls. Potential confounders such as dental caries and periodontal condition were recorded. The oral microbiome was collected using saliva samples. Microbial DNA was extracted and sequenced using shotgun sequencing. Metagenomic taxonomic and functional profiles were generated and analysed.

RESULTS

The study recruited 41 patients with CD and 24 healthy controls. Within the CD subjects, 39.0% had oral manifestations with the majority presenting with cobblestoning and/or oral ulcers. Principal coordinate analysis demonstrated distinct oral microbiome profiles between subjects with and without CD, with four key variables responsible for overall oral microbiome variance: [1] diagnosis of CD, [2] concomitant use of steroids, [3] concomitant use of azathioprine and 4] presence of oral ulcers. Thirty-two significant differentially abundant microbial species were identified, with the majority associated with the diagnosis of CD. A predictive model based on differences in the oral microbiome found that the oral microbiome has strong discriminatory function to distinguish subjects with and without CD [AUROC 0.84]. Functional analysis found that an increased representation of microbial enzymes [n = 5] in the butyrate pathway was positively associated with the presence of oral ulcers.

CONCLUSIONS

The oral microbiome can aid in the diagnosis of CD and its composition was associated with oral manifestations.

Role of Microbiota in Viral Infections and Pathological Progression

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.

Association Between Sex Hormone Levels and Gut Microbiota Composition and Diversity-A Systematic Review

GOALS/BACKGROUND

Animal studies have highlighted how the microbiota acts in a sex-specific manner with sex hormones demonstrating an association with the composition and diversity of the microbiota. This systematic review aimed to gather the available scientific evidence to explore the association between sex hormones and gut microbiota composition and diversity, in humans.

STUDY

Four bibliographic databases were searched in July 2020 using terms related to "microbiota," "microflora," "sex hormones," "testosterone," and "estrogen." Human studies that investigated the correlation between sex hormones and the microbiota composition or diversity using next-generation sequencing were included.

RESULTS

A total of 10,468 records were screened with 13 studies included in this review. In healthy women, higher estrogen levels were found to be associated with a higher abundance of Bacteroidetes, a lower abundance of Firmicutes, the Ruminococcaceae family and increased diversity. In healthy men, raised testosterone levels positively correlated with Ruminococcus, Acinetobacter, and an increased microbial diversity. Escherichia and Shigella spp. were correlated with raised testosterone in healthy women whereas Ruminococcus spp. was negatively associated with elevated testosterone levels. Women with altered testosterone/estrogen profiles (such as in polycystic ovary syndrome), had a differing gut microbiota compared with healthy women.

CONCLUSIONS

The findings gathered highlight an association between sex hormones and the gut microbiota composition/diversity and may contribute to the sex-based variations observed in disease pathogenesis. Factors such as age and medical conditions are implicated in the associations observed and should be accounted for in future studies. As the understanding of the complex symbiotic relationship between humans and their gut microbiota increases, microbiota modulation could be an attractive option for the prevention and treatment of gastrointestinal disorders.

Disease Features and Gastrointestinal Microbial Composition in Patients with Systemic Sclerosis from Two Independent Cohorts

OBJECTIVE

The study objective was to examine alterations in gastrointestinal (GI) microbial composition in patients with systemic sclerosis (SSc) and to investigate the relationship between SSc features and GI microbiota using two independent, international cohorts.

METHODS

Prospective patients with SSc from Lund University (LU), Sweden, from the University of California, Los Angeles (UCLA), United States, and control subjects provided stool specimens for 16S ribosomal RNA sequencing. Alpha and beta diversity analyses were performed. Multivariate negative binomial models identified differentially abundant genera between groups.

RESULTS

Patients from LU with SSc (n = 106) with recent SSc diagnosis (median disease duration 2.0 years) had lower abundance of commensal genera (eg, Faecalibacterium) and higher abundance of pathobiont genera (eg, Desulfovibrio) than LU-controls (n = 85). Patients from UCLA with SSc (n = 71) had a similar prevalence of females, a similar body mass index, and similar age but an increased disease duration (median 7.1 years) compared with patients from LU with SSc. Factors associated with beta diversity in patients with SSc from both LU and UCLA included disease duration (P = 0.0016), interstitial lung disease (P = 0.003), small intestinal bacterial overgrowth (P = 0.002), and immunosuppression use (P = 0.014). In multivariable analysis, the UCLA-SSc cohort had higher abundance of specific pathobiont genera (eg, Streptococcus) compared with the LU-SSc cohort.

CONCLUSION

Enrichments and depletions in certain microbial genera were observed in patients recently diagnosed with SSc, suggesting that dysbiosis is present in early SSc. Specific disease features were independently associated with fecal microbial composition in both cohorts. After controlling for these factors, the abundance of several pathobiont bacteria differed between the cohorts, suggesting that environmental factors, along with disease manifestations, should be considered in future SSc studies.

Schizophrenia and risk of new-onset inflammatory bowel disease: a nationwide longitudinal study

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) is a chronic gastrointestinal inflammatory disorder with increasing global prevalence. The risk of IBD in patients with schizophrenia remains unclear. We aim to investigate the risk of new-onset IBD in patients with schizophrenia compared with matched controls.

