The microbial metabolite I3A inhibits ferroptosis and the effectiveness of redox-based cancer therapy.

Exploring the effects of phenolic compounds and essential oils in poultry: A sustainable strategy to combat Salmonella biofilm infections.

Dietary components influence microbial composition in the digestive tract. Although often viewed as energy sources, dietary components are likely to shape microbial determinants of intestinal colonization beyond metabolism. Here, we report that a dietary long-chain fatty acid enhances the yeast Candida albicans colonization of the murine gut partly by eliciting modifications to the fungal cell surface. Mice fed an oleic acid-rich diet were readily colonized by C. albicans and exhibited higher fungal load in feces compared with rodents fed an isocaloric control diet. Surprisingly, β-oxidation, a catabolic process to break down fatty acids for energy production, was dispensable for C. albicans to colonize the high oleic acid diet-fed mice. 16S rRNA analysis detected rather modest differences in the bacterial communities between control and oleic acid-rich diets. We identified SOK1 as an oleic acid-induced kinase that dictates cell wall mannan exposure and binding to intestinal mucin under anaerobic conditions. Furthermore, oleic acid induced the expression of several C. albicans transcription factors that positively regulate intestinal colonization via remodeling of the fungal cell surface. We posit that in environments largely devoid of oxygen like the large intestine, dietary oleic acid favors a C. albicans cell surface configuration that enhances gut occupation.IMPORTANCECandida albicans is a fungal pathobiont that inhabits the digestive tract of most human adults. The fungus has roles in health and disease because it modulates prominent immune-inflammatory host responses from the gut, and in individuals with debilitated defenses, it can disseminate from the gastrointestinal tract, producing life-threatening infections. Here, we investigate how a dietary component shapes C. albicans physiology and ultimately its ability to inhabit the mammalian gut.

Gut colonization, acquisition, and persistence of β-lactamase-producing Enterobacterales among hospitalized patients in Addis Ababa, Ethiopia.

Klebsiella pneumoniaeand related species are a common cause of healthcare-associated infections. The gut is a majorKlebsiellareservoir and gut colonization is a risk factor for developing an extraintestinalKlebsiellainfection. Patients can be colonized by multipleKlebsiellastrains or even species in the gut simultaneously, and there is high concordance between the gut colonizing- and infection causing-strains. The detection and characterization of colonizing strains is critical for a better understanding of the progression to infection and for developing interventions for colonized patients. However, the association between mixed or mono-colonization and subsequent infection is unknown. In this study, we developed an amplicon-based sequencing method calledwzi-Seq that enables the detection and quantification ofKlebsiellastrains from complex samples and mixtures using the conserved capsule genewzias a molecular barcode. This method is highly accurate and precise with a sensitivity of 93% and specificity of 99.8% in mixtures containing as many as 58 uniquewzitypes. The assay was validated analytically and applied to an established case and control cohort. We determined that 63.2% (108/171) patients were mono-colonized with a singleKlebsiellastrain while 36.8% (63/171) had mixed colonization with multipleKlebsiellastrains.Controlling for patient variables in multivariate analysis, we determined that mono-colonization was significantly (p = 0.034) associated with infection. Characterization ofKlebsiellacolonizing populations could improve the accuracy of assessing infection risk and enable targeted interventions to prevent these healthcare-associated infections.ImportanceKlebsiellagut colonization is a major risk factor the development of extraintestinalKlebsiellainfections in hospitalized settings. However, it is unknown if patients are colonized by one or multiple strains ofKlebsiellaand how the population structure ofKlebsiellain the gut impacts infection risk. Here we describe the development of a novel technique,wzi-Seq, to detect and quantify multipleKlebsiellastrains from complex samples using standard techniques and rapid DNA sequencing. We appliedwzi-Seq to rectal swabs from a well-characterized patient cohort and found thatKlebsiellacolonization with a single strain was more prevalent than colonization with multiple strains. Furthermore, mono-colonized patients had a significantly higher risk of developing aKlebsiellainfection than mixed colonized patients. This work validates a new tool to studyKlebsiellapopulations and reveals that population structure in the gut influences the risk of healthcare associated infections.

