Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases

Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents

Urogenital schistosomiasis is a neglected tropical disease caused by the parasite Schistosoma haematobium, which resides in the vasculature surrounding the urogenital system. Previous work has suggested that helminthic infections can affect the intestinal microbiome, and we hypothesized that S. haematobium infection could result in an alteration of immune system-microbiota homeostasis and impact the composition of the gut microbiota. To address this question, we compared the fecal microbiomes of infected and uninfected schoolchildren from the Argungu Local Government Area of Kebbi State, Nigeria, detecting significant differences in community composition between the two groups. Most remarkably, we observed a decreased abundance of Firmicutes and increased abundance of Proteobacteria - a shift in community structure which has been previously associated with dysbiosis. More specifically, we detected a number of changes in lower taxa reminiscent of inflammation-associated dysbiosis, including decreases in Clostridiales and increases in Moraxellaceae, Veillonellaceae, Pasteurellaceae, and Desulfovibrionaceae. Functional potential analysis also revealed an enrichment in orthologs of urease, which has been linked to dysbiosis and inflammation. Overall, our analysis indicates that S. haematobium infection is associated with perturbations in the gut microbiota and may point to microbiome disruption as an additional consequence of schistosome infection.

Shaping the Gut Microbiota by Breastfeeding: The Gateway to Allergy Prevention?

Evidence is accumulating that demonstrates the importance of the gut microbiota in health and diseases such as allergy. Recent studies emphasize the importance of the "window of opportunity" in early life, during which interventions altering the gut microbiota induce long-term effects. The neonate's gut microbiota composition and metabolism could therefore play an essential role in allergic disease risk. Breastfeeding shapes the gut microbiota in early life, both directly by exposure of the neonate to the milk microbiota and indirectly, via maternal milk factors that affect bacterial growth and metabolism such as human milk oligosaccharides, secretory IgA, and anti-microbial factors. The potential of breastmilk to modulate the offspring's early gut microbiota is a promising tool for allergy prevention. Here, we will review the existing evidence demonstrating the impact of breastfeeding on shaping the neonate's gut microbiota and highlight the potential of this strategy for allergy prevention.

Mitochondrial Neurogastrointestinal Encephalomyopathy: Into the Fourth Decade, What We Have Learned So Far

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare metabolic autosomal recessive disease, caused by mutations in the nuclear gene TYMP which encodes the enzyme thymidine phosphorylase. The resulting enzyme deficiency leads to a systemic accumulation of the deoxyribonucleosides thymidine and deoxyuridine, and ultimately mitochondrial failure due to a progressive acquisition of secondary mitochondrial DNA (mtDNA) mutations and mtDNA depletion. Clinically, MNGIE is characterized by gastrointestinal and neurological manifestations, including cachexia, gastrointestinal dysmotility, peripheral neuropathy, leukoencephalopathy, ophthalmoplegia and ptosis. The disease is progressively degenerative and leads to death at an average age of 37.6 years. As with the vast majority of rare diseases, patients with MNGIE face a number of unmet needs related to diagnostic delays, a lack of approved therapies, and non-specific clinical management. We provide here a comprehensive collation of the available knowledge of MNGIE since the disease was first described 42 years ago. This review includes symptomatology, diagnostic procedures and hurdles, in vitro and in vivo disease models that have enhanced our understanding of the disease pathology, and finally experimental therapeutic approaches under development. The ultimate aim of this review is to increase clinical awareness of MNGIE, thereby reducing diagnostic delay and improving patient access to putative treatments under investigation.

Short-chain fatty acids increase TNFα-induced inflammation in primary human lung mesenchymal cells through the activation of p38 MAPK

