Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction

Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.

Adjusting the composition of gut microbiota prevents the development of post-stroke depression by regulating the gut-brain axis in mice

Disturbances in gut microbiota contribute to an imbalanced gut-brain axis, which is critical for post-stroke depression (PSD), while the underlying mechanisms remain unclear. The objective of this study was to examine the effects of modifying gut microbiota through antibiotic treatment (ABX) and fecal microbiota transplantation (FMT) on the progression of PSD. The PSD model was established by occluding the middle cerebral artery (MCAO), followed by a four-week isolated housing and restraint stress initiated three days after MCAO. For ABX, the PSD mice received antibiotic water for four weeks. While another group of PSD mice underwent FMT or fluoxetine (FLX) for four weeks. At day 35 post-MCAO, behavioral tests were conducted. Results indicated ABX and FMT significantly altered the composition of intestinal flora caused by PSD, all the treatments markedly attenuated anxiety- and depressive-like behaviors and inflammation in the gut and brain. ABX obviously alleviated PSD-induced disorder of intestinal barrier, decreased mRNA levels of TNF-α, IL-1β and IL-6, and decreased CD4+ cells in the colon. While FMT significantly decreased CD8+ cells and increased the goblet cells in colon. Furthermore, both ABX and FMT could reduce activated microglia and pro-inflammatory cytokines in the brain, alleviate decreased Nissl's bodies in the hippocampus, and reverse the decreases in 5-HT, Glu and DA in the striatum caused by PSD. Unlike ABX, FMT was similar to FLX. These findings suggest homeostasis of gut microbiota is indispensable for the development of PSD; adjusting the gut microbiota significantly improves PSD with enhanced functions of gut-brain axis.

Sesamin improved growth and overall health in young animals by enhancing gut-liver axis function

The immature gastrointestinal development of infants and young animals made them more vulnerable to stress-related damage, which affected the gut-liver axis and consequently impaired their health and growth. This study used weaned piglets as a model to investigate how dietary sesamin regulated the gut-liver axis and impacted young animal health. We assessed gut-liver tissue morphology, measured key indicators of intestinal barrier damage, mucosal repair, antioxidant and immune pathways in the gut-liver system and serum, and analyzed microbial composition. We further explored the interactions between sesamin and the gut-liver axis through PLS-PM and molecular docking analysis. Results showed that sesamin enhanced intestinal barrier function, reduced liver damage, decreased oxidative stress, promoted anti-inflammatory immune responses, and enriched beneficial microbes, thereby promoting overall growth. Sesamin can enhance the health of young animals by regulating the function of the gut-liver axis.

Administration of EPA improves lipopolysaccharide-induced intestinal dysfunction in turbot (Scophthalmus maximus L.) through modulation of TORC1 signaling

Intestinal health is crucial for digestive and absorptive functions, which are associated with fish growth performance. Searching for nutraceuticals and bioactive ingredients to improve intestinal health has become urgent for the aquaculture industry. In the present study, the effects of eicosapentaenoic acid (EPA) on intestinal function were investigated in turbot with induced intestinal damage caused by lipopolysaccharide (LPS). Juvenile turbot (initial weight 100 ± 5 g) were subjected to a 10-day enforced feeding regimen. Each fish was fed twice daily with either a 100 mg amino acid mixture (CON), an additional 1 mg of LPS (LPS), or an additional combination of 1 mg LPS and 1.7 mg EPA (LE). The results indicated that EPA supplementation restored intestinal villi integrity and the mucosal barrier. The number of goblet cells and the gene expression of MUC-2 were increased by EPA. Additionally, EPA suppressed the expression of inflammatory factors (MyD88 and NF-κB p65) and pro-inflammatory cytokines (TNFα, IL-1β, and IFN-γ). Meanwhile, post-feeding plasma free amino acid levels as well as intestinal protein synthesis were improved by EPA supplementation. The target of rapamycin (TOR) signaling pathway was significantly activated by EPA. Furthermore, EPA supplementation positively influenced intestinal microbiota, reducing the abundance of prevalent pathogens while enhancing the abundance of probiotics. Collectively, the administration of EPA effectively mitigates LPS-induced damage to the intestinal barrier, inflammatory response, and dysbiosis of microbiota through modulation of the TOR signaling pathway.

Comparison of in vitro fermentation characteristics of carob gum and guar gum

Carob gum (CG) and guar gum (GG) are widely used as additives in food processing; however, their fermentation properties in the human gut and potential effects on the human body are unclear. This study used an in vitro fermentation model to evaluate the interaction of CG and GG with intestinal flora and compare their fermentation characteristics. The results showed that CG and GG could be degraded and utilized by the intestinal flora. GG can increase the production of acetic acid, propionic acid, and butyric acid and the relative abundance of beneficial microorganisms such as Prevotella and Faecalibacterium. CG promotes propionic acid production and the relative abundance of beneficial microorganisms such as Bifidobacterium and Lactobacillus. Metabolomic studies have shown that fermented CG and GG mainly affect human metabolic pathways. GG promotes amino acid and lipid metabolism, and CG promotes amino acid metabolism and biosynthesis of secondary metabolites. This research shows that despite significant differences in how CG and GG interact with the gut microbiota, both may affect the human body.

Alterations of ocular surface microbiome in glaucoma and its association with dry eye

Introduction. Alterations in ocular surface microbiota (OSM) have been noted in both dry eye disease (DED) and glaucoma. However, the combined effects of these conditions on OSM have not been explored.Hypothesis. We hypothesized that patients with both glaucoma and dry eye would exhibit distinct changes in OSM composition and diversity compared to those with only glaucoma, only dry eye or healthy individuals.Aim. We employed amplicon sequencing to investigate OSM profiles in patients with glaucoma and/or dry eye disease.Methods. Swab samples from the conjunctiva of both eyes were collected from 28 glaucomatous patients [13 without dry eye syndrome (G-only) and 15 with dry eye syndrome (G-DED)], 13 DED patients without glaucoma (DED-only) and 31 age-matched healthy controls (HCs). After V3-V4 16S rRNA sequencing, MOTHUR tools and R language were used to elucidate and compare OSM composition and diversity between groups.Results. Our data revealed very diverse bacterial communities with 28 phyla and 785 genera. All the groups shared the three most abundant phyla, Actinobacteria (67.47%), Firmicutes (17.14%) and Proteobacteria (13.73%). Corynebacterium (54.75%), Staphylococcus (10.71%), Cutibacterium (8.77%) and Streptococcus (3.20%) were the most abundant genera. Only the G-DED group showed higher alpha diversity than the HC group (P<0.05). However, significant differences in beta diversity were observed between all three patient groups and the HC group. The Differential Expression for Sequencing 2 (DESeq2) analysis unveiled an increased presence of opportunistic bacteria across all pathological groups, with the G-DED group demonstrating the most pronounced alterations.Conclusions. Our findings confirm the predominance of Gram-positive bacteria in normal OSM and the rise of opportunistic Gram-negative bacteria in glaucoma and dry eye disease. This is the first study to characterize OSM in glaucoma patients with DED.

Fermentation of Amazonian fruit pulp (bacaba) with distinct probiotics: Impacts on chemical composition, bioaccessibility, and effects on human intestinal microbiota

Bacaba (Oenocarpus bacaba Mart.) is an underexplored Amazonian fruit rich in polyphenols that can serve as a substrate for probiotic survival and may positively impact on the composition and metabolism of the intestinal microbiota. This study aimed to evaluate the bacaba pulp fermented with probiotics Lactobacillus acidophilus 05 (LA-05) and Lacticaseibacillus casei 01 (LC1) regarding the chemical composition and probiotics survivability during fermentation (48 h), and the effect on the modulation of the intestinal microbiota of healthy adults through 16S rRNA sequencing. The probiotic-fermented bacaba pulps showed decreased pH and total soluble solids values and sugar content (maltose, glucose, fructose, and rhamnose), and increased titratable acidity values, organic acid content (lactic and tartaric acids), and phenolic compounds concentration compared to the control pulp. Furthermore, it presented adequate probiotic viability after fermentation and simulated gastrointestinal conditions. The bacaba pulp fermented with LC1 showed a higher concentration of butyric acid and phenolic compounds concentration (trans-resveratrol, cis resveratrol, catechin, procyanidin B2, and pelargonidin 3-glucoside) and bioaccessibility compared to the control pulp. The bacaba pulp fermented with LA-5 showed a higher concentration of pelargonidin 3-glucoside and procyanidin B2 compared to the control pulp and the highest bioaccessibility of some phenolic compounds (trans-resveratrol, cis-resveratrol, catechin, epicatechin, procyanidin B1, procyanidin B2, myricetin, and isorhamnetin). In vitro fecal fermentation reduced the pH and increased the abundance of Desulfovibrionales, Lactobacillales, and Peptostreptococcales-Tissierellales for all treatments. Bacaba pulp with LC1 resulted in the lowest pH values, and increased production of organic acids and concentration of phenolic compounds. Furthermore, both probiotic pulps increased the abundance of Lactobacillales and Acidaminococcales and decreased the abundance of Clostridiales. These findings provide new information about the potential of using bacaba in a functional pulp that may benefit human health through colonic microbiota changes.

