Search Results (219)

Reuse of human excreta and derivatives is becoming a common practice in areas with agricultural predominance. While in situ treated faeces through ecological sanitation (Ecosan), known as “faecal by-products” are being used to sustain soil nutrients and improve on-site sanitation, the concern remains about the health risks related to the survival of pathogens in these by-products in the community of farmers. This study assessed the survival of faecal pathogens and estimated microbial risks associated with the use of Ecosan faecal by-products in agriculture. The quantitative microbial risks assessment (QMRA) framework was used to estimate the risks posed by each faecal pathogen in solid and semi-solid faecal by-products under the probabilistic model of Monte Carlo simulation. Ascaris lumbricoides (6.5 eggs/gr), Taenia species (0.3 egg/gr), Schistosoma species (9.3 cercariae/gr), Entamoeba species (4.4 cysts/gr), and Escherichia coli (451 Cfu/gr) were detected in semi-solid faecal products. Exposure scenarios were observed throughout four critical points: vault faecal by-products removal/unloading, transport, collection, and application of faecal by-products in the gardens. Due to the presence of eggs and cysts, an estimated annual risk of infections was found in semi-solid faecal by-products with Schistosoma species (88%) and Ascaris lumbricoides (90%). Both concentrations were above World Health organisation (WHO) standards of associated infective risks of 0–10% of helminths in faecal sludge applied in the gardens. The users of faecal by-products, particularly farmers are exposed not only to high concentrations of helminth eggs but also to protozoa and bacteria with infective risks of Entamoeba species (99%) and E. coli species (62%). A stepwise implementation of faecal pathogens die-off during treatment of faecal by-products in compliance with the WHO’s 2018 guidelines can prevent the use of unsanitary faecal by-products. According to these findings, the proper control of intestinal protozoa and soil-transmitted helminths (STHs) should be enforced through personal protective measures in Burera district, Rwanda. Full article

Bacteroides 2 (Bact2) is a dysbiotic enterotype often associated with susceptibility to developing diseases such as inflammatory bowel disease (IBD). Carriers of Bact2 are found to be less responsive to therapeutic treatments like vedolizumab. This enterotype is characterised by a large amount of Bacteroides, low diversity in bacteria, fewer butyrate-producing species, and generally a low abundance of microbes in the gut. However, it remains unclear whether this dysbiosis contributes to IBD pathology or if it is merely a result of inflammation in the gut. Due to its ability to influence treatment responses, it is crucial to understand the molecular mechanisms behind this enterotype, as well as the effect of diet on this dysbiosis. A high concentration of pro-inflammatory cytokine IL-1$\beta$ was found in the faecal water of Bact2 patients, as well as an abundance of conjugated bile acids, whereas butyrate was found in decreased amounts. Through the consumption of a less industrialised diet, it could be possible to shift away from a dysbiotic enterotype like Bact2. This includes the consumption of whole-grain carbohydrates to increase the growth of butyrate-producers and maintaining a low-fat diet to decrease bile acid production. Full article

Increasing evidence suggests pancreatic cancer develops within a host–microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome–tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes. Full article

Differences in the gut microbiota are directly reflected in lung–gut axis crosstalk, which may increase susceptibility to pulmonary infections, such as those caused by the bacterium Pseudomonas aeruginosa. Deficiency of the cytokine IL-10 leads to gut inflammation, and this pro-inflammatory environment is partly due to changes in the gut microbiota. To better understand the effects of IL-10 deficiency on the gut microbiota, the intestinal microbial composition of IL-10 KO mice was assessed, and an increase in the phyla Bacteroidetes and Proteobacteria and a decrease in the phylum Firmicutes were observed in the faeces compared with the wild-type group (WT). Additionally, IL-10 KO mice had a higher pro-inflammatory immunostimulatory caecal content. Furthermore, it was found that heterologous faecal microbiota transplantation (FMT) between groups reversed this gut imbalance. IL-10 KO mice showed greater susceptibility to acute pulmonary infection by P. aeruginosa, with a higher recovery of viable bacteria in the lung and spleen, greater tissue damage and increased expression of genes encoding pro-inflammatory cytokines in the lungs. This greater susceptibility was reversed after FMT. Taken together, these results demonstrate the role of endogenous IL-10 in the gut microbiota constitution and its importance in the pulmonary immune response against P. aeruginosa infection. Full article

