Search Results (72)

Background: Antibiotics are essential for treating infections; however, they disrupt the microbiome and key microbiome-dependent functions. Clinical evidence is mixed for probiotic supplementation following antibiotics due to product heterogeneity and inconsistencies in evaluating biological mechanisms that drive clinical consequences. Accordingly, this study investigates the effects of a multi-species synbiotic on gut microbiome composition and function, and gut barrier integrity, during and following antibiotics. Methods: In a randomized, placebo-controlled trial designed to assess proof-of-mechanism, healthy adult participants received a daily synbiotic (53.6 billion AFU multi-species probiotic and 400 mg Indian pomegranate extract; DS-01) or matching placebo for 91 days. All participants also received ciprofloxacin (500 mg orally twice daily) and metronidazole (500 mg orally three times daily) for the first 7 days. Samples were collected at baseline and Days 7, 14, 49, and 91. Endpoints included fecal microbiome composition, fecal acetate and butyrate levels, urinary Urolithin A (UroA), serum p-cresol sulfate (pCS), gut barrier integrity, and safety. Results: The multi-species synbiotic significantly increased the alpha-diversity of Bifidobacterium and Lactobacillus at all timepoints compared to placebo, including short-term (Day 7, p < 0.0001) and end-of-study (Day 91, p < 0.001). The multi-species synbiotic enhanced recovery of native beneficial microbes, including butyrate-producing species and a novel Oscillospiraceae species (UMGS1312 sp900550625, p < 0.001). Beneficial microbiome-dependent metabolites increased, including fecal butyrate (119%, p < 0.05), fecal acetate (62%, p < 0.01), and UroA (13,008%, p < 0.05), whereas detrimental metabolite pCS decreased (68%, p < 0.05) compared to placebo. Functionally, the multi-species synbiotic improved gut barrier integrity rapidly (Day 7; 305%, p < 0.05) and over the long-term (Day 91; 161%, p < 0.05) compared to placebo. Conclusions: During and after antibiotics, this multi-species synbiotic promotes recovery of gut microbiome diversity and native beneficial microbes, microbiome metabolite recovery, and gut barrier function, all of which underpin antibiotic-associated gastrointestinal symptoms. Full article

Background/Objectives: Nutrition and the gut microbiota influence treatment tolerance and recovery in patients with colon cancer receiving chemotherapy. This pilot study examined changes in diet quality and fecal microbiota over 6 months of chemotherapy and evaluated longitudinal associations between diet quality and gut microbiota diversity and taxa. Methods: 48 adults with stage II–III colon cancer receiving 5-fluorouracil-based chemotherapy were assessed at baseline and 6 months post-initiation. Diet quality was measured using 3-day dietary recalls to calculate Healthy Eating Index (HEI) scores. Stool samples underwent 16S rRNA sequencing to assess Shannon diversity, Beta and taxonomic composition. Pre–post changes were analyzed using paired tests, and associations between HEI and microbiota measures were evaluated using multivariable linear regression adjusting for demographic and clinical covariates. Results: Diet quality declined during chemotherapy, with reduced intake of fiber, fruits and vegetables, and whole grains. Gut microbial alpha diversity decreased over time. At the phylum level, Actinobacteriota decreased, while Bacteroidota and Proteobacteria increased. At the genus level, only Streptococcus (decreased) and Escherichia (increased) remained significantly altered after multiple testing correction. Higher baseline diet quality and improvements over time were associated with greater microbial diversity and lower Proteobacteria abundance. Diet quality was inversely associated with Streptococcus and Escherichia and positively associated with short-chain fatty acid-producing, fiber-responsive genera (Faecalibacterium, Mediterraneibacter, Ruminococcus_E, Fusicatenibacter). Baseline gut microbiota did not significantly associate with changes in diet quality. Conclusions: Chemotherapy was associated with declines in diet quality, gut microbial alpha diversity, along with shifts in beta diversity and microbial taxa. Higher diet quality appeared protective against microbial disruption, supporting a bidirectional relationship between diet and the gut microbiome during chemotherapy. Nutritional and microbiota-focused approaches warrant further investigation in the context of chemotherapy. Full article

