Roles of the intestinal microbiota in pathogen protection. Clin Transl Immunology. 2017;6:e128. [PMID: 28243438 PMCID: PMC5311919 DOI: 10.1038/cti.2017.2]

Homeostatic T helper 17 cell responses triggered by complex microbiota are maintained in ex vivo intestinal tissue slices

Segmented filamentous bacteria (SFB) are members of the commensal intestinal microbiome. They are known to contribute to the postnatal maturation of the gut immune system, but also to augment inflammatory conditions in chronic diseases such as Crohn's disease. Living primary tissue slices are ultrathin multicellular sections of the intestine and provide a unique opportunity to analyze tissue-specific immune responses ex vivo. This study aimed to investigate whether supplementation of the gut flora with SFB promotes T helper 17 (Th17) cell responses in primary intestinal tissue slices ex vivo. Primary tissue slices were prepared from the small intestine of healthy Taconic mice with SFB-positive and SFB-negative microbiomes and stimulated with anti-CD3/CD28 or Concanavalin A. SFB-positive and -negative mice exhibited distinct microbiome compositions and Th17 cell frequencies in the intestine and complex microbiota including SFB induced up to 15-fold increase in Th17 cell-associated mediators, serum amyloid A (SAA), and immunoglobulin A (IgA) responses ex vivo. This phenotype could be transmitted by co-housing of mice. Our findings highlight that changes in the gut microbiome can be observed in primary intestinal tissue slices ex vivo. This makes the system very attractive for disease modeling and assessment of new therapies.

Interaction between Intestinal Parasites and the Gut Microbiota: Implications for the Intestinal Immune Response and Host Defence

Intestinal parasites, including helminths and protozoa, account for a significant portion of the global health burden. The gastrointestinal (GI) tract not only serves as the stage for these parasitic infections but also as the residence for millions of microbes. As the intricacies of the GI microbial milieu continue to unfold, it is becoming increasingly apparent that the interactions between host, parasite, and resident microbes help dictate parasite survival and, ultimately, disease outcomes. Across both clinical and experimental models, intestinal parasites have been shown to impact microbial composition and diversity. Reciprocally, microbes can directly influence parasitic survival, colonization and expulsion. The gut microbiota can also indirectly impact parasites through the influence and manipulation of the host. Studying this host-parasite-microbiota axis may help bring about novel therapeutic strategies for intestinal parasitic infection as well as conditions such as inflammatory bowel disease (IBD). In this review, we explore the relationship between intestinal parasites, with a particular focus on common protozoa and helminths, and the gut microbiota, and how these interactions can influence the host defence and intestinal immune response. We will also explore the impact of this tripartite relationship in a clinical setting and its broader implications for human health.

Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity

Coumarin, a phenolic compound, is a secondary metabolite produced by plants such as Tanga and Lime. Coumarin derivatives were prepared via Pechmann condensation. In this study, we performed in vitro and in vivo experiments to determine the antimicrobial and gut immune-regulatory functions of coumarin derivatives. For the in vitro antimicrobial activity assay, coumarin derivatives C1 and C2 were selected based on their pathogen-killing activity against various pathogenic microbes. We further demonstrated that the selected coumarin derivatives disrupted bacterial cell membranes. Next, we examined the regulatory function of the coumarin derivatives in gut inflammation using an infectious colitis model. In an in vivo infectious colitis model, administration of selected C1 coumarin derivatives reduced pathogen loads, the number of inflammatory immune cells (Th1 cells and Th17 cells), and inflammatory cytokine levels (IL-6 and IL-1b) in the intestinal tissue after pathogen infection. In addition, we found that the administration of C1 coumarin derivatives minimized abnormal gut microbiome shift-driven pathogen infection. Potential pathogenic gut microbes, such as Enterobacteriaceae and Staphylococcaceae, were increased by pathogen infection. However, this pathogenic microbial expansion was minimized and beneficial bacteria, such as Ligilactobacillus and Limosilactobacillus, increased with C1 coumarin derivative treatment. Functional gene enrichment assessment revealed that the relative abundance of genes associated with lipid and nucleotide metabolism was reduced by pathogen infection; however, this phenomenon was not observed in C1 coumarin derivative-treated animals. Collectively, our data suggest that C1 coumarin derivative is effective antibacterial agents that minimize pathogen-induced gut inflammation and abnormal gut microbiome modulation through their antibacterial activity.

A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection

Germ-free (GF) mice, which are depleted of their resident microbiota, are the gold standard for exploring the role of the microbiome in health and disease; however, they are of limited value in the study of human-specific pathogens because they do not support their replication. Here, we develop GF mice systemically reconstituted with human immune cells and use them to evaluate the role of the resident microbiome in the acquisition, replication and pathogenesis of two human-specific pathogens, Epstein-Barr virus (EBV) and human immunodeficiency virus (HIV). Comparison with conventional (CV) humanized mice showed that resident microbiota enhance the establishment of EBV infection and EBV-induced tumorigenesis and increase mucosal HIV acquisition and replication. HIV RNA levels were higher in plasma and tissues of CV humanized mice compared with GF humanized mice. The frequency of CCR5+ CD4+ T cells throughout the intestine was also higher in CV humanized mice, indicating that resident microbiota govern levels of HIV target cells. Thus, resident microbiota promote the acquisition and pathogenesis of two clinically relevant human-specific pathogens.

Understanding host immune responses in Clostridioides difficile infection: Implications for pathogenesis and immunotherapy

Clostridioides difficile (C. difficile) is the predominant causative agent of nosocomial diarrhea worldwide. Infection with C. difficile occurs due to the secretion of large glycosylating toxin proteins, which can lead to toxic megacolon or mortality in susceptible hosts. A critical aspect of C. difficile's biology is its ability to persist asymptomatically within the human host. Individuals harboring asymptomatic colonization or experiencing a single episode of C. difficile infection (CDI) without recurrence exhibit heightened immune responses compared to symptomatic counterparts. The significance of these immune responses cannot be overstated, as they play critical roles in the development, progression, prognosis, and outcomes of CDI. Nonetheless, our current comprehension of the immune responses implicated in CDI remains limited. Therefore, further investigation is imperative to elucidate their underlying mechanisms. This review explores recent advancements in comprehending CDI pathogenesis and how the host immune system response influences disease progression and severity, aiming to enhance our capacity to develop immunotherapy-based treatments for CDI.

