Shifts In Microbiota Research Articles

Association between changes in genital immune markers and vaginal microbiome transitions in bacterial vaginosis

Bacterial vaginosis (BV), characterized by an imbalance in the vaginal microbiota, is a prevalent condition among women of reproductive age and a risk factor for human immunodeficiency virus, sexually transmitted infections, and preterm birth. BV is generally considered to induce mucosal inflammation, but the specific pathways and cell types involved are not well characterized. This prospective study aimed to assess associations between microbial changes and mucosal immune responses in BV patients. Therefore, samples from 20 premenopausal women with BV and treated with metronidazole were analyzed. Vaginal swabs, menstrual cup, and endocervical cytobrush samples were collected before treatment, weekly for four weeks, and at 2, 4, and 6 months for Nugent scoring, immune cell populations and cytokine analysis. Of 105 study intervals, 27 (25.7%) showed improvement in Nugent category, 61 (58.1%) remained unchanged, and 17 (16.2%) worsened. Improvement correlated with decreased monocytes (p = 0.005), while worsening was linked to increased monocytes (p < 0.001) and dendritic cells (p = 0.02). B cells (p = 0.02) and IFN-γ-induced chemokines - IP-10 (p = 0.007), MIG (p = 0.049), and ITAC (p = 0.005) - were associated with improvement. In conclusion, although the T-cell-associated chemokines IP-10, ITAC, and MIG were strongly associated with improvements in Nugent category, our findings indicate that antigen-presenting cells, particularly monocytes, show the most dynamic response to shifts in the vaginal microbiota in patients with BV.

Microbiome characterization of patients with Crohn disease and the use of fecal microbiota transplantation: A review.

Inflammatory bowel disease is a chronic inflammatory condition predominantly affecting the intestines, encompassing both ulcerative colitis and Crohn disease (CD). As one of the most common gastrointestinal disorders, CD's pathogenesis is closely linked with the intestinal microbiota. Recently, fecal microbiota transplantation (FMT) has gained attention as a potential treatment for CD, with the effective reestablishment of intestinal microecology considered a crucial mechanism of FMT therapy. This article synthesizes the findings of population-based cohort studies to enhance our understanding of gut microbial characteristics in patients with CD. It delves into the roles of "beneficial" and "pathogenic" bacteria in CD's development. This article systematically reviews and compares data on clinical response rates, remission rates, adverse events, and shifts in bacterial microbiota. Among these studies, gut microbiome analysis was conducted in only 7, and a single study examined the metabolome. Overall, FMT has demonstrated a partial restoration of typical CD-associated microbiological alterations, leading to increased α-diversity in responders and a moderate shift in patient microbiota toward the donor profile. Several factors, including donor selection, delivery route, microbial state (fresh or frozen), and recipient condition, are identified as pivotal in influencing FMT's effectiveness. Future prospective clinical studies with larger patient cohorts and improved methodologies are imperative. In addition, standardization of FMT procedures, coupled with advanced genomic techniques such as macroproteomics and culture genomics, is necessary. These advancements will further clarify the bacterial microbiota alterations that significantly contribute to FMT's therapeutic effects in CD treatment, as well as elucidate the underlying mechanisms of action.

P1342 Characteristics of the gut microbiota of patients with concomitant inflammatory bowel disease and psoriatic arthritis

Abstract Background Inflammatory bowel disease (IBD) and psoriatic arthritis (PsA) are immune-mediated diseases (IMDs) that have been independently related to shifts in the gut microbiota. In this pilot study, we analyzed whether, in patients in whom both IMIDs coexist, the composition and function of the gut microbiota is different from when only one of the two IMDs exists. Methods Transversal observational study performed at a Spanish tertiary hospital. Ten patients with concomitant IBD and PsA (group A) were included. Two age, gender and disease duration matched control groups were also created, one with IBD-only patients (group B, n=20), and another with PsA-only patients (group C, n=20). Demographic and clinical characteristics were recorded. Stool samples were collected and the variable region V3–V4 of the bacterial 16S rRNA genes present in the feces was PCR-amplified and the resulting amplicons were sequenced on an Illumina NovaSeq 6000 instrument. Short chain fatty acids (SCFA) were analyzed by gas chromatography from the supernatants of the homogenized feces. Dietary assessment was registered by an online food frequency questionnaire specifically designed for intestinal disturbances; foods were transformed into nutrients and dietary compounds. For statistical analysis, ANOVA was used to compare the three groups (when the ANOVA was significant [p&amp;lt;0.05], Bonferroni's test was used for post-hoc comparisons). Results Globally, the microbiota of the different study groups did not show major rearrangements, with alpha diversity not showing statistically significant differences between them. However, beta diversity analyses indicated that the microbiotas of groups C and B were statistically different, with group A occupying an intermediate position. A linear discriminant analysis of the effect size showed that group A was enriched in certain microorganisms such as Akkermansia, while group C was enriched in Bacteroides (Figure 1). The quantification of the fecal levels of SCFA showed no statistical significant differences between the three groups. Moreover, no significant differences were observed regarding energy and nutrient intake between the assessed groups. Conclusion Our results suggest the existence of different gut microbiota profiles in subjects suffering from PsA or IDB, while patients with both conditions have an intermediate composition. These differences do not see to result from different dietary habits, since no differences in nutrient or energy intake between the groups were observed.