Liquid digestate, a by-product of excess sludge in wastewater treatment plants (WWTPs), contains high concentrations of organic matter and essential nutrients that could promote plant growth. However, it also contains a significant number of pathogenic and opportunistic pathogenic microorganisms, which present major challenges in terms of its safe application. A sample taken from WWTP “Kubratovo” was treated using plasma devices. The aim was to evaluate the effect of treatment by two types of plasma sources on the content of pathogenic bacteria as well as the chemical composition of the liquid digestate. The Surfaguide plasma source demonstrated a higher disinfection effectiveness (100% for E. coli, Clostridium sp.; over 99% for fecal and total coliforms; 98% for Salmonella sp.). The β-device effectively removed (100%) the following groups: E. coli and Clostridium sp. However, its effectiveness was significantly lower for the other groups. The obtained results show that plasma treatment induces the transformation of nitrogen and phosphorus compounds, resulting in increased nitrite and phosphate concentrations. The application of cold atmospheric plasma disinfection significantly improved the sanitary and compositional characteristics of the liquid digestate. The Surfaguide achieved significantly better results than the β-device, confirming its suitability for sustainable resource recovery and safe agricultural use. Full article

Background. The establishment and diversity of the gut microbiota during early childhood are fundamental for immune regulation and metabolic processes, with factors such as prematurity, delivery method, antibiotic treatment, and breastfeeding significantly impacting microbiome development and potential health outcomes. Objectives/Methods. This comparative study examined the gut microbiota composition in children aged 6–8 and 9–12 months, born via spontaneous labor at ≥38 weeks’ gestation, who either did not receive antibacterial therapy or required beta-lactam antibiotics. The composition of the colonic microbiota was analyzed in these fecal samples using a quantitative real-time PCR (qRT-PCR). Results. Significant differences in microbiota composition were observed between groups. Children treated with antibiotics exhibited a statistically significant reduction in alpha diversity indices (Shannon and Simpson), along with decreased colonization of key functionally important microorganisms, including obligate anaerobic bacteria such as Faecalibacterium prausnitzii, Clostridium leptum, Bacteroides spp., and metabolically active Bifidobacteria (B. bifidum, B. breve, B. longum). Conclusions. These microbiota alterations may adversely affect child health by diminishing microbial balance and functional potential, especially during this critical period of immune and metabolic development. The decline in anti-inflammatory, short-chain fatty acid-producing bacteria elevates the risk for allergic, atopic, dysbiotic, and metabolic conditions. Recognizing these impacts underscores the importance of strategies to supports microbiota restoration after antibiotic use, such as probiotics, prebiotics, and dietary interventions. Further research should focus on microbiota recovery dynamics to facilitate early intervention and optimize pediatric health outcomes. Overall, understanding antibiotic effects on gut microbiota can guide more judicious treatment approaches, reducing long-term health risks. Full article

Given the high incidence of calf diarrhea and the limited data on pathogenic and non-infectious factors in a large-scale dairy farm in Wuwei City, this study aims to investigate the pathogens associated with summer calf diarrhea and the non-infectious risk factors in local large-scale dairy farm. It included 664 diarrheic calves (1–60 days of age, from June 2024 to May 2025), detected 5 types of enteric pathogens in 81 fecal samples collected in summer via RT-qPCR, collected data on non-infectious factors, and applied binary logistic regression and ROC analysis. The annual diarrhea incidence was 14.44%, with a peak in summer. Clostridium perfringens (67.90%) and Bovine Rotavirus (48.14%) were the dominant pathogens, and the rate of mixed infections was 48.14%. Risk factors for calf diarrhea included birth in spring or summer, female, Wagyu, younger age, birth weight < 38.5 kg, primiparous dams, serum immunoglobulin level < 8.1 g/L, and dam calving score > 1; longer duration of treatment was associated with a lower recovery rate. This study identifies key pathogens, risk factors, and their thresholds, thereby providing a scientific basis for the control of calf diarrhea in similar regions. Full article

Psittacine bornavirus type-4 (PaBV-4) causes proventricular dilatation disease and death among diverse birds, most notably caged parrots and related species, with no known cure or vaccine. Infected birds can shed virus in fecal matter, urine, and feather dander but it is unknown how well PaBV-4 survives outside of the host. This study focused on assessing the persistence of PaBV-4 in common environmental situations. The presence of viral RNA was examined in aqueous solutions at varying temperatures and recovery from typical avian husbandry materials (plastic, wood, metal, and cloth). Viral RNA persistence in aqueous samples was found to be 3 weeks at 37 °C, 2 months at 24 °C (room temperature), and 3 months at 4 °C. Viral RNA was also recovered from plastic and metal surfaces up to 72 h after inoculation. Also examined were disinfection protocols comparing coverage versus contact time for a reduction in viral RNA. Complete coverage by the disinfecting agent was more important for preventing recovery of viral RNA. Additionally, PaBV-4 RNA was transferable by paper towel. These results provide the first evidence of the robust nature of PaBV-4 in an aqueous environment and show that cleaning protocols need to be carefully curated to limit possible viral spread. Full article