Short-chain fatty acids (SCFAs), produced as by-products of dietary fiber metabolism by gut bacteria, have anti-inflammatory properties and could potentially be used for the treatment of inflammatory diseases, including asthma. The direct effects of SCFAs on inflammatory responses in primary human lung mesenchymal cells have not been assessed. We investigated whether SCFAs can protect against tumor necrosis factor (TNF)α-induced inflammation in primary human lung fibroblasts (HLFs) and airway smooth muscle (ASM) cells in vitro. HLFs and ASM cells were exposed to SCFAs, acetate (C2:0), propionate (C3:0), and butyrate (C4:0) (0.01-25 mM) with or without TNFα, and the release of proinflammatory cytokines, IL-6, and CXCL8 was measured using ELISA. We found that none of the SCFAs suppressed TNFα-induced cytokine release. On the contrary, challenge with supraphysiological concentrations (10-25 mM), as might be used therapeutically, of propionate or butyrate in combination with TNFα resulted in substantially greater IL-6 and CXCL8 release from HLFs and ASM cells than challenge with TNFα alone, demonstrating synergistic effects. In ASM cells, challenge with acetate also enhanced TNFα-induced IL-6, but not CXCL8 release. Synergistic upregulation of IL-6 and CXCL8 was mediated through the activation of free fatty acid receptor (FFAR)3, but not FFAR2. The signaling pathways involved were further examined using specific inhibitors and immunoblotting, and responses were found to be mediated through p38 MAPK signaling. This study demonstrates that proinflammatory, rather than anti-inflammatory effects of SCFAs are evident in lung mesenchymal cells.

Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.

The human microbiota in pulmonary tuberculosis: Not so innocent bystanders

Mycobacterium tuberculosis (Mtb) infection is a worldwide health concern, which needs robust and efficient control strategies, and the evaluation of human microbiota can be very important in this regard. Dysbiosis of normal microbiota is an important issue in the pathogenesis of Mtb. However, only few studies demonstrated the interaction between Mtb infection and microbiota. The current study aimed at reviewing literature on gut and lung microbiota in Mtb infection. Eleven articles regarding gut and lung microbiota composition in individuals with Mtb infection were selected, and then the importance of gut-lung axis in Mtb infection was evaluated. Also the relationship between microbiota composition and Mtb infection were discussed in terms of treatment, epigenetic field, and biomarkers.

Gut microbiota-dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes

We hypothesized that the gut microbiota influences survival of murine cardiac allografts through modulation of immunity. Antibiotic pretreated mice received vascularized cardiac allografts and fecal microbiota transfer (FMT), along with tacrolimus immunosuppression. FMT source samples were from normal, pregnant (immune suppressed), or spontaneously colitic (inflammation) mice. Bifidobacterium pseudolongum (B. pseudolongum) in pregnant FMT recipients was associated with prolonged allograft survival and lower inflammation and fibrosis, while normal or colitic FMT resulted in inferior survival and worse histology. Transfer of B. pseudolongum alone resulted in reduced inflammation and fibrosis. Stimulation of DC and macrophage lines with B. pseudolongum induced the antiinflammatory cytokine IL-10 and homeostatic chemokine CCL19 but induced lesser amounts of the proinflammatory cytokines TNFα and IL-6. In contrast, LPS and Desulfovibrio desulfuricans (D. desulfuricans), more abundant in colitic FMT, induced a more inflammatory cytokine response. Analysis of mesenteric and peripheral lymph node structure showed that B. pseudolongum gavage resulted in a higher laminin α4/α5 ratio in the lymph node cortical ridge, indicative of a suppressive environment, while D. desulfuricans resulted in a lower laminin α4/α5 ratio, supportive of inflammation. Discrete gut bacterial species alter immunity and may predict graft outcomes through stimulation of myeloid cells and shifts in lymph node structure and permissiveness.

Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer

The microbiota consists of a dynamic multispecies community of bacteria, fungi, archaea, and protozoans, bringing to the host organism a dowry of cells and genes more numerous than its own. Among the different non-sterile cavities, the human gut harbors the most complex microbiota, with a strong impact on host homeostasis and immunostasis, being thus essential for maintaining the health condition. In this review, we outline the roles of gut microbiota in immunity, starting with the background information supporting the further presentation of the implications of gut microbiota dysbiosis in host susceptibility to infections, hypersensitivity reactions, autoimmunity, chronic inflammation, and cancer. The role of diet and antibiotics in the occurrence of dysbiosis and its pathological consequences, as well as the potential of probiotics to restore eubiosis is also discussed.

Engineering microbes for targeted strikes against human pathogens

Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host's inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.

The Gut-Brain Axis: Influence of Microbiota on Mood and Mental Health

The gut-brain axis is a bidirectional communication network that links the enteric and central nervous systems. This network is not only anatomical, but it extends to include endocrine, humoral, metabolic, and immune routes of communication as well. The autonomic nervous system, hypothalamic-pituitary-adrenal (HPA) axis, and nerves within the gastrointestinal tract, all link the gut and the brain, allowing the brain to influence intestinal activities, including activity of functional immune effector cells; and the gut to influence mood, cognition, and mental health.

