Effects Of Gut Bacteria Research Articles

Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts

The effect of gut bacteria on the response to immune checkpoint inhibitors (ICIs) has been studied, but the relationship between fungi and ICI responses is not fully understood. Herein, 862 fecal metagenomes from 9 different cohorts were integrated for the identification of differentially abundant fungi and subsequent construction of random forest (RF) models to predict ICI responses. Fungal markers demonstrate excellent performance, with an average area under the curve (AUC) of 0.87. Their performance improves even further, reaching an average AUC of 0.89 when combined with bacterial markers. Higher enrichment of exhausted Tcells is detected in responders, as predicted by fungal markers. Multi-kingdom network and functional analysis reveal that the fungus Schizosaccharomyces octosporus may ferment starch into short-chain fatty acids in responders. This study provides a fungal profile of the ICI response and the identification of multi-kingdom microbial markers with good performance that may improve the overall applicability of ICI therapy.

Maturation of the medaka immune system depends on reciprocal interactions between the microbiota and the intestinal tract.

The interactions between the host immune system and intestinal microorganisms have been studied in many animals, including fish. However, a detailed analysis has not been performed in medaka, an established fish model for biological studies. Here, we investigated the effect of immunodeficiency on the microbiota composition and the effect of gut bacteria on intestinal epithelial development and immune responses in medaka. Chronological analysis of the intestinal microbiota of interleukin 2 receptor subunit gamma (il2rg) mutant medaka showed a gradual decrease in the evenness of operational taxonomic units, mainly caused by the increased abundance of the Aeromonadaceae family. Exposure of wild-type medaka to high doses of an intestine-derived opportunistic bacterium of the Aeromonadaceae family induced an inflammatory response, suggesting a harmful effect on adult il2rg mutants. In addition, we established germ-free conditions in larval medaka and observed large absorptive vacuoles in intestinal epithelial cells, indicating a block in epithelial maturation. Transcriptome analysis revealed a decrease in the expression of genes involved in the defense response, including the antimicrobial peptide gene hepcidin, whose expression is induced by lipopolysaccharide stimulation in normal larvae. These results show that reciprocal interactions between the microbiome and the intestinal tract are required for the maturation of the medaka immune system.

Antibiotic-induced gut bacteria depletion has no effect on HBV replication in HBV immune tolerance mouse model

Commensal microbiota is closely related to Hepatitis B virus (HBV) infection. Gut bacteria maturation accelerates HBV immune clearance in hydrodynamic injection (HDI) HBV mouse model. However, the effect of gut bacteria on HBV replication in recombinant adeno-associated virus (AAV)-HBV mouse model with immune tolerance remains obscure. We aim to investigate its role on HBV replication in AAV-HBV mouse model. C57BL/6 mice were administrated with broad-spectrum antibiotic mixtures (ABX) to deplete gut bacteria and intravenously injected with AAV-HBV to establish persistent HBV replication. Gut microbiota community was analyzed by fecal qPCR assay and 16S ribosomal RNA (rRNA) gene sequencing. HBV replication markers in blood and liver were determined by ELISA, qPCR assay and Western blot at indicated time points. Immune response in AAV-HBV mouse model was activated through HDI of HBV plasmid or poly(I:C) and then detected by quantifying the percentage of IFN-γ+/CD8+ T cells in the spleen via flow cytometry as well as the splenic IFN-γ mRNA level via qPCR assay. We found that antibiotic exposure remarkably decreased gut bacteria abundance and diversity. Antibiotic treatment failed to alter the levels of serological HBV antigens, intrahepatic HBV RNA transcripts and HBc protein in AAV-HBV mouse model, but contributed to HBsAg increase after breaking of immune tolerance. Overall, our data uncovered that antibiotic-induced gut bacteria depletion has no effect on HBV replication in immune tolerant AAV-HBV mouse model, providing new thoughts for elucidating the correlation between gut bacteria dysbiosis by antibiotic abuse and clinical chronic HBV infection.

Secondary Bile Acids and Tumorigenesis in Colorectal Cancer.