Wastewater contamination of freshwater ecosystems is a major driver of the spread of antibiotic resistance (AR). This preliminary study investigated the impact of wastewater pollution on the AR profiles of bacterial communities in the Oued–Zénati waterway, Algeria, across a pollution gradient. From September 2017 to May 2018, water samples were collected from an upstream reference site (P1), a site downstream of urban and hospital discharges (P2), and a downstream recovery site (P3). Physicochemical and microbiological analyses revealed a critical pollution hotspot at P2, with fecal coliform concentrations reaching 9.5 × 10⁵ MPN/100 mL, nearly 40 times higher than at P1. From a representative subset of 33 bacterial isolates characterized in this study, susceptibility testing showed a high prevalence of resistance, with observed trends matching the pollution gradient. Specifically, 100% of isolates from the polluted sites (P2 and P3) were resistant to ampicillin, and 60% of isolates from the hotspot (P2) were resistant to amoxicillin/clavulanic acid. Conversely, all isolates remained susceptible to gentamicin. These initial findings suggest that direct wastewater discharge is creating a significant reservoir for AR, highlighting potential risks to public and environmental health and underscoring the urgent need for improved wastewater management infrastructure. Full article

Background/Objectives: This study investigated how phase-specific dietary strategies and weight regulation influence gut microbiota composition and diversity in competitive weightlifters. Particular emphasis was placed on integrating energy intake, macronutrient clustering, and weight fluctuations across distinct training phases. Methods: Thirteen competitive weightlifters were recruited, with 10–12 contributing complete data per phase. Fecal and dietary samples were collected during the preparation, competition, and transition phases. Gut microbiota was profiled via 16S rRNA gene sequencing, and alpha/beta diversity was analyzed using QIIME2. K-means clustering based on caloric/macronutrient intake identified dietary patterns. Taxonomic differences were assessed using DESeq2, and microbial structures were compared across training phases, weight classes, and weight-change categories. Results: Overall phylum- and genus-level profiles and diversity indices remained stable across training phases, indicating community-level resilience. However, specific genera varied with dietary and physiological factors. Enterococcus was higher during the preparation phase, whereas Lactobacillus was enriched during the competition and transition phases as well as in the high-calorie cluster. Lightweight and heavyweight athletes also showed distinct microbial structures, and pre- and post-competition weight changes were associated with shifts in selected taxa. Notably, the low-calorie group exhibited higher Shannon diversity than the high-calorie group (p = 0.0058), with Lactobacillus dominance contributing to reduced evenness in high-energy diets. Conclusions: Despite overall microbial stability, dietary energy availability and body-weight regulation modulated specific taxa relevant to performance and recovery. By integrating dietary clustering, weight-class comparison, and pre- and post-competition weight changes, this study provides novel insight into the microbiota of resistance-trained athletes, a population underrepresented in previous research. Despite the modest sample size and single-season scope, this study offers new evidence linking dietary strategies, weight regulation, and gut microbiota in weightlifters, and highlights the need for validation in broader cohorts. Full article

Spinal cord injury (SCI) is a devastating neurological state that could lead to motor, sensory, and autonomic dysfunction. In addition to its direct impact on the central nervous system, SCI exerts systemic effects, including disruption of gut homeostasis and alterations in the gut microbiota, which can contribute to sustained inflammation and hinder functional recovery. While antibiotic administration during the acute phase of SCI is clinically indicated, it may exacerbate microbial dysbiosis. In this study, we investigate the combined effects of SCI and cefazolin treatment on the gut microbiome of female rats. Animals were assigned to three groups: NAÏVE (no intervention), SHAM (cefazolin only), and INJURY (T10 spinal cord contusion plus cefazolin). Cefazolin was administered for seven days after the injury, fecal samples were collected at baseline (day 0), and on days 7, 14, 21, and 28 post-SCI. DNA was extracted and subjected to 16S rRNA gene amplicon sequencing, followed by bioinformatic analysis. Our findings revealed significant microbial dysbiosis in the INJURY group, including reduced alpha diversity and distinct shifts in microbial composition. These changes were most prominent during the acute phase post-SCI. Our findings highlight the compounding effects of spinal trauma and antibiotic exposure on the gut microbiome and suggest that maintaining microbial stability may represent a promising avenue to support recovery after SCI. Full article