P1316 Increased ultra-processed food consumption is associated with inflammation-promoting shift of gut microbiota in Inflammatory Bowel Disease

Abstract Background Previous epidemiologic studies have suggested that increased consumption of ultra-processed food (UPF) can increase the risk of developing inflammatory bowel disease (IBD) by exacerbating gut dysbiosis.1 However, studies directly linking UPF to specific microbial shift in IBD patients are limited. Our study explored differences in gut microbiota profile based on UPF intake in patients with IBD. Methods This multi-centre cohort study included 313 IBD patients from three hospitals. Patients were divided into four quartiles (Q1, Q2, Q3, Q4) based on their percentage UPF consumption, evaluated from the Korea National Health and Nutritional Examination Survey. 16S rRNA sequencing was conducted on stool samples to analyse microbial composition. Subgroup analysis was performed based on IBD activity, whereby faecal calprotectin 250 ug/g was used as a cutoff value for defining active and remission state. UPF quartiles were grouped as Q1, Q2 and Q3, Q4 when conducting subgroup analysis to maintain an adequate number of samples for comparison. Age-adjusted analysis was conducted on patients younger than 50 years. Results General characteristics of the study population showed that there were no significant differences in inflammatory markers between quartiles. However, age was significantly different (p=0.001), with the first quartile having the highest median age of 49 years. Microbial analysis showed differences in beta diversity across quartiles (p=0.046), with the abundance of Lachnospiraceae and Faecalibacterium decreasing as UPF consumption increased. Subgroup analysis showed that patients with active inflammation showed no difference in alpha or beta-diversity, but Lactobacillus was more abundant in Q1, Q2 than Q3, Q4. Patients in remission differed in beta-diversity (p=0.012), with a greater abundance of Lachnospiraceae and Faecalibacterium in Q1, Q2 and Escherichia/Shigella and Veillonella in Q3, Q4. Age-adjusted analysis showed that in active IBD, Lactobacillus was more abundant in Q1, Q2 whereas Enterobacteriaceae was more abundant in Q3, Q4. Age-adjusted analysis of patients in remission showed that Lachnospiraeae, Faecalibacterium, Bifidobacterium were more abundant in Q1, Q2 than Q3, Q4. Conclusion This study suggests that increased UPF consumption is associated with an inflammatory-promoting shift in the gut microbiome of IBD patients. Restricting UPF intake may be important for controlling gut inflammation and preventing IBD relapse.

Unraveling the shifts in the belowground microbiota and metabolome of Pinus pinaster trees affected by forest decline.

Pinus pinaster Aiton (maritime pine) stands are suffering a generalized deterioration due to different decline episodes throughout all its distribution area. It is well known that external disturbances can alter the plant associated microbiota and metabolome, which ultimately can entail the disruption of the normal growth of the hosts. Notwithstanding, very little is known about the shifts in the microbiota and the metabolome in pine trees affected by decline. The aim of our work was to unravel whether bacterial and fungal communities inhabiting the rhizosphere and root endosphere of P. pinaster trees with symptoms of decline and affected by Matsucoccus feytaudi in the National Park of Sierra Nevada (Granada, Spain) showed alterations in the structure, taxonomical profiles and associative patterns. We also aimed at deciphering potential changes in the rhizosphere and root metabolome. Trees infected by M. feytaudi and healthy individual harbored distinct microbial communities at both compositional and associative patterns. Unhealthy trees were enriched selectively in certain plant growth promoting microorganisms such as several ectomycorrhizal fungi (Clavulina) and Streptomyces, while other beneficial microorganisms (Micromonospora) were more abundant in unaffected pines. The rhizosphere of unhealthy trees was richer in secondary metabolites involved in plant defense than healthy pines, while the opposite trend was detected in root samples. The abundance of certain microorganisms was significantly correlated with several antimicrobial metabolites, thus, being all of them worthy of further isolation and study of their role in forest decline.