IUPHAR review: From gut to brain: The role of gut dysbiosis, bacterial amyloids, and metabolic disease in Alzheimer's disease

Gut microbial dysbiosis, or altered gut microbial communities, in Alzheimer's Disease suggests a pathogenic role for gut inflammation and microbial products in shaping a neuroinflammatory environment. Similarly, metabolic diseases, such as obesity and diabetes, are also associated with an increased risk of Alzheimer's Disease. As the metabolic landscape shifts during gut inflammation, and gut inflammation in turn impacts metabolic processes, we explore how these interconnected pathways may contribute to the progression of Alzheimer's Disease. Additionally, we discuss the role of bacterial amyloids produced by gut microbes, which may exacerbate amyloid aggregation in the brain and contribute to neurodegenerative processes. Furthermore, we highlight potential therapeutic strategies aimed at reducing gut inflammation, improving metabolic health, and decreasing amyloid content as a means to mitigate Alzheimer's Disease progression. These approaches, targeting the gut-brain-metabolic axis, could offer promising avenues for delaying or preventing cognitive decline in affected individuals.

Correlation of serum vitamin D levels with serum interleukin-23 levels in patients of ulcerative colitis

Ulcerative Colitis (UC) is a chronic inflammatory condition resulting from an abnormal immune response to gut microbiota, leading to cytokine dysregulation, including elevated interleukin-23 (IL-23) levels. Emerging evidence suggests that vitamin D (VD) plays a crucial role in immune modulation. However, its correlation with IL-23 in UC is not well addressed. This study aims to elucidate the relationship between serum VD and IL-23 levels in UC patients. We included forty-four UC patients and forty-four healthy controls. VD insufficiency was more common in UC patients (n = 14) compared to controls (n = 5). Significant increases in IL-23 levels were observed from remission (46.6 ± 4.3 pg/mL) to severe stages (218.5 ± 62.41 pg/mL), while VD levels did not show a similar trend. IL-23 levels also rose significantly with disease extent, from proctitis to pancolitis. A significant negative correlation was found between VD and IL-23 levels (r = -0.3175; P = 0.035). IL-23 and pulse rate were significant predictors of UC in our cohort. Our findings highlight VD insufficiency to be prevalent in UC patients, with VD levels negatively correlating with IL-23 levels, which increase with disease severity and extent. Further, understanding the interplay between VD and IL-23 will help design therapeutic interventions to modulate immune response and disease progression.

The single degree of polymerization influences the efficacy of xylooligosaccharides in shaping microbial and metabolite profiles in chicken gut to combat avian pathogenic Escherichia coli

BACKGROUND

Avian pathogenic Escherichia coli (APEC) threatens both poultry production and human health. Xylooligosaccharides (XOS) may suppress pathogenic bacteria through prebiotic actions. However, the influences of single degree of polymerization (DP) on the inhibition of APEC by XOS remain unknown. This study aimed to probe if XOS and their major monomers (xylobiose, xylotriose and xylotetraose) could differentially combat APEC via prebiotic actions using an in vitro fermentation model with chicken cecal microbiota.

METHODS

Microbiota were randomly divided into 7 groups (5 replicate tubes/group). Control group (CON) received no treatment; XOS group received commercial XOS mixtures; APEC group received APEC; XA, X2, X3 and X4 groups received APEC combined with commercial XOS mixtures, xylobiose, xylotriose and xylotetraose, respectively.

RESULTS

XOS and their major monomers mitigated APEC-induced decline (p < 0.05) in gut microbial α-diversity, with xylotetrose showing the least effect. Gut microbiota in XA, X2, X3 and X4 groups clustered together, with a relative separation observed in X4 group. XOS and their monomers elevated (p < 0.05) the abundances of Firmicutes, Bacteroidota and several probiotics (Lactobacillus, Bacteroides and Megamonas), but reduced (p < 0.05) the abundances of Proteobacteria and Escherichia-Shigella, with xylotetraose exhibiting the least efficacy. Besides, xylotriose and xylotetrose had an advantage over xylotetraose in promoting microbial production of short-chain fatty acids. Metabolomics analysis revealed that APEC challenge mainly downregulated (p < 0.05) several amino acids metabolism pathways of gut microbiota, while xylotriose had an inferiority to XOS in upregulating (p < 0.05) histidine metabolism pathway. Furthermore, microbial fermentation metabolites of all XOS monomers lowered (p < 0.05) certain virulence genes expression in APEC, with xylotriose being the most advantageous.

CONCLUSIONS

XOS and their major monomers differentially improved gut microbiota and metabolite profiles in chicken gut against APEC challenge. Overall, xylotriose exhibited the greatest inhibition against APEC abundance and virulence. Our findings underscore the role of single DP in influencing the prebiotic actions of XOS against APEC, providing a basis for the reasonable application of XOS in diets to combat bacterial challenge.

Probiotics ameliorate atopic dermatitis by modulating the dysbiosis of the gut microbiota in dogs

BACKGROUND

Canine atopic dermatitis (cAD) is a chronic inflammatory disease that significantly reduces the quality of life in dogs. Dysbiosis of the gut microbiota affects skin diseases through the gut-skin axis. Therefore, microbiota-targeted therapy may potentially serve as a new management strategy for cAD. The present study aimed to investigate the association between gut microbiota and cAD and to evaluate the effect of probiotics on the clinical symptoms of cAD and gut microbiota in dogs.

RESULTS

Gut microbiota was analyzed at baseline and after 8 and 16 weeks. Baseline analysis revealed significantly lower (p < 0.05) gut microbial diversity in dogs with cAD than in healthy dogs. Differential abundance analysis showed that Fusobacterium, Megamonas, Collinsella, unclassified Clostridiales, Bacillus, Helicobacter, and Caproiciproducens were significantly more abundant in healthy dogs. In contrast, Clostridioides, Erysipelatoclostridium, Clostridium, Terrisporobacter, and unclassified Ruminococcaceae were significantly more abundant in dogs with cAD, In addition, differential abundance analysis showed that the abundance of 46 metabolic pathways were significantly different between healthy dogs and dogs with cAD indicating the dysbiosis of the gut microbiota in cAD. Moreover, the clinical severity of cAD was negatively correlated (p < 0.05) with alpha diversity and the abundance of Fusobacterium and Megamonas. Notably, daily probiotic administration for 16 weeks significantly decreased the clinical severity (p < 0.05). Dogs with good prognoses exhibited significantly increased alpha diversity, whereas those with poor prognoses did not, suggesting that the therapeutic effects of probiotics may be mediated by changes in gut microbial diversity.

CONCLUSIONS

This study highlights the association between gut microbiota dysbiosis and cAD in dogs and demonstrates that probiotic administration can effectively ameliorate cAD by improving gut microbial dysbiosis. These findings provide a basis for novel microbiota-based therapies in cAD treatment.

Unraveling the protective mechanisms and bioactive components of litchi polysaccharides in intestinal health

In recent years, the rise in intestinal disease has driven the hunt for safer, cost-effective alternatives to traditional, side-effect-laden medications. Litchi polysaccharide (LP), derived from litchi pulp, has emerged as a potential intestinal protector, but its efficacy has not been well-established. Our study have demonstrated LP significantly preserves the integrity of the intestinal barrier in both Caenorhabditis elegans model and antibiotic-exposed mice. Furthermore, LP regulates the gut microbiota, promoting the dominance of beneficial bacteria such as Anaerostipes and Lachnoclostridium in antibiotic-exposed mice and elevating the levels of short-chain fatty acids (SCFAs). LP2-a, a key component making up 11.13 % of LP and with a molecular weight of 72,477 Da, has been isolated and identified as the main active agent. Its molecular structure, featuring galactose and arabinose and possessing a main chain composed of specific sugar units and side chains, is crucial for its protective effects. In C. elegans, LP2-a regulates the expression of intestinal structure-related genes, including up-regulating the expression of act-5 and down-regulating the levels of ajm-1, erm-1, and zoo-1, protecting the integrity of the intestinal barrier. This study provides a theoretical foundation for the potential use of LP, particularly LP2-a, in the treatment of intestinal diseases.

Neonatal gut microbiota succession in mice mapped over time, site, injury and single immunoglobulin interleukin-1 related receptor genotype

Microbial succession during postnatal gut development in mice is likely impacted by site of sampling, time, intestinal injury, and host genetics. We investigated this in wild-type and Sigirr transgenic mice that encode the p.Y168X mutation identified in a neonate with necrotizing enterocolitis (NEC). Temporal profiling of the ileal and colonic microbiome after birth to weaning revealed a clear pattern of progression from a less diverse, Proteobacteria/Escherichia_Shigella dominant community to a more diverse, Firmicutes/Bacteroidetes dominant community. Formula milk feeding, a risk factor for necrotizing enterocolitis, decreased Firmicutes and increased Proteobacteria leading to enrichment of bacterial genes denoting exaggerated glycolysis and increased production of acetate and lactate. Sigirr transgenic mice exhibited modest baseline differences in microbiota composition but exaggerated formula feeding-induced dysbiosis, mucosal inflammation, and villus injury. Postnatal intestinal microbiota succession in mice resembles human neonates and is shaped by developmental maturity, ileal vs. colonic sampling, formula feeding, and Sigirr genotype.

