Urbanization has significantly transformed dietary habits worldwide, contributing to a globally increased burden of non-communicable diseases and altered gut microbiota landscape. However, it is often overlooked that the adverse effects of these dietary changes can be transmitted from the mother to offspring during early developmental stages, subsequently influencing the predisposition to various diseases later in life. This review aims to delineate the detrimental effects of maternal urban-lifestyle diet (urbanized diet) on early-life health and gut microbiota assembly, provide mechanistic insights on how urbanized diet mediates mother-to-offspring transfer of bioactive substances in both intrauterine and extrauterine and thus affects fetal and neonatal development. Moreover, we also further propose a framework for developing microbiome-targeted precision nutrition and diet strategies specifically for pregnant and lactating women. The establishment of such knowledge can help develop proactive preventive measures from the beginning of life, ultimately reducing the long-term risk of disease and improving public health outcomes.

The human gut microbiome, crucial in various diseases, can be utilized to develop diagnostic models through machine learning (ML). The specific tools and parameters used in model construction such as data preprocessing, batch effect removal and modeling algorithms can impact model performance and generalizability. To establish an generally applicable workflow, we divided the ML process into three above-mentioned steps and optimized each sequentially using 83 gut microbiome cohorts across 20 diseases. We tested a total of 156 tool-parameter-algorithm combinations and benchmarked them according to internal- and external- AUCs. At the data preprocessing step, we identified four data preprocessing methods that performed well for regression-type algorithms and one method that excelled for non-regression-type algorithms. At the batch effect removal step, we identified the "ComBat" function from the sva R package as an effective batch effect removal method and compared the performance of various algorithms. Finally, at the ML algorithm selection step, we found that Ridge and Random Forest ranked the best. Our optimized work flow performed similarly comparing with previous exhaustive methods for disease-specific optimizations, thus is generally applicable and can provide a comprehensive guideline for constructing diagnostic models for a range of diseases, potentially serving as a powerful tool for future medical diagnostics.

Mango seed kernel polysaccharides (MSKP) were investigated for their structural characteristics, rheological properties, immunomodulatory effects, and potential benefits for gut health. The molecular weight of extracted MSKP was 4.2 × 104 Da. The primary monosaccharide in MSKP was found to be xylose, which accounted for 25.74 mol% of the total. Fucose, 22.65 mol%, rhamnose, 12.72 mol%, mannose, 11.87 mol%, ribose, 9.21 mol%, glucose, 7.87 mol%, arabinose, 6.11 mol%, and galactose, 3.81 mol%. The proposed structure of MSKP is →4) β -d-Xyl(1 → 4)α-d-Glc(1 → 4) α -d-Gal(1 → 6)β-d-Rib(1 → 3)β-d-Ara(1 → 6)α-d-Glc(1 → 2)β-d-Fuc(1 → 6)α-d-Rha(1→. MSKP solutions exhibited shear-thinning behavior, where viscosity decreased with increasing shear rates. Using an advanced extraction technique, MSKP was shown to enhance immune responses by stimulating nitric oxide production, acid phosphatase activity, and phagocytosis in RAW 264.7 murine cells. Importantly, simulated digestive tests indicated MSKP's resilience, showing no changes in molecular weight, monosaccharide content, or reducing sugar levels, suggesting it could reach the large intestine intact. This resilience promotes the increase of short-chain fatty acids (SCFAs) in the gut, highlighting MSKP's potential as a functional food for supporting gut health and preventing disease.

The gut microbiome supports both gut and overall health. Diet is known to be one of the driving factors that influences the gut microbiome. The foods we eat, the dietary and nondietary components they contain, various food consumption patterns, and the ratio of nutrients consumed have been shown to impact gut microbiome composition and function. Studies indicate that many acute and chronic diseases are associated with alterations to the gut microbiome. There are many patients who rely on enteral tube feeding for their nutrition support. More recently, enteral tube feeding formulations of "real food" have become commercially available. However, little is known about how enteral tube feeding impacts the gut microbiome in patients requiring this specialized form of nutrition therapy. This review summarizes the existing evidence regarding the food sources of commonly consumed macronutrients and their impact on the gut microbiome. Also presented is what is known regarding "standard" and real food enteral formulations on the gut microbiome. Existing evidence is suggestive that real food enteral formulations positively impact the gut microbiome. Still, more research is needed on ready-to-feed formulations, particularly in patients with various clinical conditions, and how gut microbiome modulation impacts clinical outcomes.

Diet has a profound impact in human health, which is partly driven by changes in the intestinal microbiota. Several associations between dietary intake and the intestinal microbiota composition and function have been described. Namely, the Mediterranean diet is associated with beneficial bacteria, while the intake of ultraprocessed foods is linked to dysbiosis. It is, therefore, very tempting to tailor dietary approaches to the individual needs of the microbiota; however, high-quality prospective data are lacking. Provisionally, a diet rich in fruits and vegetables and low in ultraprocessed foods is recommended to improve the intestinal microbiota composition and function.