Antimicrobial resistance (AMR) is a silently escalating global crisis, presenting a specific challenge for the One Health approach. Landscapes can serve as reservoirs of AMR bacteria and genes, while synurban wildlife may act as vectors of bidirectional exchange. However, these species can also be utilised as sentinels of landscape AMR load. Herbivorous avian bioindicators, such as the Common Wood Pigeon (Columba palumbus), continuously sample the landscape during foraging and drinking, providing a homogenous spatial overview on the state of AMR. This study aimed to investigate the potential of this species for assessing the impact of landscape diversity on bacterial communities and their AMR patterns. Toward this objective, two spatial units of 4 km in diameter located at an upstream and a downstream section of a river, relative to a provincial town, were compared using 16 cloacal samples per site. Heterotrophic plate count techniques resulted in 60 isolates, of which 48 were identified, and 35 were tested for AMR using the VITEK 2 Compact system. The association between bacteriological findings and landscape diversity was analysed using Rényi diversity profiles. The Gram-positive/Gram-negative ratio was the only parameter that proved to be significantly different between the two study sites. The investigation detected six MDR isolates, with two methicillin-resistant phenotypes (Staphylococcus gallinarum, Mammaliicoccus lentus) and two carbapenem-resistant Pseudomonas fluorescens isolates. We established that the small sample size limits drawing definitive conclusions. However, exploring the link between landscape diversity and the cultivable faecal microbiota of herbivorous birds is a promising approach for more extensive research. Full article

Underutilised, nutrient-dense legumes in their sprouted form provide promising substrates for developing functional fermented foods capable of influencing gut microbial activity and metabolite production. This study evaluated the effects of probiotic lactic acid bacteria-fermented beverages derived from sprouted Bambara groundnut (Vigna subterranea) and cowpea (Vigna unguiculata) on gut microbiota composition and short-chain fatty acid (SCFA) production using an in vitro colonic fermentation model. The beverages were fermented with either Bifidobacterium animalis BB-12 (BCBF24) or Lactiplantibacillus plantarum 75 (BCL7524). During colonic fermentation, at 0, 12, 24, and 38 h, faecal slurries were collected for SCFA analysis using gas chromatography–mass spectrometry (GC-MS) and deoxyribonucleic acid (DNA) sequencing (Oxford Nanopore Technologies). Microbial diversity decreased, indicating selective enrichment of taxa. BCL7524 induced a major shift, significantly (p < 0.05) enriching Bacillota and driving Megasphaera to ~42% dominance within 24 h. This reflected cross-feeding from L. plantarum to lactate-utilising Megasphaera spp. Spearman correlation linked Megasphaera to a broad SCFA profile, including isobutyric, isovaleric, valeric, and hexanoic acids, with a significant (p < 0.05) positive correlation observed for hexanoic acid. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated proteolysis and mapped hexanoic acid to fatty acid biosynthesis pathways, suggesting chain-elongation activity contributing to hexanoate formation. In line with this, BCL7524 produced significantly (p < 0.05) higher levels of hexanoate (3–14 mM) and valerate (10–15 mM), supporting chain-elongation activity within the community. In contrast, BCBF24 enriched Actinomycetota and Bifidobacterium, correlating with acetate production (18–23 mM). This study demonstrates that specific synbiotic beverages can modulate gut microbial ecology and metabolic output under in vitro conditions. Full article

Bacterial resistance on farms can be driven by antimicrobial use. Less is known about inter-farm transfer of resistance genes and their persistence under low antimicrobial pressure. Over two years and nine visits, we examined the shedding of resistant indicator bacteria (Escherichia coli) on one lower- and one higher-antimicrobial-usage pig farm. There was a unidirectional transfer of some less healthy pigs from the former to the latter. Faecal pools (180) were cultured on Chromagar ECC, with and without added cefotaxime or ciprofloxacin. Presumptive E. coli were phenotyped, and many ciprofloxacin-resistant isolates were whole-genome sequenced. Comparing farms, there was more (p < 0.0001) phenotypic resistance to the antimicrobial panel from the higher-usage unit, and markedly more (about ten-fold) multi-resistance. Significantly elevated individual drug resistances on this unit correlated with recently used antimicrobials. Ciprofloxacin and/or cefotaxime-resistant isolates were often present, although in low proportions. Neither of these antimicrobial classes had been administered recently, except for one fluoroquinolone course late in the study. AMR genes were more diverse from the higher-usage farm, but some resistant and multi-resistant isolates were closely related between farms. Thus, we demonstrated the maintenance of resistance genes in strains present on farms, even where selective pressure was low. Full article