Pneumocystis Pneumonia Severity Is Associated with Taxonomic Shifts in the Respiratory Microbiota.

Pneumonia caused by Pneumocystis jirovecii infection (PCP) is a potentially life-threatening illness, particularly affecting the immunocompromised. The past two decades have shown an increase in PCP incidence; however, the underlying factors that promote disease severity and fatality have yet to be fully elucidated. Recent evidence suggests that the microbiota of the respiratory tract may play a role in stimulating or repressing pulmonary inflammation, as well as the progression of both bacterial and viral pneumonia. Here, we employed 16S rRNA metataxonomic sequencing to profile the respiratory microbiota of patients with mild-moderate and severe PCP. Our results show that the upper and lower airways of PCP patients have bacterial profiles which have been associated with a pro-inflammatory response. Furthermore, we find that severe PCP is associated with lower bacterial diversity and an increase in Prevotella and a decrease in Neisseria. Functionally, severe PCP was associated with a decrease in metabolic pathways of molecules with anti-inflammatory and antimicrobial properties. To our knowledge, this is the first study showing an association of PCP severity with shifts in the respiratory microbiome and may provide some insight into which patients are more susceptible to the more severe manifestations of the disease.

Effects of prebiotics from diverse sources on dysbiotic gut microbiota associated to western diet: Insights from the human Mucosal ARtificial COLon (M-ARCOL).

Associated to various illnesses, Western Diet (WD) is acknowledged to have deleterious effects on human gut microbiota, decreasing bacterial diversity, lowering gut bacteria associated to health (such as Akkermansia muciniphila), while increasing those linked to diseases (e.g., Proteobacteria). In this study, we evaluated the potential of two new prebiotics to counteract the negative effect of WD on gut microbiota, namely raffinose family oligosaccharides (RFO) from chickpeas and laminarin (LAM) from algae, when compared to the well-known inulin (INU). The effects of prebiotics on gut microbiota composition and metabolic activities were investigated in the Mucosal-Artificial Colon, set-up to reproduce WD condition, as compared to healthy control (n=3). None of the prebiotics was able to efficiently offset the shift in microbiota induced by WD. Nevertheless, when compared to non-supplemented WD, all prebiotics showed significant impacts on microbiota composition, that were both prebiotic and donor-dependant. RFO was the only prebiotic to enhance α-diversity, while it led to an increase in Blautia and Butyricicoccaceae, associated with higher amounts of gas and butyrate. LAM and INU did not strongly impact microbial metabolic activities but were associated with a rise in Prevotella_9/Agathobacter and Faecalibacterium, respectively. To conclude, this study showed that all tested prebiotics had different impacts on human gut microbiota structure and activities, which was further donor-dependent. M-ARCOL appears as a suitable in vitro tool to better understand the mechanisms of action of prebiotic compounds in relation to gut microbes and define responders and non-responders to prebiotic supplementation, opening the possibility of customized nutritional strategies.

Impact of Food Physical Properties on Oral Drug Absorption: A Comprehensive Review.

Food-Drug Interaction (FDI) refers to the phenomenon where food affects the pharmacokinetic or pharmacodynamic characteristics of a drug, significantly altering the drug's absorption rate or absorption extent. These Interactions are considered as a primary determinant in influencing the bioavailability of orally administered drugs within the gastrointestinal tract. The impact of food on drug absorption is complex and multifaceted, potentially involving alterations in gastrointestinal physiology, increases in splanchnic blood flow rates, and shifts in the gut microbiota's composition. Up to now, extensive research has focused on the interactions between food composition (such as proteins, fats, and vitamins) and drug absorption. In contrast, the impact of food physical properties (such as viscosity, volume, and pH) has received less attention in drug development. This article reviewed the impact of food properties on oral drug absorption based on a comprehensive literature search, focusing on the influence of food volume and food viscosity. From the perspective of pharmacokinetics, we examined interaction trends between food properties and drugs across different classification based on the Biopharmaceutics Classification System (BCS). In addition, we introduced the practical application of physiologically based pharmacokinetic (PBPK) modeling in predicting oral drug absorption under the influence of food Properties.