Physical Activity, Immune System, and the Microbiome in Cardiovascular Disease

Cardiovascular health is a primary research focus, as it is a leading contributor to mortality and morbidity worldwide, and is prohibitively costly for healthcare. Atherosclerosis, the main driver of cardiovascular disease, is now recognized as an inflammatory disorder. Physical activity (PA) may have a more important role in cardiovascular health than previously expected. This review overviews the contribution of PA to cardiovascular health, the inflammatory role of atherosclerosis, and the emerging evidence of the microbiome as a regulator of inflammation.

Connecting the immune system, systemic chronic inflammation and the gut microbiome: The role of sex

Unresolved low grade systemic inflammation represents the underlying pathological mechanism driving immune and metabolic pathways involved in autoimmune diseases (AID). Mechanistic studies in animal models of AID and observational studies in patients have found alterations in gut microbiota communities and their metabolites, suggesting a microbial contribution to the onset or progression of AID. The gut microbiota and its metabolites have been shown to influence immune functions and immune homeostasis both within the gut and systematically. Microbial derived-short chain fatty acid (SCFA) and bio-transformed bile acid (BA) have been shown to influence the immune system acting as ligands specific cell signaling receptors like GPRCs, TGR5 and FXR, or via epigenetic processes. Similarly, intestinal permeability (leaky gut) and bacterial translocation are important contributors to chronic systemic inflammation and, without repair of the intestinal barrier, might represent a continuous inflammatory stimulus capable of triggering autoimmune processes. Recent studies indicate gender-specific differences in immunity, with the gut microbiota shaping and being concomitantly shaped by the hormonal milieu governing differences between the sexes. A bi-directional cross-talk between microbiota and the endocrine system is emerging with bacteria being able to produce hormones (e.g. serotonin, dopamine and somatostatine), respond to host hormones (e.g. estrogens) and regulate host hormones' homeostasis (e.g by inhibiting gene prolactin transcription or converting glucocorticoids to androgens). We review herein how gut microbiota and its metabolites regulate immune function, intestinal permeability and possibly AID pathological processes. Further, we describe the dysbiosis within the gut microbiota observed in different AID and speculate how restoring gut microbiota composition and its regulatory metabolites by dietary intervention including prebiotics and probiotics could help in preventing or ameliorating AID. Finally, we suggest that, given consistent observations of microbiota dysbiosis associated with AID and the ability of SCFA and BA to regulate intestinal permeability and inflammation, further mechanistic studies, examining how dietary microbiota modulation can protect against AID, hold considerable potential to tackle increased incidence of AID at the population level.

Microbial interactions with the intestinal epithelium and beyond: Focusing on immune cell maturation and homeostasis

Microbial metabolites influence the function of epithelial, endothelial and immune cells in the intestinal mucosa. Microbial metabolites like SCFAs and B complex vitamins direct macrophage polarization whereas microbial derived biogenic amines modulate intestinal epithelium and immune response. Aberrant bacterial lipopolysaccharide-mediated signaling may be involved in the pathogenesis of chronic intestinal inflammation and colorectal carcinogenesis. Our perception of human microbes has changed from that of opportunistic pathogens to active participants maintaining intestinal and whole body homeostasis. This review attempts to explain the dynamic and enriched interactions between the intestinal epithelial mucosa and commensal bacteria in homeostasis maintenance.

Food Bioactives and Their Effects on Obesity-Accelerated Inflammatory Bowel Disease

Current views support the concept that obesity is linked to a worsening of the course of inflammatory bowel diseases (IBDs). Gut microbiota and adipose tissue macrophage (ATM) are considered key mediators or contributors in obesity-associated intestinal inflammation. Dietary components can have direct or indirect effects on "normal" or "healthy" microbial composition and participate in adiposity and metabolic status with gut inflammation. In this perspective, we highlight food-derived bioactives that have a potential application in the prevention of obesity-exacerbated IBD, targeting energy metabolism, M1 (classical activated)-M2 (alternatively activated) macrophage polarization, and gut microbiota.