Fermented dairy products are known for their efficiency in delivering and protecting probiotic microorganisms. However, there is a growing demand for diversification of the market with plant-based products. The aim of this study was to develop an oat beverage enriched with inulin and fermented with Lacticaseibacillus rhamnosus LR B and evaluate its synbiotic effects in vitro. For this purpose, the validated dynamic colon model (the TNO Intestinal Model TIM-2) was used with focus on the composition of the gut microbiota and its production of metabolites to evaluate the functionality. The fermentation kinetics, sugars, organic acids and inulin dosage in the fermented oat beverage were also evaluated. The acidification rate was 16.91 10-3 pH units.min-1, reaching the final pH of 4.5 in 2.38 ± 0.05 h. Dosages of sucrose, glucose and lactic acid were 23.35 ± 0.45 g.L-1, 21.37 ± 0.77 g.L-1, 0.94 ± 0.05 g.L-1, respectively. After simulated in vitro digestion, the inulin concentration was partially preserved with 20.11 ± 0.21 maltose equivalent (μg.mL-1). The fermented and pre-digested oat beverage (with 7.71 ± 0.44 log CFU.mL-1) was fed into TIM-2, which was previously inoculated with feces from healthy adults. The analysis identified nine bacterial taxa that were significantly modulated compared to the standard ileal effluent medium (SIEM) control. An increase in relative abundance of Lactobacillus and Catenibacterium, and reduction in Citrobacter, Escherichia-Shigella, and Klebsiella was observed. In addition, the cumulative means of short-chain fatty acids (SCFAs) increased, especially for acetate and butyrate. These findings suggest that the developed oat beverage can positively influence the gut microbiota and its activity, highlighting possible health benefits.

The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.

Childhood obesity is a considerable public health issue. Recent research has shown that alterations in gut microbiota can have an impact on developing obesity and other metabolic health problems in children. This study aimed to investigate whether the characteristics of gut microbiota in obese children and adolescents are associated with the severity of obesity and any metabolic complications.

During May 2022 to May 2023, a total of 56 children and adolescents with obesity, aged 6-18 years, were recruited at Thammasat Hospital, situated in provincial Pathumthani in central Thailand. Participants were allocated into two groups, characterized by the severity of their obesity. Demographic data, body composition, along with resting energy expenditures were determined. Serum samples were collected for the metabolic profile and inflammatory markers. Fecal samples were obtained for gut microbiota analysis via 16S rRNA Illumina. The obese group exhibited notably greater relative abundance of Actinobacteriota in comparison to the severely obese group, along with a lower abundance of Bacteroidota. There were no statistically significant differences in the relative abundance of Firmicutes and the Firmicutes to Bacteroidota ratio between the two cohorts. Bacteroidota positively correlated with FMI, while Actinobacteriota showed a negative correlation with FMI.

The data gathered from this study illustrated that children and adolescents with obesity and severe obesity in Thailand showed differences in the relative abundance of Actinobacteriota and Bacteroidota. Certain microbiome taxa showed correlations with various body and metabolic parameters.

Dietary patterns are strongly linked to the risk of major depressive disorder (MDD). However, research on the relationship between dietary patterns and MDD with suicidal ideation (MDD + SI) are limited. The Healthy Eating Index (HEI)-2015, Dietary Inflammatory Index (DII), Comprehensive Dietary Antioxidant Index (CDAI), Oxidative Balance Score (OBS), and Dietary Index for Gut Microbiota (DI-GM) are five validated tools for assessing dietary patterns based on inflammation, antioxidant capacity, and gut microbiota diversity. This study aims to investigate the association between these dietary indices and MDD + SI.

A total of 23,621 participants from the 2007-2020 National Health and Nutrition Examination Survey were included in this study. MDD and SI were assessed using the PHQ-9. Weighted multivariable logistic regression, subgroup analyses, and restricted cubic spline (RCS) models were applied to analyze the relationships between five dietary indices and the risks of MDD and MDD + SI.

All five dietary indices showed associations with MDD to varying degrees; however, only DI-GM exhibited a significant negative association with MDD + SI after adjustment for confounding factors. Subgroup and stratified linear trend analyses revealed that this association was stronger among former smokers, obese individuals and those with hypertension or diabetes. RCS analysis showed a significant non-linear relationship between DI-GM and MDD, while a significant linear dose-response relationship was observed for DI-GM and MDD + SI.

Cross-sectional study designs cannot establish causality.

The findings of this study revealed a significant association between DI-GM and MDD + SI. Dietary interventions that promote gut microbiota diversity may help reduce the risk of MDD + SI.

Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.