METHODS

We conducted a retrospective, population-based cohort study utilising patient data from the Taiwan National Health Insurance Research Database collected between January 1, 2001, and December 31, 2011. Patients diagnosed with schizophrenia by board-certified psychiatrists without prior diagnosis of IBD were enrolled and matched to controls in 1:4 fashion by age, sex, residence, income level and medical comorbidities. Adjusted hazard ratios (HRs) for new-onset IBD and sub-analyses were determined using Cox regression analysis with adjustments.

RESULTS

Among 116 164 patients with schizophrenia and 464 656 matched controls, overall incidence of IBD among patients was significantly higher (1.14% vs. 0.25%). Average age of IBD diagnosis was 46.82 among patients with schizophrenia, versus 55.30 among controls. The HR of developing IBD among patients was 3.28, with a 95% confidence interval (95% CI) 2.49-4.33. IBD risk was higher among patients with psychiatric admissions more than once per year (HR 7.99, 95% CI 5.25-12.15) compared to those hospitalised less frequently (HR 2.72, 95% CI 2.03-3.66).

CONCLUSIONS

This population-based cohort study demonstrates a significant association between schizophrenia and subsequent IBD development. Patients with schizophrenia develop IBD at a younger age, and the risk increases with inadequately controlled schizophrenia. Physician vigilance and awareness of this correlation will improve IBD diagnosis and management among this vulnerable patient population.

Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin

The integrity of the gastrointestinal tract structure and function is seriously compromised by two pathological conditions sharing, at least in part, several pathogenetic mechanisms: inflammatory bowel diseases (IBD) and coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. IBD and COVID-19 are marked by gut inflammation, intestinal barrier breakdown, resulting in mucosal hyperpermeability, gut bacterial overgrowth, and dysbiosis together with perturbations in microbial and human metabolic pathways originating changes in the blood and fecal metabolome. This review compared the most relevant metabolic and microbial alterations reported from the literature in patients with IBD with those in patients with COVID-19. In both diseases, gut dysbiosis is marked by the prevalence of pro-inflammatory bacterial species and the shortfall of anti-inflammatory species; most studies reported the decrease in Firmicutes, with a specific decrease in obligately anaerobic producers short-chain fatty acids (SCFAs), such as Faecalibacterium prausnitzii. In addition, Escherichia coli overgrowth has been observed in IBD and COVID-19, while Akkermansia muciniphila is depleted in IBD and overexpressed in COVID-19. In patients with COVID-19, gut dysbiosis continues after the clearance of the viral RNA from the upper respiratory tract and the resolution of clinical symptoms. Finally, we presented and discussed the impact of gut dysbiosis, inflammation, oxidative stress, and increased energy demand on metabolic pathways involving key metabolites, such as tryptophan, phenylalanine, histidine, glutamine, succinate, citrate, and lipids.

Plant-Derived Exosomes as A Drug-Delivery Approach for the Treatment of Inflammatory Bowel Disease and Colitis-Associated Cancer

Inflammatory bowel disease (IBD) is a chronic recurrent intestinal disease and includes Crohn’s disease (CD) and ulcerative colitis (UC). Due to the complex etiology of colitis, the current treatments of IBD are quite limited and are mainly concentrated on the remission of the disease. In addition, the side effects of conventional drugs on the body cannot be ignored. IBD also has a certain relationship with colitis-associated cancer (CAC), and inflammatory cells can produce a large number of tumor-promoting cytokines to promote tumor progression. In recent years, exosomes from plants have been found to have the ability to load drugs to target the intestine and have great potential for the treatment of intestinal diseases. This plant-derived exosome-targeting delivery system can load chemical or nucleic acid drugs and deliver them to intestinal inflammatory sites stably and efficiently. This review summarizes the pathophysiological characteristics of IBD and CAC as well as the application and prospect of plant exosomes in the treatment of IBD and CAC.

The role of retinoic acid in the production of immunoglobulin A

Vitamin A and its derivative retinoic acid (RA) play important roles in the regulation of mucosal immunity. The effect of vitamin A metabolism on T lymphocyte immunity has been well documented, but its role in mucosal B lymphocyte regulation is less well described. Intestinal immunoglobulin A (IgA) is key in orchestrating a balanced gut microbiota composition. Here, we describe the contribution of RA to IgA class switching in tissues including the lamina propria, mesenteric lymph nodes, Peyer's patches and isolated lymphoid follicles. RA can either indirectly skew T cells or directly affect B cell differentiation. IgA levels in healthy individuals are under the control of the metabolism of vitamin A, providing a steady supply of RA. However, IgA levels are altered in inflammatory bowel disease patients, making control of the metabolism of vitamin A a potential therapeutic target. Thus, dietary vitamin A is a key player in regulating IgA production within the intestine, acting via multiple immunological pathways.

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis

Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2 × 2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after 6 weeks of treatment, versus 2 of 11 non-pretreated patients (log odds ratio: 1.69, 95% confidence interval: −0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.

Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis

Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.

Traditional Chinese Medicine Alleviates Ulcerative Colitis via Modulating Gut Microbiota

Ulcerative colitis (UC) is a chronic inflammatory bowel disorder characterized by relapsing and remitting inflammation of the bowel. In recent decades, traditional Chinese medicine (TCM) has been widely used in the therapy of UC. However, its underlying mechanisms have not been sufficiently elucidated. Accumulating studies indicate that the gut microbial dysbiosis is closely related to UC. It has been demonstrated that TCM could alter the composition of intestinal microbiota by enriching beneficial and SCFA-producing bacteria and reducing pathogenic bacteria. In this review, we discussed recent evidence regarding the TCM and its role in modulating gut microbiota for the treatment of UC.

