Yongfei Hu

Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. Actinomyces was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea. IMPORTANCE: This study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.

The increasing demand for antibiotic-free poultry production has accelerated the development of stable and effective alternatives to antibiotic growth promoters. However, the functional potential and underlying mechanisms of Lactobacillus salivarius-derived postbiotics (LSP) in broilers remain insufficiently understood. This study evaluated the effects of dietary LSP supplementation on growth performance, intestinal health, gut microbiota, and cecal metabolic profiles in broilers. A total of 720 one-day-old broilers were randomly assigned to five dietary treatments: a basal diet (CON), live L. salivarius (LS, 1000 mg/kg), or LSP supplemented at 2000 (LSPL), 4000 (LSPM), or 6000 (LSPH) mg/kg for 40 days. Compared with the CON group, LSP supplementation, particularly at 4000 mg/kg, significantly increased body weight at day 40 and average daily gain during both the later phase and the overall experimental period (P < 0.01). The optimal dosage was further validated in a large-scale commercial trial, in which LSP improved production efficiency as indicated by an increased European Production Efficiency Factor. Mechanistically, LSPM supplementation enhanced intestinal integrity by increasing the villus-height-to-crypt-depth ratio (P < 0.05) and reducing serum D-lactic acid and diamine oxidase concentrations (P < 0.05). In addition, LSP alleviated intestinal inflammatory responses by decreasing jejunal IL-2, IFN-γ levels (P < 0.05) and improving antioxidant defense by increasing hepatic catalase and glutathione S-transferase activities (P < 0.05). 16S rRNA sequencing revealed that LSPM reshaped the cecal microbiota, enriching beneficial genera such as Colidextribacter and Negativibacillus (P < 0.05). Untargeted metabolomics indicated that LSPM increased the levels of N-acyl amino acids, plant secondary metabolites, and cholest-4-en-3-one (P < 0.05). Correlation analysis further indicated close associations between microbial alterations, metabolite changes, and host intestinal health indicators. Collectively, these findings suggest that LSP enhances broiler growth performance through the coordinated regulation of the gut microbiota-metabolite-host interaction network and highlight its potential as a promising feed growth promoter for sustainable poultry production.

Dysglycaemia and periodontal inflammation frequently co-occur during pregnancy, but the microbial mechanisms linking these conditions and their potential for intervention remain incompletely understood. Here, we establish prospective pregnancy cohorts including more than 2500 volunteers and longitudinally profile oral microbiome dynamics in 534 pregnant women. We show that gestational diabetes mellitus (GDM) is associated with a progressive shift from Streptococcus-dominated oral microbiota to Prevotella/Porphyromonas-enriched dysbiosis. In mouse and cellular models, this dysbiotic oral microbiota induces periodontal inflammation, systemic IL-17 and IL-1β responses, suppression of glucagon-like peptide-1 and insulin, and exacerbation of hyperglycemia. Conversely, oral microbiota remodeling through transplantation of Streptococcus-dominated bacteria attenuates periodontal inflammation, restores glucagon-like peptide-1 and insulin levels, and improves glycaemic status in mice. Salivary metabolomics identifies docosahexaenoic acid (DHA) depletion in GDM, and in vitro assays show selective suppression of dysbiosis-associated oral pathogens by DHA. We therefore test topical gingival DHA in a double-blind randomized controlled trial of 40 pregnant women with GDM (ChiCTR2400080741), with probing depth and fasting blood glucose as primary endpoints and gingival index, attachment loss and plaque index as secondary endpoints. Daily gingival DHA application for six weeks improves probing depth and attenuates fasting glucose increase compared with placebo, with median fasting glucose changes from baseline of 0.10 versus 0.27 mmol/L. Together, these findings identify oral dysbiosis as a microbial driver of periodontal and glycaemic deterioration during pregnancy and support oral microbiome modulation as a potential adjunctive strategy for pregnancy care, although the clinical findings remain preliminary and require validation in larger trials with broader glycaemic endpoints.

Background: The gut microbiota plays a crucial role in protecting chickens against colonization by enteric pathogens, such as Salmonella . Native chickens, including Wenchang chicken and Danzhou chicken, harbor a highly diverse gut microbiota, which may contain anti-pathogenic strains. This study aimed to construct a microbial consortium from these native chicken breeds and evaluate its efficacy in protecting chicks from Salmonella infection. Results: A collection of 273 bacterial strains, representing 61 species, was isolated from the cecal digesta of Wenchang chicken and Danzhou chicken. From this collection, 29 strains were identified as exhibiting in vitro inhibitory activity against the indicator pathogens. Genomic analysis of the constituent strains in consortium BL6 revealed the genetic potential for producing antimicrobial peptides and secondary metabolites, suggesting a mechanistic basis for the inhibition. In a chick model challenged with S . Typhimurium, BL6 mitigated intestinal damage by promoting crypt restoration, enhanced barrier function, and enriched Lactobacillus , collectively contributing to improved intestinal health. Conclusions: These findings underscore the potential of a microbial consortium derived from the gut microbes of native chickens in combating Salmonella infection. This research offers valuable insights for developing innovative strategies to prevent and treat pathogen infections in broilers.

