Search Results (1,783)

The gut microbiome is essential for gut health, immune regulation, and metabolism, but pathogenic bacteria like Enterococcus and Streptococcus can disrupt these processes, increasing infection risk after colorectal surgery. Prior studies show that intravenous antibiotics and surgical bowel preparation (SBP, including mechanical preparation with oral antibiotics) significantly disrupt the gut microbiota, potentially delaying postoperative recovery. However, the effects of surgical indication (e.g., diagnosis) and operation type on gut microbiome composition and function remain unclear. This study examines how SBP, resectional and non-resectional surgery, and underlying diagnoses shape the postoperative gut microbiome and microbial recovery. Methods: Fecal samples were collected from patients undergoing colonoscopy (n = 30), non-resectional (ventral mesh rectopexy, transanal surgery; n = 25), or resectional surgery with primary anastomosis (n = 26) at baseline, intraoperatively, and on postoperative days (POD) 10, 30, and 180. Microbial diversity was assessed through 16S rRNA sequencing, and short-chain fatty acid (SCFA) levels were measured to evaluate functional changes. Results: Alpha diversity (Shannon indices) decreased across all groups, recovering by POD10 in colonoscopy patients and by POD180 in non-resectional and resectional cohorts. Beta diversity (community composition) also returned to baseline by POD10 in colonoscopy patients and POD180 in non-resectional patients, but the resectional cohort did not fully recover (p < 0.001). Both surgical cohorts showed substantial losses of commensal bacteria through POD30, with notable increases in Streptococcus in resectional patients (p < 0.0001) and Enterococcus in both surgical cohorts (p < 0.0001). Functionally, only the resectional cohort experienced significant reductions in SCFA levels (p < 0.015) relative to baseline levels. Diagnosis minimally influenced long-term microbiota recovery, although cancer patients tended to have more stable microbiomes compared to patients with diverticulitis. Conclusions: These findings indicate that perioperative factors, especially surgical resection and SBP, significantly impact gut microbial recovery, with pathogenic bacteria persisting up to 6 months post-surgery. Full article

Growth stage is a key factor influencing the composition and richness of the porcine gut microbiota. The stage-specific alterations in gut microbiota of indigenous Chinese pig breeds and cultivated breeds remain to be elucidated. This study conducted 16S rRNA sequencing analysis on fecal microbiota from Dahe black pigs across distinct growth stages. Samples included lactating sows, suckling piglets, weaned piglets, pigs weighing 50–100 kg, pigs weighing 120–150 kg, and pigs weighing > 200 kg. The results indicated that Escherichia shigella (12.4% vs. 16.2%), Lactobacillus (5.9% vs. 6.3%), and Rikenellaceae RC9 gut group (3.9% vs. 4.2%) were dominant genera shared between lactating sows and suckling piglets. The relative abundance of Eubacterium brachy group was significantly higher in lactating sows, whereas Flavonifractor was significantly lower compared to suckling piglets (p < 0.05). Compared to pigs weighing > 120 kg, lactating sows exhibited 22 differentially abundant genera, including Escherichia shigella, Cloacibacillus, Fusobacterium, Faecalibacterium, and Prevotella (p < 0.05). In suckling piglets, Firmicutes and Bacteroidota constituted 47.4% and 27.3% of the microbiota, respectively. Their relative abundance increased with body weight, reaching 52.6% and 33.3% in pigs weighing > 200 kg. Proteobacteria decreased from 17.3% in suckling piglets to 2.0% in >200 kg pigs. Spirochaetota declined from 2.5% in suckling piglets to 0.9% in weaned piglets and then increased to 6.9% in >200 kg pigs. Lactobacillus peaked at 15.7% in weaned piglets, while Escherichia shigella reached its maximum (16.2%) in suckling piglets, both gradually declining thereafter. Streptococcus abundance remained relatively stable (1.1% in suckling piglets; 4.5% in weaned piglets). Prevotellaceae NK3B31 group registered 2.9% in suckling piglets, increased to 7.1% in weaned piglets, and then declined to 2.6% in >200 kg pigs. Mitsuokella, Bilophila, Succinivibrio, Romboutsia, and Desulfovibrio were identified as the top five genera discriminating suckling and weaned piglets. Similarly, Lachnospiraceae XPB1014 group, Clostridium sensu stricto 1, Turicibacter, Quinella, and p 1088 a5 gut group were key discriminators between weaned piglets and 50–100 kg pigs. These identified microbial taxa represent potential candidate targets for modulating the developmental timing of growth phases in pigs, offering possibilities for either advancing or delaying specific physiological timepoints. Full article