Studies on the changes in rectal permeability and intestinal microbiota with developmental age in young rats

Introduction

The gut contains a diverse array of commensal microorganisms, forming a vital biological barrier within the intestine that contributes to the overall intestinal mucosal barrier. However, research on the rectal barrier during early development remains limited. This study aims to investigate the relationship between intestinal microbiota and rectal barrier function in young rats.

Methods

We evaluated the rectal barrier structure and function in rats at 2-, 4-, and 10-week-old. Methodology included histological analysis, Muc2 expression quantification, immunofluorescence localization of tight junction proteins (ZO-1, Occludin, Claudins), blood glucose monitoring after rectal insulin administration, and 16S rDNA sequencing of rectal microbiota. Spearman correlation analysis was used to explore mechanisms linking age-dependent changes in rectal permeability to microbiota dynamics.

Results

Physiological rectal permeability was significantly higher in 2-week-old rats compared to 4- and 10-week-old rats (p < 0.01), although systemic biomarkers (LPS, D-LA, and LBP) showed no significant differences. The rectal microbiota exhibited marked age-dependent shifts in composition, α/β-diversity, and metabolic pathways, with increased abundance of beneficial taxa (e.g., Muribaculaceae, Akkermansia) in older rats. Correlation analysis revealed strong associations between reduced permeability, elevated Occludin expression, and microbiota maturation (R = 0.65, p < 0.001).

Conclusion

This study demonstrates that age-dependent maturation of the rectal barrier is closely linked to microbiota composition and tight junction protein expression, providing insights into developmental mechanisms and potential strategies for pediatric rectal drug delivery.

Neonatal Food Protein-Induced Enterocolitis: Current Insights and Knowledge Gaps

Acute and chronic Food Protein-Induced Enterocolitis Syndrome (FPIES) has been well characterized in children; otherwise, neonatal FPIES (N-FPIES) remains poorly understood. In terms of pathophysiology, neonatal FPIES appears to have a more prevalent TH2 response and is characterized by specific clinical features that make the diagnosis challenging. Genetic and environmental risk factors may predispose to the development of FPIES. Recent evidence indicates that a characteristic microbiota signature may lead to barrier dysfunction, reduced regulatory T cells, and abnormal intestinal production of serotonin, responsible for the symptoms of FPIES. Regarding clinical presentation, newborns with FPIES may not fully meet the current guideline's diagnostic criteria at disease onset, being more similar to clinical entity specific of neonatal age than to acute FPIES in infants and children. Hence, differentiation from other neonatal medical and surgical conditions-particularly necrotizing enterocolitis (NEC)-remains a critical challenge for clinicians. This present review highlights our current understanding of N-FPIES, in term of pathophysiology, clinical presentation diagnosis, and treatment strategies. Refining diagnostic criteria for N-FPIES represents a clinical priority to help physicians in diagnosing and managing this challenging condition. Last, but not least, larger clinical trials are needed to optimize treatment practices in term and preterm newborns with FPIES.

Alzheimer's Disease-Derived Outer Membrane Vesicles Exacerbate Cognitive Dysfunction, Modulate the Gut Microbiome, and Increase Neuroinflammation and Amyloid-β Production

Although our understanding of the molecular biology of Alzheimer's disease (AD) continues to improve, the etiology of the disease, particularly the involvement of gut microbiota disturbances, remains a challenge. Outer membrane vesicles (OMVs) play a key role in central nervous system diseases, but the impact of OMVs on AD progression remains unclear. In this study, we hypothesized that AD-derived OMVs (OMVsAD) were a risk factor in AD pathology. To test our hypothesis, young APP/PS1 mice (AD mice) were given OMVsAD by gavage. Young AD mice were euthanized 120 days after gavage to assess the intestinal barrier, gut microbiota diversity, mediators of neuroinflammation, glial markers, amyloid burden, and short-chain fatty acid (SCFA) levels. Our results showed that OMVsAD accelerated cognitive dysfunction after 120 days of intragastric administration. Morris water maze experiment and new object recognition test showed that OMVsAD caused significantly poorer spatial ability learning and memory of the AD mice. We observed the OMVsAD-treated APP/PS1 mice display OMVs disrupting the intestinal barrier compared with controls of normal human-derived OMVs. Compared with the OMVsHC group, claudin-5 and ZO-1 related to the intestinal barrier were significantly downregulated in the OMVsAD group. The OMVsAD activate microglia in the cerebral cortex and hippocampus of AD mice, and the levels of IL-1β, IL-6, TNF-α, and NF-Κb were upregulated. We also found that OMVsAD increased Aβ production. 16S rRNA sequencing showed that OMVsAD negatively regulated the α- and β-diversity index of intestinal flora and reduced the levels of SCFA. OMVsAD may change the intestinal flora of young AD, damage the intestinal mucosa and blood-brain barrier, and accelerate AD neuropathological damage.

The impact of gut microbiota on the occurrence, treatment, and prognosis of ischemic stroke

Ischemic stroke (IS) is a cerebrovascular disease that predominantly affects middle-aged and elderly populations, exhibiting high mortality and disability rates. At present, the incidence of IS is increasing annually, with a notable trend towards younger affected individuals. Recent discoveries concerning the "gut-brain axis" have established a connection between the gut and the brain. Numerous studies have revealed that intestinal microbes play a crucial role in the onset, progression, and outcomes of IS. They are involved in the entire pathophysiological process of IS through mechanisms such as chronic inflammation, neural regulation, and metabolic processes. Although numerous studies have explored the relationship between IS and intestinal microbiota, comprehensive analyses of specific microbiota is relatively scarce. Therefore, this paper provides an overview of the typical changes in gut microbiota following IS and investigates the role of specific microorganisms in this context. Additionally, it presents a comprehensive analysis of post-stroke microbiological therapy and the relationship between IS and diet. The aim is to identify potential microbial targets for therapeutic intervention, as well as to highlight the benefits of microbiological therapies and the significance of dietary management. Overall, this paper seeks to provide key strategies for the treatment and management of IS, advocating for healthy diets and health programs for individuals. Meanwhile, it may offer a new perspective on the future interdisciplinary development of neurology, microbiology and nutrition.

Regulation of Intestinal Barrier Function and Gut Microbiota by Hot Melt Extrusion-Drug Delivery System-Prepared Mulberry Anthocyanin in an Inflammatory Bowel Disease Model

Background/Objectives: Anthocyanins (ACNs) derived from mulberry (Morus alba L.) exhibit potent antioxidant and anti-inflammatory activities. However, their low stability and bioavailability in physiological environments limit their therapeutic potential. This study aimed to enhance the stability and controlled release ACNs using a hot-melt extrusion drug delivery system (HME-DDS) formulation, HME-MUL-F2, and evaluate its effects on gut barrier function and microbiota composition in a DSS-induced colitis model. Methods: The anthocyanin content of HME-MUL-F2 was quantified and compared with that of raw mulberry extract. The formulation's protective effects were assessed in Caco-2 and RAW 264.7 cells, confirming its biocompatibility and anti-inflammatory properties. The therapeutic efficacy was further evaluated in a dextran sulfate sodium (DSS)-induced inflammatory bowel disease (IBD) model, focusing on gut barrier integrity, inflammatory cytokine modulation, and gut microbiota composition. Results: HME-MUL-F2 significantly improved gut barrier function by upregulating tight junction proteins and reducing inflammatory cytokine levels in the colitis model. Moreover, the formulation modulated gut microbiota composition, promoting beneficial bacteria while suppressing pathogenic strains. HME-MUL-F2 administration led to a significant increase in the Bacteroidetes-to-Firmicutes ratio, which is associated with improved gut health. These results indicate that HME-MUL-F2 significantly enhances anthocyanin bioavailability, leading to improved gut health and potential therapeutic applications for inflammatory conditions. Conclusions: This study highlights the potential of HME technology for improving the stability, bioavailability, and therapeutic efficacy of anthocyanins. HME-MUL-F2 is a sustained-release formulation that enhances gut barrier function and modulates intestinal microbial balance in a DSS-induced inflammatory bowel disease model. These findings strongly suggest that the observed therapeutic effects of HME-MUL-F2 are primarily due to enhanced anthocyanin bioavailability and targeted delivery to the colon, although further clinical studies will provide more definitive confirmation.