Friend or Foe: Exploring the Relationship between the Gut Microbiota and the Pathogenesis and Treatment of Digestive Cancers

Digestive cancers are among the leading causes of cancer death in the world. However, the mechanisms of cancer development and progression are not fully understood. Accumulating evidence in recent years pointing to the bidirectional interactions between gut dysbiosis and the development of a specific type of gastrointestinal cancer is shedding light on the importance of this "unseen organ"-the microbiota. This review focuses on the local role of the gut microbiota imbalance in different digestive tract organs and annexes related to the carcinogenic mechanisms. Microbiota modulation, either by probiotic administration or by dietary changes, plays an important role in the future therapies of various digestive cancers.

Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism

BACKGROUND

Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.

CASE PRESENTATION

To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.

CONCLUSION

This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.

Interactions between microsporidia and other members of the microbiome

The microbiome is the collection of microbes that are associated with a host. Microsporidia are intracellular eukaryotic parasites that can infect most types of animals. In the last decade, there has been much progress to define the relationship between microsporidia and the microbiome. In this review, we cover an increasing number of reports suggesting that microsporidia are common components of the microbiome in both invertebrates and vertebrates. These microsporidia infections can range from mutualistic to pathogenic, causing several physiological phenotypes, including death. Infection with microsporidia often causes a disruption in the normal microbiome, with both increases and decreases of bacterial, fungal, viral, and protozoan species being observed. This impact on the microbiome can occur through upregulation and downregulation of innate immunity as well as morphological changes to tissues that impact interactions with these microbes. Other microbes, particularly bacteria, can inhibit microsporidia and have been exploited to control microsporidia infections. These bacteria can function through regulating immunity, secreting anti-microsporidia compounds, and, in engineered versions, expressing double-stranded RNA targeting microsporidia genes. We end this review by discussing potential future directions to further understand the complex interactions between microsporidia and the other members of the microbiome.

Profile of the gut microbiota of Pacific white shrimp under industrial indoor farming system

The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.

Listeria monocytogenes infection in pregnant macaques alters the maternal gut microbiome†

OBJECTIVES

The bacterium Listeria monocytogenes (Lm) is associated with adverse pregnancy outcomes. Infection occurs through consumption of contaminated food that is disseminated to the maternal-fetal interface. The influence on the gastrointestinal microbiome during Lm infection remains unexplored in pregnancy. The objective of this study was to determine the impact of listeriosis on the gut microbiota of pregnant macaques.

METHODS

A non-human primate model of listeriosis in pregnancy has been previously described. Both pregnant and non-pregnant cynomolgus macaques were inoculated with Lm and bacteremia and fecal shedding were monitored for 14 days. Non-pregnant animal tissues were collected at necropsy to determine bacterial burden, and fecal samples from both pregnant and non-pregnant animals were evaluated by 16S rRNA next-generation sequencing.

RESULTS

Unlike pregnant macaques, non-pregnant macaques did not exhibit bacteremia, fecal shedding, or tissue colonization by Lm. Dispersion of Lm during pregnancy was associated with a significant decrease in alpha diversity of the host gut microbiome, compared to non-pregnant counterparts. The combined effects of pregnancy and listeriosis were associated with a significant loss in microbial richness, although there were increases in some genera and decreases in others.

CONCLUSIONS

Although pregnancy alone is not associated with gut microbiome disruption, we observed dysbiosis with listeriosis during pregnancy. The macaque model may provide an understanding of the roles that pregnancy and the gut microbiota play in the ability of Lm to establish intestinal infection and disseminate throughout the host, thereby contributing to adverse pregnancy outcomes and risk to the developing fetus.

Association of nicotine dependence and gut microbiota: a bidirectional two-sample Mendelian randomization study

Background

Nicotine dependence is a key factor influencing the diversity of gut microbiota, and targeting gut microbiota may become a new approach for the prevention and treatment of nicotine dependence. However, the causal relationship between the two is still unclear. This study aims to investigate the causal relationship between nicotine dependence and gut microbiota.

Methods

A two-sample bidirectional Mendelian randomization (MR) study was conducted using the largest existing gut microbiota and nicotine dependence genome-wide association studies (GWAS). Causal relationships between genetically predicted nicotine dependence and gut microbiota abundance were examined using inverse variance weighted, MR-Egger, weighted median, simple mode, weighted mode, and MR-PRESSO approaches. Cochrane's Q test, MR-Egger intercept test, and leave-one-out analysis were performed as sensitivity analyses to assess the robustness of the results. Multivariable Mendelian randomization analysis was also conducted to eliminate the interference of smoking-related phenotypes. Reverse Mendelian randomization analysis was then performed to determine the causal relationship between genetically predicted gut microbiota abundance and nicotine dependence.

Results

Genetically predicted nicotine dependence had a causal effect on Christensenellaceae (β: -0.52, 95% CI: -0.934-0.106, P = 0.014). The Eubacterium xylanophilum group (OR: 1.106, 95% CI: 1.004-1.218), Lachnoclostridium (OR: 1.118, 95% CI: 1.001-1.249) and Holdemania (OR: 1.08, 95% CI: 1.001-1.167) were risk factors for nicotine dependence. Peptostreptococcaceae (OR: 0.905, 95% CI: 0.837-0.977), Desulfovibrio (OR: 0.014, 95% CI: 0.819-0.977), Dorea (OR: 0.841, 95% CI. 0.731-0.968), Faecalibacterium (OR: 0.831, 95% CI: 0.735-0.939) and Sutterella (OR: 0.838, 95% CI: 0.739-0.951) were protective factor for nicotine dependence. The sensitivity analysis showed consistent results.

Conclusion

The Mendelian randomization study confirmed the causal link between genetically predicted risk of nicotine dependence and genetically predicted abundance of gut microbiota. Gut microbiota may serve as a biomarker and offer insights for addressing nicotine dependence.

Gut microbiota of the small intestine as an antimicrobial barrier against foodborne pathogens: Impact of diet on the survival of S. Typhimurium and L. monocytogenes during in vitro digestion