Visceral leishmaniasis (VL) is transmitted by Leishmania-infected sand fly bites and malnutrition is a known risk factor in human VL. Models using sand fly transmission or malnutrition promote parasite dissemination. By investigating features of L. donovani-Lutzomyia longipalpis transmission to malnourished mice, we show that a comparable IL1-β-driven acute inflammation is maintained in malnourished (MN-SF) and well-nourished (WN-SF) sand fly-infected mice. However, parasite dissemination was more pronounced in MN-SF that had a significantly higher acute (P ≤ 0.001) and chronic (P ≤ 0.0001) splenic parasite burden compared to WN-SF. Compared to WN-SF, MN-SF exhibited chronic clinical symptoms (P ≤ 0.0001), neutrophilia (P ≤ 0.001), lymphocytopenia (P ≤ 0.0001), increased heme oxygenase-1 (P ≤ 0.001) and IL17-A (P ≤ 0.0001) levels, dysregulation of liver enzymes, lymph node barrier dysfunction, and augmented dysbiosis, all associated with enhanced VL severity. Combining vector-transmission and malnutrition provides an improved model to study VL pathogenesis and host defense.

Digestive diseases have a high incidence worldwide, with various geographic, age, and gender factors influencing the occurrence and development of the diseases. The main etiologic factors involve genetics, environment, lifestyle, and dietary habits. In a low-oxygen environment, however, the body's tissue cells activate hypoxia-inducible factor (HIF), which produces different inflammatory mediators. Hypoxia impacts health at the molecular level by modulating cellular stress responses, metabolic pathways, and immune functions. It also alters gene expression and cellular behavior, thereby affecting gastrointestinal function. Under normal physiological conditions, the gastrointestinal mucus system serves as a crucial protective barrier, defending against mechanical injury, pathogenic invasion, and exposure to harmful chemicals. The integrity and functionality of this barrier are dependent on the synthesis and regulation of mucins and mucus, which are influenced by multiple factors. Additionally, the composition and diversity of the gastric microbiota are shaped by factors such as Helicobacter pylori infection, diet, and lifestyle. A balanced gastric microbiota supports gastrointestinal health and fortifies the mucus barrier. However, hypoxia can disrupt this equilibrium, leading to inflammation, alterations in the mucus layer, and destabilization of the gastric microbiota. Understanding the interplay between hypoxia, the mucus system, and the gastric microbiota is essential for identifying novel therapeutic strategies. Future research should elucidate the mechanisms through which hypoxia influences these systems and develop interventions to mitigate its adverse effects on gastrointestinal health. We examined the impact of hypoxia on the gastrointestinal mucus system and gastric microbiota, highlighting its implications for human health and potential therapeutic approaches.

A number of investigations have shown that gut microbiome influences humans' ability to communicate with others, and impairments in social interactions are linked to alterations in gut microbiome composition and diversity, via epigenetic mechanisms. This article reviews the links among gut microbiome, social behavior, and epigenetic shifts relevant to gut microbiome-derived metabolites. First, we discuss how different social determinants of health, such as socioeconomic status, diet, environmental chemicals, migration, ecological conditions, and seasonal changes may influence gut microbiome composition, diversity, and functionality, along with epigenetic alterations and thereby affect social behavior. Next, we consider how gut microbiome-derived metabolites, diet, probiotics, and fecal microbiome transplantation may reduce impairments in social interactions through the adjustment of epigenetic aberrations (e.g., DNA methylation, histone modifications, and microRNAs expression) which may suppress or increase gene expression patterns. Finally, we present the potential benefits and unresolved challenges with the use of gut microbiome-targeted therapeutics in reducing social deficits.

The human gut microbiota is closely associated with human health, influencing not only overall well-being but also the incidence and treatment outcomes of diseases. Altitudinal gradients are considered to impact gut microbial community characteristics through factors such as environmental temperature, humidity, and lifestyle. While previous studies have reported altitudinal variations in human gut microbiota in specific regions, a comprehensive exploration of these patterns at a global scale is still lacking. In this study, we analyzed 16S rRNA amplicon sequencing data from healthy human gut microbiota, spanning altitudes from 3 m to 3850 m, obtained from multiple open-access databases. The analysis focused on elucidating the altitudinal patterns of microbial diversity, community composition, and functional profiles.

After screening, a total of 6702 sequences from 15 countries were obtained. The diversity of human gut microbiota decreased with increasing altitude (R = -0.047, P < 0.001), but no consistent results were acquired among continents. The relative abundances of the genera Faecalibacterium and Blautia decreased with rising altitude (R = -0.131 and R = -0.135, respectively, P < 0.001 for both), while the relative abundance of the genus Prevotella increased with altitude (R = 0.336, P < 0.001). However, taxa such as Bacilliota, Bacteroides, and Bifidobacterium exhibit no consistent trends across different continents. The abundance of genes associated with the metabolism of terpenoids and polyketides, lipid metabolism, neurodegenerative diseases, and aging increased with altitude (R = 0.146, 0.037, 0.366, and 0.317, respectively; lipid metabolism P = 0.003, others P < 0.001). Conversely, the abundance of genes related to the immune system and carbohydrate metabolism decreased with increasing altitude (R = -0.166 and R = -0.219, respectively; P < 0.001 for both).

Altitude significantly influences diversity, composition, and functional attributes of the human gut microbiota.

