BMC Microbiology

The genus Gardnerella comprises a group of fastidious bacteria associated with the female urogenital tract and has undergone extensive taxonomic revision in recent years. In this study, a bacterial strain, designated CCPDSM, was isolated from the female urinary microbiome and subjected to a comprehensive polyphasic taxonomic characterization. The 16S rRNA gene sequence confirmed that this strain is a member of the genus Gardnerella, and phylogenetic analyses based on cpn60 sequences, together with phylogenomic reconstruction placed strain CCPDSM within the genus Gardnerella as a distinct and well-supported lineage. Genome-based relatedness indices (ANIb, ANIm, TETRA and dDDH), demonstrated clear separation of CCPDSM from all validly published Gardnerella species. In contrast, comparisons with two publicly available closely related genomes yielded values above accepted species delineation thresholds, supporting their assignment to the same taxon. Phenotypic characterization, together with genome-based functional predictions, revealed a fastidious, fermentative metabolic profile that further differentiated CCPDSM from its closest relatives, while remaining consistent with traits characteristic of the genus. On the basis of combined phylogenetic, genomic and phenotypic evidence, strain CCPDSM is proposed as representing a novel species within the genus Gardnerella, for which the name Gardnerella fastidiominuta sp. nov. is proposed, with strain CCPDSM (=CECT 31324=CCP 588) designated as the type strain. This study expands the recognized diversity of Gardnerella and highlights the female urinary tract as a reservoir of previously uncharacterized species within this genus.

Yarrowia lipolytica is a yeast of industrial interest exhibiting remarkable lipolytic and proteolytic capacities, with a high potential for white biotechnology applications. This yeast can be isolated from a wide range of natural, polluted or anthropogenic environments, including various food products. The present study aims to increase the data on Y. lipolytica phenotypic diversity by evaluating the growth parameters and secreted enzymatic activities of 28 wild-type Y lipolytica (and Yarrowia sp.) strains isolated from various environments across 10 countries. These data could facilitate the selection of appropriate strains for specific research purposes, particularly when wild-type strains are prioritized over genetically engineered ones, like for food-related applications. Notably, strain SWJ-1b exhibited an outstanding combination of favourable characteristics, with optimum (or near) performances for both growth and enzymatic parameters.

Industrial waste containing hydrophobic pollutants, like oils and hydrocarbons, is toxic and difficult to degrade, posing both ecological and human health risks. Biosurfactants are eco-friendly surface-active compounds produced by microorganisms, known for their ability to lower surface and interfacial tension, enhancing the solubility and bioavailability of hydrophobic compounds, facilitating their breakdown. The current study focuses on isolating biosurfactant-producing bacteria from industrial waste sources near Dhaka, Bangladesh, and characterizing their properties, determining potential usage. Using diesel-enriched nutrient agar, bacterial strains were isolated and screened for biosurfactant production by oil displacement, emulsification index (E24%), and drop collapse assay. The most promising isolates were characterized according to their biochemical activities and 16S rRNA amplicon-based sequencing. Isolation and characterization of the surfactants have been carried out using chromatographic techniques. The identified bacteria passed the drop collapse and oil displacement tests. CTAB agar assay, indicates their anionic nature, showing an emulsification index ranging 10-41%. The potential biosurfactant producers belong to Bacillus, Pseudomonas, Acinetobacter, and Enterobacterium genera. The surfactants showed antibacterial, antifungal, and plant growth promotion activity and have been characterized in terms of pH stability, salinity, adhesion, and temperature tolerance. The study successfully identified and characterized potential biosurfactant-producing bacteria from industrial waste, highlighting their efficiency in breaking down hydrophobic pollutants and hydrocarbons. These microorganisms provide a green and economical substitute for synthetic surfactants due to their biodegradability and lower toxicity. Upon further research and scaling, these bacteria can be a good source of biosurfactants for potential applications in industrial, agricultural, and biomedical fields. IMPORTANCEThe study carries high significance as it creates multi-disciplinary scopes for utilizing these environmentally adapted biosurfactant-producing bacteria in industry, agriculture, and medicine. Since the bacterial isolates have hydrocarbon degradation ability, upon optimization for higher production, industrial usage in oil refinery and other industries can be adopted. Due to their biodegradable nature, usage in wound healing bandages and as antimicrobial agents in medicine will be noteworthy. The isolates have plant growth promotion ability and utilizing them as biofertilizer will reduce the dependency on chemical fertilizers. This is the first detailed report on biosurfactant-producing bacteria from this industrial waste-polluted Turag River of Dhaka City. Moreover, it compiles detailed screening protocols and methods for analyzing such environmentally friendly microbes. Such characterization also opens the scope for optimizing the production of the surfactant compounds on a large scale and utilizing them commercially.