The human gastrointestinal tract employs an assortment of chemical, enzymatic and immune barriers to impede pathogen colonization. An essential component of these barriers is the gut microbiota, which infers protection against ingested pathogens through its colonization resistance mechanisms. Specifically, the gut microbiota of the distal small intestine (ileum) renders a crucial line of defense, given that this location is regarded as an important interaction site. This study aimed to evaluate the impact of the ileal microbiota on the survival of the foodborne pathogens Salmonella enterica serotype Typhimurium and Listeria monocytogenes, utilizing an in vitro digestion model system. Moreover, the effect of diet on the gut microbiota colonization resistance mechanisms was assessed, by comparing a healthy (high fiber/low sugar) and a western diet (low fiber/high sugar). For S. Typhimurium, the results revealed that the digestion of a healthy diet led to a similar inactivation compared to the western diet, with the values of total log reduction being 0.83 and 0.82 log(CFU), respectively; yet the lack of readily accessible nutrients in the healthy diet combined with the acidic shock during gastric digestion caused the induction of stress tolerance to the pathogen. This resulted in increased pathogen survival in the presence of gut microbiota, with S. Typhimurium proliferating during the ileal phase with a maximum specific growth rate of 0.16 1/h. On the contrary, for L. monocytogenes, the healthy diet was associated with a greater inactivation than the western diet (total log reduction values: 3.08 and 1.30 log(CFU), respectively), which appeared strongly influenced by the encounter of the pathogen with the gut microbiota. Regarding the latter, the species Escherichia coli and Bacteroides thetaiotaomicron appeared to be the most prevalent in most cases. Finally, it was also demonstrated that the ileal microbiota colonization resistance mechanisms largely relied on competitive responses. The obtained knowledge of this research can contribute to the development and/or complementation of defensive strategies against pathogen infection, while also underlining the value of in vitro approaches.

Nonrestrictive diet does not increase infections during post-HSCT neutropenia: data from a multicenter randomized trial

Infections are a major cause of morbidity and mortality during neutropenia after hematopoietic stem cell transplantation (HSCT). The use of a low-microbial protective diet (PD) in the peritransplantation period is a standard of care, although its efficacy has never been tested prospectively. We conducted a multicenter, randomized, noninferiority trial, enrolling all consecutive adult patients undergoing high-dose induction chemotherapy or HSCT with the objective to compare nonrestrictive diet (NRD) vs PD. Overall, 222 patients were enrolled, randomly assigned, and analyzed. One hundred seventy-five subjects (79%) received autologous HSCT (auto-HSCT), 41 (18%) received allogeneic HSCT (allo-HSCT), and 6 (3%) patients received high-dose induction chemotherapy. There was no significant difference in terms of incidence of grade ≥2 infections and death during neutropenia in the 2 arms. In multivariable analysis, only multiple myeloma diagnosis, fluoroquinolone prophylaxis, and the absence of mucositis were associated with a lower incidence of grade ≥2 infections. We did not report any significant variation in terms of hospitalization length, incidence of mucositis and gastrointestinal infections, body weight, and serum albumin variations in the 2 arms. In allo-HSCT recipients, the incidence of acute graft-versus-host disease grade ≥3 was similar. NRD was associated with higher patient-reported satisfaction. In conclusion, NRD is not inferior to a traditional PD during neutropenia after HSCT, and our results demonstrated that implementing a restrictive diet unnecessary burdens patients' quality of life. The clinical trial was registered prospectively in the clinical trial registry of the Istituto Nazionale dei Tumori of Milan as INT54/16.

The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health

Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.

Diet- and salinity-induced modifications of the gut microbiota are associated with differential physiological responses to ranavirus infection in Rana sylvatica

Greater knowledge of how host-microbiome interactions vary with anthropogenic environmental change and influence pathogenic infections is needed to better understand stress-mediated disease outcomes. We investigated how increasing salinization in freshwaters (e.g. due to road de-icing salt runoff) and associated increases in growth of nutritional algae influenced gut bacterial assembly, host physiology and responses to ranavirus exposure in larval wood frogs (Rana sylvatica). Elevating salinity and supplementing a basic larval diet with algae increased larval growth and also increased ranavirus loads. However, larvae given algae did not exhibit elevated kidney corticosterone levels, accelerated development or weight loss post-infection, whereas larvae fed a basic diet did. Thus, algal supplementation reversed a potentially maladaptive stress response to infection observed in prior studies in this system. Algae supplementation also reduced gut bacterial diversity. Notably, we observed higher relative abundances of Firmicutes in treatments with algae-a pattern consistent with increased growth and fat deposition in mammals-that may contribute to the diminished stress responses to infection via regulation of host metabolism and endocrine function. Our study informs mechanistic hypotheses about the role of microbiome mediation of host responses to infection that can be tested in future experiments in this host-pathogen system. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.

Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract†

The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host-microbe or microbe-microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.

The gut dysbiosis-cancer axis: illuminating novel insights and implications for clinical practice

The human intestinal microbiota, also known as the gut microbiota, comprises more than 100 trillion organisms, mainly bacteria. This number exceeds the host body cells by a factor of ten. The gastrointestinal tract, which houses 60%-80% of the host's immune cells, is one of the largest immune organs. It maintains systemic immune homeostasis in the face of constant bacterial challenges. The gut microbiota has evolved with the host, and its symbiotic state with the host's gut epithelium is a testament to this co-evolution. However, certain microbial subpopulations may expand during pathological interventions, disrupting the delicate species-level microbial equilibrium and triggering inflammation and tumorigenesis. This review highlights the impact of gut microbiota dysbiosis on the development and progression of certain types of cancers and discusses the potential for developing new therapeutic strategies against cancer by manipulating the gut microbiota. By interacting with the host microbiota, we may be able to enhance the effectiveness of anticancer therapies and open new avenues for improving patient outcomes.

Gut-on-a-Chip Models: Current and Future Perspectives for Host-Microbial Interactions Research

The intestine contains the largest microbial community in the human body, the gut microbiome. Increasing evidence suggests that it plays a crucial role in maintaining overall health. However, while many studies have found a correlation between certain diseases and changes in the microbiome, the impact of different microbial compositions on the gut and the mechanisms by which they contribute to disease are not well understood. Traditional pre-clinical models, such as cell culture or animal models, are limited in their ability to mimic the complexity of human physiology. New mechanistic models, such as organ-on-a-chip, are being developed to address this issue. These models provide a more accurate representation of human physiology and could help bridge the gap between clinical and pre-clinical studies. Gut-on-chip models allow researchers to better understand the underlying mechanisms of disease and the effect of different microbial compositions on the gut. They can help to move the field from correlation to causation and accelerate the development of new treatments for diseases associated with changes in the gut microbiome. This review will discuss current and future perspectives of gut-on-chip models to study host-microbial interactions.

Multifunctional hydrogels based on chitosan, hyaluronic acid and other biological macromolecules for the treatment of inflammatory bowel disease: A review

Hydrogel is a three-dimensional network polymer material rich in water. It is widely used in the biomedical field because of its unique physical and chemical properties and good biocompatibility. In recent years, the incidence of inflammatory bowel disease (IBD) has gradually increased, and the disadvantages caused by traditional drug treatment of IBD have emerged. Therefore, there is an urgent need for new treatments to alleviate IBD. Hydrogel has become a potential therapeutic platform. However, there is a lack of comprehensive review of functional hydrogels for IBD treatment. This paper first summarizes the pathological changes in IBD sites. Then, the action mechanisms of hydrogels prepared from chitosan, sodium alginate, hyaluronic acid, functionalized polyethylene glycol, cellulose, pectin, and γ-polyglutamic acid on IBD were described from aspects of drug delivery, peptide and protein delivery, biologic therapies, loading probiotics, etc. In addition, the advanced functions of IBD treatment hydrogels were summarized, with emphasis on adhesion, synergistic therapy, pH sensitivity, particle size, and temperature sensitivity. Finally, the future development direction of IBD treatment hydrogels has been prospected.