Modulation of chronic obstructive pulmonary disease progression by antioxidant metabolites from Pediococcus pentosaceus: enhancing gut probiotics abundance and the tryptophan-melatonin pathway

ABSTRACT Chronic obstructive pulmonary disease (COPD), a condition primarily linked to oxidative stress, poses significant health burdens worldwide. Recent evidence has shed light on the association between the dysbiosis of gut microbiota and COPD, and their metabolites have emerged as potential modulators of disease progression through the intricate gut-lung axis. Here, we demonstrate the efficacy of oral administration of the probiotic Pediococcus pentosaceus SMM914 (SMM914) in delaying the progression of COPD by attenuating pulmonary oxidative stress. Specially, SMM914 induces a notable shift in the gut microbiota toward a community structure characterized by an augmented abundance of probiotics producing short-chain fatty acids and antioxidant metabolisms. Concurrently, SMM914 synthesizes L-tryptophanamide, 5-hydroxy-L-tryptophan, and 3-sulfino-L-alanine, thereby enhancing the tryptophan-melatonin pathway and elevating 6-hydroxymelatonin and hypotaurine in the lung environment. This modulation amplifies the secretion of endogenous anti-inflammatory factors, diminishes macrophage polarization toward the M1 phenotype, and ultimately mitigates the oxidative stress in mice with COPD. The demonstrated efficacy of the probiotic intervention, specifically with SMM914, not only highlights the modulation of intestine microbiota but also emphasizes the consequential impact on the intricate interplay between the gastrointestinal system and respiratory health.

Specialized Feed-Additive Blends of Short- and Medium-Chain Fatty Acids Improve Sow and Pig Performance During Nursery and Post-Weaning Phase.

The present study investigates the impact of supplementing diets with a synergistic blend of short- and medium-chain fatty acids (SCFAs-MCFAs) during the peripartum and lactation phases on early microbial colonization and the subsequent growth performance of newborn pigs. The experiment involved 72 sows and their litters, with a follow-up on 528 weaned pigs. Sows were fed either a control diet or a diet supplemented with SCFAs-MCFAs and the pigs were monitored for their growth performance and microbial populations. Subsequently, selected weaned pigs were allotted to an SCFAs-MCFAs diet according to the maternal diet. Results showed that SCFAs-MCFAs supplementation led to reduced backfat loss in sows and improved pig weight and uniformity at weaning (p < 0.05). Additionally, suckling pigs exhibited significant shifts in gut microbiota, including increased lactic acid bacteria and reduced Streptococcus suis populations (p < 0.05). Although there was no influence of maternal diet on pig growth after weaning, there was a modulation on bacterial populations at 7 and 35 days post-weaning. Pigs fed SCFAs-MCFAs demonstrated improved feed efficiency with notable reductions in E. coli and Streptococcus suis counts. The findings suggest that maternal dietary supplementation with SCFAs-MCFAs can positively influence both sow and pig performance, offering a potential strategy to enhance productivity and health in the commercial swine production.

Long-term adaptation to dietary shifts of gut microbiota in gilthead seabream (Sparus aurata)

In many meta-analyses and literature reviews on fish microbiota, the provenance of the animals (farmed vs. wild) is often overlooked. Given the well-established role of diet as a key factor in shaping gut microbiota, this study investigates the impact of dietary nature by comparing the microbiota of gilthead seabream (Sparus aurata) fed a commercial diet versus a wild-type diet, all reared within a recirculating aquaculture system. Over a 60-day period, we tracked changes in gut bacterial diversity, structure, and composition following a shift from a commercial feed to a diet exclusively based on pink shrimp (Parapenaeus longirostris). Gut bacterial communities were assessed using 16S rRNA gene sequencing (Illumina MiSeq platform) with primers targeting the V3-V4 hypervariable regions. Twenty days after the dietary change, microbial diversity (Shannon index) increased in fish fed the shrimp diet compared to those fed the commercial diet, while Dominance index values decreased. Additionally, inter-individual (beta-) diversity based on Bray-Curtis distances also differed between dietary treatments. These results support further that microbiota comparisons between farmed/captive and wild fish are challenging due to the unpredictable feeding regimes and dietary variations in wild fish. However, the diet impact on microbiota diminished over time, with the differences in intra- and inter-individual diversity being reduced after 40 days, which suggests an adaptation of microbial communities to dietary changes. At this point, gut microbial communities also showed a similar taxonomical composition. Moreover, a core microbiota consisting of species belonging to the genera Ralstonia, Paraburkholderia, Fulvimonas, Pseudomonas, and Cutibacterium was maintained in all sampling times under both dietary treatments. Overall, this study serves as a conceptual approach that shows a long-term adaptation of the gut microbiota after a radical dietary change, probably driven by host-inherent factors. Furthermore, these results may be a valuable insight for feed manufacturers aiming to develop sustainable and cost-effective ingredients since they suggest that some alternative feeds and ingredients do not have adverse long-term effects on fish gut microbiota.

Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial

BackgroundNowadays, obesity has become a major health issue. In addition to negatively affecting body composition and metabolic health, recent evidence shows unfavorable shifts in gut microbiota in individuals with obesity. However, the effects of weight loss on gut microbes and metabolites remain controversial. Therefore, the purpose of this study was to investigate the effects of a 12-week program on gut microbiota and metabolic health in patients with obesity.MethodsWe conducted a controlled trial in 23 male and female patients with obesity. Twelve participants completed a 12-week program of caloric restriction combined with strength and HIIT training (INT, pre-BMI 37.33 ± 6.57 kg/m2), and eleven participants were designated as non-intervention controls (pre-BMI 38.65 ± 8.07 kg/m2). Metagenomic sequencing of the V3-V4 region of the 16S rDNA gene from fecal samples allowed for gut microbiota classification. Nuclear magnetic resonance spectroscopy characterized selected serum and fecal metabolite concentrations.ResultsWithin INT, we observed a significant improvement in body composition; a significant decrease in liver enzymes (AST, ALT, and GMT); a significant increase in the relative abundance of the commensal bacteria (e.g., Akkermansia muciniphila, Parabacteroides merdae, and Phocaeicola vulgatus); and a significant decrease in the relative abundance of SCFA-producing bacteria (e.g., the genera Butyrivibrio, Coprococcus, and Blautia). In addition, significant correlations were found between gut microbes, body composition, metabolic health biomarkers, and SCFAs. Notably, the Random Forest Machine Learning analysis identified predictors (Butyrivibrio fibrisolvens, Blautia caecimuris, Coprococcus comes, and waist circumference) with a moderate ability to discriminate between INT subjects pre- and post-intervention.ConclusionsOur results indicate that a 12-week caloric restriction combined with strength and HIIT training positively influences body composition, metabolic health biomarkers, gut microbiota, and microbial metabolites, demonstrating significant correlations among these variables. We observed a significant increase in the relative abundance of bacteria linked to obesity, e.g., Akkermansia muciniphila. Additionally, our study contributes to the ongoing debate about the role of SCFAs in obesity, as we observed a significant decrease in SCFA producers after a 12-week program.Trial registrationThe trial was registered on [05/12/2014] with ClinicalTrials.gov (No: NCT02325804).

Basic Molecular Biology, Metabolic and Immunological Mechanisms of Fecal Microbiota Transplantation

Aim: demonstration of basic molecular biological, metabolic and immunological effects of fecal microbiota transplantation (FMT), on the example of a rare case of acute graft-versus-host disease (GVHD) with intestinal damage in a patient after allogeneic hematopoietic stem cell transplantation (allo-HSCT).Materials and methods. To monitor the basic effects of FMT, we performed targeted DNA sequencing of 16S rRNA gene (V3–V4) using MiSeq platform as well as multiplex real-time PCR, MS/gas chromatography technique, immunophenotyping of blood lymphocytes, histological and immunohistochemical techniques.Clinical case. A 40-year-old female patient diagnosed with myelodysplastic syndrome, with a history of two unsuccessful allo-HSCTs due to graft failure, underwent the third haploidentical HSCT (haplo-HSCT) from her father as ‘salvage’ therapy. Due to early viral/bacterial colitis post-transplant associated with a multidrug-resistant strain of K. pneumoniae and herpes virus type 6, FMT was performed on days 46 and 47 after allo-HSCT. Complete resolution of the enteropathy symptoms was noted following FMT. However, immunosuppressive therapy was canceled on D+106 after haplo-HSCT due to the detection of minimal residual disease causing development of the ‘overlap’-type GVHD with damage skin lesions grade 4, and intestinal mucous membranes grade 3. This complication required resumption and subsequent intensification of immunosuppressive therapy with complete resolution of GVHD symptoms. Following FMT treatment, the patient showed complete resolution of clinical colitis symptoms. According to results of 16S rRNA sequencing, the species-specific diversity of fecal microbiota increased significantly, along with decreased relative contents of opportunistic bacteria (Klebsiella, Enterococcus, Streptococcus genera). A significant growth was revealed for commensal Bacteroidota, and re-emergence of Faecalibacterium, Blautia, Roseburia. Acute gastrointestinal GVHD promoted by tacrolimus withdrawal was associated with repeated depletion of intestinal microbiota. Upon resolution of GVHD and resumed immunosuppression, increased microbiota diversity (Shannon index) was again recorded, and the parameters of patient’s fecal microbiota reached the donor values. The microbiota shifts at all clinical stages (before and after FMT, at the peak of acute intestinal GVHD and intensive immunosuppressive therapy) showed some relations with metabolism of bile and fatty acids in blood plasma and immune parameters.Conclusions. FMT may be a component of complex therapy aimed at early reconstitution of immune system and organic acid metabolism in patients after allo-HSCT. The composition of fecal microbiota, metabolic profile and spectrum of lymphocyte subpopulations may be markers for monitoring complex rehabilitation after allo-HSCT.

Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice

ABSTRACT Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1 ∆IEC mice carrying an intestinal epithelial deletion of the Crohn’s disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1 ∆IEC pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1 ∆IEC mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.

Effect of dietary fat source on the composition of the cecal microbiome in maturing broiler chicken.

Diet has been found to significantly influence gut microbiota throughout various life stages, and gut microbiota have been increasingly shown to influence host physiology, health, and behavior. This study uses 16S rRNA sequencing to examine the effects of six different fat-supplemented diets (canola oil, coconut oil, fish oil, flaxseed oil, lard, and olive oil) on broiler chicken cecal microbial composition and predicted function in comparison with a common and inexpensive fat source (poultry fat). Groups of broilers were fed each of these diets and then evaluated on day 41 and day 55 of age. For both 41- and 55-day samples, Firmicutes and Bacteroidetes phyla were the dominant bacteria in the ceca accounting for 99% of the microbial community. Across the 41- and 55-day samples, treatment time was associated with a stronger and more significant microbiota shift (p < 0.001) than differences in dietary treatment alone (p = 0.117), but dietary treatment combined with treatment time is a significant factor as well (p = 0.047). Sparse partial least squares discriminant analysis was used to explore the more discriminating taxa for each treatment group. For identified species, butyrate production appears to be affected in a diet-specific manner, with many butyrate-producing species being evident for the fish-based diet at day 41 and a few of these species for the flaxseed-based diet at day 55. Predicted functions, as conducted with PICRUSt2, were significant for comparisons between the control and the flaxseed-based dietary treatment group at day 55, with indications of host health benefit for the flaxseed-based diet. Predicted functions found to be significant were for enzymes and pathways such as propionate CoA ligase, aminobutyraldehyde dehydrogenase, vitamin B12-transporting ATPase, thiamine kinase, acetylneuraminate epimerase, and L-tryptophan biosynthesis. This study provides insight surrounding specific dietary fat-based treatments to be investigated further and highlights the importance of polyunsaturated fat sources in poultry feed that may offer a favorable cecal microbial modulation compared to saturated fat sources.

Effects of Increasing Temperature on Bacterial Community Diversity in Mixed Stands of Artemisia argyi and Solidago canadensis in Eastern China.

Global climate change and invasive plants significantly impact biodiversity and ecosystem functions. This study focuses on the effects of progressive warming on microbial communities within the Solidago canadensis invasion community, simulated through six stages of invasion progression, from minimal to dominant S. canadensis presence alongside native Artemisia argyi, in bulk soils collected from a natural habitat and cultivated under controlled greenhouse conditions. Utilizing high-throughput sequencing and microbial community analysis on 72 samples collected from the S. canadensis invasion community, the shifts in soil microbiota under varying warming scenarios were investigated (+0 °C, +1.15 °C and +1.86 °C). We observed significant shifts in invasion community soil bacteria in response to warming, with Acidobacteria, Actinobacteria, and others showing distinct responses between baseline and warmed conditions, while groups like Chlorobi and Cyanobacteria only differed significantly at higher temperature extremes. The random forests algorithm identified 14 taxa as biomarkers and a model was established to correlate S. canadensis invasion community soil microbiota with progressive warming. Co-occurrence network analysis revealed that moderate warming enhances microbial connectivity and the presence of a super-generalist, ASV 1160. However, further warming disrupts these networks by eliminating key generalists, revealing a potential reduction in network stability and diversity. These findings illuminate the dynamic responses of microbes in S. canadensis invasion community soil to varying temperature regimes, suggesting a model for successional dynamics and offering a deeper comprehension of microbial community shifts amid climatic fluctuations. This study delineates how warming significantly reshapes the soil microbial composition, potentially impacting S. canadensis's invasion success unfavorably, thereby highlighting the importance of considering microbial dynamics in ecological management.