The gut microbiota plays a crucial role in early childhood development. Dysbiosis in this community has been linked to risk of disease. The transition from an exclusive milk-based diet to complementary feeding and eventual weaning is crucial for the development and maturation of the gut microbiota. However, the impact of breastfeeding duration during the complementary feeding period (typically 6 to 24 months of age) on microbial development trajectories remains incompletely characterized. Here, we investigated whether prolonged breastfeeding during the complementary feeding window influences gut microbiota succession by comparing children who continued breastfeeding with those who were fully weaned at the same ages. We analyzed 16S rRNA gene sequencing profiles of fecal samples collected from a cohort of Peruvian children at 6, 12, 18, and 24 months of age. Samples were categorized into two groups: a complementary feeding group (BF), which received both complementary foods and breast milk, and a post-weaning group (NBF), which had stopped receiving breast milk for over 7 days. We conducted both alpha and beta diversity to assess within- and between-sample microbial variation. Relative abundances of microbial taxa at the phylum and genus levels were also quantified. The results showed a clear age-related increase in both species richness and species evenness across early childhood, while BF had more gradual changes relative to NBF. Marked differences in community composition were observed between BF and NBF children at 12, 18, and 24 months, respectively. Children who continued breastfeeding maintained a Bifidobacterium-rich, lower-diversity microbiota for a longer period, whereas weaned children at the same age exhibited accelerated microbiota development toward an adult-like profile enriched in Bacteroidota and Bacillota (formerly Firmicutes). These findings suggest that breastfeeding during the complementary feeding period exerts a significant influence on gut microbiota development through the first two years of life, which is most likely independent of complementary food. The study provides potential implications for children’s health and nutrition guidelines from a perspective of gut microbiota succession. Full article

Undaria pinnatifida fucoidan (UPF), a sulphated polysaccharide derived from brown seaweed, has attracted scientific and clinical interest for its wide-ranging anti-inflammatory and neurodegenerative properties. A growing body of research shows that UPF inhibits NF-κB and MAPK signalling pathways, reduces pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), decreases ROS production, and suppresses iNOS and COX-2 activity, thereby mitigating oxidative and inflammatory damage in vitro. In vivo studies confirm these actions, demonstrating reduced systemic inflammation, promoted antioxidant defence, modulated gut microbiota composition, and improved production of beneficial microbial metabolites. In parallel, emerging evidence highlights UPF’s neuroprotective potential, characterised by protection against neuroinflammation and oxidative stress, the attenuation of amyloid-beta deposition, and improvement in neuronal function. Importantly, low- to medium-molecular-weight and highly sulphated UPF fractions consistently exhibit stronger bioactivities, suggesting a structural basis for its therapeutic potential. This review integrates mechanistic evidence from cellular, preclinical, and emerging clinical studies, highlighting UPF as a versatile marine-derived agent with therapeutic relevance for inflammatory and neurodegenerative diseases, and outlines future research directions toward clinical translation. Full article