Stably transmitted defined microbial community in honeybees preserves Hafnia alvei inhibition by regulating the immune system

The gut microbiota of honeybees is highly diverse at the strain level and essential to the proper function and development of the host. Interactions between the host and its gut microbiota, such as specific microbes regulating the innate immune system, protect the host against pathogen infections. However, little is known about the capacity of these strains deposited in one colony to inhibit pathogens. In this study, we assembled a defined microbial community based on phylogeny analysis, the 'Core-20' community, consisting of 20 strains isolated from the honeybee intestine. The Core-20 community could trigger the upregulation of immune gene expressions and reduce Hafnia alvei prevalence, indicating immune priming underlies the microbial protective effect. Functions related to carbohydrate utilization and the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS systems) are represented in genomic analysis of the defined community, which might be involved in manipulating immune responses. Additionally, we found that the defined Core-20 community is able to colonize the honeybee gut stably through passages. In conclusion, our findings highlight that the synthetic gut microbiota could offer protection by regulating the host immune system, suggesting that the strain collection can yield insights into host-microbiota interactions and provide solutions to protect honeybees from pathogen infections.

Pigs' intestinal barrier function is more refined with aging

The high mortality upon enteric virus infection in piglets causes huge economic losses. To control these infections, potential causes for this high susceptibility for enteric virus infections in younger piglets were analyzed by comparing the intestinal barrier between 1-week, 2-week and 4-week-old piglets. In this study, histological staining was used to analyze morphological differences in intestinal villi, real-time qPCR was performed to assess mRNA expression levels of genes that were related to viral infection and differentiation of immune cells, and flow cytometry was utilized to measure the frequencies of T cells. According to the results obtained, 1-week-old piglets have intestinal villi with shallower crypts, less well developed epithelial cells and a more immature immune system compared to older pigs. Moreover, high amounts of enteric virus invasion-assisting proteins but low amounts of resistant proteins in 1-week piglets could also be a reason for the high susceptibility of 1-week-old piglets.

Role of short chain fatty acids in gut health and possible therapeutic approaches in inflammatory bowel diseases

Inflammatory bowel diseases (IBDs) are characterized by inflammation in the gastrointestinal tract and include Ulcerative Colitis and Crohn’s Disease. These diseases are costly to health services, substantially reduce patients’ quality of life, and can lead to complications such as cancer and even death. Symptoms include abdominal pain, stool bleeding, diarrhea, and weight loss. The treatment of these diseases is symptomatic, seeking disease remission. The intestine is colonized by several microorganisms, such as fungi, viruses, and bacteria, which constitute the intestinal microbiota (IM). IM bacteria promotes dietary fibers fermentation and produces short-chain fatty acids (SCFAs) that exert several beneficial effects on intestinal health. SCFAs can bind to G protein-coupled receptors, such as GPR41 and GPR43, promoting improvements in the intestinal barrier, anti-inflammatory, and antioxidant effects. Thus, SCFAs could be a therapeutic tool for IBDs. However, the mechanisms involved in these beneficial effects of SCFAs remain poorly understood. Therefore, this paper aims to provide a review addressing the main aspects of IBDs, and a more detailed sight of SCFAs, focusing on the main effects on different aspects of the intestine with an emphasis on IBDs.

Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis

Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.

Effect of Dietary Zinc Methionine Supplementation on Growth Performance, Immune Function and Intestinal Health of Cherry Valley Ducks Challenged With Avian Pathogenic Escherichia coli

This study was carried out to evaluate the effects of supplemental zinc methionine (Zn-Met) on growth performance, immune function, and intestinal health of meat ducks challenged with avian pathogenic Escherichia coli (APEC). A total of 480 1-day-old Cherry Valley male ducks were randomly assigned to 8 treatments with 10 replicates, each replicate containing 10 ducks. A 4 × 2 factor design was used with four dietary zinc levels (0, 30, 60, 120 mg Zn/kg in the form Zn-Met was added to the corn-soybean basal diet) and challenged with or without APEC at 8-days-old ducks. The trial lasted for 14 days. The results showed that a dietary Zn-Met supplementation significantly increased body weight (BW) of 14 days and BW gain, and decreased mortality during 7-14-days-old ducks (p < 0.05). Furthermore, dietary 30, 60, 120 mg/kg Zn-Met supplementation noticeably increased the thymus index at 2 days post-infection (2 DPI) and 8 DPI (p < 0.05), and 120 mg/kg Zn-Met enhanced the serum IgA at 2 DPI and IgA, IgG, IgM, C3 at 8 DPI (p < 0.05). In addition, dietary 120 mg/kg Zn-Met supplementation dramatically increased villus height and villus height/crypt depth (V/C) of jejunum at 2 DPI and 8 DPI (p < 0.05). The TNF-α and IFN-γ mRNA expression were downregulated after supplemented with 120 mg/kg Zn-Met in jejunum at 8 DPI (p < 0.05). Moreover, dietary 120 mg/kg Zn-Met supplementation stimulated ZO-3, OCLN mRNA expression at 2 DPI and ZO-2 mRNA expression in jejunum at 8 DPI (p < 0.05), and improved the MUC2 concentration in jejunum at 2 DPI and 8 DPI (p < 0.05). At the same time, the cecal Bifidobacterium and Lactobacillus counts were increased (p < 0.05), and Escherichia coli counts were decreased (p < 0.05) after supplemented with Zn-Met. In conclusion, inclusion of 120 mg/kg Zn-Met minimizes the adverse effects of APEC challenge on meat ducks by improving growth performance and enhancing immune function and intestinal health.

Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection by Vibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium, Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected with V. cholerae when compared to stool from uninfected persons. However, if and how P. aminovorans interacts with V. cholerae has not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors of V. cholerae to affect the disease outcome is unclear. Here, we show that P. aminovorans and V. cholerae together form dual-species biofilm structure at the air–liquid interface, with previously uncharacterized novel features. Importantly, the presence of P. aminovorans within the murine small intestine enhances V. cholerae colonization in the same niche that is dependent on the Vibrio exopolysaccharide and other major components of mature V. cholerae biofilm. These studies illustrate that multispecies biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections.