The Relationship between Physical Activity, Physical Exercise, and Human Gut Microbiota in Healthy and Unhealthy Subjects: A Systematic Review

Simple Summary

To date, the influence that physical activity (PA)/physical exercise (PE) can exert on the human gut microbiota (GM) is still poorly understood. Several issues arise in structuring research in this area, starting from the association between PA/PE and diet. Indeed, the diet of an individual is a key factor for the composition of the GM and those who regularly practice PA/PE, generally, have dietary patterns favorable to the creation of an ideal environment for the proliferation of a GM capable of contributing to the host’s health. It is therefore difficult to establish with certainty whether the effects generated on the GM are due to a PA protocol, the type of diet followed, or to both. In addition, most of the available studies use animal models to investigate a possible correlation between PA/PE and changes in the GM, which may be not necessarily applied to humans. Evidence suggests that aerobic PA/PE seems capable of producing significant changes in GM; training parameters, likewise, can differentially influence the GM in young or elderly people and these changes appear to be transient and reversible.

Abstract

Several studies have been conducted to find at least an association between physical activity (PA)/ physical exercise (PE) and the possibility to modulate the gut microbiome (GM). However, the specific effects produced on the human GM by different types of PA/PE, different training modalities, and their age-related effects are not yet fully understood. Therefore, this systematic review aims to evaluate and summarize the current scientific evidence investigating the bi-directional relationship between PA/PE and the human GM, with a specific focus on the different types/variables of PA/PE and age-related effects, in healthy and unhealthy people. A systematic search was conducted across four databases (Web of Science, Medline (PubMed), Google Scholar, and Cochrane Library). Information was extracted using the populations, exposure, intervention, comparison, outcomes (PICOS) format. The Oxford Quality Scoring System Scale, the Risk of Bias in Non-Randomized Studies of Interventions (ROBINS-I) tool, and the JBI Critical Appraisal Checklist for Analytical Cross-Sectional Studies were used as a qualitative measure of the review. The protocol was registered in PROSPERO (code: CRD42022302725). The following data items were extracted: author, year of publication, study design, number and age of participants, type of PA/PE carried out, protocol/workload and diet assessment, duration of intervention, measurement tools used, and main outcomes. Two team authors reviewed 694 abstracts for inclusion and at the end of the screening process, only 76 full texts were analyzed. Lastly, only 25 research articles met the eligibility criteria. The synthesis of these findings suggests that GM diversity is associated with aerobic exercise contrary to resistance training; abundance of Prevotella genus seems to be correlated with training duration; no significant change in GM richness and diversity are detected when exercising according to the minimum dose recommended by the World Health Organizations; intense and prolonged PE can induce a higher abundance of pro-inflammatory bacteria; PA does not lead to significant GM α/β-diversity in elderly people (60+ years). The heterogeneity of the training parameters used in the studies, diet control, and different sequencing methods are the main confounders. Thus, this systematic review can provide an in-depth overview of the relationship between PA/PE and the human intestinal microbiota and, at the same time, provide indications from the athletic and health perspective.

Nutraceuticals in the Modulation of the Intestinal Microbiota: Current Status and Future Directions

Pharmaceutical interest in the human intestinal microbiota has increased considerably, because of the increasing number of studies linking the human intestinal microbial ecology to an increasing number of non-communicable diseases. Many efforts at modulating the gut microbiota have been made using probiotics, prebiotics and recently postbiotics. However, there are other, still little-explored opportunities from a pharmaceutical point of view, which appear promising to obtain modifications of the microbiota structure and functions. This review summarizes all in vitro, in vivo and clinical studies demonstrating the possibility to positively modulate the intestinal microbiota by using probiotics, prebiotics, postbiotics, essential oils, fungus and officinal plants. For the future, clinical studies investigating the ability to impact the intestinal microbiota especially by using fungus, officinal and aromatic plants or their extracts are required. This knowledge could lead to effective microbiome modulations that might support the pharmacological therapy of most non-communicable diseases in a near future.

Efficacy and Safety of Probiotics Combined With Traditional Chinese Medicine for Ulcerative Colitis: A Systematic Review and Meta-Analysis

Background: The combination of probiotics and traditional Chinese medicine (TCM) is a prospective therapy for ulcerative colitis (UC), and its efficacy and safety need to be urgently evaluated.

Objective: This study aims to comprehensively assess the efficacy and safety of probiotics combined with TCM for the treatment of UC.

Methods: The Pubmed, EMBASE, Cochrane library, China Academic Journals (CNKI), Wan-fang database, Chinese biomedical literature service system (CBM), and Chinese Science and Technology Journals (CQVIP) were searched. Subgroup analysis were designed in accordance with different control drugs, treatment courses, and types of probiotics. The Review Manager software (version 5.4.1) was utilized for statistical analysis.

Results: 14 original studies containing 1,154 patients were analyzed and showed that probiotics with TCM was more effective than 5-aminosalicylic acid (5-ASA), probiotics or TCM used individually. Moreover, probiotics combined with TCM could inhibit the intestinal inflammation, reduce the recurrence rate and the incidence of adverse events. The subgroup analysis showed that a mixture of different probiotics was more effective than a single strain.