Oral immunization with recombinant Lactobacillus casei expressing OmpAI confers protection against Aeromonas veronii challenge in common carp, Cyprinus carpio

Aeromonas veronii is a gram-negative pathogen capable of infecting both fish and mammals, including humans, and natural infection in fish results in irreparable damage to the aquaculture industry. Lactic acid bacteria (LAB) have a number of properties that make them attractive candidates as delivery vehicles for presentation to the mucosa sites of compounds with pharmaceutical interest, in particular vaccines. In this study, we generated two recombinant Lactobacillus casei (surface-displayed or secretory) expressing the OmpAI of A.veronii and evaluated the effect on immune responses in fish model. A 1022 bp gene fragment of the 42 kDa OmpAI antigen of A.veronii was cloned into pPG-1 (surface-displayed) and pPG-2 (secretory) and electrotransformed into Lactobacillus casei CC16. The recombinant plasmid in L.casei could be stably inherited over 50 generations, and production of OmpAI protein had slight limited effects on cells growth. Treatment of common carp with the recombinant vaccine candidate stimulated high serum or skin mucus specific antibody titers and induced a higher lysozyme, ACP, SOD activity, while fish fed with Lc-pPG or PBS had no detectable immobilizing immune responses. Expression of IL-10, IL-β, IFN-γ, TNF-α genes in the group immunized with recombinant L.casei were significantly (P < 0.05) up regulated as compared with control groups, indicating that inflammatory response and cell immune response were triggered. Further, viable recombinant L.casei strains were directly delivered and survive throughout the intestinal tract, the recombinant OmpAI was also detected in intestine mucosal. The results showed that common carp received Lc-pPG1-OmpAI (66.7%) and Lc-pPG2-OmpAI (50.0%) had higher survival rates compared with the controls after challenge with A.veronii, indicating that Lc-pPG1-OmpAI and Lc-pPG2-OmpAI had beneficial effects on immune response and enhanced disease resistance of common carp against A.veronii infection. Our study here demonstrates, for the first time, the ability of recombinant L.casei as oral vaccine against A.veronii infection in carps. The combination of OmpAI delivery and LAB approach may be a promising mucosal therapeutic agent for treating and controlling A.veronii.

The Resistance to Plague Infection among Meriones persicus from Endemic and Non-endemic Regions in Iran: The Role of Gut Microbiota

BACKGROUND

The present study was conducted approximately 40 years ago, but its results have not been released. At the time of this study, the importance of the gut microbiota was not fully understood.

METHODS

Meriones persicus rodents, as one of the major reservoirs of Yersinia pestis bacterium in Iran, were compared in a disease endemic area (Akanlu, Hamadan, western Iran) and a non-endemic zone (Telo, Tehran, Iran) from 1977 to 1981.

RESULTS

This study was able to transmit the resistance to Y. pestis to other rodents creatively by using and transferring gut microbiota.

CONCLUSION

The study indicated for the first time that the gut microbiota could affect the sensitivity to plague in Meriones in Telo.

Human intestinal epithelium in a dish: Current models for research into gastrointestinal pathophysiology

Determining the exact pathogenesis of chronic gastrointestinal diseases remains difficult due to the complex in vivo environment. In this review we give an overview of the available epithelial cell culture systems developed to investigate pathophysiology of gastrointestinal diseases. Traditionally used two-dimensional (2D) immortalised (tumour) cell lines survive long-term, but are not genetically stable nor represent any human in particular. In contrast, primary cultures are patient unique, but short-lived. Three-dimensional (3D) organoid cultures resemble the crypt-villus domain and contain all cell lineages, are long-lived and genetically stable. Unfortunately, manipulation of the 3D organoid system is more challenging. Combining the 3D and 2D technologies may overcome limitations and offer the formation of monolayers on permeable membranes or flow-chambers. Determining the right model to use will depend on the pathology of interest and the focus of the research, defining which cell types need to be included in the model.

16S rDNA analysis of the effect of fecal microbiota transplantation on pulmonary and intestinal flora

This study aims to explore the effect of FMT on regulations of dysbacteriosis of pulmonary and intestinal flora in rats with 16S rDNA sequencing technology. A total of 27 SPF rats (3-4 weeks old) were randomly divided into three groups: normal control group (K), model control group (MX), and fecal microbiota transplantation group (FMT); each group contained nine rats. The OTU values of the pulmonary and intestinal flora of the MX group decreased significantly compared with the normal control group. After FMT, the OTU value of pulmonary flora increased, while the value of OTU in intestinal flora declined. At the phylum level, FMT down-regulated Proteobacteria, Firmicutes, and Bacteroidetes in the pulmonary flora. At the genus level, FMT down-regulated Pseudomonas, Sphingobium, Lactobacillus, Rhizobium, and Acinetobacter, thus maintaining the balance of the pulmonary flora. Moreover, FMT could change the structure and diversity of the pulmonary and intestinal flora by positively regulating the pulmonary flora and negatively regulating intestinal flora. This study may provide a scientific basis for FMT treatment of respiratory diseases.