Background/ObjectivesGlucagon-Like Peptide-1 (GLP-1) is a key incretin hormone that regulates glucose homeostasis and energy metabolism. Impaired GLP-1 signaling contributes to the development of obesity, metabolic syndrome, and type 2 diabetes. Emerging evidence indicates that gut microbiota-derived components can influence GLP-1 secretion, highlighting the therapeutic potential of microbial modulators. Akkermansia muciniphila, a next-generation probiotic associated with improved metabolic health, remains underexplored for its capacity to stimulate GLP-1 release. This study aimed to investigate the GLP-1- stimulatory effects of live and pasteurized (dead) A. muciniphila strains in human enteroendocrine cells. MethodsHuman enteroendocrine L-cells (NCI-H716) were treated with varying doses of live and dead A. muciniphila from Vidya Herbss proprietary VHAKM strain and a commercially available marketed strain (dead form). Following incubation, GLP-1 levels were quantified from culture supernatants using enzyme-linked immunosorbent assay (ELISA). Comparative analyses assessed differences in GLP-1 secretion between strains and treatment forms. ResultsBoth live and pasteurized VHAKM strains significantly increased GLP-1 secretion compared to untreated controls. The live VHAKM strain exhibited higher GLP-1 stimulatory activity than its pasteurized counterpart and the marketed strain. The results suggest a strain-specific and viability-dependent modulation of GLP-1 secretion in human L-cells. ConclusionsThis study demonstrates that A. muciniphila VHAKM enhances GLP-1 secretion in a strain- and form-dependent manner, with live cells showing superior efficacy. These findings provide foundational insights for developing microbiome-targeted interventions to boost endogenous GLP-1 levels and improve metabolic health outcomes.

BackgroundInflammatory bowel disease (IBD) is a chronic inflammatory disorder characterized by gut microbial dysbiosis and immune dysregulation. While compositional changes in the microbiome are well studied, the functional mechanisms through which microbes influence host signalling remain poorly understood. PurposeThis study aimed to investigate microbial-host molecular mimicry in IBD and to elucidate its role in modulating immune and neuronal pathways through a newly proposed Microbial Signal Recognition and Neuronal Mimicry (SRNM) axis. MethodsShotgun metagenomic datasets from IBD patients and healthy controls were analyzed using a custom Molecular Mimicry In Silico Pipeline (MMIP). Reads were assembled, annotated, and subjected to protein homology mapping, Gene Ontology enrichment, PFAM domain analysis, and taxonomic profiling to identify microbial proteins mimicking human functional pathways. ResultsIBD-associated microbiomes exhibited significantly higher functional complexity and enrichment of eukaryote-like proteins compared to healthy controls. Microbial proteins mimicking host pathways involved in neuron projection development, signal recognition particle (SRP)-mediated protein targeting, immune signaling, and stress responses were markedly enriched in IBD. Key human-like targets included TRPV1, CAMK2D, SNCA, MTCP1, TCL1B, and PEAK3. PFAM analysis revealed overrepresentation of kinase domains, zinc-finger motifs, ankyrin repeats, and ABC transporters. These signatures were predominantly contributed by IBD-enriched taxa such as Gammaproteobacteria, Fusobacteria, and Betaproteobacteria. ConclusionThis study identifies a previously unrecognized SRNM axis in IBD, revealing how microbial molecular mimicry may influence neuroimmune signaling and disease pathogenesis, and highlight potential targets for microbiome-based therapeutic intervention.