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

Background/Objectives: Loss and fragmentation of habitat from agricultural conversion led to the near extirpation of the pygmy rabbit (Brachylagus idahoensis Merriam, 1891) population in the Columbia Basin (CB) of Washington, USA. Recovery efforts began in 2002 and included captive breeding, translocations from other regions for genetic rescue, and reintroduction into native habitat in three sites: Sagebrush Flat (SBF), Beezley Hills (BH), and Chester Butte (CHB). Methods: We used noninvasive and invasive genetic sampling to evaluate demographic and population genetic parameters on three translocated populations of pygmy rabbits over eight years (2011–2020). For each population, our goal was to use fecal DNA sampling and 19 microsatellite loci to monitor spatial distribution, apparent survival rates, genetic diversity, reproduction, effective population size, and the persistence of CB ancestry. Over the course of this study, 1978 rabbits were reintroduced as part of a cooperative conservation effort between state and federal agencies. Results: Through winter and summer monitoring surveys, we detected 168 released rabbits and 420 wild-born rabbits in SBF, 13 released rabbits and 2 wild-born in BH, and 16 released rabbits in CHB. Observed heterozygosity (H_o) values ranged from 0.62–0.84 (SBF), 0.59–0.80 (BH), and 0.73–0.77 (CHB). Allelic richness (AR) ranged from 4.67–5.35 (SBF), 3.71–5.41 (BH), and 3.69–4.65 (CHB). Effective population (N_e) within SBF varied from 12.3 (2012) to 44.3 (2017). CB ancestry persisted in all three wild populations, ranging from 15 to 27%. CB ancestry persisted in 99% of wild-born juveniles identified in SBF. Apparent survival of juvenile rabbits differed across years (1–39%) and was positively associated with release date, release weight, and genetic diversity. Survival of adults (0–43%) was positively influenced by release day, with some evidence that genetic diversity also positively influenced adult apparent survival. Conclusions: Noninvasive genetic sampling has proven to be an effective and efficient tool in monitoring this reintroduced population, assessing both demographic and genetic factors. This data has helped managers address the goals of the Columbia Basin recovery program of establishing multiple sustainable wild populations within the sagebrush steppe habitat of Washington. Full article

Antibiotics may be used for gastrointestinal enteropathies but research has demonstrated significant microbiota dysmetabolism, fermentation pattern alterations, and prolonged dysbiosis following treatment. The objective of this study was to determine how dietary fiber or fecal microbial transplant (FMT) treatments impacted the fecal characteristics, metabolite concentrations, and microbiota populations of cats treated with metronidazole. Twenty-five healthy adult cats (6.75 ± 1.20 yr) were fed a commercial kibble diet for 2 wk, administered metronidazole (20 mg/kg BW BID) for 2 wk, then monitored for 4 wk. Cats were allotted to one of three interventions (diet, diet + beet pulp, diet + FMT) for 1 wk, interventions ceased, then recovery was monitored for 4 wk. Fresh fecal samples were collected at the end of each phase and at the mid-points of recovery. As anticipated, metronidazole increased fecal scores and moisture (p < 0.05), reduced fecal bacterial alpha diversity (p < 0.0001), and reduced fecal metabolite concentrations. Few treatment effects were detected, with antibiotic recovery contributing to many of the results observed. Dysbiosis was persistent throughout the study, with 4/25 cats still demonstrating mild dysbiosis after 9 wk. Overall, dietary or FMT treatments may aid in accelerated antibiotic recovery in cats but further research is needed to refine treatments for greater efficacy. Full article