Background: The gut microbiota and the gut epithelium play a central role in maintaining systemic and brain homeostasis from early life. Stressful experiences during sensitive developmental windows can disrupt this balance, increasing long-term susceptibility to psychiatric disorders. However, the mechanisms through which early-life alterations in the microbiota influence brain development and function remain poorly understood. Here, the sex-specific impact of prenatal stress (PNS) on gut integrity and microbial composition in adult offspring was explored. Methods: Thirty dams were mated and randomly assigned to PNS or control. Offspring microbiota was analysed through 16S rRNA sequencing, intestinal morphology with morphometric analyses, and tight junctions using qPCR and immunofluorescence. Results: Exposure to PNS was associated with reduced intestinal surface area in males and shortened crypts in females. In both sexes, PNS caused a decrease in the expression of ZO-1, suggesting impaired gut barrier integrity. 16S rRNA sequencing revealed, furthermore, that PNS exposure was associated with a decrease in beneficial genera, including Akkermansia in males and Clostridia vadinBB60 in females, along with an increase in the pro-inflammatory genus Anaerotruncus, regardless of sex. Notably, some of these alterations were more pronounced in PNS-exposed animals that showed impaired sociability, highlighting gut microbiota inter-individual variability in the response to early-life adversity. Moreover, selected microbial changes show significant correlations with the behavioural outcomes, as well as with intestinal morphology or brain inflammatory markers. Conclusions: Together, these findings pinpoint the gut as a central player in stress vulnerability and highlight specific microbial signatures as promising biomarkers and therapeutic targets for stress-related disorders. Full article

Recent studies increasingly highlight the complex interaction between gut microbiota and mental health, drawing attention to the role of the microbiota–gut–brain axis (MGBA) in the pathophysiology of mental and neurodevelopmental disorders. Changes in the composition of the gut microbiota—dysbiosis—are associated with conditions such as depression, schizophrenia, bipolar disorder (BD), autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), and neurodegenerative diseases such as Parkinson’s and Alzheimer’s. These microbial imbalances can affect brain function through a variety of mechanisms, including activation of the immune system, alteration of intestinal permeability, modulation of the digestive and central nervous systems, and changes in the production of neuroactive metabolites such as short-chain fatty acids, serotonin, and tryptophan derivatives. The aim of this paper is to review the current state of knowledge on therapeutic strategies targeting the gut microbiome—including probiotics, prebiotics, synbiotics, personalized dietary interventions, and fecal microbiota transplantation (FMT)—which are becoming promising adjuncts or alternatives to conventional psychopharmacology, offering a forward-looking and individualized approach to mental health treatment. Understanding the bidirectional and multifactorial nature of MGBA may pave the way for new, integrative treatment paradigms in psychiatry and neurology, requiring further research and exploration of their scope of application. Full article

Background: Self-directed lifestyle modifications are essential for managing symptoms in individuals diagnosed with irritable bowel syndrome (IBS). This study incorporated longitudinal multi-omics profiling to estimate the mechanisms underlying responses to a nurse-led person-centered self-management intervention in young adults with IBS. Methods: This pre-post study was nested within a 12-week parent randomized controlled trial (NCT03332537). Biospecimens (stool and blood) and clinical outcomes were collected at baseline and post-intervention. Symptoms were assessed using the Brief Pain Inventory and PROMIS^® short forms. Host transcriptomic profiling was performed using RNA sequencing, and gut microbial composition was analyzed via 16S rRNA sequencing. Host transcriptomic co-expression and microbial co-abundance modules were identified via weighted gene co-expression network analysis. Associations between multi-omics modules and symptoms were evaluated using linear mixed-effect models. Results: Among the 20 participants, most were non-Hispanic (75%), White (75%), and female (65%). The intervention significantly reduced self-reported pain severity (p = 0.019) and pain interference (p = 0.013). Decreased associations were observed between pain phenotypes and a microbial module enriched in core metabolic pathways (interference: β = −4.7, p < 0.001; severity: β = −2.4, p = 0.02). Anxiety strengthened associations with host transcriptomic cellular energy metabolism pathways post-intervention (p < 0.05). The intervention attenuated associations between fatigue, sleep disturbance, and immune–inflammatory transcriptomic and microbial adaptation modules (p < 0.05). Conclusions: Findings suggest that the IBS self-management intervention induces symptom-specific biological responses, implicating distinct host–microbe pathways. Larger longitudinal studies are warranted to validate these omics-based symptom signatures. Full article