The Bacillus genus comprises physiologically versatile, endospore-forming bacteria widely distributed in natural environments. In this study, we report the isolation and genomic characterization of strain Bva_UNVM-123, recovered from agricultural soil in Pergamino, Argentina. Whole-genome sequencing using Illumina technology yielded a 5.1 Mbp draft genome assembled in 67 contigs with a GC content of 36%. Comparative genomic analyses using the TYGS server and digital DNADNA hybridization (dDDH) values supported its classification as a potentially novel species within the Bacillus sensu lato (s.l.) group. Genome annotation revealed 4,866 protein-coding genes, including multiple determinants conferring resistance to antibiotics (e.g., fosfomycin, tetracycline, beta-lactams) and toxic heavy metals (e.g., arsenic, cadmium, mercury), supporting its potential application in bioremediation. Additionally, PathogenFinder predicted a low probability of human pathogenicity (0.207), reinforcing its safety for environmental use. Functional classification based on Swiss-Prot further supported a metabolically versatile profile and revealed the presence of resistance-related categories associated with environmental adaptation. This study adds to the growing knowledge of environmental Bacillus species and their biotechnological potential

BackgroundIdiopathic epilepsy (IE) is the most common chronic nervous system disorder of dogs, and its cause is poorly understood. Emerging evidence suggests that microbiome alterations can occur with IE via the microbiota-gut-brain axis. Therefore, we analyzed the fecal microbiomes of 98 dogs (49 IE, 49 control) in a pairwise case-control observational study using 16S rRNA gene sequencing. ResultsAlthough the microbial community was mostly similar between groups, IE was associated with a modest but significant shift in Weighted-Unifrac distance (P = 0.042). We used six differential abundance (DA) methods to identify differentially abundant amplicon sequencing variants (ASVs) between IE and control groups. Notably, one Collinsella ASV was found to be significantly more abundant in IE dogs by all six methods. The gut microbial compositions varied drastically across households (accounting for about 69% of the total variation), but did not have significant differences between sex, age, or breed. Phenobarbital administration in IE dogs had a significant effect on seizure control, and was not associated with changes in the microbiome. ConclusionOur findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.

BackgroundStunting, defined as height-for-age below -2 standard deviations of the WHO child growth standards median, is influenced by nutritional and environmental factors. It remains a public health challenge in Tanzania, particularly in Iringa (prevalence 57%, exceeding the national average of 30%), despite abundant food production. This study explored the gut bacteriome as a potential biomarker for child growth and its association with water, sanitation, and hygiene (WaSH) practices in food-secure settings. MethodsA community-based cross-sectional study (September-October 2024) enrolled children aged 5-23 months in Iringa, collecting fecal samples and household data on growth metrics, WaSH, feeding practices, and illness. The V3-V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed with QIIME2 and R for alpha and beta diversity, differential abundance (ANCOM-BC), and random forest (RF) modelling. ResultsOverall, 60.5% of 297 children were stunted. Stunting was associated with older age, male gender, discontinued breastfeeding, poor feeding diversity, toilet sharing, and residence location (p < 0.001, p = 0.049, p = 0.001, p = 0.001, p = 0.001, and p = 0.005, respectively). Significant differences in bacterial community composition were observed between stunted and normally growing children (Shannon p = 0.0053; Bray-Curtis p = 0.001). A shared core bacteriome was identified in both groups, influenced by environmental and dietary factors. Normally growing children were enriched with Bifidobacterium, Rothia, Olsenella, Slackia, Lactobacillus, Gemella, and Oscillibacter, while stunted children showed enrichment of Prevotella, Akkermansia, Fusobacterium, Acinetobacter, Alistipes, Odoribacter, Fournierella, and the Ruminococcus torques group. ConclusionAge was the most consistent predictor of gut microbial diversity. Stunting does not appear to be caused by a completely different gut microbiome; instead, shared environmental and dietary factors shape both gut bacteria and child growth. Promoting diverse complementary feeding, continued breastfeeding, and improved hygiene could mitigate risks and inform targeted interventions in food-secure regions.