Background/Objectives: This study aimed to examine the effects of a Fucoidan-rich extract from Saccharina latissima (SLE-F) on differential gut microbiota composition, intestinal inflammation status, and microbial functional gene expression in participants infected with Dengue or Oropouche virus at the Hermanos Ameijeiras Hospital in Havana, Cuba. Methods: Fecal samples were collected at baseline, day 28, and day 90 from 90 healthy adults, some of whom contracted the virus during the study period. Functional gene analysis was conducted using two approaches—the Kruskal–Wallis H test and linear discriminant analysis effect size—applied to ortholog-level data normalized by read count and gene copy number. Results: Infected participants exhibited significantly lower Lachnospiraceae-to-Enterobacteriaceae (LE) ratios, indicating increased intestinal inflammation. High-dose SLE-F treatment led to a significant reduction in the LE ratio (p = 0.006), suggesting a strong anti-inflammatory effect. Microbiome analysis revealed a shift from dysbiosis to a more balanced composition by the end of the study, characterized by increased abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and B. longum, along with decreased pro-inflammatory taxa such as Fusobacterium. Conclusions: Genetic analysis provided distinct yet complementary insights into the microbiome’s functional responses to infection and therapeutic modulation by Fucoidan. These findings highlight the therapeutic potential of high-dose Fucoidan in reducing gut inflammation and promoting microbiome recovery following viral infections. Full article

Background and aim: Neurobehavioral changes associated with food allergies have been reported, but the therapeutic effects of probiotics have not been fully explored. Our study aimed to investigate the impact of multi-strain probiotics on neurobehavioral outcomes and to elucidate the underlying mechanism via the microbiota-gut-brain axis. Methods: C57BL/6J Male mice were randomly divided into the following three groups: (1) control group; (2) OVA-sensitized group; (3) OVA-sensitized group treated with multi-strain probiotics (OVA + P). Anaphylactic reactions and behavioral abnormalities were assessed by histological, immunological, and behavioral analyses. To further elucidate the underlying mechanisms, the prefrontal cortex was collected for microglial morphological analysis, while serum and fecal samples were obtained for untargeted metabolomic profiling and 16S rDNA-based gut microbiota analysis, respectively. Results: Multi-strain probiotics significantly alleviated anaphylactic reactions in OVA-sensitized mice, as evidenced by reduced serum IgE levels, decreased Th2 cytokines, and reduced epithelial damage. Meanwhile, neurobehavioral symptoms were alleviated, including anxiety-like and depression-like behaviors, repetitive behaviors, social avoidance, and impaired attention. Mechanistically, probiotics administration suppressed production of inflammatory cytokines (TNF-α, IL-1β and IL-6) and inhibited activation of M1 microglia in the prefrontal cortex, which might contribute to neuron recovery. Furthermore, multi-omics analysis revealed that amino acid metabolism restoration in OVA + P mice, particularly carboxylic acids and derivatives, which was remarkably correlated with alterations in gut microbiota and behaviors related to FA. Conclusions: Gut microbiota and its amino acid metabolites mediate the therapeutic effects of multi-strain probiotics on FA-induced behavioral abnormalities. These effects occur alongside the suppression of neuroinflammation and microglial activation in the prefrontal cortex. Our findings highlight the neuroimmune regulatory role of the gut-microbiota-brain axis and support the potential use of probiotics as an intervention for FA-induced brain dysfunctions. Full article

Antibiotics are commonly used to aid in the remission of gastrointestinal diseases, but usage may lead to prolonged dysbiosis. The objective of this study was to evaluate the effects of metronidazole on fecal microbiota, fecal metabolites, and serum bile acids and uremic toxins of healthy adult cats. Twelve healthy adult cats (4.7 ± 0.4 yr) received metronidazole (20 mg/kg BW PO BID) for 14 days (day 0–14) and were monitored during a 28-day recovery period (day 15–42). Fecal and blood samples were collected at baseline (day 0), after metronidazole (day 14), and weekly during recovery (on days 21, 28, 35, and 42). Fecal samples were analyzed for microbiota and bacterial metabolites. Serum samples were analyzed for bile acids and uremic toxins. Metronidazole increased dysbiosis index and fecal lactate concentrations (p < 0.0001) and decreased fecal propionate, butyrate, and secondary bile acid concentrations (p < 0.0001) for up to 28 days. Prolonged dysbiosis and Peptacetobacter (Clostridium) hiranonis reductions were observed in 10/12 (83%) cats. Serum uremic toxins were also reduced (p < 0.0001) after metronidazole administration. The observed changes after metronidazole administration illustrate how changes in the gut microbiome alter microbial metabolism and its relation to host dysmetabolism. In conclusion, metronidazole is a potent antibiotic with persistent effects observed in the microbiome and metabolome, even up to one month after administration. Full article