Conclusion: It is suggested that probiotics combined with TCM could effectively control clinical symptoms, inhibit intestinal inflammatory response, and finally slow down the disease progress and reduce the disease recurrence with less adverse events. The mixture of different probiotics used in conjunction with individually tailored TCM is a potential clinical strategy for UC.

Modulating gut dysbiosis and mitochondrial dysfunction in oxazolone-induced ulcerative colitis: the restorative effects of β-glucan and/or celastrol

Objectives

Microbiome–Mitochondria interaction is gaining a significant attention; thus, studying its mechanism emerges as a must to provide restorative lines in managing diseases. The aim is to study the mechanistic effects of β-Glucan and/or Celastrol in oxazolone-induced ulcerative colitis (UC).

Methods

75 Wistar rats were allocated into 5 equal groups. Group I: control group. Group II: UC group, Group III: β-Glucan-treated UC group, Group IV: Celastrol-treated UC group & Group V: mutual treatment group. All groups were subjected to the detection of free fatty acid receptor 2 (FFAR-2) and peroxisome proliferator-activated receptor gamma co-activator1α (PGC-1α) mRNA gene expressions. Citrate synthase (CS) activity, mitochondrial membrane potential (MMP), ATP concentration, reactive oxygen species (ROS) were detected. Trimethylamine N-oxide (TMAO) concentration was measured.

Results

After treatment we monitored significant upregulation of FFAR-2 and PGC-1α mRNA expression. Likewise, ATP level and CS activity were significantly increased. On the contrary, there was a significant lessening in ROS and TMAO levels with improvement of MMP.

Conclusion

Mutual use of β- Glucan and Celastrol had a greater effect than each alone against UC, which is considered a novel finding highlighting the ameliorative effects of this combined treatment in modulating Microbiome/Mitochondria axis, thus launching promising avenues for UC.

Gut microbiota-derived short chain fatty acids are potential mediators in gut inflammation

Gut inflammation is a challenging concern in humans and animals, which disturbs normal growth and leads to severe bowel diseases. Short chain fatty acids (SCFA) are the gut microbiota metabolites produced from fermentation of non-digestible carbohydrates, and have been reported to modulate gut inflammation. SCFA have been implicated as the potential therapeutic bioactive molecules for gut inflammatory diseases, and could be an alternative to antibiotic growth promoters (AGP). In this review, the existing knowledge about the types of SCFA, the related gut microbes producing SCFA, the roles of SCFA in maintaining gut homeostasis, and how SCFA modulate gut inflammation is summarized. The therapeutic application of SCFA in the treatment of inflammatory bowel disease (IBD) is also highlighted.

Immunoregulatory Intestinal Microbiota and COVID-19 in Patients with Type Two Diabetes: A Double-Edged Sword

Coronavirus disease 2019, or COVID-19, is a major challenge facing scientists worldwide. Alongside the lungs, the system of organs comprising the GI tract is commonly targeted by COVID-19. The dysbiotic modulations in the intestine influence the disease severity, potentially due to the ability of the intestinal microbiota to modulate T lymphocyte functions, i.e., to suppress or activate T cell subpopulations. The interplay between the lungs and intestinal microbiota is named the gut-lung axis. One of the most usual comorbidities in COVID-19 patients is type 2 diabetes, which induces changes in intestinal microbiota, resulting in a pro-inflammatory immune response, and consequently, a more severe course of COVID-19. However, changes in the microbiota in this comorbid pathology remain unclear. Metformin is used as a medication to treat type 2 diabetes. The use of the type 2 diabetes drug metformin is a promising treatment for this comorbidity because, in addition to its hypoglycemic action, it can increase amount of intestinal bacteria that induce regulatory T cell response. This dual activity of metformin can reduce lung damage and improve the course of the COVID-19 disease.

Balancing reactive oxygen species generation by rebooting gut microbiota

Reactive oxygen species (ROS; free radical form O₂ ^•‾ , superoxide radical; OH^• , hydroxyl radical; ROO^• , peroxyl; RO^• , alkoxyl and non-radical form ¹ O₂ , singlet oxygen; H₂ O₂ , hydrogen peroxide) are inevitable companions of aerobic life with crucial role in gut health. But, overwhelming production of ROS can cause serious damage to biomolecules. In this review, we have discussed several sources of ROS production that can be beneficial or dangerous to the human gut. Microorganisms, organelles and enzymes play crucial role in ROS generation, where, NOX1 is the main intestinal enzyme, which produce ROS in the intestine epithelial cells. Previous studies have reported that probiotics play significant role in gut homeostasis by checking the ROS generation, maintaining the antioxidant level, immune system and barrier protection. With current knowledge, we have critically analyzed the available literature and presented the outcome in the form of bubble maps to suggest the probiotics that help in controlling the ROS-specific intestinal diseases, such as inflammatory bowel disease (IBD) and colon cancer. Finally, it has been concluded that rebooting of the gut microbiota with probiotics, postbiotics or fecal microbiota transplantation (FMT) can have crucial implications in the structuring of gut communities for the personalized management of the gastrointestinal (GI) diseases.