Urinary tract infection (UTI) is one of the most common community-acquired bacterial infections mainly caused by extraintestinal pathogenic Escherichia coli (ExPEC) strains. The high-risk Escherichia coli ST131 clone is a major global cause of this disease. The lineage rapid dissemination is associated to multidrug resistance (MDR), production of extended-spectrum beta-lactamase (ESBL), and multiple virulence-associated genes. Although we lack information about ExPEC high-risk clones in Latin America, we recently reported an increase in ST131 dissemination in Rio de Janeiro from 2015 to 2019. The present study aims to characterize virulence and resistance molecular and phenotypic features that may contribute to dissemination of E. coli ST131 in Rio de Janeiro, Brazil. We assessed a 133 E. coli ST131 strains collection obtained from urine of outpatients with suspected UTI, in 2019. We determined antimicrobial susceptibility, fluoroquinolones resistance genes, virulence factors associated genes and biofilm production of all strains and analyzed the frequencies by each clade or subclade. A higher incidence of women (92%) and elderly (65%) subjects was observed. Overall resistance to first- and second-line treatment for UTI antimicrobials ampicillin, ciprofloxacin and sulfamethoxazole-trimethoprim was detected in high rates (40%), with a major impact of subclade C2 strains that were resistant to almost all antimicrobials tested, 52% carry ESBL and 66% of strains harbor the aac(6)-Ib-cr ciprpofloxacin resistance gene. Clade B and subclade C2 showed higher virulence scores among the other clades. They present unique virulence profiles characterized by the presence of papGIII, sfa/focDE, and especially ibeA genes in clade B, and the afa/DrBC, papGII, hlyA, cnf1 genes in subclade C2. Over 50% of our strains are biofilm producers, characterized by weak (24%) and strong producers (32%). ESBL and MDR strains harbor mainly papA, papGII, hlyA, cnf1 and kpsMTII genes that plays a key role in ST131 colonization. Subclade C1 is the major biofilm producer (78%), despite its lower virulence score. We also detected higher incidence of papA (27%), hlyA (19%) genes and the RPAI(malX) marker (84%) in biofilm producer strains with a statistical association of sfa/focDE gene (9%). We can infer that Clade C strains might be responsible for ST131 dissemination and persistence in Rio de Janeiro.

BackgroundGut microbiome disruption is often characterized by loss of obligate anaerobic bacteria, which may lead to altered production of microbial metabolites that can be detected peripherally. The application of widely used sequencing-based microbiome analyses to clinical settings is limited by cost, turnaround time, and challenges with patients with very low stool output. Since some products of strictly bacterial metabolism detectable in blood, peripheral metabolites may provide a potentially rapid and scalable indicator of gut microbiome composition and function. We performed a systematic review and meta-analysis of studies reporting circulating microbial metabolites and gut microbiome composition to evaluate whether peripheral microbial metabolites could identify gut microbiome perturbation. ResultsCandidate metabolites were identified systematically across an independent set of studies reporting metabolite-microbiome associations, enabling assessment of reproducibility across disease states and cohorts. We performed a meta-analysis of 19 human cohorts comprising 3242 participants with paired blood metabolite and stool microbiome data. Anaerobe depletion (obligate anaerobe relative abundance <0.70 by sequencing) was associated with decreased products of anaerobic microbial metabolism. Combinations of metabolites distinguished individuals with anaerobe-depleted microbiomes from those without. Circulating metabolite levels distinguished between cases and controls with similar performance as gut microbiome composition across a range of health/disease states, and changed markedly within patients experiencing gut anaerobe depletion after antibiotic exposure. ConclusionsCirculating microbial metabolites are potentially informative indicators of gut microbiome disruption and may serve as a rapid and method for patient stratification in clinical trials or acute care settings. ImportanceCirculating microbial metabolites represent a practical and scalable approach to detecting significant gut microbiome disruption, particularly loss of obligate anaerobes. Unlike stool-based sequencing, which can be logistically challenging and slow, blood-based metabolite profiling could be actionably integrated into existing clinical workflows. Our findings suggest metabolites capture compositional consequences of microbiome collapse, with performance comparable to direct microbiome profiling in distinguishing disease states. Enabling diagnostic enrichment and real-time monitoring of microbiome injury (e.g., during antibiotic use or critical illness) has potential implications for both clinical care and research, including selection of patients for investigation of microbiome-targeted therapies. With further validation, circulating metabolites could provide an accessible surrogate for gut microbiome composition in settings where sequencing is impractical.

Structured AbstractO_ST_ABSINTRODUCTIONC_ST_ABSAdults with Down syndrome (DS) have a higher risk of developing Alzheimers disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS. METHODSFecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing. Major Neurocognitive Disorder (NcD) was diagnosed according to DSM-5 criteria. Plasma levels of p-Tau181, NfL, and GFAP were measured using the Simoa platform. RESULTSCompared with CTRL, DS showed significant changes in UBA1819 and Intestinibacter genera, previously reported to be associated with mild cognitive impairment. Furthermore, DS with NcD were characterized by a reduced abundance of Roseburia genus, which was also negatively associated with plasma levels of AD biomarkers. CONCLUSIONAdults with DS display AD-associated changes in GM partially resembling those previously reported in euploid AD patients

RationaleBronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility. ObjectivesTo comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development. MethodsTracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age. Measurements and Main ResultsMicrobial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition. ConclusionsOur findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.