Microbiota in the gastrointestinal tract play a crucial role in nutrient digestion, health and so forth in equines. As the research attention on gut microbes has increased, several studies have investigated the composition of the gastrointestinal microbial flora in equines. This article reviews the effects of breed, age, intestinal site, nutritional management and diseases on the gastrointestinal microbiota of horses and donkeys, thus offering references for improving the gastrointestinal microecological environment in these animals and preventing and controlling disease occurrence in them.

Dysbiosis refers to the disruption of the gut microbiota balance and is the pathological basis of various diseases. The main pathogenic mechanisms include impaired intestinal mucosal barrier function, inflammation activation, immune dysregulation, and metabolic abnormalities. These mechanisms involve dysfunctions in the gut-brain axis, gut-liver axis, and others to cause broader effects. Although the association between diseases caused by dysbiosis has been extensively studied, many questions remain regarding the specific pathogenic mechanisms and treatment strategies. This review begins by examining the causes of gut microbiota dysbiosis and summarizes the potential mechanisms of representative diseases caused by microbiota imbalance. It integrates clinical evidence to explore preventive and therapeutic strategies targeting gut microbiota dysregulation, emphasizing the importance of understanding gut microbiota dysbiosis. Finally, we summarized the development of artificial intelligence (AI) in the gut microbiota research and suggested that it will play a critical role in future studies on gut dysbiosis. The research combining multiomics technologies and AI will further uncover the complex mechanisms of gut microbiota dysbiosis. It will drive the development of personalized treatment strategies.

The composition of animal gut microbiota is significantly affected by a variety of factors. Seasonal variation in environmental factors is believed to have a significant impact on the composition of mammalian gut microbiota. Therefore, studying the seasonal differences in gut microbiota diversity in wildlife is of great importance to explore their ecological adaptability. This study compared the diversity of gut microbiota of the short-faced moles (Scaptochirus moschatus) in spring, summer, and autumn by using 16S rRNA amplification sequencing. Our results reveal significant seasonal differences in the diversity and function of the short-faced moles gut microbiota. Compared to spring, the diversity and function of the gut microbiota in summer and autumn of short-faced moles are more similar to each other. The relative abundance of Firmicutes is higher in spring than in summer and autumn, while the relative abundance of Proteobacteria in summer and autumn is higher than that of spring. There are significant differences in carbohydrate metabolism between spring and summer, and between spring and autumn. The correlation analysis results suggest that climatic factors are strongly associated with seasonal variation in gut microbiota of the short-faced moles, especially temperature and relative humidity. The present study discusses the seasonal variations in the gut microbiota diversity of short-faced moles and the significant impact of climatic factors on gut microbiota diversity. These results will highlight the potential impact of climatic factors on the seasonal changes of the gut microbiota of subterranean mammals and provide a new view for comprehensively understanding the ecological adaptation of subterranean mammals.

This review provides an updated overview of the gut microbiota's involvement in spondyloarthritis (SpA) from a clinical perspective. It explores mechanisms by which the gut microbiota may influence SpA pathogenesis and considers the therapeutic implications of targeting the microbiome in SpA treatment.

The pathogenesis of SpA is multifactorial, involving genetic predisposition, external factors and dysregulation of the immune system. Recent studies have identified alterations in the gut microbiome of patients with SpA, including changes in microbial diversity and specific taxa linked to disease activity. HLA-B27 status seems to influence gut microbiota composition, potentially impacting disease progression. In HLA-B27 transgenic rats, the association between gut microbiota and SpA development has been confirmed, supporting findings from human studies. A compromised gut barrier, influenced by proteins like zonulin, may allow microbial antigens to translocate, triggering immune responses associated with SpA.

These findings highlight the potential for microbiota-modulating therapies, such as probiotics, prebiotics, diet and exercise, in managing SpA. However, methodological variability in human studies exposes the need for more rigorous research to better understand these associations. This may offer the opportunity to refine treatment strategies, offering a personalized approach to managing the disease.

This study aimed to investigate the effects of Boletus edulis Bull: Fr. polysaccharide (BEP), extracted using a deep eutectic solvent based on l-lactic acid and glycine, on glucose and lipid metabolism in high-fat diet (HFD)-fed mice. The primary mechanism by which BEP improves symptoms of glucose and lipid imbalances involves the modulation of gut microbiota. Key beneficial bacteria, including S24-7, Lachnospiraceae, [Prevotella], and Lactobacillus, were significantly enriched in the intestines of BEP-treated mice, with abundances 2.48-, 1.62-, 6.33- and 2.60-fold higher, respectively, compared to the HFD group. In contrast, the abundance of harmful bacteria, particularly Desulfovibrio, was reduced by 1.81-fold. These microbial shifts contributed to the alleviation of intestinal mucus layer damage and a 50 % reduction in serum lipopolysaccharide (LPS) levels, a key driver of systemic inflammation, compared to the HFD group. As a result, BEP effectively inhibited LPS-induced activation of the hepatic TLR4/Myd88/MAPK signaling pathway, thereby normalizing the expression of proteins related to glucose and lipid metabolism. A fecal microbiota transplantation study further demonstrated that the gut microbiota changes induced by BEP were central to its anti-metabolic syndrome effects. Overall, BEP may serve as a dietary supplement for preventing and treating diet-induced metabolism disorders by targeting the gut microbiota.