Enterococci, particularlyE. faecalis, can survive in diverse settings within and outside human hosts. The capacity ofE. faecalisto colonize these locations relies on its ability to adapt by altering gene expression in response to environmental exposures. One mechanism for quickly altering gene expression is through regulation by small noncoding RNAs (sRNAs); sRNAs can regulate one or many target genes and either up- or down-regulate transcript stability and protein expression. While many sRNAs have been predicted inE. faecalis,few have experimentally established target mRNAs or physiological functions. Here, we investigate the targets, function, and mechanism of Enterococcus sRNA 84. We found that sRNA 84 is conserved within the family Enterococcaceae, suggesting that it plays a role in the regulation of core genes and functions. RNA sequencing and proteomic analysis revealed that the absence of sRNA 84 led to downregulation of many cell surface proteins, including mucin-binding proteins. Consistent with these findings, an sRNA 84 knockout strain had reduced binding to mucinin vitroand impaired intestinal colonization of specific-pathogen-free mice. Taken together, these data support a model whereby sRNA 84 upregulates cell surface adhesins, which subsequently facilitate host colonization through binding to mucin. sRNA 84 is one of the first sRNAs in enterococci with demonstrated targets and function. This finding establishes the conserved sRNA 84 as a potential key regulator of enterococcal host adaptation, providing insight into how these organisms adapt their gene expression to survive both within and outside animal hosts.

Isolation and characterization of an antibiofilm bacteriophage against Klebsiella michiganensis and evaluation of its therapeutic potential in an insect larval gut colonization model

Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers (R0) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential (R0 = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 (R0 = 1.18) and ST131-C2 (R0 = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.

A prebiotic hydrogel based on gellan gum and arabinoxylan from flaxseed (Linum usitatissimum) for advanced probiotic delivery.

BackgroundMaternal microbiota during pregnancy plays a crucial role in establishing the neonatal gut microbiota, which is essential for infant health. This study aimed to trace maternal microbial sources contributing to early neonatal gut colonization and assess the effect of prenatal probiotic supplementation on maternal–to–neonatal microbial transmission.MethodsA total of 26 mother–neonate pairs undergoing full-term vaginal delivery were enrolled. From gestational week 32 until delivery, the intervention group received a probiotic supplement containing Bifidobacterium longum, Lactobacillus delbrueckii bulgaricus, and Streptococcus thermophilus twice daily, while the control group received no supplementation. Maternal fecal, vaginal, and placental samples were collected at full term, and neonatal fecal samples were collected longitudinally at Days 1, 3, 14, and 6 months postpartum. Microbial community profiling was performed using 16 S rRNA gene sequencing. Microbial source attribution was conducted using the FEAST algorithm.ResultsAlpha and beta diversity analyses showed that prenatal probiotics transiently altered the composition of neonatal meconium microbiota, with no significant differences observed at later time points. Volatility analysis revealed enhanced microbial stability in the probiotic group during Days 1 to 3 (P < 0.001). FEAST source-tracking indicated that maternal gut and placenta were the major contributors to neonatal meconium colonization, with gut-derived input increasing over time and vaginal contributions remaining minimal throughout. Probiotic supplementation significantly increased the placental contribution to meconium microbiota (P = 0.02), with a sustained but non-significant elevation observed through later stages. Meanwhile, gut-derived and vaginal-derived inputs were consistently reduced in the probiotic group, though these differences did not reach statistical significance.ConclusionThis study highlights the dynamic nature of maternal-to-neonatal microbial transmission and demonstrates that prenatal probiotic supplementation can transiently reshape early colonization patterns by modulating source contributions.Trial registrationClinicalTrials.gov, NCT06241222 (https://clinicaltrials.gov/study/NCT06241222); retrospectively registered on 2024-01-17 (study start 2018-01-01; completion 2021-12-31; first posted 2024-02-05).Supplementary InformationThe online version contains supplementary material available at 10.1186/s12967-025-07293-6.

Gut colonization by Extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E), is increasing among nonhospitalized children, but the impact of ESBL-E carriage on the intestinal microbiota remains unknown. In this study, we compared the fecal bacterial composition in 24 children (3-11 years old) that were carriers of Escherichia producing ESBL (ESBL-Es) to that of an age- and gender-matched group of non-carriers using 16S rRNA gene amplicon sequencing. Alpha diversity of the community was similar in both groups. No significant differences in relative abundance at the phylum, class, and order levels were found. Significant differences at the genus and species level were identified. The genus Blautia and the species Blautia obeum were more abundant in non-carriers, whereas the genus Coprococcus and Coprococcus eutactus species were more abundant in carriers. Generalized linear models, confirmed these differences and identified additional ones at the family (Tannerellaceae is more abundant in carries), genus (Parabacteroides is more abundant in carriers), and species (Bifidobacterium longum and Ruminococcus gauvreauii are more abundant in non-carriers, and Parabacteroides distasonis in carriers) levels. However, statistical significance was lost in all cases after applying multiple testing correction. Altogether, this study uncovers a differential microbiological signature between pediatric ESBL-Es carriers and non-carriers, despite an overall similar diversity and composition of their gut microbiota. Further studies are required to explore if these differences predispose to, or are a consequence of ESBL-Es carriage, and if modulation of the gut microbiota community may help to prevent or eliminate ESBL-Es colonization.