Despite the importance of wastewater environmental monitoring in disease prevention and response strategies, its use remains poorly documented in Senegal. In addition, there is more onsite sanitation than sewer networks in Dakar, and open drains channel for rainwater are also used as clandestine wastewater discharge into the sea. This study aimed to assess the presence of specific pathogens in wastewater, faecal sludge, and bathing water (the sea). Samples were taken at treatment plants, an open drain, and in the receiving environment (the sea) from June to December 2023. Total nucleic acid was subjected to multiplex qualitative qPCR using SeeGene Allplex™ kits targeting 34 gastrointestinal pathogens. Descriptive statistics, multiple correspondence analysis (MCA) and logistic regression were performed. Considering all matrices, across 51 analysed samples, the results revealed strong bacterial (96.08%, n = 49), parasitic (84.31%, n = 43), and viral (68.63%, n = 35) presence. These results showed high levels of Aeromonas spp. (96.08%), Blastocystis hominis (80.39%), Enterocytozoon (58.82%), and Norovirus GII (74.51%) among bacteria, protozoa, helminths, and viruses, respectively. Moreover, faecal sludge and pumping station samples show more identified pathogen than wastewater treatment plant and seawater samples. The MCA revealed that the dry season is spatially associated with a greater number of pathogens than the rainy season, but the latter showed a greater species diversity. Logistic regression showed that certain physicochemical parameters, including BOD5, turbidity, pH, and suspended solids, influence pathogen detection. However, qualitative detection and sampling period may constitute limitations. These results reveal that wastewater and bathing water can serve as sources of information on the circulation of pathogens of interest with epidemic potential. Therefore, this valuable epidemiological tool could serve as an adjunct to clinical surveillance in order to prevent future epidemics. Full article

Metabolic Dysfunction-Associated Steato-Hepatitis (MASH) is a multiple-hit disease. Endotoxins, ethanol, and other metabolites of certain gut microbiota can reach the liver and accelerate inflammation and disease progression. Targeting ethanol-producing colonic bacteria with rifaximin could affect the progress of MASH. In the present study, thirty mice were assigned to three groups (n = 10 mice per group). Mice received either a normal diet, a Western diet, or a Western diet with oral rifaximin. After 12 weeks, liver function, serum levels of TNF-α, interleukin (IL)-1β, IL-6, and lipopolysaccharides (LPS) were measured. Liver specimens were assessed for pathological changes, lipid deposition, and fibrosis. Expression of p53, GFAP, CD68, and TLR-4 in the liver was also assessed. Faecal samples were evaluated for ethanol contents. Lactobacillus acidophilus, in addition to ethanol-producing Klebsiella pneumoniae and Escherichia coli, were isolated, quantified, and tested for sensitivity to rifaximin. Rifaximin was able to ameliorate Western diet-induced biochemical changes and elevated TNF-α, IL-1β, IL-6, and LPS levels. Changes in liver histology, fibrosis, and lipid content were attenuated. Expressions of p53, GFAP, CD68, and TLR-4 in the liver were all reduced. The Western diet-induced increases in faecal ethanol or ethanol-producing bacteria were not corrected by rifaximin. After 12 weeks, isolated bacteria from the rifaximin group were rifaximin-resistant. Our findings imply that the protective impact of rifaximin in the MASH model is unlikely to be mediated by alteration of ethanol-producing colonic bacteria because of acquired rifaximin resistance. Rifaximin-induced reduction in endotoxemia and inflammation in the liver appears to be a more relevant explanation. Full article