Colorectal cancer (CRC) is one of the most common and deadly cancers in the world and is a typical inflammatory tumor. In recent years, the incidence of CRC has been increasing year by year. There is evidence that the intake of high-fat diet and overweight are associated with the incidence of CRC, among which bile acids play a key role in the pathogenesis of the disease. Studies on the relationship between bile acid metabolism and the occurrence of CRC have gradually become a hot topic, improving the understanding of metabolic factors in the etiology of colorectal cancer. Meanwhile, intestinal flora also plays an important role in the occurrence and development of CRC In this review, the classification of bile acids and their role in promoting the occurrence of CRC are discussed, and we highlights how a high-fat diet affects bile acid metabolism and destroys the integrity of the intestinal barrier and the effects of gut bacteria.

Bioremediation of selenium-contaminated soil using earthworm Eisenia fetida: Effects of gut bacteria in feces on the soil microbiome

Selenium (Se) contamination in the soil poses a food safety risk to humans. The present study was to investigate the role of earthworm Eisenia fetida in soil Se remediation. When exposed to selenite at 4 mg Se/kg, E. fetida efficiently concentrated Se in tissues (24.53 mg Se/kg dry weight), however, only accounting for a minor portion of the added Se. Microbial analysis shows 12 out of 15 functional genera became more abundant in the worm-inhabited soil when exposed to Se, suggesting E. fetida contributed to Se remediation mainly by introducing Se-reducing bacteria to the soil via feces, which were dominated by the genera Pseudomonas (∼62.65%) and Aeromonas (∼29.99%), whose abundance was also significantly boosted in the worm-inhabited soil. However, when isolated from worm feces at 200 mg Se/L, Pseudomonas strains only displayed a high tolerance to Se rather than removal capacity. In contrast, among 4 isolated Aeromonas strains, A. caviae rapidly removing 85.74% of the added selenite, mainly through accumulation (67.38%), while A. hydrophila and A. veronii were more effective at volatilizing Se (27.77% and 24.54%, respectively), and A. media performed best by reducing Se by ∼49.00% under anaerobic conditions. Overall, our findings have highlighted the importance of E. fetida as a key contributor of functional bacteria to the soil microbiome, building a strong foundation for the development of an earthworm-soil system for Se bioremediation.

Effects of gut bacteria and their amyloids on mental health and neurodegeneration in Parkinson’s disease

Effects of gut bacteria and their amyloids on mental health and neurodegeneration in Parkinson’s disease

The role of the gut microbiome in opioid use.

Although the gut and brain are separate organs, they communicate with each other via trillions of intestinal bacteria that collectively make up one's gut microbiome. Findings from both humans and animals support a critical role of gut microbes in regulating brain function, mood, and behavior. Gut bacteria influence neural circuits that are notably affected in addiction-related behaviors. These include circuits involved in stress, reward, and motivation, with substance use influencing gut microbial abnormalities, suggesting significant gut-brain interactions in drug addiction. Given the overwhelming rates of opioid overdose deaths driven by abuse and addiction, it is essential to characterize mechanisms mediating the abuse potential of opioids. We discuss in this review the role of gut microbiota in factors that influence opioid addiction, including incentive salience, reward, tolerance, withdrawal, stress, and compromised executive function. We present clinical and preclinical evidence supporting a bidirectional relationship between gut microbiota and opioid-related behaviors by highlighting the effects of opioid use on gut bacteria, and the effects of gut bacteria on behavioral responses to opioids. Further, we discuss possible mechanisms of this gut-brain communication influencing opioid use. By clarifying the relationship between the gut microbiome and opioid-related behaviors, we improve understanding on mechanisms mediating reward-, motivation-, and stress-related behaviors and disorders, which may contribute to the development of effective, targeted therapeutic interventions in opioid dependence and addiction.

Trimethylamine-N-oxide is present in human follicular fluid and is a negative predictor of embryo quality.