Effective decolonization strategies for intestinal carriers of carbapenem-resistant Enterobacterales are essential to prevent severe life-threatening infections. In this work, we established gut colonization in Zophobas morio larvae (ZmL) using an OXA-48-producing Salmonella enterica ST198 strain (Sk-1) and assessed the commercial INTESTI bacteriophage cocktail (INTESTIbc) for decolonization. ZmL were fed with food contaminated with Sk-1 (INTESTIbc-susceptible) for 3 days and then maintained on a non-contaminated diet until day 14 (T14). At T3, ZmL were grouped in untreated, dPBS- or INTESTIbc-treated (oral force-feeding on T3 and T5). At specified intervals, ZmL were sampled for quantification and characterization of Sk-1 (antibiotic/INTESTIbc susceptibility and whole-genome sequencing). ZmL microbiota was also investigated by 16S rRNA amplicon sequencing. ZmL were rapidly colonized by Sk-1 across all groups (T3: 4.3 × 106 CFU/mL). Untreated and dPBS-treated larvae remained consistently colonized (T10: 3.4-9.1 × 104 CFU/mL; T14: 2.9-5.9 × 104 CFU/mL), whereas INTESTIbc treatment induced a significant Sk-1 regrowth (T10: 4.0 × 106 CFU/mL; P < 0.05 vs. controls). Sk-1 strains recovered under different conditions between T7 and T14 did not show phenotypic and genotypic changes. Bacteriophages administration resulted in reduced relative abundance of potential bacterial competitors of Sk-1 (i.e., Pseudocitrobacter). ZmL can be used as a new in vivo model of intestinal colonization with S. enterica. However, INTESTIbc administration failed to achieve decolonization and instead promoted hazardous overgrowth of the inoculated pathogen. These findings highlight the need for further investigations to clarify the therapeutic potential or possible risks of broad-spectrum bacteriophage cocktails against intestinal infections/colonization caused by hyperepidemic S. enterica clones.

VE202 is an oral, defined 16-strain bacterial consortium with properties that may diminish dysbiosis and alleviate symptoms of inflammatory bowel disease. This phase 1 study evaluated VE202 safety and tolerability and assessed strain colonization. Thirty-one healthy adults received oral vancomycin 125 mg four times daily for 5 days to decrease gut microbial burden, followed by a single dose of VE202 at 1 × 109 or 1 × 1010 colony-forming units (CFUs), or 14-days of the lower dose (1.4 × 1010 total CFU). Adverse events were monitored through week 12, with follow-up at week 24. Stool was collected for VE202 strain detection and abundance during screening and pretreatment, day 2, day 4, day 7, day 14, week 4, week 8, week 12, and optionally at week 24. VE202 and vancomycin pretreatment were well tolerated. Among VE202 recipients, the most frequent adverse events (>20% of subjects) were abdominal discomfort, diarrhea, headache, and fatigue. Most treatment-related adverse events were gastrointestinal. Two serious adverse events were reported; these were not treatment-related and occurred weeks after dosing completion. VE202 strain detection and relative abundance in the vancomycin-perturbed gut occurred as soon as day 2, sustained through 2 weeks postdosing, then declined slowly but remained substantially above baseline through week 24. Colonization was dose- and duration-dependent, with 14-day dosing providing more durable VE202 colonization. VE202 was well tolerated. Following antibiotic pretreatment, rapid and durable gut colonization of VE202 strains was observed, most significantly in participants administered multiple doses (NCT03931447).

The human gut microbiome, comprising trillions of microorganisms, plays a crucial role in host metabolism, immune function, and overall health. Environmental microbiota from diverse sources, including diet, soil, air, water, and built environments, significantly influence the composition and functional capacity of the human gut microbiome throughout life. This comprehensive study examines the bidirectional relationship between environmental microbiota and the human gut microbiome, analysing recent research that demonstrates how environmental pollutants, dietary factors, antibiotics, and lifestyle changes reshape microbial communities. Through analysis of metagenomic data, metabolomic profiling, and immune response assessments across 2,500 participants from urban, rural, and industrial environments, we reveal that environmental exposures can select for specific microbial functions, including xenobiotic degradation pathways, while disrupting beneficial microbial networks. Our findings indicate that environmental microbiota not only serve as a reservoir for gut colonisation but also influence host-microbe interactions that determine health outcomes. The integration of multi-omics approaches with germ-free animal model validation provides compelling evidence that environmental microbiota management represents a promising therapeutic target for preventing and treating microbiome-associated diseases. Understanding these complex ecological relationships is essential for developing personalised microbiome-based interventions and public health strategies.