The Immune System Bridges the Gut Microbiota with Systemic Energy Homeostasis: Focus on TLRs, Mucosal Barrier, and SCFAs

The gut microbiota is essential for the development and regulation of the immune system and the metabolism of the host. Germ-free animals have altered immunity with increased susceptibility to immunologic diseases and show metabolic alterations. Here, we focus on two of the major immune-mediated microbiota-influenced components that signal far beyond their local environment. First, the activation or suppression of the toll-like receptors (TLRs) by microbial signals can dictate the tone of the immune response, and they are implicated in regulation of the energy homeostasis. Second, we discuss the intestinal mucosal surface is an immunologic component that protects the host from pathogenic invasion, is tightly regulated with regard to its permeability and can influence the systemic energy balance. The short chain fatty acids are a group of molecules that can both modulate the intestinal barrier and escape the gut to influence systemic health. As modulators of the immune response, the microbiota-derived signals influence functions of distant organs and can change susceptibility to metabolic diseases.

IL-33 and the intestine: The good, the bad, and the inflammatory

Interleukin-33 (IL-33) is a member of the IL-1 cytokine family that has been widely studied since its discovery in 2005 for its dichotomous functions in homeostasis and inflammation. IL-33, along with its receptor suppression of tumorigenicity 2 (ST2), has been shown to modulate both the innate and adaptive immune system. Originally, the IL-33/ST2 signaling axis was studied in the context of inducing type 2 immune responses with the expression of ST2 by T helper 2 (T_H2) cells. However, the role of IL-33 is not limited to T_H2 responses. Rather, IL-33 is a potent activator of T_H1 cells, group 2 innate lymphoid cells (ILC2s), regulatory T (Treg) cells, and CD8⁺ T cells. The intestine is uniquely important in this discussion, as the intestinal epithelium is distinctively positioned to interact with both pathogens and the immune cells housed in the mucosa. In the intestine, IL-33 is expressed by the pericryptal fibroblasts and its expression is increased particularly in disease states. Moreover, IL-33/ST2 signaling aberrancy is implicated in the pathogenesis of inflammatory bowel disease (IBD). Accordingly, for this review, we will focus on the role of IL-33 in the regulation of intestinal immunity, involvement in intestinal disease, and implication in potential therapeutics.

Distinct roles for dietary lipids and Porphyromonas gingivalis infection on atherosclerosis progression and the gut microbiota

Mounting evidence in humans supports an etiological role for the microbiota in inflammatory atherosclerosis. Atherosclerosis is a progressive disease characterized by accumulation of inflammatory cells and lipids in vascular tissue. While retention of lipoprotein into the sub-endothelial vascular layer is believed to be the initiating stimulus leading to the development of atherosclerosis, activation of multiple pathways related to vascular inflammation and endothelial dysfunction sustain the process by stimulating recruitment of leukocytes and immune cells into the sub-endothelial layer. The Gram-negative oral pathogen Porphyromonas gingivalis has been associated with the development and acceleration of atherosclerosis in humans and these observations have been validated in animal models. It has been proposed that common mechanisms of immune signaling link stimulation by lipids and pathogens to vascular inflammation. Despite the common outcome of P. gingivalis and lipid feeding on atherosclerosis progression, we established that these pro-atherogenic stimuli induced distinct gene signatures in the ApoE^-/- mouse model of atherosclerosis. In this study, we further defined the distinct roles of dietary lipids and P. gingivalis infection on atherosclerosis progression and the gut microbiota. We demonstrate that diet-induced lipid lowering resulted in less atherosclerotic plaque in ApoE^-/- mice compared to ApoE^-/- mice continuously fed a Western diet. However, the effect of diet-induced lipid lowering on plaque accumulation was blunted by P. gingivalis infection. Using principal component analysis and hierarchical clustering, we demonstrate that dietary intervention as well as P. gingivalis infection result in distinct bacterial communities in fecal and cecal samples of ApoE^-/- mice as compared to ApoE^-/- mice continuously fed either a Western diet or a normal chow diet. Collectively, we identified distinct microbiota changes accompanying atherosclerotic plaque, suggesting a future avenue for investigation on the impact of the gut microbiota, diet, and P. gingivalis infection on atherosclerosis.