The microbiota and microbiome associated with zooplankton remains rather understudied compared to other animal groups and/or taxa. The present study aimed at investigating the whole-body bacterial microbiota of Daphnia spp. in two contrasting Greek lakes, the shallow and hypertrophic Lake Koronia vs. the deep and mesotrophic Lake Vegoritida, including both egg-bearing and non-egg-bearing individuals. In both lakes, 2,060 bacterial operational taxonomic units (OTUs) were found, with 223 of them being conditionally rare (crOTUs) with low contribution even for the dominant phyla, with L. Vegoritida having more crOTUs than L. Koronia. The individuals microbiota had inconsiderable overlap with the surrounding water microbiota in both lakes. The two lakes showed significant differences in their Daphnia -associated microbiota. L. Koronia had richer OTUs and rather homogeneous bacterial communities, with higher occupancy. Overall, no significant differences in between the microbiota of egg-bearing and non-egg-bearing Daphnia individuals in both lakes. However, regarding the most important OTUs (miOTUs), the L. Koronia miOTUs were highly overlapped between the individuals with and without eggs, with only one missing from the individuals without eggs. In L. Vegoritida the individuals without eggs had only six miOTUs and while egg-bearing individuals had nine different ones; the two lakes had no shared miOTUs., considerable differences occurred.. A total of 27 miOTUs, was found and belonged to the Pseudomonadota, unclassified Bacteria, Cyanobacteria, Bacteroidota, Bacillota and Actinomycetota. Those miOTUs, where assignment to the genus level was possible, they were related to Cyanobium, Mucilaginibacter, Flavobacterium and Staphylococcus. This study showed that lake morphotype and ecological status can exert some impact on Daphnia-associated bacterial microbiota, with more pronounced effects on egg-bearing and non-egg-bearing individuals.

The emergence of antimicrobial resistance (AMR) has driven the search for alternative therapeutic strategies, including antivirulence approaches targeting bacterial quorum sensing (QS). Azelaic acid (AzA), a naturally occurring dicarboxylic acid with known antimicrobial properties, has not previously been characterized as a QS inhibitor in Gram-negative pathogens. This study evaluated the dual antimicrobial and antivirulence activity of AzA against reference strains and clinical isolates of Pseudomonas aeruginosa, Enterobacteriaceae, and Staphylococcus aureus through in vitro assays and molecular docking analyses. Minimum inhibitory concentration (MIC) values ranged from 250 to 1000 {micro}g/mL, with lower MICs observed in clinical isolates of E. coli and S. aureus. Subinhibitory concentrations (250, 500 and 750 {micro}g/mL) were used to assess QS-regulated virulence factors in P. aeruginosa, including pyocyanin, elastase, alginate, and protease production. AzA exhibited a significant, dose-dependent inhibition of all evaluated virulence factors across both reference and multidrug-resistant (MDR) and pan-drug-resistant (PDR) clinical strains (p < 0.001), achieving inhibition levels exceeding 90% in several cases, particularly for protease activity. Molecular docking analyses revealed that AzA interacts with key QS-related proteins (LasI, LasR, PqsD, and PqsR), showing moderate binding affinities (-5.3 to -6.5 kcal/mol) and stable interactions within conserved ligand-binding domains. These findings suggest a multitarget modulatory mechanism affecting interconnected QS pathways. Overall, this study demonstrates, for the first time, that AzA acts as a quorum sensing inhibitor in P. aeruginosa, attenuating virulence without directly affecting bacterial growth, highlighting its potential as a promising antivirulence therapeutic strategy.