Establishment and evaluation of a specific antibiotic-induced inflammatory bowel disease model in rats

Physical and chemical methods for generating rat models of enteritis have been established; however, antibiotic induction has rarely been used for this purpose. The present study aimed to establish and evaluate a rat model of inflammatory bowel disease (IBD) using antibiotics. A total of 84 Sprague-Dawley (SD) rats were divided into the following groups, according to the dosage and method of administration of the antibiotics: A, control; B, low-dose clindamycin; C, medium-dose clindamycin; D, high-dose clindamycin; E, low-dose clindamycin, ampicillin and streptomycin; F, medium-dose clindamycin, ampicillin and streptomycin; and G, high-dose clindamycin, ampicillin and streptomycin. Antibiotic administration was stopped on day 7; the modeling period covered days 1-7, and the recovery period covered days 8-15. Half of the animals were dissected on day 11, with the remaining animals dissected on day 15. Food and water intake, body weight and fecal weight were recorded. Intestinal flora was analyzed via microbial culture and quantitative PCR. The content of TNF-α, IL1-β, IL-6 and C-reactive protein (CRP) was assessed in abdominal aorta blood. Colonic and rectal tissues were examined pathologically via hematoxylin-eosin staining to assess leukocyte infiltration and intestinal mucosal changes as indicators of inflammation. Rat weight, food intake, water intake and 2-h fecal weight were significantly different across the experimental groups (P = 0.040, P = 0.016, P<0.001 and P = 0.009, respectively). Microbial cultures revealed no significant differences between group A and B,C (P = 0.546,0.872) but significant differences betwenn group A and the other experimental groups (all P<0.001). Furthermore, significant differences in the levels of Bacteroides, Faecalibacterium prausnitzii and Dialister invisus on day 4 between groups A, C and F (P = 0.033, P = 0.025 and P = 0.034, respectively). Significant differences were detected in the levels of TNF-α, IL1-β, IL-6 and CRP between the groups (all P<0.001). The colonic and rectal pathological inflammation scores of the experimental groups were significantly different compared with group A (B vs. A, P = 0.002; others, all P<0.001). These findings indicated that an antibiotic-induced IBD model was successfully established in SD rats; this animal model may serve as a useful model for clinical IBD research.

Gut Microbiota, Macrophages and Diet: An Intriguing New Triangle in Intestinal Fibrosis

Intestinal fibrosis is a common complication in inflammatory bowel disease (IBD) without specific treatment. As macrophages are the key actors in inflammatory responses and the wound healing process, they have been extensively studied in chronic diseases these past decades. By their exceptional ability to integrate diverse stimuli in their surrounding environment, macrophages display a multitude of phenotypes to underpin a broad spectrum of functions, from the initiation to the resolution of inflammation following injury. The hypothesis that distinct macrophage subtypes could be involved in fibrogenesis and wound healing is emerging and could open up new therapeutic perspectives in the treatment of intestinal fibrosis. Gut microbiota and diet are two key factors capable of modifying intestinal macrophage profiles, shaping their specific function. Defects in macrophage polarisation, inadequate dietary habits, and alteration of microbiota composition may contribute to the development of intestinal fibrosis. In this review, we describe the intriguing triangle between intestinal macrophages, diet, and gut microbiota in homeostasis and how the perturbation of this discreet balance may lead to a pro-fibrotic environment and influence fibrogenesis in the gut.

The effect of a hydrolyzed protein diet on the fecal microbiota in cats with chronic enteropathy

The effect of a hydrolyzed protein diet on the fecal microbiota has not been studied in feline chronic enteropathy (CE). Our study aimed to (1) compare the fecal microbiota of cats with CE to control cats with no gastrointestinal signs and (2) determine the effect of a hydrolyzed protein diet on the fecal microbiota of cats with CE and whether this differs between dietary responders and non-responders. The fecal microbiome of cats with CE (n = 36) showed decreased α-diversity in terms of genus richness (P = 0.04) and increased β-diversity in terms of Bray–Curtis Dissimilarity (P < 0.001) compared to control cats (n = 14). Clostridium was the only genera significantly over-represented in cats with CE compared to control cats (adjusted P < 0.1). After 6-weeks of feeding the diet, fifteen cats were classified as responders and 18 as non-responders, based on clinical signs. At the genus level, α-diversity was increased in non-responders versus responders at diagnosis, but decreased after dietary intervention in both groups (P < 0.05). At the family level, non-responders became increasingly dissimilar after dietary intervention (P = 0.012). In general, the abundance of bacteria decreased with feeding a hydrolyzed diet, with the genera most significantly affected being more frequently observed in non-responders. Bifidobacterium was the only genus that increased significantly in abundance post-diet and this effect was observed in both responders and non-responders. Both Oscillibacter and Desulfovibrionaceae_unclassified were most abundant in non-responders at diagnosis but were rarely observed post diet in neither responders nor non-responders. Cats with CE had similar microbiota changes to those described in human inflammatory bowel disease. Whether the presence of Oscillibacter and Desulfovibrionaceae_unclassified are indicators of non-response to the diet at diagnosis requires further investigation. Despite the hydrolyzed diet reducing α-diversity in all cats with CE, this did not resolve gastrointestinal signs in some cats. However, responders metabolized the diet in a similar manner, reflected by sustained β-diversity, while the microbiome of non-responders became increasingly dissimilar compared to diagnosis at the family level. Therefore, the microbiome may not be as tightly regulated in cats with CE that are non-responders and therefore, these cats would require additional therapy for remission of clinical signs.

The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease

The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.