Curcumin Mitigates Gut Dysbiosis and Enhances Gut Barrier Function to Alleviate Metabolic Dysfunction in Obese, Aged Mice.

The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis in aged mice fed a high-fat, high-sugar diet (HFHSD). Eighteen- to twenty-one-month-old male C57BL/6 mice were divided into groups fed a normal chow diet or HFHSD, with or without curcumin supplementation (0.4% w/w) for 8 and 15 weeks. We assessed body weight, food intake, insulin sensitivity, gut microbiota composition, and gene expression in the gut and liver and performed histological analysis of gut tissues. Curcumin supplementation prevented HFHSD-induced weight gain and metabolic disturbances. In the gut, curcumin-treated mice showed a higher abundance of beneficial bacterial genera, such as Lachnospiraceae, Akkermansia, Mucispirillum, and Verrucomicrobiota, alongside a lower abundance of harmful bacterial genera like Desulfobacteria, Alistipes, and Muribaculaceae compared to control. This shift in gut microbiota was associated with improved gut integrity, as demonstrated by increased expression of the tight junction protein occludin and reduced levels of the pro-inflammatory marker interleukin-1β in the ileum. Additionally, curcumin modulated hepatic gene expression involved in bile acid homeostasis, suggesting a positive effect on liver health. Curcumin supplementation can alleviate the negative effects of aging and an HFHSD on the gut microbiome, improve gut barrier integrity, and maintain bile acid homeostasis. These findings highlight curcumin's potential as a dietary intervention for managing obesity- and age-associated gut health issues.

TLR2/TLR5 Signaling and Gut Microbiota Mediate Soybean-Meal-Induced Enteritis and Declined Growth and Antioxidant Capabilities in Large Yellow Croaker (Larimichthys crocea)

Soybean meal, renowned for its high yield, cost efficiency, and protein richness, serves as a pivotal plant-based alternative to fish meal. However, high soybean meal inclusion in Larimichthys crocea diets is linked to enteritis and oxidative damage, with unknown mechanisms. Our study aims to elucidate the molecular basis of soybean-meal-induced enteritis and its impact on intestinal microbiota in L. crocea. To this end, four isonitrogenous and isolipidic diets with varying soybean meal levels (0% FM, 15% SBM15, 30% SBM30, and 45% SBM45) were administered to L. crocea for 8 weeks. The results indicated that the SBM30 and SBM45 treatments significantly hindered fish growth, digestive efficiency, and protein utilization. Furthermore, high soybean meal levels (SBM30 and SBM45) activated intestinal Toll-like receptors (TLR2A, TLR2B, TLR5, and TLR22), stimulating C-Rel and mTOR protein expression and elevating ERK phosphorylation. This led to increased pro-inflammatory cytokine production (IL-1β, IL-6, and TNF-α) and decreased anti-inflammatory cytokine expression (IL-4/13A, IL-4/13B, and TGF-β), suggesting a potential signaling pathway for soybean-meal-induced enteritis. Furthermore, enteritis induced by high soybean meal levels led to oxidative damage, evident from increased MDA levels and decreased antioxidant enzyme activities (SOD and CAT). The SBM30 and SBM45 treatments increased Firmicutes and Bacteroidetes abundance in fish gut microbiota, while Proteobacteria abundance decreased. This microbiota shift may enhance soybean meal nutrient utilization, yet high soybean meal concentrations still impair growth. A soybean-meal-rich diet promotes harmful bacteria like Rhodococcus and depletes probiotics like Ralstonia, increasing disease risks. L. crocea has limited tolerance for soybean meal, necessitating advanced processing to mitigate anti-nutritional factors. Ultimately, exploring alternative protein sources beyond soybean meal for fish meal replacement is optimal for L. crocea.

Western diet promotes endometriotic lesion growth in mice and induces depletion of Akkermansia muciniphila in intestinal microbiota.