The gut microbiota of seabirds can undergo shifts during the moulting period due to fasting. Understanding the characteristics of gut microbiota in African penguins (Spheniscus demersus) throughout moulting is meaningful for the conservation and management of this critically endangered seabird species. A total of 12 captive African penguins reared in Shanghai Zoo were divided into three sampling stages: (1) pre-moulting (Pre); (2) mid-moulting (Mid); and (3) post-moulting (Post). The 16S rDNA gene sequencing of faecal samples was performed to evaluate differences in diversity, composition, and predicted function of the gut microbiota across the moulting period. The results showed that Firmicutes, Proteobacteria, and Actinobacteria were the predominant bacterial phyla in African penguins throughout moulting. Moulting significantly altered the diversity and composition of gut microbiota in captive African penguins. Pre-moulting penguins exhibited higher abundances of Bacilli and Lactobacillales compared with mid- and post-moulting groups, whereas mid- and post-moulting penguins had increased abundances of several potentially harmful bacteria. In addition, the functional prediction analysis indicated that pre-moulting penguins had a higher abundance of protein N-glycosylation pathway compared with both mid- and post-moulting penguins. The pre-moulting group also exhibited a decreased abundance of the vitamin E biosynthesis pathway compared with the mid-moulting group. The present study has revealed that the gut environment of African penguins is more vulnerable during the mid- and post-moulting periods. The findings provide reference information for improving the management of endangered seabird species during moult. Full article

Background: The human gut microbiome is highly complex, and its composition is strongly influenced by dietary patterns. Alterations in microbiome structure have been associated with a range of diseases, including type 2 diabetes mellitus. However, the underlying mechanisms for this remain poorly understood. In this study, a novel in vitro approach was utilized to investigate the interplay between gut bacteria, dietary metabolites, and metabolic dysfunction. Methods: Two representative gut bacterial species—Bacteroides thetaiotaomicron and Lactobacillus fermentum—were isolated from human faecal samples and subjected to controlled dietary manipulation to mimic eubiotic and dysbiotic conditions. Metabolites produced under these conditions were extracted, characterized, and quantified. To assess the functional impact of these metabolites, we utilized the INS-1 832/3 insulinoma cell line, evaluating insulin sensitivity through glucose-stimulated insulin secretion and ERK1/2 activation. Results: Our findings demonstrate that metabolites derived from high-carbohydrate/high-fat diets exacerbate metabolic dysfunction, whereas those generated under high-fibre conditions significantly enhance insulin secretion and glucose-dependent ERK1/2 activation in co-culture compared to monocultures. Conclusions: This work systematically disentangles the complex interactions between gut microbiota, diet, and disease, providing mechanistic insights into how microbial metabolites contribute to the onset of metabolic disorders. Full article

Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy. Full article

Background: Parkinson’s disease (PD) involves progressive neurodegeneration with clinical or subclinical disturbance of the gut–brain axis, including altered gastrointestinal motility and enteric nervous system involvement. Clinical studies have reported gut microbiome alterations in PD, with shifts in taxa associated with inflammatory signalling and short-chain fatty acid (SCFA) metabolism. Photobiomodulation (PBM), a non-invasive light therapy, has been investigated as a potential adjunctive treatment for PD, with proposed effects on neural, metabolic, and immune pathways. We previously reported the five-year clinical outcomes in a PBM-treated Parkinson’s disease case series. Here we report the five-year gut microbiome outcomes based on longitudinal samples collected from the same participants. This was an exploratory, open-label longitudinal study without a control group. Objective: Our objective was to assess whether long-term PBM was associated with changes in gut microbiome diversity and composition in the same Parkinson’s disease cohort as previously assessed for changes in Parkinson’s symptoms. Methods: Six participants from the earlier PBM proof-of-concept study who had been diagnosed with idiopathic PD and who had continued treatment (transcranial light emitting diode [LED] plus abdominal and neck laser) for five years had their faecal samples analysed by 16S rDNA sequencing to assess microbiome diversity and taxonomic composition. Results: Microbiome analysis revealed significantly reduced evenness (α-diversity) and significant shifts in β-diversity over five years, as assessed by Permutational Multivariate Analysis of Variance (PERMANOVA). At the phylum level, Pseudomonadota and Methanobacteriota decreased in four of the six participants. Both of these phyla are often increased in the Parkinson’s microbiome compared with the microbiomes of healthy controls. Family-level changes included increased acetate-producing Bifidobacteriaceae (five of the six participants); decreased pro-inflammatory, lipopolysaccharide (LPS)-producing Enterobacteriaceae (two of the three participants who have this bacterial family present); and decreased LPS- and H₂S-producing Desulfovibrionaceae (five of six). At the genus level, Faecalibacterium, a key butyrate producer, increased in four of the six participants, potentially leading to more SCFA availability, although other SCFA-producing bacteria were decreased. This was accompanied by reductions in pro-inflammatory LPS and H₂S-producing genera that are often increased in the Parkinson’s microbiome. Conclusions: This five-year case series represents the longest follow-up of microbiome changes in Parkinson’s disease, although the interpretation of results is limited by very small numbers, the lack of a control group, and the inability to control for lifestyle influences such as dietary changes. While causal relationships cannot be inferred, the parallel changes in improvements in mobility and non-motor Parkinson’s symptoms observed in this cohort, raises the hypothesis that PBM may interact with the gut–brain axis via the microbiome. Controlled studies incorporating functional multi-omics are needed to clarify potential mechanistic links between microbial function, host metabolism, and clinical outcomes. Full article