Tea Polyphenols: A Natural Antioxidant Regulates Gut Flora to Protect the Intestinal Mucosa and Prevent Chronic Diseases

The intestinal tract of a healthy human body hosts many microorganisms that are closely linked to all aspects of people’s lives. The impact of intestinal flora on host health is no longer limited to the gut but can also affect every organ in the body through various pathways. Studies have found that intestinal flora can be altered by external factors, which provides new ideas for treating some diseases. Tea polyphenols (TP), a general term for polyphenols in tea, are widely used as a natural antioxidant in various bioactive foods. In recent years, with the progress of research, there have been many experiments that provide strong evidence for the ability of TP to regulate intestinal flora. However, there are very few studies on the use of TP to modify the composition of intestinal microorganisms to maintain health or treat related diseases, and this area has not received sufficient attention. In this review, we outline the mechanisms by which TP regulates intestinal flora and the essential role in maintaining suitable health. In addition, we highlighted the protective effects of TP on intestinal mucosa by regulating intestinal flora and the preventive and therapeutic effects on certain chronic diseases, which will help further explore measures to prevent related chronic diseases.

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.

Inflammatory Bowel Disease Therapeutics: A Focus on Probiotic Engineering

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of gastrointestinal (GI) tract with dysregulated mucosal immune functions and disturbed commensal ecosystem of the intestinal lumen. IBD is categorized into two major subsets: Crohn's disease (CD) and ulcerative colitis (UC). Though advent of biologics has shifted the treatment with relatively longer remission compared to small molecule pharmaceuticals, patients still suffer from long-term complications. Since gut-microbiome is now accepted as another human organ holding potential for long-lasting human health, probiotics, and its engineering hold great promises to treat several previously untreatable chronic inflammatory conditions including IBD. Several emerging biological engineering tools have unlimited potential to manipulate probiotic bacterial system. These can produce useful therapeutic biologics with a goal to either ameliorate and/or treat previously untreatable chronic inflammatory conditions. As gut-microbiome is diverse and vary in different ethnic, geographic, and cultural human population, it will be important to develop vision for personalized probiotic treatment and develop the technology thereof to make personalized probiotic options a reality. The aim of this review paper is to present an overview of the current knowledge on both pharmacological and nonpharmacological IBD treatment modalities with a special emphasis on probiotic strains that are developed through the probiotic engineering. These engineered probiotics contain the most anti-inflammatory cytokines found within the human immune response and are currently being used to treat the intestinal inflammation in IBD for the IBD treatment.

Impending Mental Health Issues During Coronavirus Disease 2019 - Time for Personalized Nutrition Based on the Gut Microbiota to Tide Over the Crisis?

Coronavirus disease 2019 (COVID-19) is a major pandemic facing the world today caused by SARS-CoV-2 which has implications on our mental health as well. The uncertain future, fear of job loss, lockdown and negative news all around have taken a heavy toll on the mental health of individuals from across the world. Stress and anxiety can affect the COVID-19 patients even more. Recent study suggests COVID-19 infection may lead to post-traumatic stress disorder (PTSD). Certain prebiotics and probiotics have been shown to have anxiolytic effect through gut microbiota modulation. Incidentally, preliminary report also suggests a differential microbial profile in COVID-19 patients as compared to healthy individuals. Gut microbiota's role in anxiety and depression is well studied. The importance of the "gut-brain" axis has been implicated in overall mental health. It is known that diet, environmental factors and genetics play an important role in shaping gut microbiota. Trials may be initiated to study if personalized diet and supplementation based on individual's gut microbiome profile may improve the general mental well-being of people prone to anxiety during this pandemic. Also, COVID-19 patients may be provided personalized nutritional therapy based on their gut microbiota profile to see if PTSD and anxiety symptoms can be alleviated.

Pediococcus pentosaceus CECT 8330 protects DSS-induced colitis and regulates the intestinal microbiota and immune responses in mice

Background

Compelling evidences demonstrated that gut microbiota dysbiosis plays a critical role in the pathogenesis of inflammatory bowel diseases (IBD). Therapies for targeting the microbiota may provide alternative options for the treatment of IBD, such as probiotics. Here, we aimed to investigate the protective effect of a probiotic strain, Pediococcus pentosaceus (P. pentosaceus) CECT 8330, on dextran sulfate sodium (DSS)-induced colitis in mice.

Methods

C57BL/6 mice were administered phosphate-buffered saline (PBS) or P. pentosaceus CECT 8330 (5 × 10⁸ CFU/day) once daily by gavage for 5 days prior to or 2 days after colitis induction by DSS. Weight, fecal conditions, colon length and histopathological changes were examined. ELISA and flow cytometry were applied to determine the cytokines and regulatory T cells (Treg) ratio. Western blot was used to examine the tight junction proteins (TJP) in colonic tissues. Fecal short-chain fatty acids (SCFAs) levels and microbiota composition were analyzed by targeted metabolomics and 16S rRNA gene sequencing, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of orthologous groups of proteins (COG) pathway analysis were used to predict the microbial functional profiles.