STUDY QUESTIONAre levels of trimethylamine-N-oxide (TMAO) in human follicular fluid (FF) related to IVF outcomes?SUMMARY ANSWERHigher levels of TMAO are a negative predictor of oocyte fertilization and embryo quality.WHAT IS KNOWN ALREADYTMAO is a metabolic product of dietary choline and l-carnitine produced via subsequent enzymatic modifications by the intestinal microbiota and hepatocytes. TMAO promotes inflammatory and oxidative stress pathways and has been characterized as a causative biomarker for the development of cardiometabolic disease.STUDY DESIGN, SIZE, DURATIONFor the present cross-sectional study, samples (FF and plasma) from 431 modified natural cycle (MNC)-IVF cycles of 132 patients were collected prospectively between October 2014 and March 2018 in a single academic medical center.PARTICIPANTS/MATERIALS, SETTING, METHODSTMAO and its precursors (choline, l-carnitine and gamma-butyrobetaine) were measured by ultra-high-performance liquid chromatography/mass spectrometry in (i) matched FF and plasma from 63 MNC-IVF cycles, in order to compare metabolite levels in the two matrices and (ii) FF from 232 MNC-IVF cycles in which only one oocyte was retrieved at follicular puncture. The association between metabolite levels and oocyte fertilization, embryo fragmentation percentage, embryo quality and the occurrence of pregnancy was analyzed using multilevel generalized estimating equations with adjustment for patient and cycle characteristics.MAIN RESULTS AND THE ROLE OF CHANCEThe level of choline was higher in FF as compared to matched plasma (P < 0.001). Conversely, the levels of TMAO and gamma-butyrobetaine were lower in FF as compared to plasma (P = 0.001 and P = 0.075, respectively). For all metabolites, there was a positive correlation between FF and plasma levels. Finally, levels of TMAO and its gut-derived precursor gamma-butyrobetaine were lower in FF from oocytes that underwent normal fertilization (TMAO: odds ratio [OR] 0.66 [0.49–0.90], P = 0.008 per 1.0-μmol/L increase; gamma-butyrobetaine: OR 0.77 [0.60–1.00], P = 0.047 per 0.1-μmol/L increase) and developed into top-quality embryos (TMAO: OR 0.56 [0.42–0.76], P < 0.001 per 1.0-μmol/L increase; gamma-butyrobetaine: OR 0.79 [0.62–1.00], P = 0.050 per 0.1-μmol/L increase) than in FF from oocytes of suboptimal development.LIMITATIONS, REASONS FOR CAUTIONThe individual contributions of diet, gut bacteria and liver to the metabolite pools have not been quantified in this analysis.WIDER IMPLICATIONS OF THE FINDINGSMore research on the contribution of diet and the effect of gut bacteria on FF TMAO is warranted. Since TMAO integrates diet, microbiota and genetic setup of the person, our results indicate potential important clinical implications for its use as biomarker for lifestyle interventions to improve fertility.STUDY FUNDING/COMPETING INTEREST(S)No external funding was received for this project. The Department of Obstetrics and Gynecology of the University Medical Center Groningen received an unrestricted educational grant of Ferring Pharmaceutical BV, the Netherlands. The authors have no other conflicts of interest.TRIAL REGISTRATION NUMBERNetherlands Trial Register number NTR4409.

1751-P: Human Islet Response to Selected Type 1 Diabetes Associated Bacteria

Type 1 diabetes (T1D) is a chronic autoimmune disease that results from destruction of pancreatic β-cells. A role of gut bacteria in T1D has been suggested. However, the nature of that role remains largely unknown. Bacterial blooms are reported to be increased in gut prior to incidence of autoimmunity. One hypothesis is that these bacteria might elicit a response from human islets associated with immune cells recruitment. We have tested this hypothesis using 3 bacteria, namely Bacteroides dorei (BD), Ruminococcus gnavus (RG), both increased before T1D and Escherichia coli (EC), ubiquitous bacteria. Briefly, human islets were exposed to one of these bacteria for 6 and 24h. After that, RNA-Seq analysis was performed. The three bacteria altered expression of a number of genes at 6 and 24h. Additionally, each bacteria displayed a unique set of differentially expressed genes (DEG). Ingenuity pathway analysis of DEG revealed that top activated pathways and diseases included Th17 activation and inflammatory response respectively. A common set of DEG was also noted among different treatments at both 6 and 24h. The commonly upregulated genes were mostly cytokines (42.5%) including members of C-C and C-X-C motif chemokines followed by enzymes (13%) e.g., PTGS2 and SOD2, suggesting a selective effect of gut bacteria on islet immune and biosynthetic pathways. Immunoblotting for NAMPT, SOD2 and TRAF3IP2 revealed similar trends to those observed in RNA-Seq. From the list of tested cytokines, only CXCL8 was significantly increased, with its release being highest in EC. When injected into the pancreas through the bile ducts of normal mice, each bacteria elicited a unique pattern of islet inflammation. However, diabetes doesn’t not result from these injections, indicating other missing factors e.g., genetics or environment. Our data reveal several details about islet response to T1D associated bacteria. Understanding the changes induced by host-microbiome interaction could help for diabetes prevention by their reversal. Disclosure A.M. Abdellatif: None. N.E. Sarvetnick: None. Funding National Institute of Allergy and Infectious Diseases; The Leona M. and Harry B. Helmsley Charitable Trust; JDRF; J.W. Kieckhefer Foundation