Effects of a high-fat diet on gut microbiota and possible implications for bone health in male Wistar rats

Diet plays an important role in the composition of gut microbiota. Emerging research suggests that bone homeostasis can also be influenced by the gut microbiota. The aim of this study was to assess possible alterations in gut microbiota in an experimental obesity model induced by a high-fat diet (HFD) and the possible effects on parameters of bone metabolism and remodeling. Male Wistar rats were fed a HFD (60% lipids) or standard (control) diet for 14 weeks. Biochemical and hormonal parameters, bone histomorphometry, bone protein levels, and gut microbiota composition were analyzed. HFD animals exhibited a greater gut microbiota α-diversity represented by the Shannon Index and an increased relative abundance of the Proteobacteria phylum. Histomorphometry detected lower bone formation in the HFD group, accompanied by increased levels of serum and bone leptin and FGF-23 (fibroblast growth factor-23). The Shannon Index was correlated directly with bone FGF-23 (R 0.96, p = 0.04) and inversely with the osteoblastic surface (R -0.95, p = 0.04). The present study disclosed a significant increase in gut microbiota α-diversity and relative abundance of Proteobacteria phylum in obese animals fed a high-fat diet in parallel with increased levels of bone and serum leptin and FGF-23 and lower bone formation. The associations of Shannon Index with bone levels of FGF-23 and reduced osteoblastic surface suggest a link between HFD-induced higher gut microbiota diversity and low bone formation.

Harnessing the human gut microbiota: an emerging frontier in combatting multidrug-resistant bacteria

Antimicrobial resistance (AMR) has become a major and escalating global health threat, undermining the effectiveness of current antibiotic and antimicrobial therapies. The rise of multidrug-resistant bacteria has led to increasingly difficult-to-treat infections, resulting in higher morbidity, mortality, and healthcare costs. Tackling this crisis requires the development of novel antimicrobial agents, optimization of current therapeutic strategies, and global initiatives in infection surveillance and control. Recent studies highlight the crucial role of the human gut microbiota in defending against AMR pathogens. A balanced microbiota protects the body through mechanisms such as colonization resistance, positioning it as a key ally in the fight against AMR. In contrast, gut dysbiosis disrupts this defense, thereby facilitating the persistence, colonization, and dissemination of resistant pathogens. This review will explore how gut microbiota influence drug-resistant bacterial infections, its involvement in various types of AMR-related infections, and the potential for novel microbiota-targeted therapies, such as fecal microbiota transplantation, prebiotics, probiotics, phage therapy. Elucidating the interactions between gut microbiota and AMR pathogens will provide critical insights for developing novel therapeutic strategies to prevent and treat AMR infections. While previous reviews have focused on the general impact of the microbiota on human health, this review will specifically look at the latest research on the interactions between the gut microbiota and the evolution and spread of AMR, highlighting potential therapeutic strategies.

Principles of gut microbiota assembly

The gut microbiota plays a critical role in human health, yet its taxonomic complexity, interpersonal variability, and resistance to change in adulthood present challenges for understanding the factors driving shifts in its composition and function. Here, we propose a hierarchy of ecological factors governing gut microbiota assembly, stability, and resilience. At the apex of this hierarchy is habitat filtering by host-derived electron acceptors, which dictates the ecological guilds that dominate distinct gut regions. Host dietary behavior shapes niche availability within these ecological guilds by regulating nutrient availability. Priority effects preserve taxonomic stability whereas microbial antagonism governs competition for open ecological positions. This framework highlights how host control over microbial energy metabolism directs microbiota self-assembly and maintains gut homeostasis.

Omega-3 polyunsaturated fatty acids attenuates cognitive impairment via the gut-brain axis in diabetes-associated cognitive dysfunction rats

Diabetes-related cognitive dysfunction (DACD) is a comorbidity of type 2 diabetes that has a negative effect on patients' quality of life. Research has indicated that disruption of the gut microbiota (GM) may be linked to dementia with altered cognitive performance. Conversely, omega-3 polyunsaturated fatty acids (n-3 PUFAs) may reverse DACD. The present study aimed to assess the effects of an n-3 PUFA intervention and fecal microbiota transplantation (FMT) on high-fat and streptozotocin-induced DACD model rats. In DACD rats, n-3 PUFA treatment restored fasting blood glucose (FBG) levels and cognitive function, increased the expression of anti-inflammatory cytokines and downregulated the expression of proinflammatory cytokines in the cortex and colon. Additionally, the expression of the postsynaptic density protein-95 mRNA and protein varied with n-3 PUFA treatment. Treatment with n-3 PUFAs also increased the expression of tight junction proteins. Beneficial and short-chain fatty acid-producing bacteria were more abundant when rats were exposed to n-3 PUFAs. After FMT from the rats with DACD symptoms that were improved by the n-3 PUFA dietary intervention into another batch of DACD rats, we observed recovery in recipient DACD rats. These results indicated that the alleviation of DACD symptoms by n-3 PUFAs was attributed to gut microbiota remodeling.

Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism

Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa. Results show that zoo-housed gorillas in the U.S. exhibit the most diverse gut microbiomes and markers of increased protein and carbohydrate fermentation, at the expense of microbial metabolic traits associated with plant cell-wall degradation. Machine learning models identified unique microbial traits in U.S. gorillas with cardiometabolic distress; including reduced metabolism of sulfur-containing amino acids and hexoses, increased abundance of potential enteric pathogens, and low fecal butyrate and propionate production. These findings show that cardiometabolic disease in gorillas is potentially associated with altered gut microbial function, influenced by zoo-specific diets and environments.

Differential effects of polyvinyl chloride microplastics and kaolin particles on gut immunity of mussels at environmental concentrations

Both microplastics (MPs) and kaolin are marine suspended particles capable of influencing the physiology of bivalve mollusks. However, the current research on MPs lacks the analysis of their own physical and chemical toxicity, and the comparative study of the toxicity of microplastics and natural suspended particles (NSPs) in aquatic environment. In this work, three experiments are layered, with Experiment 1 directly comparing polyvinyl chloride MPs (PVC MPs) and kaolin and showing that MPs have greater deleterious effects on thick-shelled mussels than kaolin, with the exception of physical damage and effects on gut microorganisms. As the presence or absence of chemicals may be the main difference between MPs and kaolin, in Experiment 2 the toxicity drivers of PVC MPs itself were investigated, demonstrating that the chemicals in MPs are indeed toxic and that the harmful effects of MPs on mussels may be due to the superposition of their own physical and chemical toxicity. Finally, in Experiment 3 mussels were exposed to the chemicals in PVC MPs and kaolin in a composite and found that the toxicity of the composite exposure was greater than that of the single exposure to kaolin, suggesting that the chemicals may be the main factor contributing to the difference in toxicity between PVC MPs and kaolin. In conclusion, this work addresses the lack of a natural particle control group in current studies of MPs, confirms that the toxicity drivers of MPs are due to both physical and chemical factors, highlights the role of NSPs in the environment, and provides new insights for evaluating the toxic effects of MPs in the natural marine environment.

Dietary manipulation of intestinal microbes prolongs survival in a mouse model of Hirschsprung disease

Enterocolitis is a common and potentially deadly manifestation of Hirschsprung disease (HSCR) but disease mechanisms remain poorly defined. Unexpectedly, we discovered that diet can dramatically affect the lifespan of a HSCR mouse model ( Piebald lethal , sl/sl ) where affected animals die from HAEC complications. In the sl/sl model, diet alters gut microbes and metabolites, leading to changes in colon epithelial gene expression and epithelial oxygen levels known to influence colitis severity. Our findings demonstrate unrecognized similarity between HAEC and other types of colitis and suggest dietary manipulation could be a valuable therapeutic strategy for people with HSCR.

Abstract

Hirschsprung disease (HSCR) is a birth defect where enteric nervous system (ENS) is absent from distal bowel. Bowel lacking ENS fails to relax, causing partial obstruction. Affected children often have "Hirschsprung disease associated enterocolitis" (HAEC), which predisposes to sepsis. We discovered survival of Piebald lethal ( sl/sl ) mice, a well-established HSCR model with HAEC, is markedly altered by two distinct standard chow diets. A "Protective" diet increased fecal butyrate/isobutyrate and enhanced production of gut epithelial antimicrobial peptides in proximal colon. In contrast, "Detrimental" diet-fed sl/sl had abnormal appearing distal colon epithelium mitochondria, reduced epithelial mRNA involved in oxidative phosphorylation, and elevated epithelial oxygen that fostered growth of inflammation-associated Enterobacteriaceae . Accordingly, selective depletion of Enterobacteriaceae with sodium tungstate prolonged sl/sl survival. Our results provide the first strong evidence that diet modifies survival in a HSCR mouse model, without altering length of distal colon lacking ENS.

Highlights

Two different standard mouse diets alter survival in the Piebald lethal ( sl/sl ) mouse model of Hirschsprung disease, without impacting extent of distal colon aganglionosis (the region lacking ENS). Piebald lethal mice fed the "Detrimental" diet had many changes in colon epithelial transcriptome including decreased mRNA for antimicrobial peptides and genes involved in oxidative phosphorylation. Detrimental diet fed sl/sl also had aberrant-appearing mitochondria in distal colon epithelium, with elevated epithelial oxygen that drives lethal Enterobacteriaceae overgrowth via aerobic respiration. Elimination of Enterobacteriaceae with antibiotics or sodium tungstate improves survival of Piebald lethal fed the "Detrimental diet".