BackgroundProbiotics, as common regulators of the gut microbiota, have been used in research to alleviate clinical symptoms of atopic dermatitis (AD).ObjectiveOur research team has previously identified a potential relieving effect of Clostridium butyricum on the treatment of AD, but the specific mechanism of how Clostridium butyricum alleviates AD has not yet been confirmed.MethodsIn this study, we explored the relieving effect of Clostridium butyricum on AD through in vivo and in vitro experiments. AD mice induced by 2,4-dinitrofluorobenzene (DNFB) were orally administered with 1 × 108 CFU of Clostridium butyricum for three consecutive weeks.ResultsOral administration of Clostridium butyricum reduced ear swelling, alleviated back skin lesions, decreased mast cell and inflammatory cell infiltration, and regulated the levels of inflammation-related cytokines. Clostridium butyricum activated the intestinal immune system through the TLR4/MyD88/NF-κB signaling pathway, suppressed the expression of inflammatory factors IL-10 and IL-13, and protected the damaged intestinal mucosa.ConclusionClostridium butyricum administration improved the diversity and abundance of the gut microbiota, enhanced the functionality of the immune system, and protected the epidermal barrier.

Kombucha, a fermented beverage obtained from a Symbiotic Culture of Bacteria and Yeast, has shown potential in modulating gut microbiota, although no clinical trials have been done.

We aimed to evaluate the effects of regular black tea kombucha consumption on intestinal health in individuals with and without obesity.

A pre-post clinical intervention study was conducted lasting 8 wk. Forty-six participants were allocated into 2 groups: normal weight + black tea kombucha (n = 23); and obese + black tea kombucha (n = 23). Blood, urine, and stool samples were collected at baseline (T0) and after 8 wk of intervention (T8).

A total of 145 phenolic compounds were identified in the kombucha, primarily flavonoids (81%) and phenolic acids (19%). Kombucha favored commensal bacteria such as Bacteroidota and Akkermanciaceae, especially in the obese group. Subdoligranulum, a butyrate producer, also increased in the obese group after kombucha consumption (P = 0.031). Obesity-associated genera Ruminococcus and Dorea were elevated in the obese group at baseline (P < 0.05) and reduced after kombucha consumption, becoming similar to the normal weight group (Ruminococcus: obese T8 × normal weight T8: P = 0.27; Dorea: obese T8 × normal weight T0: P = 0.57; obese T8 × normal weight T8: P = 0.32). Fungal diversity increased, with a greater abundance of Saccharomyces in both groups and reductions in Exophiala and Rhodotorula, particularly in the obese group. Pichia and Dekkera, key microorganisms in kombucha, were identified as biomarkers after the intervention.

Regular kombucha consumption positively influenced gut microbiota in both normal and obese groups, with more pronounced effects in the obese group, suggesting that it may be especially beneficial for those individuals. This trial was registered at Brazilian Clinical Trial Registry - ReBEC as UTN code U1111-1263-9550 (https://ensaiosclinicos.gov.br/rg/RBR-9832wsx).

Dysbiosis is a feature of patients with systemic sclerosis (SSc). While a causal relationship between the gastrointestinal (GI) microbiota and SSc pathogenesis has not been established, alterations in the GI microbiota are appreciated early in the SSc disease course. Moreover, recent research has illuminated specific microbial signatures that define SSc phenotypes. This review summarizes new research on the GI microbiome in SSc with a focus on technical advancements and the emerging study of the GI metabolome. This review also addresses diverse modalities for manipulating the GI microbiome with the hope of developing preventative treatment strategies to avert progression of SSc.

Antibiotic resistance has become a global health concern, driving the need for sustainable alternatives in animal husbandry. This study explores the potential of natural feed additives as a viable solution to enhance poultry growth and health while reducing reliance on antibiotics. Chinese herbal medicines and probiotics have been widely studied as green, healthy, and safe antibiotic alternatives in livestock and poultry production. A total of 120 chickens were randomly divided into four groups: a control group and three treatment groups supplemented with 1% Pulsatilla chinensis powder, 3% fresh Acer truncatum, or 1% Clostridium butyricum. The results showed that Pulsatilla chinensis powder significantly increased gamma-glutamylcysteine (p < 0.05), UDP-N-acetylglucosamine (p < 0.05), tyramine (p < 0.01), and leucine (p < 0.05). Acer truncatum notably altered cecal metabolites, including L-tyrosine (p < 0.05), α-ketoisovaleric acid (p < 0.01), myristoleic acid (p < 0.01), glutathione (p < 0.05), and PGA1 (p < 0.05). Clostridium butyricum modified cecal metabolites such as L-glutamine (p < 0.05), riboflavin (p < 0.05), L-Carnitine (p < 0.05), ergocalciferol (p < 0.01), and α-tocotrienol (p < 0.05).

Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.