Endometriosis, affecting 10% of women in their reproductive years, remains poorly understood. Both individual and environmental unexplained factors are implicated in this heterogenous condition. This study aims to examine the influence of a Western diet on endometriosis lesion development in mice and to uncover the mechanisms involved. Mice were fed either a control diet or a Western diet (high in fatty acids and low in fiber) for 4weeks. Endometriosis was then surgically induced, and lesion development was monitored by ultrasound. After 7weeks, the mice were sacrificed for analysis of lesion characteristics through RT-qPCR, immunohistochemistry, and flow cytometry. Additionally, the intestinal microbiota was assessed using 16S rRNA gene sequencing. Mice on the Western diet developed lesions that were significantly twice as large compared to those on the control diet. These lesions exhibited greater fibrosis and proliferation, alongside enhanced macrophage activity and leptin pathway expression. Changes in the intestinal microbiota were significantly noted after endometriosis induction, regardless of diet. Notably, mice on the Western diet with the most substantial lesions showed a loss of Akkermansia Muciniphila in their intestinal microbiota. A Western diet significantly exacerbates lesion size in a mouse model of endometriosis, accompanied by metabolic and immune alterations. The onset of endometriosis also leads to substantial shifts in intestinal microbiota, suggesting a potential link between diet, intestinal health, and endometriosis development.

Tegoprazan-Amoxicillin Dual Therapy for Helicobacter pylori Eradication: A Prospective, Randomized, Multicenter Study in Fujian, China.

Few studies have investigated the efficacy and safety of tegoprazan-amoxicillin (TA) dual therapy for Helicobacter pylori eradication. We aim to evaluate the effectiveness and safety of different dosages of TA dual therapy for H. pylori eradication. This prospective, randomized, open-label, multicenter study was conducted at four centers in Fujian, China. H. pylori-infective patients were randomized 1:1:1 to receive one of the following treatments: bismuth quadruple therapy (BQT, esomeprazole 20 mg twice daily + potassium bismuth citrate 240 mg twice daily + amoxicillin 1 g twice daily + clarithromycin 500 mg twice daily), tegoprazan-amoxicillin dual therapies (TA-qd, tegoprazan 50 mg once daily + amoxicillin 1 g thrice daily; TA-bid, tegoprazan 50 mg twice daily + amoxicillin 1 g thrice daily) for 14 days. The primary outcome was noninferiority in eradication rates of the different TA groups compared to the BQT group. Secondary outcomes encompassed an assessment of adverse reactions and clinical symptom relief. Additionally, exploratory outcomes were focused on the shifts in gut microbiota and a cost-effectiveness analysis. A total of 321 patients were enrolled. The eradication rates in the BQT group, TA-qd group, and TA-bid group were 85.05% (91/107), 85.98% (92/107), and 85.98% (92/107) in the intention-to-treat analysis (ITT) (BQT vs. TA-qd, 95% CI -8.50% to 10.36%, noninferiority p = 0.012; BQT vs. TA-bid, 95% CI -8.50% to 10.36%, noninferiority p = 0.012); 91.00% (91/100), 91.09% (92/101), and 92.93% (92/99) in the modified intention-to-treat analysis (mITT) (BQT vs. TA-qd, 95% CI -7.81% to 7.98%, noninferiority p = 0.006; BQT vs. TA-bid, 95% CI -5.62% to 9.48%, noninferiority p < 0.001); 90.81% (89/98), 91.00% (91/100), and 93.81% (91/97) in the per-protocol analysis (PP) (BQT vs. TA-qd, 95% CI -7.83% to 8.19%, noninferiority p = 0.006; BQT vs. TA-bid, 95% CI 4.46% to 10.46%, noninferiority p < 0.001). The incidence of adverse reactions in the TA-qd and TA-bid groups was significantly lower than in the BQT group (13.33%, 14.56%, and 27.18%, respectively; p = 0.017). The complete remissions of clinical symptoms for BQT, TA-qd, and TA-bid were 36.89%, 65.71%, and 68.93%, respectively, had significant differences (p < 0.001). Two weeks of TA therapy altered gut microbiota diversity and composition, but that recovered 4 weeks after discontinuation. The cost-effectiveness ratios (CERs) for BQT, TA-qd, and TA-bid were 1.85 CNY, 2.08 CNY, and 3.69 CNY, respectively. Both TA dual therapies provided satisfactory eradication rates of > 90% for eradicating H. pylori, fewer adverse reactions, and greater clinical symptom relief compared to BQT, with a mild, reversible impact on gut microbiota. In addition, the TA dual therapy with low doses of tegoprazan showed better cost-effectiveness. Chinese Clinical Trial Register and registration No.: ChiCTR2300071997.