In humans, the bioactivity of polyphenols is highly dependent on dose intake and their interactions with the gastrointestinal tract and gut microbiota, which metabolize polyphenols into bioactive or inactive derivatives. Polyphenols are only partially absorbed in the small intestine, where enzymatic hydrolysis releases aglycone forms that may cross the gut barrier. A significant proportion of polyphenols escapes absorption and reaches the colon, where resident microbes convert them into simpler phenolic metabolites. Such molecules are often more bioavailable than the parent compounds and can enter systemic circulation, leading to distant effects. Although higher polyphenol consumption has been associated with preventive and therapeutic outcomes, even low intake or poor intestinal absorption may still confer benefits, as polyphenols in the colon can positively modulate gut microbiota composition and function, contributing to favorable shifts in the microbial metabolome. These interactions can influence host metabolic, immune, and neurological pathways, particularly through the gut–liver–brain axis. To provide a comprehensive understanding of these relationships, this review examines the dose-related activity of polyphenols, their microbiota-mediated biotransformation, their bioavailability, and the health effects of their metabolites, while also presenting a comparative overview of key studies in the field. We underscore the importance of integrating microbiome and polyphenol research to recapitulate and contextualize the health benefits of dietary polyphenols. Full article

Background: Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by social communication deficits, repetitive behaviors, and frequent gastrointestinal comorbidities. Emerging research suggests gut microbiota alterations contribute to ASD symptoms and gastrointestinal dysfunction, but detailed microbial profiles and clinical correlations remain underexplored. Methods: This study analyzed gut microbiota in 45 children aged 2–18 years diagnosed with ASD. Stool samples underwent 16S rRNA gene sequencing. Clinical assessments included ASD diagnostic subtype, adaptive functioning using the Vineland Adaptive Behavior Scale, gastrointestinal symptoms as per the Rome IV criteria, dietary patterns, and demographic variables. Statistical analyses correlated microbiota profiles with clinical features. Results: Gut microbiota composition was significantly influenced by delivery mode, age, sex, and diet. Vaginally delivered children had higher beneficial SCFA-producing bacteria, whereas Cesarean section was linked to increased pathogenic Clostridiales. High-calorie and protein-rich diets correlated with shifts toward pro-inflammatory taxa. Microbial diversity and specific genera correlated with adaptive behavior domains (communication, socialization, motor skills) and severity of gastrointestinal symptoms. Both pro-inflammatory and anti-inflammatory bacteria variably impacted neurodevelopmental outcomes. Conclusions: Gut microbiota composition in children with ASD is shaped by multifactorial influences and connected to neurobehavioral and gastrointestinal phenotypes. The findings of this study support the potential of microbiota-targeted interventions to ameliorate ASD-associated symptoms and improve quality of life. Full article

Background/Objectives: Recent evidence suggests that gut microbiota plays an important role in anxiety and stress-related disorders through interactions along the gut–brain axis. Our aim was to determine the microbiological diversity of intestinal microorganisms in individuals with acute and remission phases of PD when compared to healthy individuals. Another aim was also to analyze the differences in the metabolic pathways occurring in the intestinal microbiota of individuals from the three analyzed groups. Methods: A diagnosis was established using the Mini-International Neuropsychiatric Interview (M.I.N.I). The gut’s microbiota composition was analyzed through bacterial 16S rRNA gene sequencing (V1–V2 regions). The clinical evaluations included a BMI measurement, Short Form-36 Health Survey (SF-36), Hamilton Anxiety Scale (HAM-A), Montgomery–Åsberg Depression Rating Scale (MADRS), Columbia-Suicide Severity Rating Scale (C-SSRS), and State-Trait Anxiety Inventory (STAI). Results: We recruited 62 participants (31 PD and 31 controls). After conducting quality control filtering, data from 54 participants were analyzed (25 PD, 11 acute, 14 remission, and 29 controls). Observed richness was lower in the acute PD (63) group than in the control (74) and remission (66) (p = 0.038) groups, whereas the Shannon and Simpson indices and beta diversity (PERMANOVA) were not significantly different. The Ruminococcus gnavus group was enriched in acute PD; no other deconfounded differences in microbial composition were detected. Predicted functional differences were detected by edgeR only and included the pathways that are related to steroid biosynthesis and innate immune signaling. Conclusions: Distinct gut microbial signatures were associated with PD, implicating both the metabolic and inflammatory pathways in disease pathophysiology. Full article