Background/Objectives: Childhood obesity is a growing global concern linked to metabolic disorders such as nonalcoholic fatty liver disease (NAFLD). Small intestinal bacterial overgrowth (SIBO) may exacerbate these conditions by promoting systemic inflammation and metabolic dysfunction. This review evaluates the prevalence of SIBO in obese children, its association with inflammatory and metabolic markers, and the efficacy of diagnostic and therapeutic strategies. Methods: A systematic search of PubMed, Scopus, and Web of Science (2010-present) was conducted using Boolean operators: ('small intestinal bacterial overgrowth' OR 'SIBO') AND 'prevalence' AND ('low-grade inflammatory markers' OR 'metabolic status') AND 'gut microbiome' AND 'dysbiosis' AND 'obese children'. Results: The data show that SIBO is frequently observed in obese pediatric populations and is associated with gut dysbiosis, impaired nutrient absorption, and reduced production of short-chain fatty acids. These changes contribute to increased intestinal permeability, endotoxemia, and chronic low-grade inflammation. Several microbial taxa have been proposed as biomarkers and therapeutic targets. Diagnostic inconsistencies persist, but treatments such as probiotics, prebiotics, dietary interventions, and selective antibiotics show potential, pending further validation. Conclusions: Early identification and treatment of SIBO with tailored strategies may help reduce metabolic complications and improve outcomes in children with obesity.

Pouchitis is the most common complication after ileal pouch-anal anastomosis (IPAA) for ulcerative colitis. Induction and maintenance of remission is a crucial therapeutic goal. We investigated curcumin's efficacy in treatment of pouchitis.

The double-blind trial included an induction cohort of refractory pouchitis patients and a maintenance cohort of patients without pouchitis after IPAA. Patients received either placebo or curcumin for 8 weeks. The pouchitis activity were assessed before and after and was compared between cohorts or groups. Laboratory inflammation indicators, nutritional status and quality of life were also appraised.

52 patients were included, with 39 and 13 patients entering the maintenance cohort and induction cohort, respectively. In maintenance cohort, the proportion of clinical remission elevated from 11 to 89% in curcumin group (p = 0.005), whereas there was no significant difference in placebo group (10% vs 5%, p = 1).In induction cohort, 67% (4/6) patients achieved clinical response after 8 weeks' intervention of curcumin, whereas none treated with placebo (p = 0.021). Patients treated with curcumin appeared less inflammation and there was no significant difference in indicators changes between two cohorts.

Curcumin has preventive and therapeutic effects on pouchitis. Curcumin supplementation can reduce the disease activity and improve the nutritional status of patients with after IPAA.

ChiCTR, ChiCTR1900022243. Registered 31 March 2019, https://www.chictr.org.cn/historyversionpub.aspx?regno=ChiCTR1900022243.

Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.

This study aimed to assess the global burden of Clostridioides difficile infection (CDI) from 1990 to 2019, focusing on disability-adjusted life years (DALYs) rates, mortality, and trends. Data were extracted from the Global Burden of Disease Study 2019 and analyzed globally, regionally, and nationally by age, sex, region, and socio-demographic index (SDI). Measures included age-standardized DALYs rate (ASDR), mortality rate (ASMR), and average annual percentage changes (AAPCs). Decomposition analysis and Bayesian age-period-cohort model were used to evaluate factors affecting CDI trends and predict future progress, respectively. Globally, the overall ASDR and ASMR of CDI showed an increasing trend (AAPCASDR = 1.39, 95% CI: 1.23-1.55; AAPCASMR = 2.79, 95% CI: 2.66-2.93). High SDI countries showed the highest ASDR (18.86, 95% CI: 17.46-20.24) and ASMR (0.99, 95% CI: 0.87- 1.11), with the fastest growth rate (AAPCASDR = 2.84, 95% CI: 2.64-3.04; AAPCASMR = 4.26, 95% CI: 3.98-4.55). Conversely, the low SDI regions exhibit negative growth; however, some low-middle SDI regions, such as South Africa, experienced a heavy disease burden. While most of the disease burden occurs in people over 70 years of age, the burden of children under 5 years of age should also be considered. Moreover, the increased burden on high SDI regions is primarily driven by epidemiological changes. CDI burden has risen globally, particularly in high SDI regions. Moreover, clinicians should take care to consider the burden in individuals under 5 years of age.IMPORTANCEThe global burden of Clostridioides difficile infection (CDI) is increasing, with notable disparities across regions, age groups, and socioeconomic levels. The higher mortality and disability risks, particularly among older adults, children under 5, and in high socio-demographic index regions, highlight the urgent need for targeted public health interventions and policy adjustments to address these vulnerabilities and reduce the impact of CDI on global health.