Effect of Dietary Supplementation of Bacillus subtilis and Terribacillus saccharophillus on Innate Immune Responses of a Tropical Freshwater Fish, Labeo rohita

Objective: Indiscriminate use of antibiotics to control fish diseases has led to the development and propagation of antibiotic resistant bacteria in aquatic ecosystems. Amongst the various alternatives proposed, enhancing immunity in fish using probiotics is the most widely accepted approach. Several earlier studies indicated the possibility of more potent effects of bacteria on fish when administered in live condition than as inactivated cells. But very few studies have explored the effect of gut bacteria on innate immune responses of fishes. Hence an attempt is made to study immunostimulatory effects of dietary supplementation of Bacillus subtilis and Terribacillus saccharophillus isolated from the gut of an edible Indian freshwater fish, Labeo rohita, in the same species. Methods: Long term administration (for 30 and 60 days) of B. subtilis or T. saccharophillus isolated from the gut wall of L. rohita were tested in the same species for their ability to improve innate immunity through measurement of the phagocytic activity, respiratory burst, myeloperoxidase activity, serum IgM levels, serum lectins, haemagglutination and haemolytic activity. Results: Dietary administration of 107 cfu/g of B.subtilis/T. saccharophillus for 30 (B1) or 60 (B2) days resulted in a significant increase in immune and humoral responses of L. rohita. Serum phagocytic activity, respiratory burst activity, myeloperoxidase activity, serum lectins, haemagglutination and haemolytic activity increased upon administration of B.subtilis / T. saccharophillus, except serum IgM levels which increased only in B1. A positive correlation was observed between the duration of supplementation of diets and the responses in both the cases. Conclusion: The results suggest that T. saccharophillus can also be used as a potent probiont similar to B.subtilis and both will have significant applications in fish feed formulations and disease prevention.

P082 Divergent effects of gut bacteria altered in dysbiosis of inflammatory bowel disease on monocytes and macrophage polarisation

Background: Fistulae are a frequent complication in Crohn’s disease patients. Epithelial to mesenchymal transition (EMT) has been identified as an important driving force of their formation. On the other hand, the importance of ER stress and related pathways in intestinal inflammation has been demonstrated by recent evidence from animal models, the phenotype of human IBD, as well as genetic data. We showed previously, that ER stress leads to the onset of EMT in intestinal epithelial cells. Here, we investigated candidate signaling pathways and therapeutic substances. Methods: HT-29 cells were stimulated with the ER stress inducer tunicamycin (TM). In order to identify candidate pathways, we used specific inhibitors targeting JNK, Src, Smad or siRNA targeting Ets1 transcription factor prior to stimulation with TM. Polyamines, butyrates and bile acids were tested for their potential therapeutic effect by pre-treating the cells with the substances followed by addition of TM. The extent of ER stress and EMT was determined by measuring typical markers by Western blot and quantitative real time PCR. Results: Upon treatment with TM induction of the transcription factor Ets1 was found, which is known to be induced upon ER stress and to play a role in induction of EMT. However, knockdown of Ets1 by siRNA did not influence mRNA levels of the typical fibroblast markers vimentin, beta-6-integrin or the ER stress marker gp96. Similar, inhibiting Smad only lead to slightly reduced levels of beta-6-integrin. On the other hand, stimulation with JNK inhibitor II revealed that induction of Ets, beta-6-integrin and gp96 was JNK-dependent. In addition, the Src kinase inhibitor PP2 reduced the expression of Ets1 and gp96, while induction of beta-6-integrin was found to be Src-independent. Analysing potential therapeutic substances, neither spermidine nor sodium phenylbutyrate could counteract the effect of TM. However, pre-incubation of the cells with 10 mM of the bile acid tauroursodeoxycholic acid decreased significantly the levels of vimentin, beta-6-integrin and gp96. Conclusions: Our data suggest that the JNK and Src pathway are involved in the regulation of ER stress-mediated EMT during fistula formation in Crohn’s disease. The bile acid tauroursodeoxycholic acid represents a therapeutic treatment option.