The breast microbiome remains stable throughout a woman’s life. The breast is not a sterile organ, and its microbiota exhibits a distinct composition compared to other body sites. The breast microbiome is a community characterized by an abundance of Proteobacteria and Firmicutes, which represent the result of host microbial adaptation to the fatty acid environment in the tissue. The breast microbiome demonstrates dynamic adaptability during lactation, responding to maternal physiological changes and infant interactions. This microbial plasticity modulates local immune responses, maintains epithelial integrity, and supports tissue homeostasis, thereby influencing both breast health and milk composition. Disruptions in this balance, the dysbiosis, are closely linked to inflammatory breast conditions such as mastitis. Risk factors for breast cancer (BC) include genetic mutations, late menopause, obesity, estrogen metabolism, and alterations in gut microbial diversity. Gut microbiota can increase estrogen bioavailability by deconjugating estrogen-glucuronide moieties. Perturbations of this set of bacterial genes and metabolites, called the estrobolome, increases circulating estrogens and the risk of BC. Fusobacterium nucleatum has recently been associated with BC. It moves from the oral cavity to other body sites hematogenously. This review deals with the characteristics of the breast microbiome, with a focus on F. nucleatum, highlighting its dual role in promoting tumor growth and modulating immune responses. F. nucleatum acts both on the Wnt/β-catenin pathway by positively regulating MYC expression and on apoptosis by inhibiting caspase 8. Furthermore, F. nucleatum binds to TIGIT and CEACAM1, inhibiting T-cell cytotoxic activity and protecting tumor cells from immune cell attack. F. nucleatum also inhibits T-cell function through the recruitment of myeloid suppressor cells (MDSCs). These cells express PD-L1, which further reduces T-cell activation. A deeper understanding of F. nucleatum biology and its interactions with host cells and co-existing symbiotic microbiota could aid in the development of personalized anticancer therapy. Full article

The gut microbiota of red deer is a topic of growing interest, particularly with regard to its ecological and physiological importance. The diversity and composition of these microbial communities is influenced by environmental variables, diet and interactions with other organisms in their habitat. Fecal samples were collected in 10 hunting reserves in the Friuli-Venezia Giulia region, Italy. In each hunting reserve, five individual samples were taken from the ground for a total of 50 samples. After DNA extraction, the V3–V4 16s rRNA regions were sequenced. The raw data were uploaded to QIIME2 and taxonomic annotation was performed. Significant differences between the deer sampled in the hunting reserves (p < 0.05) were calculated for the phyla Firmicutes and Cyanobacteriota and for the ratio of Firmicutes to Bacteroidota, especially for the mountain reserves in the north and northeast compared to the reserves in the hills in the west. Shannon and Chao1 alpha diversity indices varied between reserves (p < 0.01) and the Bray–Curtis beta diversity index also indicated differences in microbiota between hunting reserves. The different habitats and vegetation of the reserves could explain the differences observed. Understanding the dynamics of the microbiota of red deer provides important information about their health and feeding behavior and also has far-reaching implications for species conservation. Full article