Gut microbiota variations in response to environmental and nutritional factors are of great significance as gut microbiota plays an integral role in nutrient metabolism, immunity, health, and disease conditions. In this context, limited studies investigated variations of gut microbiota in response to different feeding systems and environmental conditions. The current study obtained fresh fecal samples from house-fed (LS) and grazing yaks (LF) from Linzhou County. 16 S rRNA amplicon sequencing of the V3-V4 and internal transcribed spacer 2 (ITS2) domains generated 16,332 bacterial and 2345 fungus amplicon sequence variants (ASVs). Alpha and beta diversity indices revealed significant variations (p > 0.05) in gut microflora between the two groups. At the phylum level, Firmicutes, Actinobacteriota, Bacteroidota, and Patescibacteria regarding bacteria, and Ascomycota and Basidiomycota regarding fungi dominated. At the genus level, UCG-005, Rikenellaceae_RC9_gut_group, Clostridium_sensu_stricto_1, g__Muribaculaceae, UCG-010, [Eubacterium]_coprostanoligenes_group, Turicibacter, Alistipes, Prevotellaceae_UCG-003, UCG-009, Blautia, dgA-11_gut_group, Candidatus_Saccharimonas dominated in LS, while Anthrobacter and Terrisporobacter dominated in the LF group. Fungal genera like Myrothecium and Plectosphaerella dominated the LS group, while Neoascochyta, Paraphaeosphaeria, and Hypocreales dominated the LF group. Also, significant variations (p > 0.05) in gene expressions were found between the two groups. These findings provide insights into yak gut microbiota adaptations and metabolic changes in response to varied environmental conditions and can provide valuable information, optimizing feeding strategies after identifying specific differences between grazing and house-fed yaks, reducing environmental impacts, and improving yaks' health and productivity in specific geographical settings.

Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.

we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.

Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.

A number of studies have reported on the improvement in physical and psychological diseases through diet; however, the findings for these ameliorative effects have differed. Such differences may be due to the varying metabolism of the nutrient content in food among subjects. It has been reported that differences in the enterotypes of gut microbiota are associated with metabolic differences, and enterotypes vary between countries and regions. This study investigated whether differences in gut microbiota affect the relationship between dietary habits and stress responses.

We administered a questionnaire to 810 subjects who participated in the "Sukoyaka Health Survey" regarding their dietary habits and stress reactions. We also performed an analysis of the gut microbiota from fecal samples.

The gut microbiota was grouped into four clusters based on the abundance of genus strains. The relationship between dietary habits and stress responses revealed two patterns of eating: one where more frequent intakes were associated with a lower stress response, and another with a higher stress response. We investigated the relationship between dietary habits and stress responses for each gut microbiota cluster. The results showed that the relationship between dietary habits and stress responses differed for each cluster.

Our analysis showed that dietary habits affect stress responses, but the relationship varies depending on the gut microbiota. This finding suggests that one of the factors for the difference in the ameliorative efficacy of physical and psychological diseases through diet is the difference in the abundance ratio of the gut microbiota (enterotype).

The ARFID InitiativE Sweden (ARIES) investigates the genetic and environmental factors contributing to avoidant/restrictive food intake disorder (ARFID) in children and adolescents aged 6-14 years. ARIES will establish a national biobank and research registry. It aims to provide data for immediate research and track ARFID outcomes and clarify genetic links between ARFID and other conditions and analyse the gut microbiome to guide nutrition interventions.

The study will involve 1500 Swedish children and adolescents with ARFID and a control group of 500 Swedish children and adolescents without ARFID. Parents/guardians and their children will complete online questionnaires assessing ARFID and other eating disorder (ED) pathology, co-occurring conditions, quality of life and parental stress and ED pathology. All participants will provide a saliva sample for comprehensive genetic analyses. Additionally, a subset of participants will provide a stool sample to investigate the gut microbiome in ARFID.

ARIES was approved by the Swedish Ethical Review Authority (Dnr 2023-04638). All participants will give assent and their parents will complete informed consent. Data will be made available by the authors on reasonable request. Findings will be published in scientific journals and shared with the public and stakeholders in accessible ways, for example, via social media.

Rotavirus vaccines are less effective in high mortality regions. A rotavirus vaccine administered at birth may overcome challenges to vaccine uptake posed by a complex gut microbiome. We investigated the association between the microbiome and vaccine responses following RV3-BB vaccine (G3P[6]) administered in a neonatal schedule (dose 1: 0-5 days), or infant schedule (dose 1: 6-8 weeks) in Indonesia (Phase 2b efficacy study) (n = 478 samples/193 infants) (ACTRN12612001282875) and in Malawi (Immunigenicity study) (n = 355 samples/186 infants) (NCT03483116). Vaccine responses assessed using anti-rotavirus IgA seroconversion (IgA), stool shedding of vaccine virus and vaccine take (IgA seroconversion and/or shedding). Here we report, high alpha diversity, beta diversity differences and high abundance of Bacteroides is associated with positive vaccine take and shedding following RV3-BB administered in the neonatal schedule, but not with IgA seroconversion, or in the infant schedule. Higher alpha diversity was associated with shedding after three doses of RV3-BB in the neonatal schedule compared to non-shedders, or the placebo group. High abundance of Streptococcus and Staphylococcus is associated with no shedding in the neonatal schedule group. RV3-BB vaccine administered in a neonatal schedule modulates the early microbiome environment and presents a window of opportunity to optimise protection from rotavirus disease.