The Ukrainian brook lamprey (UBL) (Eudontomyzon mariae) spreads in Poland and often replaces the European brook lamprey (EBL) (Lampetra planeri) in rivers contaminated by wastewater effluents. We aimed to investigate whether this phenomenon is associated with differences in the intestinal microbiota of the two lamprey species. We analysed seasonal changes in the midgut microbial content of the UBL ammocoetes collected from a section of the River Gać affected by wastewater treatment plant effluent. The numbers of cultivable psychrophilic (autochthonous) and mesophilic (allochthonous) microorganisms, along with Escherichia coli and faecal streptococci, were compared to those found in the EBL from the same site. Higher levels of the faecal indicator microorganisms were observed in the UBL gut content compared to the EBL across most seasons, particularly in the winter (all mesophiles), in contrast to the levels of psychrophilic bacteria. This may suggest a relatively greater accumulation of mesophilic, sewage-associated bacteria in the UBL gut. Varying intestinal bacterial counts in the UBL gut did not reflect trends observed for the microorganisms in surrounding water during the studied seasons. These findings support the hypothesis that the UBL potentially benefits from the uptake of faecal bacteria. Such adaptation may contribute to its dominance in contaminated freshwater ecosystems, where EBL populations decline. Full article

Bathing water quality (BWQ) monitoring and prediction are essential to safeguard public health by informing bathers about the risk of exposure to faecal indicator bacteria (FIBs). Traditional monitoring approaches, such as manual sampling and laboratory analysis, while effective, are often constrained by delayed reporting, limited spatial and temporal coverage, and high operational costs. The integration of artificial intelligence (AI), particularly machine learning (ML), with automated data sources such as environmental sensors and satellite imagery has offered novel predictive and real-time monitoring opportunities in BWQ assessment. This systematic literature review synthesises current research on the application of AI in BWQ assessment, focusing on predictive modelling techniques and remote sensing approaches. Following the PRISMA methodology, 63 relevant studies are reviewed. The review identifies dominant modelling techniques such as Artificial Neural Networks (ANN), Deep Learning (DL), Decision Tree (DT), Random Forest (RF), Multiple Linear Regression (MLR), Support Vector Machine (SVM), and Hybrid and Ensemble Boosting algorithms. The integration of AI with remote sensing platforms such as Google Earth Engine (GEE) has improved the spatial and temporal solution of BWQ monitoring systems. The performance of modelling approaches varied depending on data availability, model flexibility, and integration with alternative data sources like remote sensing. Notable research gaps include short-term faecal pollution prediction and incomplete datasets on key environmental variables, data scarcity, and model interpretability of complex AI models. Emerging trends point towards the potential of near-real-time modelling, Internet of Things (IoT) integration, standardised data protocols, global data sharing, the development of explainable AI models, and integrating remote sensing and cloud-based systems. Future research should prioritise these areas while promoting the integration of AI-driven BWQ systems into public health monitoring and environmental management through multidisciplinary collaboration. Full article