Graphical abstract

Integrating gut and IgA-coated microbiota to identify Blautia as a probiotic for enhancing feed efficiency in chickens

This study explores the role of IgA-coated bacteria in improving feed efficiency in chickens, offering a novel perspective for probiotic screening. Chickens with high feed efficiency were found to have a greater abundance of Gram-positive bacteria, while low feed efficiency chickens exhibited higher levels of Gram-negative bacteria and potential pathogens. Through fecal microbiota transplantation (FMT) and integrating analysis of cecal and IgA-coated microbiota, we precisely identified Blautia as a key genus linked to improved feed efficiency. Further validation demonstrated that Blautia coccoides, a representative species of this genus, enhances feed efficiency and activates B cells to produce Immunoglobulin A (IgA), both in vivo and in vitro. Our findings provide new insights into the potential of IgA-coated bacteria as functional probiotics, offering a promising strategy for enhancing feed efficiency in animal production.

Role of the gut microbiome in psychological symptoms associated with inflammatory bowel diseases

The brain-gut axis constitutes the basis for the bidirectional communication between the central nervous system and the gastrointestinal tract driven by neural, hormonal, metabolic, immunological, and microbial signals. Alterations in the gut microbiome composition as observed in inflammatory bowel diseases can modulate brain function and emerging empirical evidence has indicated that interactions among the brain-gut microbiome-axis seem to play a significant role in the pathogenesis of both inflammatory bowel diseases and psychiatric disorders and their comorbidity. Yet, the immunological and molecular mechanisms underlying the co-occurrence of inflammatory bowel diseases and psychological symptoms are still poorly understood. The aim of this narrative review is to highlight contemporary empirical findings supporting a pivotal role of the gut microbiome in the pathophysiology of highly prevalent neuropsychiatric symptoms in inflammatory bowel diseases such as fatigue, depression, and anxiety. Finally, we focus on microbiome modulation as potential treatment option for comorbid neuropsychiatric symptoms in immune-mediated diseases and especially in inflammatory bowel diseases. High-quality clinical trials are required to clarify how microbiome modulation through dietary interventions or probiotic, prebiotic or synbiotic treatment can be used clinically to improve mental health and thus quality of life of patients with inflammatory bowel diseases.

Yeast cell wall polysaccharides accelerate yet in-feed antibiotic delays intestinal development and maturation via modulating gut microbiome in chickens

BACKGROUND

It is important to promote intestinal development and maturation of chicks for feed digestion and utilization, intestinal health, and disease resistance. This study aimed to investigate the effects of dietary yeast cell wall polysaccharides (YCWP) addition on intestinal development and maturation of chickens and its potential action mechanism.

METHODS

180 one-day-old male Arbor Acres broilers were randomly assigned to three groups containing control (basal diets without any antibiotics or anticoccidial drug), bacitracin methylene disalicylate (BMD)-treated group (50 mg/kg) and YCWP-supplemented group (100 mg/kg).

RESULTS

Compared with control group, in-feed antibiotic BMD continuous administration significantly decreased crypt depth (d 21) and villus height (d 42) along with mucosal maltase activity (d 42) in the ileum (P < 0.05). Also, BMD markedly downregulated gene expression levels of β-catenin, lysozyme, occludin and FABP-2 (d 21) and innate immune related genes CD83 and MHC-I mRNA levels (d 42, P < 0.05), and decreased goblet cell counts in the ileum of chickens (d 21 and d 42, P < 0.05). While, TLR-2, TLR-6 and iNOS mRNA abundances were notably upregulated by BMD treatment (d 42, P < 0.05). Nevertheless, dietary YCWP addition significantly increased the ratio of villus height to crypt depth (d 21), villus surface area (d 21 and d 42), ileal alkaline phosphatase and maltase activities as well as goblet cell (d 21 and d 42) and IgA-producing plasma cell numbers as compared to BMD treatment (d 21, P < 0.05). YCWP addition also upregulated gene expression levels of Lgr5, Wnt/β-catenin signaling pathway related gene (Wnt3, β-catenin, d 21; β-catenin, d 42), intestinal cells proliferation marker Ki-67 and barrier function related genes (occludin, d 21 and d 42, P < 0.05). Moreover, YCWP significantly increased antigen presenting cell marker related genes (MHC-II, d 21; CD83 and MHC-I, d 42), TLR-1, TLR-2 and TLR-6 mRNA levels (d 21, P < 0.05). Cecal microbiome analysis showed that YCWP addition obviously improved cecal microbial composition, as indicated by increasing relative abundance of Fournierella, Psychrobacter and Ruminiclostridium on d 21, and Alistipes and Lactobacillus on d 42, which were positively related with gut development and maturation related indexes (P < 0.05).

CONCLUSION

Collectively, YCWP promoted yet antibiotic BMD delayed intestinal morphological and immunological development linked with modulating gut microbiome in chickens.

Shenmai injection revives cardiac function in rats with hypertensive heart failure: involvement of microbial-host co-metabolism

Heart failure (HF) is a complex syndrome marked by considerable expenditures and elevated mortality and morbidity rates globally. Shenmai injection (SMI), a form of Traditional Chinese Medicine-based therapy, has demonstrated effectiveness in treating HF. Recent research suggests that Traditional Chinese Medicine (TCM) may induce beneficial changes in microbial-host co-metabolism, potentially providing cardiovascular protection. This study used a rat model of hypertensive heart failure (H-HF) to explore the mechanism of SMI. The possible compounds and key targets of SMI against H-HF were investigated using network pharmacology. The pharmacodynamics of SMI were validated using the H-HF animal model, with analysis of fecal gut microbiota integrating metabolomics and 16S rRNA sequencing. Metorigin metabolite traceability analysis and the MetaboAnalyst platform were utilized to explore the action mechanism. To evaluate changes in serum TMAO levels, targeted metabolomics was performed. Finally, the study looked at the intrinsic relationships among modifications in the intestinal flora, metabolite profile changes, and the targets of SMI compounds to clarify how they might be used to treat H-HF. According to metabolomics and 16S rRNA sequencing, by reestablishing homeostasis in the gut microbiota, SMI affects vital metabolic pathways, such as energy metabolism, amino acid metabolism, and bile acid metabolism. Increased serum TMAO levels were identified to be a risk factor for H-HF, and SMI was able to downregulate the levels of TMAO-related metabolites. Network pharmacology analysis identified 13 active components of SMI targeting 46 proteins, resulting in differential expression changes in 8 metabolites and 24 gut microbes. In conclusion, this study highlights the effectiveness of SMI in alleviating H-HF and its potential to modulate microbial-host co-metabolism. Through a comprehensive discussion of the interconnected relationships among the components, targets, metabolites, and gut microbiota, it provided fresh light on the therapeutic mechanism of SMI on H-HF.

Bowel preparation before colonoscopy: Consequences, mechanisms, and treatment of intestinal dysbiosis

The term "gut microbiota" primarily refers to the ecological community of various microorganisms in the gut, which constitutes the largest microbial community in the human body. Although adequate bowel preparation can improve the results of colonoscopy, it may interfere with the gut microbiota. Bowel preparation for colonoscopy can lead to transient changes in the gut microbiota, potentially affecting an individual's health, especially in vulnerable populations, such as patients with inflammatory bowel disease. However, measures such as oral probiotics may ameliorate these adverse effects. We focused on the bowel preparation-induced changes in the gut microbiota and host health status, hypothesized the factors influencing these changes, and attempted to identify measures that may reduce dysbiosis, thereby providing more information for individualized bowel preparation for colonoscopy in the future.

Emerging Concepts in Periprosthetic Joint Infection Research: The Human Microbiome

Microorganisms, including bacteria, fungi, and viruses, that reside on and within the human body are collectively known as the human microbiome. Dysbiosis, or disruption in the microbiome, has been implicated in several disease processes, including asthma, obesity, autoimmune diseases, and numerous other conditions. While the Human Microbiome Project and the generation of descriptive studies it inspired established correlations between characteristic patterns in the composition of the microbiome and specific disease phenotypes, current research has begun to focus on elucidating the causal role of the microbiome in disease pathogenesis. Within the field of orthopaedic surgery, researchers have proposed the concept of a "gut-joint axis," whereby the intestinal microbiome influences joint health and the development of diseases, such as osteoarthritis and periprosthetic joint infection (PJI). It is theorized that intestinal dysbiosis increases gut permeability, leading to the translocation of bacteria and their metabolic products into the systemic circulation and the stimulation of proinflammatory response cascades throughout the body, including within the joints. While correlative studies have identified patterns of dysbiotic derangement associated with osteoarthritis and PJI, translational research is needed to clarify the precise mechanisms by which these changes influence disease processes. Additionally, an emerging body of literature has challenged the previously held belief that certain body sites are sterile and do not possess a microbiome, with studies identifying distinct microbial genomic signatures and a core microbiome that varies between anatomic sites. A more thorough characterization of the joint microbiome may have profound implications for our understanding of PJI pathogenesis and our ability to stratify patients based on risk. The purpose of this review was to outline our current understanding of the human microbiome to describe the gut-joint axis and its role in specific pathologies, including PJI, and to highlight the potential of microbiome-based therapeutic interventions in the field of orthopaedics.