Background: With the emergence of drug-resistant strains and an unprecedented threat to control initiatives, tuberculosis remains to be a major public health risk in Ethiopia. Resistance to rifampicin (RR) is an important indicator, since RR is an acceptable surrogate for multidrug-resistant TB (MDR-TB). Over 95% of RR is based on mutations in an 81base pair segment of the rpoB gene, detected using rapid molecular assays. Despite this, detailed molecular epidemiological information is scarce. This study characterized the specific rpoB gene mutation patterns among patients in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted in 753 Mycobacterium tuberculosis complex (MTBC) clinical samples, corroborated as positive for MTBC from 2020 to 2024; respective probe mutation patterns were generated by the Xpert MTB/RIF platform. Demographic and clinical variables were also assessed for detecting the potential risk factors. Results: The overall RR-TB rate was 2.3% (17/753). Molecular analysis showed a distinct pattern of mutation, with codon 526 mutations being the most frequent, occurring in 54.3% of the resistance mechanisms. This was followed by those at codons 531 (21.7%) and 533 (15.2%). Most significant was the fact that 100% of RR-TB was observed among treatment-naive patients, providing unequivocal evidence that primary transmission is the exclusive cause of resistance in this population. Moreover, there were no statistically significant correlations between RR-TB and demographic factors, including sex, age, or HIV co-infection. Conclusion: The study demonstrates a steady, low-grade epidemic of RR-TB in Addis Ababa, dominated by a virulent bacterial strain with a distinctive mutation at codon 526. These observations highlight the imperative necessity for a strategic shift from a reactive, clinically-oriented model to proactive public health measures. To effectively break the chains of transmission, we recommend the universal application of drug susceptibility testing, enhanced and socially-directed contact tracing, and integrating molecular surveillance into the TB control program.

The incidence of colorectal cancer (CRC) has been increasing in Taiwan and is associated with multiple risk factors, including aging, obesity, and dietary habits. Increasing evidence suggests that gut microbiota dysbiosis contributes to CRC development. This study aimed to characterize microbial and metabolic alterations across premalignant and malignant colorectal lesions and to identify potential microbiome-associated biomarkers. Individuals undergoing colonoscopy for screening or surveillance at Taipei Veterans General Hospital were enrolled. Gut microbial composition was analyzed using full-length 16S rRNA gene sequencing to achieve high-resolution taxonomic profiling. Predicted functional pathways were inferred from microbial communities, and targeted metabolomic profiling was performed to evaluate microbial metabolic outputs. A total of 122 individuals were included, comprising 62 healthy controls, 15 adenoma cases, and 45 CRC cases. Progressive shifts in microbial composition and predicted functional pathways were observed along the adenoma-carcinoma sequence. Several bacterial taxa, including Phocaeicola dorei, Anaerotignum faecicola, Negativibacillus massiliensis, and Dysosmobacter segnis, were enriched in CRC. At the functional level, CRC samples showed enrichment of pathways associated with energy metabolism and bacterial stress responses. Metabolomic analysis further revealed increased levels of tauro-ursocholanic acid in CRC samples, whereas short-chain fatty acids (SCFAs) were reduced compared with controls. Integrative analysis combining full-length 16S sequencing, functional pathway prediction, and metabolomic profiling revealed coordinated microbial and metabolic alterations across the adenoma-carcinoma sequence. These findings provide insight into microbiome-associated processes in colorectal tumorigenesis and suggest potential microbial and metabolic biomarkers for CRC. ImportanceColorectal cancer (CRC) develops through a adenoma-carcinoma sequence, yet the microbial and metabolic alterations accompanying this progression remain incompletely understood. In this study, we integrated full-length 16S rRNA gene sequencing with metabolomic profiling to characterize taxonomic, functional, and metabolic changes across healthy controls, adenoma, and CRC. Our results reveal synchronized shifts in specific microbial taxa, predicted metabolic pathways, and fecal metabolites along the adenoma-carcinoma sequence. Several bacterial species, including Phocaeicola dorei, Anaerotignum faecicola, and Dysosmobacter segnis, increased in CRC, whereas short-chain fatty acids decreased progressively from controls to adenoma and CRC. Functional pathway analysis further indicated alterations in microbial fermentation, amino acid metabolism, and energy-related pathways. Together, these findings highlight the potential role of microbiome-associated metabolic changes in colorectal tumorigenesis and suggest candidate microbial and metabolic markers that may aid in understanding disease development and improving risk stratification.