The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.

Obesity, characterized by excessive fat accumulation, stems from an imbalance between energy intake and expenditure, with the gut microbiota playing a crucial role. This review highlights how gut microbiota influences metabolic pathways, inflammation, and adipose tissue regulation in obesity. Specific bacteria and metabolites, such as lipopolysaccharides (LPS) and short-chain fatty acids (SCFAs), modulate gut permeability, inflammation, and energy harvest, impacting obesity development. Certain gut bacteria, including Clostridium XIVb, Dorea spp., Enterobacter cloacae, and Collinsella aerofaciens, promote obesity by increasing energy harvest, gut permeability, and inflammatory response through LPS translocation into the bloodstream. Conversely, beneficial bacteria like Akkermansia muciniphila, Lactobacillus spp., and Bifidobacterium spp. enhance gut barrier integrity, regulate SCFA production, and modulate fasting-induced adipose factor, which collectively support metabolic health by reducing fat storage and inflammation. Metabolites such as SCFAs (acetate, propionate, and butyrate) interact with G-protein coupled receptors to regulate lipid metabolism and promote the browning of white adipose tissue (WAT), thus enhancing thermogenesis and energy expenditure. However, LPS contributes to insulin resistance and fat accumulation, highlighting the dual roles of these microbial metabolites in both supporting and disrupting metabolic function. Therapeutic interventions targeting gut microbiota, such as promoting WAT browning and activating brown adipose tissue (BAT), hold promise for obesity management. However, personalized approaches are necessary due to individual microbiome variability. Further research is essential to translate these insights into microbiota-based clinical therapies.

Wild primates face a wide range of anthropogenic influences globally that impact their health, fitness, and survival. One area of potential impact that has been particularly understudied is the supplementation of wild primate diets with human foods. Although the consumption of human foods represents a substantial dietary change for wild primates, knowledge of how it impacts their physiology and behavior is limited. Here we explore how human food supplementation impacts wild primates by comparing the gut microbiomes of free-ranging brown howler monkeys (Alouatta guariba) in periurban Brazil that do or do not have access to human foods. We found that howler monkeys consuming human foods had reduced gut microbial diversity and reduced relative abundances of fiber degrading microbial taxa, which has been associated with negative health consequences in other animals, including humans. However, the effect size of these differences was relatively small and varied over time. Additionally, the composition of the gut microbiome varied significantly across months, regardless of the access to human foods. We suggest that the biology of this howler monkey population is minimally impacted by human foods. Further empirical research will help clarify the relationship between human food supplementation and health across primate populations, facilitating conservation applications.

In microbiota research, whole stool sampling is the conventional approach but can be problematic or infeasible for certain patients. This study aims to validate the use of rectal swabbing as an alternative method for microbiota analysis and determine optimal storage conditions suitable for various clinical settings, including intensive care units. We evaluated different sampling techniques and storage temperatures. Our findings indicated that rectal swabs yield microbiota diversity comparable to whole stool samples. Notably, storage conditions significantly impacted microbiota profiles, with increased E. coli and Enterococcus sp. quantifications observed at room temperature (RT). Consequently, we recommend immediate refrigeration of rectal swabs to reliably assess aerobic and total microbiota, particularly for patients requiring urgent care, such as antibiotic treatment.

We developed a pragmatic approach to study total and aerobic gut microbiota, applicable in numerous clinical units, such as intensive care or emergency units, where whole stool sampling is often impractical. This approach employs ESwab devices, which are already commonly used in hospitals.

Dietary patterns significantly impact health outcomes and gut microbiota composition. However, longitudinal studies associating ultra-processed food consumption with gut microbiota composition, especially among adolescents in low- and middle-income countries, are lacking. This study aimed to explore this association using data collected from 364 participants at ages 6, 11, and 12 years from the 2004 Pelotas (Brazil) Birth Cohort. Microbiota data was obtained at age 12 after 16S rRNA gene sequencing of self-collected fecal samples. Linear or logistic regression models evaluated the relationship between age groups and gut microbiota outcomes (alpha diversity, beta diversity and relative abundances at the phylum and genus levels), considering dietary covariates and demographic, socioeconomic, health-related, and behavioral factors. No significant associations between ultra-processed food consumption and alpha diversity were observed after multiple testing corrections, and there was no strong evidence linking ultra-processed food consumption and beta diversity, with unweighted metrics explaining little variance at ages 11 and 12. Nominal associations were found between ultra-processed food and relative abundances of Actinobacteria (p = 0.032) and Proteobacteria (p = 0.045) (phyla), Bacteroides (p = 0.037 at age 6; p = 0.015 at age 11) and Peptostreptococcus (p = 0.025 at age 6; p = 0.010 at age 11) (genera). However, these associations lost statistical significance after adjustments for multiple comparisons. These findings highlight the need for more longitudinal studies to better understand the complex interaction between ultra-processed food intake and gut microbiota composition in adolescent populations in low- and middle-income countries.