Photodynamic therapy with a novel photosensitizer inhibits DSS-induced ulcerative colitis in rats via the NF-κB signaling pathway

Introduction

Ulcerative colitis (UC) is an inflammatory bowel disease characterized by inflammation and ulceration of the digestive tract.

Methods

Photodynamic therapy (PDT) with a novel photosensitizer LD4 was used to treat UC rat models to explore the therapeutic effect and mechanism of LD4-PDT on UC. 16S ribosomal RNA was used to detect the composition of Gut microbiota.

Results

Our findings indicate that LD4-PDT could protect the integrity of the colonic mucosa, alleviate the inflammatory response and promote the healing of colonic mucosa. Mechanism studies demonstrated that LD4-PDT could inhibit the NF-κB signaling pathway, downregulated the expression of the inflammatory factors' tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and myeloperoxidase (MPO), increased the contents of glutathione (GSH) and superoxide dismutase (SOD) and decreased the content of malondialdehyde (MDA). Additionally, analysis of gut microbiota revealed that LD4-PDT treatment could decrease the abundance of the Proteobacteria phylum in fecal samples, while no significant differences were observed in the Firmicutes, Bacteroidetes, or Actinobacteria phyla among the three groups using 16S rRNA analysis.

Discussion

In summary, our data suggested that LD4-PDT could inhibit DSS-induced UC in rats via the NF-κB signaling pathway, indicating its potential as a novel photosensitizer for the treatment of UC.

Effects of orally administered clioquinol on the fecal microbiome of horses

BACKGROUND

Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.

OBJECTIVES

Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.

STUDY DESIGN

Experimental prospective cohort study using a single horse group.

METHODS

Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).

RESULTS

The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.

MAIN LIMITATIONS

Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.

CONCLUSIONS

Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.

Liver damage and immune responses

Chronic liver disease (CLD) has massive systemic repercussions including major impacts on the body's immune system. Abnormalities in phenotype, function and numbers of various immune cell subsets have been established by a large number of clinical and pre-clinical studies. The loss of essential immune functions renders CLD-patients exceptionally susceptible to bacterial and viral infections and also impairs the efficacy of vaccination. Consequently, infections represent a major clinical issue causing significant morbidity and mortality in these patients. Mechanistically, the immune dysfunction associated with CLD results from the increased translocation of bacteria and bacterial cues from the intestine. These trigger a signaling axis around the cytokines IFN I and IL-10 in hepatic myeloid cells, which aside from impairing the function of the myeloid cells themselves, also has notable negative impacts on the functionality of other immune cells. T cells in CLD-patients and -models are especially affected by this signaling axis and display a variety of quantitative and qualitative defects. Due to the high clinical relevance, understanding the mechanisms underlaying CED-associated immune dysfunction is of critical importance to discover and develop new therapeutic targets.

Dietary Capsaicin Supplementation Mitigates Calving-Induced Stress and Enhances Antioxidant Capacity, Immune Function, and Gut Microbiota in Periparturient Dairy Cows

This study investigated the effects of dietary capsaicin supplementation on antioxidant capacity, immune function, and gut microbiota in periparturient dairy cows. Twenty Holstein cows with an average parity of 2.5 ± 0.76, milk production of 31.30 ± 2.39 kg, and 36.10 ± 2.38 days to calving were randomly assigned to either a control group fed a basal diet or a treatment group supplemented with 1.2 g/head/day of capsaicin. The supplementation was administered during an evaluation period spanning from 28 days before delivery to 21 days after delivery using a randomized block experimental design. Results showed that capsaicin significantly reduced milk somatic cell count and pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) while enhancing serum antioxidant enzymes (SOD, GSH-Px, and CAT) and immunoglobulin levels (IgG, IgA, and IgM). Moreover, capsaicin altered gut microbiota composition, increasing the relative abundance of beneficial genera. These findings suggest that dietary capsaicin supplementation during the transition period improves lactation performance and supports immune function, as well as alleviates oxidative stress. This study highlights the potential of capsaicin as a practical dietary strategy for enhancing productivity in dairy farming.

The baseline fecal microbiome differs in patients with and without anastomotic leakage after colorectal cancer surgery

Background

Anastomotic leakage (AL) is a severe complication of colorectal surgery. The risk of AL is affected by both surgery and patient factors. Gut microbiomes can be generated from the residual material from the fecal immunochemical test (FIT). We, therefore, examined if AL after colorectal cancer surgery could be associated with specific baseline microbiomes in the FIT screening sampling tubes collected weeks before surgery.

Methods

Samples from patients participating in the Danish colorectal cancer screening program were biobanked from 2016 to 2018, and samples from patients who had surgery for screening-detected cancer were included. They were matched with patients without AL in a 1:2 ratio based on age, sex, location of anastomosis (colonic/rectal), ASA classification, and smoking habits. Bacterial DNA was extracted from the sampling tubes, and the fecal microbiomes were analyzed with targeted 16S ribosomal RNA third-generation sequencing.

Results

18 patients who developed AL after surgery were matched with 36 without AL. The alpha diversity was lower in the AL group (p = 0.035), and the AL group separated from the Controls in the PCoA plot (p < 0.001). This was due to the patients undergoing rectal resections, with significant differences in alpha- and beta diversity (p = 0.025 and p = 0.002, respectively). The prevalence of bacteria with the potential to produce collagenase was higher in patients who developed AL (odds ratio 1.29 (95% CI 1.28-1.30), p < 0.001).

Conclusions

We found differences in the baseline microbiome profile associated with subsequent development of AL after surgery for screening-detected rectal cancer.

Evaluating the Effects of Sugar Shift® Symbiotic on Microbiome Composition and LPS Regulation: A Double-Blind, Placebo-Controlled Study

(1) Background: This study evaluated the effects of BiotiQuest® Sugar Shift®, a novel probiotic formulation, for its impact on gut microbiome composition and metabolic health in type 2 diabetes mellitus (T2D). T2D is characterized by chronic inflammation and gut microbiome imbalances, yet the therapeutic potential of targeted probiotics remains underexplored. (2) Methods: In a 12-week randomized, double-blind, placebo-controlled trial, 64 adults with T2D received either Sugar Shift or placebo capsules twice daily. Each dose provided 18 billion CFU of eight GRAS-certified bacterial strains and prebiotics. Clinical samples were analyzed for metabolic markers, and microbiome changes were assessed using 16S rRNA sequencing and metagenomics. (3) Results: Sugar Shift significantly reduced serum lipopolysaccharide (LPS) levels, improved insulin sensitivity (lower HOMA-IR scores), and increased short-chain fatty acid (SCFA)-producing genera, including Bifidobacterium, Faecalibacterium, Fusicatenibacter, and Roseburia. Pro-inflammatory taxa like Enterobacteriaceae decreased, with reduced LPS biosynthesis genes and increased SCFA production genes. The Lachnospiraceae:Enterobactericeae ratio emerged as a biomarker of reduced inflammation. (4) Conclusions: These findings demonstrate the potential of Sugar Shift to restore gut homeostasis, reduce inflammation, and improve metabolic health in T2D. Further studies are warranted to explore its long-term efficacy and broader application in metabolic disease management.

The Efficacy of Fecal Microbiota Transplantation in Mouse Models Infected with Clostridioides difficile from the Perspective of Metabolic Profiling: A Systematic Review

Objectives: This systematic review evaluates the effectiveness of fecal microbiota transplantation (FMT) in treating Clostridioides difficile infection (CDI) in mouse models using a metabolomics-based approach. Methods: A comprehensive search was conducted in three databases (PubMed, Scopus, Google Scholar) from 10 April 2024 to 17 June 2024. Out of the 460 research studies reviewed and subjected to exclusion criteria, only 5 studies met all the inclusion criteria and were analyzed. Results: These studies consistently showed that FMT effectively restored gut microbiota and altered metabolic profiles, particularly increasing short-chain fatty acids (SCFAs) and secondary bile acids, which inhibited C. difficile growth. FMT proved superior to antibiotic and probiotic treatments in re-establishing a healthy gut microbiome, as evidenced by significant changes in the amino acid and carbohydrate levels. Despite its promise, variability in the outcomes-due to factors such as immune status, treatment protocols, and donor microbiome differences-underscores the need for standardization. Rather than pursuing immediate standardization, the documentation of factors such as donor and recipient microbiome profiles, preparation methods, and administration details could help identify optimal configurations for specific contexts and patient needs. In all the studies, FMT was successful in restoring the metabolic profile in mice. Conclusions: These findings align with the clinical data from CDI patients, suggesting that FMT holds potential as a therapeutic strategy for gut health restoration and CDI management. Further studies could pave the way for adoption in clinical practice.