Results

P. pentosaceus CECT 8330 treatment protected DSS-induced colitis in mice as evidenced by reducing the weight loss, disease activity index (DAI) score, histological damage, and colon length shortening. P. pentosaceus CECT 8330 decreased the serum levels of proinflammatory cytokines (TNF-α, IL-1β, and IL-6), and increased level of IL-10 in DSS treated mice. P. pentosaceus CECT 8330 upregulated the expression of ZO-1, Occludin and the ratio of Treg cells in colon tissue. P. pentosaceus CECT 8330 increased the fecal SCFAs level and relative abundances of several protective bacteria genera, including norank_f_Muribaculaceae, Lactobacillus, Bifidobacterium, and Dubosiella. Furthermore, the increased abundances of bacteria genera were positively correlated with IL-10 and SCFAs levels, and negatively associated with IL-6, IL-1β, and TNF-α, respectively. The KEGG and COG pathway analysis revealed that P. pentosaceus CECT 8330 could partially recover the metabolic pathways altered by DSS.

Conclusions

P. pentosaceus CECT 8330 administration protects the DSS-induced colitis and modulates the gut microbial composition and function, immunological profiles, and the gut barrier function. Therefore, P. pentosaceus CECT 8330 may serve as a promising probiotic to ameliorate intestinal inflammation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03235-8.

Enriched CD45RA-CD62L+ central memory T and decreased CD3+CD56+ natural killer T lymphocyte subsets in the rectum of ulcerative colitis patients

OBJECTIVES

To investigate the distinctive features of lymphocytes promoting inflammation in ulcerative colitis.

METHODS

We performed flow cytometric analysis of peripheral blood mononuclear cells (PBMCs) and colorectal mucosa lymphocytes in ulcerative colitis patients (n = 13) and control patients (n = 5).

RESULTS

CD62L⁺/CD3⁺CD4⁺ (35.7 ± 14.0% vs. 19.9 ± 6.4%) and CD62L⁺/CD3⁺CD4^- cells (17.1 ± 17.4% vs. 2.4 ± 3.9%) were higher in the rectum of ulcerative colitis patients than in control patients. Subpopulation analysis revealed that CD45RA^-CD62L⁺/CD3⁺CD4⁺, that is, central memory T cell fraction in CD4⁺ T cells, was significantly increased in the rectum of ulcerative colitis, compared to that in control patients (23.3 ± 10.5% vs. 8.2 ± 4.0%). Comparison of rectum and colon samples in ulcerative colitis patients indicated that CD56⁺/CD3⁺ was decreased in the rectum compared to that in the colon (11.3 ± 12.5% vs. 21.3 ± 16.5%). The ratio of CD56⁺/CD3⁺ was also decreased in the rectum of active ulcerative colitis patients compared to that in ulcerative colitis patients at the endoscopic remission stages (2.8 ± 1.7% vs. 18.5 ± 13.3%).

CONCLUSION

We demonstrated that CD62L⁺ T lymphocytes, particularly the CD45RA^-CD62L⁺ T cell subset that represents central memory T cells, were increased in the rectum of patients with ulcerative colitis. In addition, the CD56⁺/CD3⁺ subset (natural killer T cells) was decreased in the rectum compared to that of less inflamed colonic mucosa. These results suggest that the enrichment of central memory T lymphocytes and the reduction of natural killer T cells in the gut mucosa are involved in the pathogenesis of ulcerative colitis.

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.

Native and Engineered Probiotics: Promising Agents against Related Systemic and Intestinal Diseases

Intestinal homeostasis is a dynamic balance involving the interaction between the host intestinal mucosa, immune barrier, intestinal microecology, nutrients, and metabolites. Once homeostasis is out of balance, it will increase the risk of intestinal diseases and is also closely associated with some systemic diseases. Probiotics (Escherichia coli Nissle 1917, Akkermansia muciniphila, Clostridium butyricum, lactic acid bacteria and Bifidobacterium spp.), maintaining the gut homeostasis through direct interaction with the intestine, can also exist as a specific agent to prevent, alleviate, or cure intestinal-related diseases. With genetic engineering technology advancing, probiotics can also show targeted therapeutic properties. The aims of this review are to summarize the roles of potential native and engineered probiotics in oncology, inflammatory bowel disease, and obesity, discussing the therapeutic applications of these probiotics.

Host microbiomes in tumor precision medicine: how far are we?

The human gut microbiome has received a crescendo of attention in recent years, due to the countless influences on human pathophysiology, including cancer. Research on cancer and anticancer therapy is constantly looking for new hints to improve the response to therapy while reducing the risk of relapse. In this scenario, the gut microbiome and the plethora of microbial-derived metabolites are considered a new opening in the development of innovative anticancer treatments for a better prognosis. This narrative review summarizes the current knowledge on the role of the gut microbiome in the onset and progression of cancer, as well as in response to chemo-immunotherapy. Recent findings regarding the tumor microbiome and its implications for clinical practice are also commented on. Current microbiome-based intervention strategies (i.e., prebiotics, probiotics, live biotherapeutics and fecal microbiota transplantation) are then discussed, along with key shortcomings, including a lack of long-term safety information in patients who are already severely compromised by standard treatments. The implementation of bioinformatic tools applied to microbiomics and other omics data, such as machine learning, has an enormous potential to push research in the field, enabling the prediction of health risk and therapeutic outcomes, for a truly personalized precision medicine.