This study develops a methodological framework that combines conventional antimicrobial susceptibility testing with Particle Swarm Optimisation (PSO) to enhance toothpaste formulations, employing Escherichia coli isolated from the oral cavity as a model organism. We used the agar well diffusion method to see if two fluoride toothpastes (Oral B and My-my) could kill oral E. coli isolates at 6.25%, 12.5%, 25%, 50%, and 100% concentrations. A surrogate Random Forest model was created using these experimental data to link formulation parameters to antimicrobial activity. Then, PSO was used to find the best formulation traits. Multi-objective optimisation that looks at the trade-offs between antimicrobial effectiveness and cytotoxicity was shown as a conceptual framework. Both toothpastes showed antimicrobial activity that depended on the concentration, with Oral B being more effective (23.0 mm at 100% concentration) than My-my (20.0 mm). The PSO framework, utilised as a methodological illustration while explicitly recognising data constraints, determined hypothetical formulation parameters (sodium fluoride 1100 ppm, hydrated silica abrasive, 2.5% SLS) with an anticipated zone of inhibition of 26.3 mm. These predictions are mathematically optimal for a surrogate model that was trained on very little data (n=10 formulation points). They need a lot of experimental testing before any claims about the formulation can be made. This work is presented as a proof-of-concept methodological framework, not as validated formulation guidance.

1.Fermentable fibres such as inulin can support metabolic health but may exacerbate gastrointestinal symptoms in individuals with irritable bowel syndrome (IBS) due to rapid fermentation and gas production. The gel-forming fibre psyllium improves IBS symptoms, although the underlying mechanisms remain unclear. We hypothesised that fibre gelation alters fermentation by modulating microbial access to substrates. To test this, we compared psyllium with methylcellulose, a chemically modified, gel-forming fibre, to determine the effects of gelation on inulin fermentation. Inulin alone or combined with psyllium or methylcellulose was fermented for 48 hrs in a colonic fermentation model inoculated with healthy human faeces. Gas production, metabolite profiles, microbial community composition and microbial localisation within fibre gels were assessed. Bioactivity of fermentation products was evaluated in STC-1 cells. Psyllium co-fermentation significantly accelerated fermentation and enhanced production of metabolites, while methylcellulose had minimal effects. Psyllium maintained higher diversity and enriched polysaccharide-degrading taxa including Bacteroides and Phoecaeicola species, which were strongly associated with metabolic activity. Bacterial penetration into the psyllium matrix was observed but not into methylcellulose. Fermentation products from psyllium but not methylcellulose stimulated GLP-1 and 5-HT secretion in STC-1 cells. These findings demonstrate that delayed-onset fermentable gel-forming fibres enhance microbial access to entrapped substrates, driving metabolic and hormonal responses.

BackgroundGlobally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. ResultsOur cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts. ConclusionOur work provides a detailed genomic and phenotypic analysis of bacteria isolated from Z. marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.

Rock-inhabiting fungi thrive in subaerial oligotrophic environments such as desert rocks, solar panels and marble monuments where organic carbon and nitrogen are scarce. We tested whether the rock-inhabiting fungus Knufia petricola showed a preference regarding nitrogen ([Formula] or [Formula]) and carbon (glucose or sucrose) sources and whether it was sensitive towards carbon and nitrogen limitation. As this fungus produces the carbon-rich, nitrogen-free 1,8-dihydroxynaphthalene (DHN) melanin, we tested whether a melanin-deficient mutant would be less sensitive to carbon limitation. The carbon and nitrogen concentrations were the primary predictors of growth, with a broad optimum partially explained by an optimal fungal C:N ratio. Limiting carbon or nitrogen supply decreased biomass formation, CO2 production and biofilm thickness but promoted substratum penetration through filamentous growth. The nitrogen content of the biomass was flexible within limits, increasing upon increasing nitrogen supply or decreasing carbon supply. The carbon use efficiency was fairly constant, whereas melanization correlated with a higher nitrogen content of the biomass despite melanin being nitrogen-free. In conclusion, in vitro, K. petricola switches to explorative growth under nutrient limitations, like fast-growing fungi, revealing universal fungal resource-acquisition patterns. Graphical abstract text and imageCarbon and nitrogen availability affect biofilm growth and morphology of the extremotolerant fungus Knufia petricola Abolfazl Dehkohneh, Julia Schumacher, Bastiaan J. R. Cockx, Karin Keil, Tessa Camenzind, Jan-Ulrich Kreft, Anna A. Gorbushina, Ruben Gerrits Growth of the rock-inhabiting fungus Knufia petricola was studied by varying carbon and nitrogen sources and concentrations. Overall, growth was best predicted by the carbon and nitrogen concentrations. Carbon and nitrogen limitation promoted substratum penetration through filamentous growth. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/712823v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@6d98bdorg.highwire.dtl.DTLVardef@146aac5org.highwire.dtl.DTLVardef@757fa8org.highwire.dtl.DTLVardef@ff709_HPS_FORMAT_FIGEXP M_FIG C_FIG