Neuroprotective Effect of a Multistrain Probiotic Mixture in SOD1G93A Mice by Reducing SOD1 Aggregation and Targeting the Microbiota-Gut-Brain Axis

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by the selective loss of motor neurons. A bidirectional communication system known as the "microbiota-gut-brain" axis has a regulatory function in neurodegenerative disorders. The impact of probiotics on ALS through the "microbiota-gut-brain" axis remains uncertain. A longitudinal investigation was conducted to examine the alterations in the structure of the ileum and colon in mutant superoxide dismutase 1 (SOD1G93A) transgenic mice models of ALS by using immunofluorescence and Western blotting. Subsequently, the mice were administered a multistrain probiotic mixture (LBE) or vehicle orally, starting from 60 days of age until the terminal stage of the disease. The effects of these agents on the behavior, gut microbiota, microbial metabolites, and pathological processes of the spinal and intestine of SOD1G93A mice were analyzed, with a focus on exploring potential protective mechanisms. SOD1G93A mice exhibit various structural abnormalities in the intestine. Oral administration of LBE improved the proinflammatory response, reduced aberrant superoxide dismutase 1 (SOD1) aggregation, and protected neuronal cells in the intestine and spinal cord of SOD1G93A mice. Furthermore, LBE treatment resulted in a change in intestinal microbiota, an increase in short-chain fatty acid levels, and an enhancement in autophagy flux. SOD1G93A mice exhibited various structural abnormalities in the intestine. LBE can improve the proinflammatory response, reduce aberrant SOD1 aggregation, and protect neuronal cells in the spinal cord and intestine of SOD1G93A mice. The positive effect of LBE can be attributed to increased short-chain fatty acids and enhanced autophagy flux.

Blended Tea Ameliorates T2DM via Modulation of Gut Microflora

Increasing evidences suggest that type 2 diabetes mellitus (T2DM) is closely related to gut microflora dysbiosis, which can be improved by dietary intervention. Four natural plant products, including Cyclocarya paliurus, Fu brick tea, Ampelopsis grossedentata, and Lithocarpus litseifolius, were blended to form a blended tea product for obtaining the better flavor. The blended tea was also expected to have excellent pharmacological activity. Therefore, the ameliorative effect of blended tea on T2DM and underlying mechanisms were studied in this study. The results showed that the blended tea extract effectively attenuated the symptoms of glucose and lipid metabolism-related disorders in T2DM mice fed by high-fat and high-sucrose diet. Furthermore, blended tea extract intervention significantly attenuated gut microbiota dysbiosis, the abundance of bacteria such as Bacteroidetes and Firmicutes, which aid in the hydrolysis and utilization of carbohydrates, significantly increased, while the abundance of pathogenic bacteria such as Proteobacteria significantly decreased. Certain core microorganisms involved in energy metabolism, including Ruminococcaceae_UCG-005, Butyricimonas, Roseburia, Oscillibacter, [Eubacterium]_nodatum_group, Muribaculaceae, Prevotellaceae UCG 001, were also found to be improved by blended tea extract. Collectively, our results demonstrated that the blended tea may ameliorate T2DM through modulation of gut microflora. The blended tea may serve as novel functional drink for the treatment of T2DM and dysbiosis of gut microbiota.

Accumulation and depuration of tire wear particles in zebrafish (Danio rerio) and toxic effects on gill, liver, and gut

The toxic effects of tire wear particles (TWPs) in the environment are a growing concern for a variety of aquatic organisms. However, studies about TWPs toxicity on aquatic organisms are limited. This study investigated the accumulation and depuration of TWPs in zebrafish at three different concentrations (5 mg/L, 10 mg/L, and 20 mg/L), as well as the toxic effects on the gill, liver, and gut. We found that TWPs could accumulate in the gill and gut for a long time, and the number of TWPs at the high-concentration (20 mg/L) was higher than at the low-concentration (5 mg/L). TWPs induced oxidative stress in the gill and liver. The liver transcriptome profiles indicated that the high concentration of TWPs tended to up-regulate metabolic processes, whereas the low concentration of TWPs was inclined to down-regulate cellular processes. The high-concentration treatment significantly increased xenobiotic biodegradation and metabolism, and lipid metabolism-related pathways, whereas the low-concentration treatment distinctly altered amino acid metabolism-related pathways. The expression of gstt1b, ugt1a1, mgst3b, miox, hsd17b3, and cyp8b1 gene was up-regulated in all TWPs treatments. In addition, Gemmobacter and Shinella enriched in the high-concentration treatment were closely correlated with the degradation of TWPs. These findings provided objective evidence for the toxicity evaluation of TWPs on zebrafish.

The human gut microbiome in health and disease: time for a new chapter?

The gut microbiome, composed of the colonic microbiota and their host environment, is important for many aspects of human health. A gut microbiome imbalance (gut dysbiosis) is associated with major causes of human morbidity and mortality. Despite the central part our gut microbiome plays in health and disease, mechanisms that maintain homeostasis and properties that demarcate dysbiosis remain largely undefined. Here we discuss that sorting taxa into meaningful ecological units reveals that the availability of respiratory electron acceptors, such as oxygen, in the host environment has a dominant influence on gut microbiome health. During homeostasis, host functions that limit the diffusion of oxygen into the colonic lumen shelter a microbial community dominated by primary fermenters from atmospheric oxygen. In turn, primary fermenters break down unabsorbed nutrients into fermentation products that support host nutrition. This symbiotic relationship is disrupted when host functions that limit the luminal availability of host-derived electron acceptors become weakened. The resulting changes in the host environment drive alterations in the microbiota composition, which feature an elevated abundance of facultatively anaerobic microbes. Thus, the part of the gut microbiome that becomes imbalanced during dysbiosis is the host environment, whereas changes in the microbiota composition are secondary to this underlying cause. This shift in our understanding of dysbiosis provides a novel starting point for therapeutic strategies to restore microbiome health. Such strategies can either target the microbes through metabolism-based editing or strengthen the host functions that control their environment.

Propyl acetate protects intestinal barrier during parenteral nutrition in mice and Caco-2 cells

BACKGROUND

Gut microbiota dysbiosis induces intestinal barrier damage during parenteral nutrition (PN). However, the underlying mechanisms remain unclear. This study aimed to investigate gut microbiota dysbiosis, luminal short-chain fatty acids, and autophagy in a mouse model and how these short-chain fatty acids regulate autophagy.

METHODS

Eight-week-old male specific-pathogen-free mice were randomly divided into a Chow group (standard diet and intravenous normal saline infusion) and a PN group (continuous infusion of PN nutrient solution) for 7 days. Caco-2 cells were also treated with intestinal rinse solutions from Chow and PN mouse models.

RESULTS

Compared with the Chow group, the PN group exhibited increased Proteobacteria and decreased Firmicutes, correlating with decreased propyl acetate. In the PN group, intestinal tissue exhibited elevated adenosine monophosphate-activated protein kinase (AMPK) phosphorylation, LC3II protein levels, and Atg3 and Atg7 messenger RNA levels. P62 protein levels were decreased, indicating an increase of autophagy flux in the PN group. In the Caco-2 cell model, cells treated with PN solution plus propyl acetate exhibited increased Claudin-1 and occluding along with decreased interleukin-6 and tumor necrosis factor α compared with those treated with PN solution alone. Propyl acetate addition inhibited the AMPK-mammalian target of rapamycin (mTOR) pathway, mitigating the excessive autophagy induced by the PN intestinal rinse solution in Caco-2 cells.

CONCLUSION

PN led to a significant reduction in propyl acetate levels in the intestine, excessive activation of autophagy, and barrier dysfunction. Propyl acetate inhibited excessive autophagy via the AMPK/mTOR signaling pathway and protected the intestinal barrier during PN.

Fecal microbiota of diarrheic calves: Before, during, and after recovering from disease

BACKGROUND

It is unknown if gastrointestinal dysbiosis in diarrheic calves causes disease or is a consequence of the disease.

OBJECTIVES

Describe the fecal microbiota of calves before, during, and after recovering from diarrhea.

ANIMALS

Fifteen female Holstein calves of 0 to 21 days old from a single farm. Seven calves remained healthy throughout the study, and 8 developed diarrhea on Day 14.

METHODS

Longitudinal cohort study. Microbiota composition was characterized by amplifying the V4 region of the 16S rRNA gene.

RESULTS

Diversity (Shannon index) increased with age in healthy and diarrheic calves from Day 3 to 21, but diarrheic calves had a lower diversity on the day diarrhea was first observed (Day 14). By Day 21, diversity increased in calves that recovered from diarrhea and was not significantly different from that of their healthy counterparts (P > .05). Weighted UniFrac distance showed significant differences in the fecal microbiota between diarrheic and healthy calves at Day 14 of age (PERMANOVA, P < .05), but not before or after diarrhea (PERMANOVA, P > .05). Lactobacillus, Clostridium Sensu Stricto 1, and Collinsella were differentially abundant on Day 10 in calves that developed diarrhea on Day 14 (P < .05).