Determine independent gut microbiota-diseases association by eliminating the effects of human lifestyle factors

Lifestyle and physiological variables on human disease risk have been revealed to be mediated by gut microbiota. Low concordance between case-control studies for detecting disease-associated microbe existed due to limited sample size and population-wide bias in lifestyle and physiological variables. To infer gut microbiota-disease associations accurately, we propose to build machine learning models by including both human variables and gut microbiota. When the model's performance with both gut microbiota and human variables is better than the model with just human variables, the independent gut microbiota -disease associations will be confirmed. By building models on the American Gut Project dataset, we found that gut microbiota showed distinct association strengths with different diseases. Adding gut microbiota into human variables enhanced the classification performance of IBD significantly; independent associations between occurrence information of gut microbiota and irritable bowel syndrome, C. difficile infection, and unhealthy status were found; adding gut microbiota showed no improvement on models' performance for diabetes, small intestinal bacterial overgrowth, lactose intolerance, cardiovascular disease. Our results suggested that although gut microbiota was reported to be associated with many diseases, a considerable proportion of these associations may be very weak. We proposed a list of microbes as biomarkers to classify IBD and unhealthy status. Further functional investigations of these microbes will improve understanding of the molecular mechanism of human diseases.

Orally pH-activated "nano-bomb" carrier combined with berberine by regulating gene silencing and gut microbiota for site-specific treatment of ulcerative colitis

Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease that features colonic epithelial barrier dysfunction and gut dysbiosis. Preclinical studies demonstrated that inhibiting the overexpression of CD98 via small...

Advancement of Traditional Chinese Medicine in Regulation of Intestinal Flora: Mechanism-based Role in Disease Management

Intestinal microecology is the largest and most complex human microecology. The intestinal microflora plays an important role in human health. Imbalance of intestinal microflora contributes to the occurrence and development of many diseases. Recently, the treatment of human diseases by regulating intestinal microflora has become a research topic of interest. Traditional Chinese medicine considers the whole human body as the central concept in disease treatment strategies. It advocates maintaining the coordination and balance of the functions of various organs and systems of the human body, including the intestinal microflora. Traditional Chinese medicine improves the metabolism and immune function of the human body by regulating the intestinal microflora. The intestinal microflora could trigger pharmacological activity or reduce toxicity of drugs through regulating metabolism, which enables traditional Chinese medicine formulations to exert their best therapeutic effects. This review summarized the relationship between the intestinal microflora and digestive system, tumors, and other diseases. Furthermore, the role of traditional Chinese medicine in the treatment of tumors, and other diseases is discussed. The relationship among traditional Chinese medicine and the common intestinal microflora, pathogenesis of human diseases, and effective intervention methods were elaborated. In addition, we explored the research progress of traditional Chinese medicine in the treatment of various human diseases by regulating intestinal microflora to provide new treatment concepts. There is a close relationship between traditional Chinese medicine and the intestinal microflora. Traditional Chinese medicine formulations contribute to maintain the natural balance of the intestinal tract and the intestinal microflora to achieve treatment effects. This paper summarizes the mechanism of action of traditional Chinese medicine formulations in regulating the intestinal microflora in the prevention and treatment of various diseases. Furthermore, it summarizes information on the application of the interaction between traditional Chinese medicine preparations and the regulation of intestinal microflora in the treatment of common human diseases. Intestinal microflora plays a key role in traditional Chinese medicine in maintaining the natural balance of physiology and metabolism of human body. It will provide a theoretical basis for the traditional Chinese medicine preparations in the prevention and treatment of common human diseases, and simulate future research on this aspect.

Structural Changes in Trabecular Bone, Cortical Bone and Hyaline Cartilage as Well as Disturbances in Bone Metabolism and Mineralization in an Animal Model of Secondary Osteoporosis in Clostridium perfringens Infection

There is no information regarding whether changes in the microbiological balance of the gastrointestinal tract as a result of an infection with Clostridium perfringens influence the development of metabolic bone disorders. The experiment was carried out on male broiler chickens divided into two groups: control (n = 10) and experimental (n = 10). The experimental animals were infected with Clostridium perfringens between 17 and 20 days of age. The animals were euthanized at 42 days of age. The structural parameters of the trabecular bone, cortical bone, and hyaline cartilage as well as the mineralization of the bone were determined. The metabolism of the skeletal system was assessed by determining the levels of bone turnover markers, hormones, and minerals in the blood serum. The results confirm that the disturbed composition of the gastrointestinal microflora has an impact on the mineralization and metabolism of bone tissue, leading to the structural changes in cortical bone, trabecular bone, and hyaline cartilage. On the basis of the obtained results, it can be concluded that changes in the microenvironment of the gastrointestinal tract by infection with C. perfringens may have an impact on the earlier development of osteoporosis.

Microbial pathogenesis in inflammatory bowel diseases

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal system. Previously, it is considered the disease of the western world but now the incidence and prevalence of IBD are increasing globally with urbanization and modernization. Additionally, the major problem is the highest incidence of IBD among children and adolescents. The precise etiology of IBD is unknown and there is no cure for IBD, which is also the reason for increasing the number of cases worldwide. The IBD is a complex interplay of environment, immune system, and microbiota in a genetically susceptible host. Among these factors, the alteration in intestinal microbiota has been detected in IBD patients. The bacterial species associated with IBD include Mycobacterium paratuberculosis, adherent-invasive E. coli (AIEC), Helicobacter pylori, and Campylobacter concisus. Moreover, the efficacy of antibiotics and probiotics further suggests the role of microbes in IBD. However, no study confirmed the bacterial species as a cause of IBD as per Koch's postulates. Thus, still controversies exist regarding the role of microbes in IBD. Therefore, this paper aims to review the current literature to evaluate the role of microbes in IBD that would be a useful inventory of researchers working in this area.