Specific Strains of Honeybee Gut Lactobacillus Stimulate Host Immune System to Protect against Pathogenic Hafnia alvei

Honeybee gut microbiota plays an important role in host physiology and metabolism. Recent studies have shown that the influence of the resident microorganisms in the regulation of honeybee immune system is profound, which protects against the pathogen Serratia marcescens. However, only few of the core gut members in the regulation of immune functions have been studied. Here, we explored how different bee gut bacterial species aided in the clearance of the pathogenic Hafnia alvei, which causes bee septicemia with a high mortality rate. We found that both Gilliamella apicola W8136 and Lactobacillus apis W8172 protect honeybees from the opportunistic pathogen, while two other strains from Gilliamella and Lactobacillus did not affect the invasion of H. alvei. Transcriptomic analysis revealed that gut species induced different expression profiles in the gut. Specifically, two regulator genes from the Toll pathway, PGRP-S3 recognizing Gram-positive and Spätzle that bind to the Toll protein for the downstream signal transduction, were elevated by L. apis. Correspondingly, multiple genes encoding antibacterial proteins were also stimulated by L. apis. Interestingly, we found an increased expression of apidaecin, which also exhibited a high in vitro inhibitory effect on H. alvei. To elucidate the difference of strains in the host’s immune regulation, comparative genomic analyses indicate that the S-layer proteins unique to L. apis are potentially involved in honeybee Toll signaling and the activation of antibacterial protein production.

IMPORTANCE Honeybees are essential pollinators supporting global agricultural economies and food supplies. Recent honeybee decline has been linked to several factors, while pathogen infection is considered one of the most significant contributing factors. Although a limited number of bacterial pathogens have been identified, Hafnia alvei is one of the pathogens causing septicemia in adult bees. In this study, we showed that two bee gut members, Gilliamella and Lactobacillus, can clear H. alvei from invasion. Mono-colonization of specific strains can stimulate the host Toll signaling pathway and the downstream expression of AMPs. Specifically, apidaecin upregulated by the gut symbionts is more effective against the pathogen. Moreover, our genomic analysis suggests that the surface-layer proteins specific to Lactobacillus strains are an important driver of Toll signaling, highlighting the variation of bee gut strains in regulating the host immune system.

Microbial biogeography of the wombat gastrointestinal tract

Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region-the putative site of primary plant fermentation in wombats-are distinct from the distal colon, and that faecal samples may have limitations in capturing the diversity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.

Clinical Decision Support Systems to Reduce Unnecessary Clostridoides difficile Testing Across Multiple Hospitals

BACKGROUND

Inappropriate C. difficile testing has adverse consequences for the patient, hospital, and public health. Computerized Clinical Decision Supports (CCDS) in the Electronic Health Record (EHR) may reduce C. difficile test ordering; however, effectiveness of different approaches, ease of use, and best fit into the healthcare providers' (HCP) workflow, are not well understood.

METHODS

Nine academic and 6 community U.S. hospitals participated in this 2-year cohort study. CCDS (hard- or soft-stop) triggered when duplicate C. difficile test order attempted, or if laxatives were recently received. The primary outcome was the difference in testing rates pre- and post-CCDS interventions, using incident rate ratios (IRR) and mixed effect Poisson regression models. We performed qualitative evaluation (contextual inquiry, interviews, focus groups) based on a human factors model. We identified themes using a codebook with primary- and sub-nodes.

RESULTS

In 9 hospitals implementing hard-stop CCDS and 4 hospitals implementing soft-stop CCDS, C. difficile testing IRR reduction was 33% (95% CI, 30-36%), and 23% (95% CI 21-25%), respectively. Two hospitals implemented a non-EMR based human intervention with IRR reduction of 21% (95% CI 15-28%). HCPs reported generally favorable experiences, and highlighted time efficiencies such as inclusion of the patients most recent laxative administration on the CCDS. Organizational factors including hierarchical cultures, and communication between HCPs caring for the same patient, impact CCDS acceptance and integration.

CONCLUSIONS

CCDS reduced unnecessary C. difficile testing and were perceived positively by HCPs when integrated into their workflow, and when displayed relevant patient specific information needed for decision-making.

Diet leaves a genetic signature in a keystone member of the gut microbiota

Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet causes microbiota imbalances that underlay many pathological conditions (i.e., dysbiosis). Although the effects of dietary changes on microbiota composition and functions are well documented, their impact in gut bacterial evolution remains unexplored. We followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly in the gut and Western-style diet selected for mutations that promote degradation of mucin-derived glycans. Periodic dietary changes caused fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intraspecies genetic diversity compared to constant dietary regimens. These results show that dietary changes leave a genetic signature in microbiome members and suggest that B. thetaiotaomicron genetic diversity could be a biomarker for dietary differences among individuals.

Bacterial biofilm thickness and fungal-inhibitory bacterial richness both prevent establishment of the amphibian fungal pathogen, Batrachochytrium dendrobatidis

Host-associated microbial biofilms can provide protection against pathogen establishment. In many host-microbe symbioses (including, but not limited to: humans, plants, insects, and amphibians), there is a correlation between host-associated microbial diversity and pathogen infection risk. Diversity may prevent infection by pathogens through sampling effects and niche complementarity- but an alternative hypothesis may be that microbial biomass is confounded with diversity, and that host-associated biofilms are deterring pathogen establishment through space pre-emption. In this study, we use the amphibian system as a model for host-microbe-pathogen interactions to ask two questions: (1) is bacterial richness confounded with biofilm thickness or cell density, and (2) to what extent does biofilm thickness, cell density, and bacterial richness each deter the establishment of the amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd)? To answer these questions, we built a custom biofilm microcosm that mimics the host-environment interface by allowing nutrients to diffuse out of a fine-pore biofilm scaffolding. This created a competitive environment in which bacteria and the fungal pathogen compete for colonization space. We then challenged bacterial biofilms ranging in community richness, biofilm thickness, bacterial cell density, and Bd-inhibitory metabolite production with live Bd zoospores to determine how Bd establishment success on membranes vary. We found that biofilm thickness and Bd-inhibitory isolate richness work in complement to reduce Bd establishment success. This work underscores that physical aspects of biofilm communities can play a large role in pathogen inhibition and in many studies, these traits are not studied. IMPORTANCE Our finding highlights the fact that diversity, as measured through 16S rDNA sequencing, may obscure the true mechanisms behind microbe-mediated pathogen defence, and that physical space occupation by biofilm-forming symbionts may significantly contribute to pathogen protection. These findings have implications across a wide range of host-microbe systems, since 16S rDNA sequencing is a standard tool used across many microbial systems. Further, our results are potentially relevant to many host-pathogen systems, since host-associated bacterial biofilms are ubiquitous.