CONCLUSION AND CLINICAL IMPORTANCE

The fecal microbiota of healthy and diarrheic calves evolved similarly during the first 10 days of age but differed significantly on the day of onset of diarrhea. Enriching Lactobacillus, Clostridium Sensu Stricto 1, and Collinsella before diarrhea onset could have been contributed to the development of diarrhea.

Physical Exercise and the Gut Microbiome: A Bidirectional Relationship Influencing Health and Performance

Background/Objectives: The human gut microbiome is a complex ecosystem of microorganisms that can influence our health and exercise habits. On the other hand, physical exercise can also impact our microbiome, affecting our health. Our narrative review examines the bidirectional relationship between physical activity and the gut microbiome, as well as the potential for targeted probiotic regimens to enhance sports performance. Methods: We conducted a comprehensive literature review to select articles published up till January 2024 on the topics of physical exercise, sports, probiotics, and gut microbiota from major scientific databases, incorporating over 100 studies. Results: We found that the impact of physical activity on the gut microbiome varies with the type and intensity of exercise. Moderate exercise promotes a healthy immune system, while high-intensity exercise for a long duration can cause a leaky gut and consequent systemic inflammation, which may disrupt the microbial balance. Combining aerobic and resistance training significantly affects bacterial diversity, linked to a lower prevalence of chronic metabolic disorders. Furthermore, exercise enhances gut microbiome diversity, increases SCFA production, improves nutrient utilization, and modulates neural and hormonal pathways, improving gut barrier integrity. Our findings also showed probiotic supplementation is associated with decreased inflammation, enhanced sports performance, and fewer gastrointestinal disturbances, suggesting that the relationship between the gut microbiome and physical activity is mutually influential. Conclusions: The bidirectional relationship between physical activity and the gut microbiome is exemplified by how exercise can promote beneficial bacteria while a healthy gut microbiome can potentially enhance exercise ability through various mechanisms. These findings underscore the importance of adding potential tailored exercise regimens and probiotic supplementation that consider individual microbiome profiles into exercise programs.

Co-frequency or contrary? The effects of Qiwei Baizhu Powder and its bioactive compounds on mucosa-associated microbiota of mice with antibiotic-associated diarrhea

Qiwei Baizhu Powder (QWBZP) has been proven effective in treating antibiotic-associated diarrhea (AAD), and the mechanism is associated with regulating the gut microbiota. However, the role of the bioactive compounds of QWBZP in regulating the gut microbiota is still unclear. In this study, 24 mice were divided into a normal control group (N), a model group (R), a QWBZP decoction group (TW), and a QWBZP-TG group (TG). AAD mouse models were established by mixed antibiotic administration. After modeling, mice in the TW group and TG group were treated with QWBZP decoction and QWBZP-TG, respectively. Mice in the N group and R group were gavaged with sterile water. 16S rRNA gene sequencing was used to investigate the changes of mucosa-associated microbiota (MAM) in the small intestine of mice. Moreover, the levels of diamine oxidase (DAO), D-Lactate, secretory immunoglobulin A (sIgA), interleukin 6 (IL-6), IL-10, and tumor necrosis factor-α (TNF-α) were detected using enzyme-linked immunosorbent assay (ELISA) kits. The results showed that QWBZP-TG significantly altered the diversity, structure, and abundance of MAM in the AAD mice. QWBZP-TG exerted a stronger suppression effect on Escherichia and Clostridium compared with QWBZP decoction. Meanwhile, QWBZP-TG downregulated the abundance of Lactobacillus, which elicited an opposite effect to QWBZP decoction. Prevotella was the signature bacteria that responded to the QWBZP-TG intervention. Furthermore, both QWBZP decoction and QWBZP-TG decreased the levels of DAO, D-Lactate, sIgA, IL-6, and TNF-α in the AAD mice. The role of glycosides is to help QWBZP ameliorate diarrhea symptoms by inhibiting the proliferation of diarrhea-associated bacteria, reducing inflammation and regulating immunity.

Host-pathobiont interactions in Crohn's disease

The mammalian intestine is colonized by trillions of microorganisms that are collectively referred to as the gut microbiota. The majority of symbionts have co-evolved with their host in a mutualistic relationship that benefits both. Under certain conditions, such as in Crohn's disease, a subtype of inflammatory bowel disease, some symbionts bloom to cause disease in genetically susceptible hosts. Although the identity and function of disease-causing microorganisms or pathobionts in Crohn's disease remain largely unknown, mounting evidence from animal models suggests that pathobionts triggering Crohn's disease-like colitis inhabit certain niches and penetrate the intestinal tissue to trigger inflammation. In this Review, we discuss the distinct niches occupied by intestinal symbionts and the evidence that pathobionts triggering Crohn's disease live in the mucus layer or near the intestinal epithelium. We also discuss how Crohn's disease-associated mutations in the host disrupt intestinal homeostasis by promoting the penetration and accumulation of pathobionts in the intestinal tissue. Finally, we discuss the potential role of microbiome-based interventions in precision therapeutic strategies for the treatment of Crohn's disease.

Physiological role and complex regulation of O2-reducing enzymes in the obligate anaerobe Clostridioides difficile

Clostridioides difficile, the major cause of antibiotic-associated diarrhea, is a strict anaerobic, sporulating Firmicutes. However, during its infectious cycle, this anaerobe is exposed to low oxygen (O2) tensions, with a longitudinal decreasing gradient along the gastrointestinal tract and a second lateral gradient with higher O2 tensions in the vicinity of the cells. A plethora of enzymes involved in oxidative stress detoxication has been identified in C. difficile, including four O2-reducing enzymes: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). Here, we investigated the role of the four O2-reducing enzymes in the tolerance to increasing physiological O2 tensions and air. The four enzymes have different, yet overlapping, spectra of activity. revRbr2 is specific to low O2 tensions (<0.4%), FdpA to low and intermediate O2 tensions (0.4%-1%), revRbr1 has a wider spectrum of activity (0.1%-4%), and finally FdpF is more specific to tensions > 4% and air. These different O2 ranges of action partly arise from differences in regulation of expression of the genes encoding those enzymes. Indeed, we showed that revrbr2 is under the dual control of σA and σB. We also identified a regulator of the Spx family that plays a role in the induction of fdp and revrbr genes upon O2 exposure. Finally, fdpF is regulated by Rex, a regulator sensing the NADH/NAD+ ratio. Our results demonstrate that the multiplicity of O2-reducing enzymes of C. difficile is associated with different roles depending on the environmental conditions, stemming from a complex multi-leveled network of regulation.

IMPORTANCE

The gastrointestinal tract is a hypoxic environment, with the existence of two gradients of O2 along the gut, one longitudinal anteroposterior decreasing gradient and one proximodistal increasing from the lumen to the epithelial cells. O2 is a major source of stress for an obligate anaerobe such as the enteropathogen C. difficile. This bacterium possesses a plethora of enzymes capable of scavenging O2 and reducing it to H2O. In this work, we identified the role of the four O2-reducing enzymes in the tolerance to the physiological O2 tensions faced by C. difficile during its infectious cycle. These four enzymes have different spectra of action and protect the vegetative cells over a large range of O2 tensions. These differences are associated with a distinct regulation of each gene encoding those enzymes. The complex network of regulation is crucial for C. difficile to adapt to the various O2 tensions encountered during infection.

The intestinal microbiome of infants with cow's milk-induced FPIES is enriched in taxa and genes of enterobacteria

OBJECTIVES

Food protein-induced enterocolitis syndrome (FPIES) is a severe type of non-IgE (immunoglobulin E)-mediated (NIM) food allergy, with cow's milk (CM) being the most common offending food. The relationship between the gut microbiota and its metabolites with the inflammatory process in infants with CM FPIES is unknown, although evidence suggests a microbial dysbiosis in NIM patients. This study was performed to contribute to the knowledge of the interaction between the gut microbiota and its derived metabolites with the local immune system in feces of infants with CM FPIES at diagnosis.

METHODS

Twelve infants with CM FPIES and a matched healthy control group were recruited and the gut microbiota was investigated by 16S amplicon and shotgun sequencing. Fatty acids (FAs) were measured by gas chromatography, while immune factors were determined by enzyme-linked immunosorbent assay and Luminex technology.

RESULTS

A specific pattern of microbiota in the gut of CM FPIES patients was found, characterized by a high abundance of enterobacteria. Also, an intense excretion of FAs in the feces of these infants was observed. Furthermore, correlations were found between fecal bifidobacteria and immune factors.

CONCLUSION

These fecal determinations may be useful to gain insight into the pathophysiology of this syndrome and should be taken in consideration for future studies of FPIES patients.