Gestational diabetes mellitus (GDM) is a common complication of pregnancy associated with various perinatal risks in mothers and heightened risks of long-term obesity and metabolic syndrome in their children. Understanding the effect of GDM on infant health is crucial. Infant gut colonization has generated significant interest owing to its profound impact on health and potential role in later disease development. Here we conducted a thorough analysis of the microbiota and metabolome of neonatal meconium to understand how GDM in mothers affects microbial colonization in the early lives of their offspring. This study included 49 healthy-term neonates born to mothers with GDM (n=29) and normoglycemic mothers (n=20) between March 2022 and February 2023 at Chang Gung Memorial Hospital (Linkou branch). Fecal samples were collected in sterilized containers before the infants reached 5 days of age. To analyze the meconium microbiota, 16S rRNA gene sequencing was performed, and proton nuclear magnetic resonance was used to examine the metabolome. Neonates born to mothers with diet-controlled GDM exhibited a notable decrease in α-diversity and a shift in β-diversity compared to those born to normoglycemic mothers. A functional analysis revealed increased peroxisome proliferator-activated receptor and adipocytokine signaling pathway activation in the GDM group. Metabolomic analysis revealed significant changes in the fumarate and succinate levels, indicating metabolic shifts associated with maternal GDM. These findings highlight the potential effects of pregnancy-related complications on the establishment of gut bacteria in neonates. Further comprehensive studies are required to understand the long-term implications of these microbial changes on infant health.

The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves’ gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-20111-9.

Klebsiella pneumoniae is an escalating public health threat driven by the emergence of antibiotic-resistant and hyper-encapsulated strains that spread systemically from the gut. The immune defenses preventing gut colonization and dissemination remain poorly defined. Herein, we uncover distinct and context-dependent roles for complement proteins C3 and C4 in host defense following K. pneumoniae infection. Following gut colonization, C3 and C4 levels rise significantly. In addition to inducing alternative pathway-mediated C3b deposition on K. pneumoniae grown under gut-relevant conditions, C3 is critical for recruiting myeloid cells to the gut, promoting local opsonophagocytosis, and preventing lethal systemic spread. Depletion of systemic C3 reveals mucosal-derived C3 controls K. pneumoniae GI colonization, whereas systemic C3 is essential for limiting fatal dissemination. In contrast, C4 is dispensable for controlling GI colonization, dissemination, and myeloid recruitment under conditions of natural acquisition. However, C4 becomes critical for controlling GI burden and systemic disease following antibiotic-induced dysbiosis and supercolonization with antibiotic-resistant K. pneumoniae. Notably, mice deficient in CD21/35—a receptor for cleaved C3 and C4 fragments important for B cell activation and antigen retention—exhibit a defect similar to C4−/− mice, with significantly increased GI burden under antibiotic-induced supercolonization, suggesting distinct complement-dependent pathways are involved in mucosal protection. Collectively, these findings reveal a dual-layered immune strategy: C3-driven opsonophagocytosis is critical for controlling colonization and dissemination under baseline conditions, while C4 and CD21/35 become indispensable following antibiotic-induced supercolonization. This work advances our understanding of complement-dependent mucosal immune protection and identifies potential targets for preventing gut-to-bloodstream transition of this pathogen.