The crosstalk between gut microbiota, intestinal immunological niche and visceral adipose tissue as a new model for the pathogenesis of metabolic and inflammatory diseases: the paradigm of type 2 diabetes mellitus

Gut microbiota (GM) comprises more than one thousand microorganisms between bacterial species, viruses, fungi, and protozoa, and represents the main actor of a wide net of molecular interactions, involving, among others, the endocrine system, immune responses, and metabolism. GM influences many endocrine functions such as adrenal steroidogenesis, thyroid function, sexual hormones, IGF-1 pathway and peptides produced in gastrointestinal system. It is fundamental in glycaemic control and obesity, while also exerting an important function in modulating the immune system and associated inflammatory disease. The result of this crosstalk in gut mucosa is the formation of the intestinal immunological niche. Visceral adipose tissue (VAT) produces about 600 different peptides, it is involved in lipid and glucose metabolism and in some immune reactions through several adipokines. GM and VAT interact in a bidirectional fashion: while gut dysbiosis can modify VAT adipokines and hormone secretion, VAT hyperplasia modifies GM composition. Acquired or genetic factors leading to gut dysbiosis or increasing VAT (i.e., Western diet) induce a proinflammatory condition, which plays a pivotal role in the development of dysmetabolic and immunologic conditions, such as diabetes mellitus. Diabetes is clearly associated with specific patterns of GM alterations, with an abundance or reduction of GM species involved in controlling mucosal barrier status, glycaemic levels and exerting a pro- or anti-inflammatory activity. All these factors could explain the higher incidence of several inflammatory conditions in Western countries; furthermore, besides the specific alterations observed in diabetes, this paradigm could represent a common pathway acting in many metabolic conditions and could pave the way to a new, interesting therapeutic approach.

Effects of Lactobacillus pentosus combined with Arthrospira platensis on the growth performance, immune response, and intestinal microbiota of Litopenaeus vannamei

Litopenaeus vannamei is one of the most productive shrimp species in the world. However, shrimp farming is suffering from adverse environmental conditions and disease outbreaks. Typically, Lactobacillus pentosus and Arthrospira platensis are used as substitutes for some antibiotics. In the present study, we assessed the effects of dietary supplements along with living bacteria or cell-free extracts of L. pentosus combined with A. platensis on the growth performance, immune response, intestinal microbiota, and disease resistance of L. vannamei against Vibrio alginolyticus. Shrimp fed L. pentosus live bacteria combined with A. platensis showed the best growth performance and lowest feed conversion rate. The supplementation diet with L. pentosus live bacteria and A. platensis could significantly enhance the trypsin activity in shrimp after the feeding trial. Given the lowest feed conversion rate in shrimp fed L. pentosus live bacteria combined with A. platensis, we reasonably speculated that the decrease in feed conversion rate may be related to the increase in trypsin activity. In addition, dietary cell-free extracts of L. pentosus combined with A. platensis enhanced the expression of immune-related genes after the feeding trial or challenge test. Moreover, results of the bacterial challenge test indicated that the shrimp fed cell-free extracts of L. pentosus combined with A. platensis diet resulted in the highest survival rate, which suggested that cell-free extracts of L. pentosus and A. platensis could improve the disease resistance against V. alginolyticus by up-regulating the expressions of immune-related genes. Dietary L.pentosus or A. platensis, or their combination, reduced the abundance of harmful bacteria, including Proteobacteria in shrimp intestine, which suggested that L. pentosus and A. platensis could improve the growth performance and health of shrimp by regulating the structure of the intestinal microbiota. The findings of this study demonstrated that L. pentosus live bacteria and A. platensis exerted synergistic effects on the growth performance and digestion in shrimp, while cell-free extracts of L. pentosus and A. platensis showed synergistic effects on the immune response and disease resistance of shrimp against V. alginolyticus.

Probiotics and gut microbiota: mechanistic insights into gut immune homeostasis through TLR pathway regulation

Consumption of probiotics as a useful functional food improves the host's wellbeing, and, when paired with prebiotics (indigestible dietary fibre/carbohydrate), often benefits the host through anaerobic fermentation.

Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice

AIMS

The composition, overtly abundance, and diversity of gut microbiota, play a significant role in maintaining physiological homeostasis with age. Reports revealed that the gut microbial profile might be correlated with immunity and metabolism. It is, therefore, tantamount to know if an older individual can achieve the immunity and metabolic profile of a younger individual by receiving the gut microbiome of a younger individual. In the current report, we have studied the effects of cecal microbiota transplantation (CMT) from younger to older mice.

MATERIALS AND METHODS

In this study, older BALB/c mice (23 weeks) received CMT from younger BALB/c mice (3 weeks).

KEY FINDINGS

CMT recipient mice showed altered expressions of immune and tight junction protein genes in the colon of mice, while the non-CMT recipient mice did not. Older mice were treated with AVNM to make them compatible with CMT. Further data from metabolite studies revealed that AVNM treatment mainly affected the aromatic amino acid biosynthesis pathway while CMT mostly affected the metabolism of different carbohydrates. We repeated the analysis in C57BL/6 mice without any significant effects of CMT.

SIGNIFICANCE

Results revealed that mice who received CMT showed more efficient restoration of gut microbiota than non-CMT recipient mice. CMT caused the alleviation of Salmonella infection and efficient recovery of the cecal index in the mice following antibiotics treatment.

Host Factors in Dysregulation of the Gut Barrier Function during Alcohol-Associated Liver Disease

Chronic alcohol consumption and alcohol-associated liver disease (ALD) represent a major public health problem worldwide. Only a minority of patients with an alcohol-use disorder (AUD) develop severe forms of liver disease (e.g., steatohepatitis and fibrosis) and finally progress to the more advanced stages of ALD, such as severe alcohol-associated hepatitis and decompensated cirrhosis. Emerging evidence suggests that gut barrier dysfunction is multifactorial, implicating microbiota changes, alterations in the intestinal epithelium, and immune dysfunction. This failing gut barrier ultimately allows microbial antigens, microbes, and metabolites to translocate to the liver and into systemic circulation. Subsequent activation of immune and inflammatory responses contributes to liver disease progression. Here we review the literature about the disturbance of the different host defense mechanisms linked to gut barrier dysfunction, increased microbial translocation, and impairment of liver and systemic inflammatory responses in the different stages of ALD.