Fatty liver hemorrhagic syndrome (FLHS) is a critical disease threatening the laying hen industry. Inulin, a widely used prebiotic, has shown promise in alleviating metabolic disorders, but its role in mitigating FLHS in laying hens is not fully understood. Here, we investigated the effects and underlying mechanisms of inulin-mediated alleviation of FLHS in a high-carbohydrate low-protein diet (HCD)-induced laying hen model. We found that inulin supplementation significantly ameliorated HCD-induced hyperlipidemia, hyperglycemia, hepatic steatosis, liver injury, and oxidative stress. These phenotypic improvements were accompanied by enhanced fatty acid oxidation and suppressed lipid synthesis and inflammation. Microbiota analysis revealed that inulin reshaped the HCD-perturbed cecal microbiota, with Faecalibacterium identified as the only dominant genus substantially depleted by HCD and restored by inulin. Targeted metabolomics showed that inulin elevated cecal spermidine levels, which strongly correlated with Faecalibacterium abundance and improved metabolic traits. Fecal microbiota transplantation (FMT) from inulin-treated donors replicated the protective effects, confirming the causal role of gut microbiota in mediating inulin's anti-FLHS activity. Further mechanistic investigation using the representative species Faecalibacterium prausnitzii demonstrated that inulin enhanced spermidine production through transcriptional activation of the spermidine biosynthetic pathway. Spermidine, in turn, upregulated hepatic ALDH1A2 expression, enhancing retinoic acid synthesis and activating the AMPK-SIRT1 axis, thereby reducing lipid accumulation in hepatocytes. Collectively, these findings establish a novel Faecalibacterium-spermidine-ALDH1A2-retinoic acid-AMPK-SIRT1 axis through which inulin alleviates FLHS, highlighting inulin as a dietary intervention targeting the gut-liver axis and offering novel therapeutic avenues for preventing this disorder in laying hens.

Probiotics have been demonstrated to be effective and safe for hyperuricemia (HUA) and gout treatment. Hence, identifying microbes with high uric acid- or purine-metabolizing ability is highly important. Due to the high load of uric acid in chicken feces, we hypothesized that the chicken gut would be an excellent source for new uric acid or purine-metabolizing microbes. In this study, we examined chicken gut contents to isolate an Enterococcus faecalis strain (designated CML390) that displayed high uric acid-degrading ability. In vitro experiments indicated that E. faecalis CML390 could effectively metabolize uric acid under both aerobic and anaerobic conditions, and the richer the nutrients, the higher the rate of uric acid degradation. By integrating genomics, transcriptomics, and metabolomics analyses, we revealed two pathways involved in aerobic and anaerobic uric acid degradation, respectively, in this isolate. E. faecalis CML390 relies on oxygen to metabolize uric acid into substances such as allantoin under aerobic conditions, while it also harbors a conserved uric acid-inducible gene cluster for anaerobic uric acid metabolism. An in vivo experiment showed that gavage with live E. faecalis CML390 in a mouse model of HUA (established using a combination of uric acid and potassium oxonate) significantly reduced serum uric acid levels and alleviated HUA. Our findings contribute to the exploration of the pathways and mechanisms of uric acid metabolism in intestinal microorganisms and provide a candidate probiotic for the treatment of HUA and gout.

Multiple factors, including genetics, nutrition, and health, influence the vertical transmission of microbiota from mothers to their offspring. Recent studies have shown that avian microbiota can be passed to the next generation via the eggshell and egg albumen. However, it remains unclear whether these microbial communities are regulated by nutrition and how they are associated with the host genotype. Chickens, with their controlled rearing conditions and stable genotypes, provide a promising model for investigating microbiome transmission in birds. This study aims to determine whether host genotype‐associated bacteria are vertically transmitted between generations, and how maternal nutritional intervention with soyasaponin modulates this microbial transfer, thereby shaping chick intestinal development and informing effective nutritional strategies. We established a microbial vertical transmission model across various anatomical sites in breeder hens, chicken embryos, and chicks. Avian gut microbiota and reproductive tract microbiota can both be found in chicks at various developmental stages. Supplementing breeder hen diets with soyasaponin interacts with vertically transmitted Bifidobacterium adolescentis to produce γ‐aminobutyric acid. This compound modulates offspring intestinal development through distinct mechanisms in chick epithelial cells, including the inhibition of LC3 and caspase3‐associated autophagy and apoptosis pathways, as well as the promotion of proliferation and differentiation pathways mediated by LGR5 and Olfm4. Our study highlights that avian gut and reproductive tract microbiota are transmitted to chicks through the cloaca, with the yolk sac also being instrumental in this vertical transfer. The incorporation of soyasaponin in avian diets affects microbial transfer, providing a theoretical basis for studying maternal effects in poultry and formulating corresponding dietary strategies.

Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance. In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance. Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control.