Due to persistent poaching and habitat fragmentation, wild forest musk deer (Moschus berezovskii) in China have sharply declined; although captive breeding helps, frequent gut diseases limit further expansion. This study used high-throughput 16S rRNA sequencing to analyze the effects of age, season variation, and compound probiotics on the gut microbiota of captive individuals. The results demonstrated that compound probiotics exerted a significantly greater influence on gut microbial composition, α-diversity, and functional variation compared to the effects of age or seasonal factors. β-diversity analysis confirmed greater differences between probiotic-treated and control groups than among age or seasonal groups. Microbial community assembly was mainly driven by deterministic processes, with stochastic processes also playing a role in winter. Compound probiotics markedly reshaped dominant bacterial taxa at both phylum and genus levels, with Acinetobacter identified as a key biomarker. They also significantly modulated metabolic and phenotypic traits, decreasing functions related to Gram-positive and aerobic bacteria while enhancing those linked to Gram-negative characteristics. Environmental correlation analysis further demonstrated that compound probiotics exerted a stronger influence than both age and seasonal factors. The findings underscore the value of dietary and probiotic strategies for enhancing gut health and resilience in endangered forest musk deer. Full article

Cardiovascular disease (CVD) remains the leading cause of global mortality, despite advances in adult-focused prevention and therapy. Mounting evidence supports the Developmental Origins of Health and Disease (DOHaD) paradigm, which identifies early-life exposures as critical determinants of long-term cardiovascular health. Among the key mechanistic pathways, oxidative stress and gut microbiota dysbiosis have emerged as central, interrelated contributors to cardiovascular programming. Prenatal and postnatal insults can induce sustained redox imbalance and disrupt microbial homeostasis. This disruption creates a feed-forward loop that predisposes offspring to CVD later in life. Antioxidants offer a promising reprogramming strategy by targeting both oxidative stress and gut microbiota composition. Preclinical studies demonstrate that maternal antioxidant interventions—such as vitamins, amino acids, melatonin, polyphenols, N-acetylcysteine, and synthetic agents—can restore redox homeostasis, modulate gut microbial communities, and attenuate cardiovascular risk in offspring. This review synthesizes current evidence on how oxidative stress and gut microbiota act together to shape cardiovascular trajectories. It also examines how antioxidant-based therapies may disrupt this pathological axis during critical developmental windows. Although human data remain limited due to ethical and practical constraints, advancing microbiota-targeted antioxidant interventions may offer a transformative approach to prevent CVD at its origins. Full article

Next-generation sequencing has overturned the dogma of biliary sterility, revealing low-biomass microbiota along the gut–biliary axis with metabolic and immunologic effects. This review synthesizes evidence on composition, function, and routes of colonization across benign and malignant disease. In cholelithiasis, Proteobacteria- and Firmicutes-rich consortia provide β-glucuronidase, phospholipase A₂, and bile salt hydrolase, driving bile supersaturation, nucleation, and recurrence. In primary sclerosing cholangitis, primary biliary cholangitis, and autoimmune hepatitis, intestinal dysbiosis and disturbed bile acid pools modulate pattern recognition receptors and bile acid signaling (FXR, TGR5), promote Th17 skewing, and injure cholangiocytes; bile frequently shows Enterococcus expansion linked to taurolithocholic acid. Distinct oncobiomes characterize cholangiocarcinoma subtypes; colibactin-positive Escherichia coli and intratumoral Gammaproteobacteria contribute to DNA damage and chemoresistance. In hepatocellular carcinoma, intratumoral microbial signatures correlate with tumor biology and prognosis. We critically appraise key methodological constraints—sampling route and post-sphincterotomy contamination, antibiotic prophylaxis, low biomass, and heterogeneous analytical pipelines—and outline a translational agenda: validated microbial/metabolomic biomarkers from bile, tissue, and stent biofilms; targeted modulation with selective antibiotics, engineered probiotics, fecal microbiota transplantation, and bile acid receptor modulators. Standardized protocols and spatial, multi-omic prospective studies are required to enable risk stratification and microbiota-informed therapeutics. Full article