The impact of the host intestinal microbiome on carcinogenesis and the response to chemotherapy

The microbiome consists of all microbes present on and within the human body. An unbalanced, or 'dysbiotic' intestinal microbiome is associated with inflammatory bowel disease, diabetes and some cancer types. Drug treatment can alter the intestinal microbiome composition. Additionally, some chemotherapeutics interact with microbiome components, leading to changes in drug safety and/or efficacy. The intestinal microbiome is a modifiable target, using strategies such as antibiotic treatment, fecal microbial transplantation or probiotic administration. Understanding the impact of the microbiome on the safety and efficacy of cancer treatment may result in improved treatment outcome. The present review seeks to summarize relevant research and look to the future of cancer treatment, where the intestinal microbiome is recognized as an actionable treatment target.

Vancomycin-Induced Changes in Host Immunity and Behavior: Comparative Genomic and Metagenomic Analysis in C57BL/6 and BALB/c Mice

BACKGROUND

The consequence of treatment with antibiotics on the gut microbiota can be destructive. The antibiotics, however, can be utilized to understand the role of gut microbiota on the host physiology.

AIM

Earlier, we reported the efficacy of vancomycin in gut microbiota perturbation. We continued to understand the effect of restoration kinetics of perturbed gut microbiota on the immunity and behavior of Th1 (C57BL/6)- and Th2 (BALB/c)-biased mice.

METHODS

We studied restoration kinetics of the gut microbiota for two months following the withdrawal of vancomycin treatment in both mice strains. We analyzed cecal microbiome composition, different behavioral assays, and expression of select genes associated with stress and barrier function in gut and brain.

RESULTS

Metagenomic analysis of gut microbiota revealed that the treatment with vancomycin caused a significant decrease in the relative abundance of Firmicutes and Bacteroidetes phyla with a time-dependent increase in Proteobacteria and Verrucomicrobia phyla. Maximum restoration (> 70%) of gut microbiota happened by the 15th day of withdrawal of vancomycin. BALB/c mice showed a more efficient restoration of gut microbiota compared to C57BL/6 mice. We established the correlation patterns of gut microbiota alteration and its effect on (a) the behavior of mice, (b) expression of key brain molecules, and (c) immunity-related genes.

CONCLUSIONS

The results revealed that the gut microbiome profiling, behavior, and immune responses varied significantly between Th1- and Th2-biased mice. By withdrawing the treatment with vancomycin of major gut microbes, important physiological and behavioral changes of both mice strains returned to the normal (untreated control) level.

The Role of Glucocorticoids in Inflammatory Diseases

For more than 70 years, glucocorticoids (GCs) have been a powerful and affordable treatment option for inflammatory diseases. However, their benefits do not come without a cost, since GCs also cause side effects. Therefore, strong efforts are being made to improve their therapeutic index. In this review, we illustrate the mechanisms and target cells of GCs in the pathogenesis and treatment of some of the most frequent inflammatory disorders affecting the central nervous system, the gastrointestinal tract, the lung, and the joints, as well as graft-versus-host disease, which often develops after hematopoietic stem cell transplantation. In addition, an overview is provided of novel approaches aimed at improving GC therapy based on chemical modifications or GC delivery using nanoformulations. GCs remain a topic of highly active scientific research despite being one of the oldest class of drugs in medical use.

Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices

Culture-independent approaches now represent the gold standard for the investigation of both environmental and host-associated complex microbial communities. Nevertheless, despite the great advantages offered by these novel methodologies based on the use of next-generation DNA sequencing approaches, a number of bias sources have been identified. Among the latter, free DNA contained in biological matrices is one of the main sources of inaccuracy in reconstructing the resident microbial population of viable cells. For this reason, the photoreactive DNA-binding dye propidium monoazide (PMAxx^™) has been developed by improving standard PMA. This compound binds and inactivates free DNA, thus preventing its amplification and sequencing. While the performances of PMA have been previously investigated, the efficiency with PMAxx^™ has been tested mainly for amplicon-based profiling approaches on a limited number of biological matrices. In this study, we validated the performance of PMAxx^™ for shotgun metagenomics approaches employing various human-associated matrices. Notably, results revealed that the effectiveness of PMAxx^™ in inactivating free DNA of prokaryotes and eukaryotes tends to vary significantly based on the biological matrices analyzed.

In-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products

Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to Lacticaseibacillus&nbsp;paracasei strains NSMJ15 and NFFJ04, Lentilactobacillus parabuchneri NSMJ16, Levilactobacillus&nbsp;brevis NSMJ23, and Schleiferilactobacillus harbinensis NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (v/v) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of Bacillus, Escherichia, Leclercia, Morganella, and Vagococcus were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.

Symbiosis and Dysbiosis of the Human Mycobiome

The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.

The gut microbiome: what the oncologist ought to know

The gut microbiome (GM) has been implicated in a vast number of human pathologies and has become a focus of oncology research over the past 5 years. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation and protection against pathogens. Strong evidence is emerging to support the effects of the GM on the development of some malignancies but also on responses to cancer therapies, most notably, immune checkpoint inhibition. Tools for manipulating the GM including dietary modification, probiotics and faecal microbiota transfer (FMT) are in development. Current understandings of the many complex interrelationships between the GM, cancer, the immune system, nutrition and medication are ultimately based on a combination of short-term clinical trials and observational studies, paired with an ever-evolving understanding of cancer biology. The next generation of personalised cancer therapies focusses on molecular and phenotypic heterogeneity, tumour evolution and immune status; it is distinctly possible that the GM will become an increasingly central focus amongst them. The aim of this review is to provide clinicians with an overview of microbiome science and our current understanding of the role the GM plays in cancer.

Nanoplastics Induce More Serious Microbiota Dysbiosis and Inflammation in the Gut of Adult Zebrafish than Microplastics

Microplastics (MPs) (< 5 mm) and nanoplastics (NPs) (< 100 nm) are emerging environmental pollutants and have been proved could cause a series of toxicity in aquatic organisms. In this study, the effects on gut microbiota of adult zebrafish exposed for 21 days to 10 μg/L and 1 mg/L of MPs (8 μm) and NPs (80 nm) were evaluated. We analyzed the intestinal microbial community of zebrafish using high throughput sequencing of the 16S rRNA gene V3-V4 region and also performed transcriptional profiling of the inflammation pathway related genes in the intestinal tissues. Our results showed that both spherical polystyrene MPs and NPs could induce microbiota dysbiosis in the gut of zebrafish. The flora diversity of gut microbiota significantly increased under a high concentration of NPs. At the phylum level, the abundance of Proteobacteria increased significantly and the abundance of Fusobacteria, Firmicutes and Verrucomicrobiota decreased significantly in the gut after 21-day exposure to 1 mg/L of both MPs and NPs. Furthermore, interestingly, the abundance of Actinobacteria decreased in the MPs treatment groups but increased in the NPs treatment groups. At the genus level, revealed that the relative abundance of Aeromonas significantly increased both in the MPs and NPs treatment groups. Moreover, it was observed that NPs increased mRNA levels of il8, il10, il1β and tnfα in the gut, but not in MPs exposure group, indicating that the NPs may have a more serious effect on the gut of zebrafish than MPs to induce microbiota dysbiosis and inflammation in the gut.

Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird

Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.

Microbiota and epigenetics: promising therapeutic approaches?

The direct/indirect responsibility of the gut microbiome in disease induction in and outside the digestive tract is well studied. These results are usually from the overpopulation of certain species on the cost of others, interaction with beneficial microflora, interference with normal epigenetic control mechanisms, or suppression of the immune system. Consequently, it is theoretically possible to cure such disorders by rebalancing the microbiome inside our bodies. This can be achieved by changing the lifestyle pattern and diet or by supplementation with beneficial bacteria or their metabolites. Various approaches have been explored to manipulate the normal microbial inhabitants, including nutraceutical, supplementations with prebiotics, probiotics, postbiotics, synbiotics, and antibiotics, or through microbiome transplantation (fecal, skin, or vaginal microbiome transplantation). In the present review, the interaction between the microbiome and epigenetics and their role in disease induction is discussed. Possible future therapeutic approaches via the reestablishment of equilibrium in our internal micro-ecosystem are also highlighted.

Therapeutic Applications of Resveratrol in Hepatic Encephalopathy through Its Regulation of the Microbiota, Brain Edema, and Inflammation

Hepatic encephalopathy is a common complication in patients with liver cirrhosis and portosystemic shunting. Patients with hepatic encephalopathy present a variety of clinical features, including neuropsychiatric manifestations, cognitive dysfunction, impaired gut barrier function, hyperammonemia, and chronic neuroinflammation. These pathogeneses have been linked to various factors, including ammonia-induced oxidative stress, neuronal cell death, alterations in the gut microbiome, astrocyte swelling, and blood-brain barrier disruptions. Many researchers have focused on identifying novel therapeutics and prebiotics in the hope of improving the treatment of these conditions. Resveratrol is a natural polyphenic compound and is known to exert several pharmacological effects, including antioxidant, anti-inflammatory, and neuroprotective activities. Recent studies suggest that resveratrol contributes to improving the neuropathogenic effects of liver failure. Here, we review the current evidence describing resveratrol's effects in neuropathogenesis and its impact on the gut-liver axis relating to hepatic encephalopathy. We highlight the hypothesis that resveratrol exerts diverse effects in hepatic encephalopathy and suggest that these effects are likely mediated by changes to the gut microbiota, brain edema, and neuroinflammation.

Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d'Ivoire

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.

Intestinal response characteristic and potential microbial dysbiosis in digestive tract of Bufo gargarizans after exposure to cadmium and lead, alone or combined

The gastrointestinal tract is the largest immune organ in the body and meanwhile, accommodates a large number of microorganisms. Heavy metals could disturb the intestinal homeostasis and change the gut microbial composition. However, the information regarding the links between dysbiosis of gut microbiota and imbalance of host intestinal homeostasis induced by the mixture of heavy metals is insufficient. The present study investigates the effects of Cd/Pb, both single and combination exposure, on the growth performance, intestinal histology, digestive enzymes activity, oxidative stress and immune parameters, and intestinal microbiota in Bufo gargarizans tadpoles. Our results revealed that co-exposure of Cd-Pb induced more severe impacts not only on the host, but the intestinal microbiota. On the one hand, co-exposure of Cd-Pb significantly induced growth retardation, intestinal histological injury, decreased activities of digestive enzymes. On the other hand, Cd and Pb exposure, especially in mixed form, changed the diversity and richness, structure of microbiota. Also, the intestinal microbial composition was altered by Cd/Pb exposure (alone and combination) both at the different levels. Proteobacteria, act as front-line responder, was significantly increased in tadpoles under the exposure of metals. Finally, the functional prediction revealed that the disorders of metabolism and immune responses of intestinal microbiota was increased in tadpoles exposed to Cd/Pb (especially the mixture of Cd and Pb). Our research complements the understanding of links between changes in host fitness loss and intestinal microbiota and will add a new dimension of knowledge to the ecological risks of mixed heavy metals in amphibian.

Significance of African Diets in Biotherapeutic Modulation of the Gut Microbiome

Diet plays an essential role in human development and growth, contributing to health and well-being. The socio-economic values, cultural perspectives, and dietary formulation in sub-Saharan Africa can influence gut health and disease prevention. The vast microbial ecosystems in the human gut frequently interrelate to maintain a healthy, well-coordinated cellular and humoral immune signalling to prevent metabolic dysfunction, pathogen dominance, and induction of systemic diseases. The diverse indigenous diets could differentially act as biotherapeutics to modulate microbial abundance and population characteristics. Such modulation could prevent stunted growth, malnutrition, induction of bowel diseases, attenuated immune responses, and mortality, particularly among infants. Understanding the associations between specific indigenous African diets and the predictability of the dynamics of gut bacteria genera promises potential biotherapeutics towards improving the prevention, control, and treatment of microbiome-associated diseases such as cancer, inflammatory bowel disease, obesity, type 2 diabetes, and cardiovascular disease. The dietary influence of many African diets (especially grain-base such as millet, maize, brown rice, sorghum, soya, and tapioca) promotes gut lining integrity, immune tolerance towards the microbiota, and its associated immune and inflammatory responses. A fibre-rich diet is a promising biotherapeutic candidate that could effectively modulate inflammatory mediators' expression associated with immune cell migration, lymphoid tissue maturation, and signalling pathways. It could also modulate the stimulation of cytokines and chemokines involved in ensuring balance for long-term microbiome programming. The interplay between host and gut microbial digestion is complex; microbes using and competing for dietary and endogenous proteins are often attributable to variances in the comparative abundances of Enterobacteriaceae taxa. Many auto-inducers could initiate the process of quorum sensing and mammalian epinephrine host cell signalling system. It could also downregulate inflammatory signals with microbiota tumour taxa that could trigger colorectal cancer initiation, metabolic type 2 diabetes, and inflammatory bowel diseases. The exploitation of essential biotherapeutic molecules derived from fibre-rich indigenous diet promises food substances for the downregulation of inflammatory signalling that could be harmful to gut microbiota ecological balance and improved immune response modulation.