BackgroundTigecycline remains a last-resort antibiotic for treating multidrug-resistant (MDR) Gram-negative pathogens. The emergence of tet(X4)-mediated high-level tigecycline resistance in Escherichia coli has raised global concern, yet its prevalence in healthy human populations remains limited.MethodsWe conducted a community-based surveillance study involving 245 fecal samples from healthy individuals in three urban communities in Shenzhen, China. Tigecycine-resistant strains were isolated using MacConkey agar supplemented with 2 mg/L tigecycline and confirmed by PCR detection of tet(X). Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and phylogenetic analysis were performed.ResultsTigecycline-resistant E. coli were detected in 1.6% (4/245) of samples. All isolates carried tet(X4) and exhibited an MDR phenotype. WGS revealed that tet(X4) was located on IncY (n=1) and IncFIA8-IncHI1/ST17 plasmids (n=3), which closely resembled previously described plasmids and co-harbored additional resistance genes. The core tet(X4)-carrying region in all four plasmids, associated with ISCR2, was highly similar to that of p47EC—the first tet(X4)-bearing plasmid identified in porcine E. coli in China. Notably, the three IncFIA-IncHI1/ST17 plasmids shared an identical 12,536-bp region structured as IS1–catD–tet(X4)–ISCR2–ΔISCR2–floR–ΔISCR2. Virulence-associated genes involved in adhesion, iron acquisition, biofilm formation, and secretion systems were also identified in four tet(X4)-positive isolates. The four isolates belonged to globally distributed sequence types ST10, ST201, ST877, and ST1308. Phylogenomic analysis demonstrated close genetic relatedness between these community isolates and strains from diverse geographical regions and hosts.ConclusionsThis study reveals silent intestinal colonization by tet(X4)-positive MDR E. coli among healthy urban residents, highlighting the role of community reservoirs in the dissemination of last-resort antibiotic resistance. These findings underscore the urgent need for One Health-oriented antimicrobial resistance surveillance and intervention strategies that extend beyond clinical settings.

This descriptive and exploratory observational case series examined intestinal colonisation and subsequent bacteraemia due to ESBL-producing Klebsiella pneumoniae (ESBL-Kp) in preterm neonates in Morocco. Prospective bacteriological cultures and antibiotic susceptibility testing were supported by phenotypic methods, including Brilliance ESBL Agar and the NG-Test CARBA-5 assay, for the rapid detection of ESBL and carbapenemase producers. Molecular analysis using PCR was also undertaken to identify specific resistance genes. A total of 567 rectal swabs were collected from 339 preterm neonates, yielding 293 K. pneumoniae isolates. ESBL-producing strains were identified in 53.6% of the neonates (182/339). Detected resistance genes included blaSHV (26.3%), blaCTX-M-1 (42.8%), blaTEM (30.2%), blaOXA-48 (50.0%), blaNDM(15.3%), and blaVIM (4.9%). Principal risk factors for colonisation were low birth weight (OR 1.69), very preterm birth (OR 6.24), enteral tube feeding (OR 2.02), and prolonged use of third-generation cephalosporins (OR 1.26). Among the neonates studied, 32 (9.4%) developed healthcare-associated bacteraemia, with 56.2% of these cases preceded by intestinal colonisation with ESBL-Kp. Clinically, severe respiratory distress and alveolar haemorrhage were strongly associated with increased mortality (aRR = 29.32 and 4.45, respectively). The findings highlight the clinical importance of early screening to guide infection control and antimicrobial stewardship in neonatal intensive care settings.

Quorum-sensing (QS) interference is a promising antivirulence strategy in aquaculture. This study investigated six indigenous bacterial strains for their ability to degrade N-hexanoyl homoserine lactone, a key QS signaling molecule. All strains demonstrated significant QS interference, indicating potential as biocontrol agents. Furthermore, we assessed the key in vitro traits relevant to probiotic application. These included growth rate, pH tolerance and salinity resilience. MYUG presented the fastest growth, followed by KSNUG, PMUG01, LFUG, PMUG02, and HSNUG, representing promising establishment potential within production systems and in fish guts. All strains tolerated pH (3—9) and salinity (1%—4%), supporting their adaptability to aquaculture environments and dynamic GIT conditions. Glycan diversity analysis revealed distinct lectin-glycan interaction profiles, with HSNUG displaying the highest glycan diversity index, potentially enhancing its gut adhesion and colonization capacity. Functional-trait scoring based on these in vitro characteristics ranked the six strains’ probiotic suitability as: KSNUG > LFUG > PMUG01 > MYUG > HSNUG > PMUG02. A sporulation assay showed that four Bacillaceae strains (HSNUG, LFUG, PMUG01, and PMUG02) formed spores, an advantageous trait for stability during probiotic feed formulation, storage and administration. Antibiotic susceptibility screening confirmed that PMUG01 and PMUG02 had no concerning patterns, while HSNUG and LFUG exhibited resistance to certain antibiotics, warranting further molecular analysis. Finally, biosafety and gut colonization assays in axenic zebrafish embryos confirmed the in vivo safety and gut colonization potential. Within the spore-forming group, additional trait-based scoring ranked probiotic-suitability as: LFUG > PMUG01 > PMUG02 > HSNUG. Overall, these findings support in vitro-based selection of safe and effective probiotic candidates for sustainable aquaculture.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04157-3.