Abstract Objective Endometrial cancer (EC) is a common gynecologic malignancy globally, but the role of the intratumoral microbiome remains poorly defined. While microbial dysbiosis is increasingly linked to cancer, the composition, function, and clinical relevance of the microbiota in EC are underexplored. This study aims to systematically profile the microbiome in EC patients by integrating culturomics and 16S rDNA sequencing, and to evaluate the functional properties of key bacterial strains in relation to tumor progression. Methods We collected cancerous tissues (CATs), non-cancerous adjacent tissues (NATs), and vaginal swabs from 32 EC patients. Culturomics was performed on 57 samples from 19 patients to isolate and identify bacteria, while 16S rDNA sequencing assessed microbial diversity and composition. Functional assays, including flow cytometry for invasion efficiency and ELISA, were used to evaluate pro-inflammatory capacity. Results Culturomics identified 79 bacterial species, with Staphylococcus , Streptococcus , and Cutibacterium emerging as core genera shared across the vagina, NATs, and CATs. Functional analysis revealed that strains such as Staphylococcus epidermidis and Streptococcus anginosus exhibited high invasion efficiency (up to 84.8%) and significantly upregulated pro-inflammatory responses. 16S rDNA sequencing showed that Lactobacillus dominated the vaginal microbiota, whereas endometrial tissues were enriched with opportunistic pathogens (e.g., Stenotrophomonas ). Critically, specific genera were associated with aggressive clinical features: Slackia with poorly differentiated (G3) tumors and Porphyromonas with deep myometrial invasion (≥ 50%). Conclusion This study uncovers a distinct, translocally disseminated core microbiota in EC, with key strains demonstrating invasive and pro-inflammatory capacities that may play a role in tumor progression. These findings provide a foundation for microbial biomarkers and targeted interventions, highlighting the transformative potential of microbiome research in gynecologic oncology.

The relationship between gut microbiota and human health has become one of the focal point in medical research. Probiotics, which modulate the gut microbiome, hold considerable promise for both prophylaxis and therapeutic intervention. This requires deeper insights into the kinetic changes and molecular mechanisms upon probiotic entry into the body. In this study, we utilized advanced molecular imaging to delineate the in vivo kinetic dynamics of two Lacticaseibacillus paracasei Zhang (L. paracasei Zhang, LPZ) formulations: a liquid culture and a lyophilized powder. Our results provide new insights into the gastrointestinal transit and growth kinetics of the different probiotics formulations. Strikingly, the liquid LPZ achieved its peak growth phase within a relatively short period of 6 to 8 h post-ingestion, culminating in a 270- to 680-fold increase in residues at the 24th hour post-ingestion when compared to the lyophilized powder LPZ. Furthermore, during peak in vivo replication, LPZ enhanced gut microbial diversity and enriched beneficial commensal communities. Functionally, LPZ ingestion attenuated virulence factors while upregulating carbohydrate-active enzymes. Notably, LPZ significantly reduced xanthine levels, a metabolite associated with hyperuricemia, thereby providing a mechanistic basis for the observed relief from gout symptoms. This supports the mechanism of prior clinical findings and paves the way for future clinical trials and therapeutic use of LPZ and related probiotics.IMPORTANCEThe innovation of this study lies in visualizing the kinetic changes of two Lacticaseibacillus paracasei Zhang (L. paracasei Zhang, LPZ) formulations (a liquid culture and lyophilized powder) within the gastrointestinal tract. It was found that liquid LPZ proliferates in vivo with a higher retention rate. Furthermore, we also found that when liquid LPZ reaches its peak proliferation phase in vivo, it not only effectively promotes the proliferation of other beneficial bacteria and the production of their metabolites but also generates more carbohydrate-active enzymes while reducing virulence factors, thereby amplifying the functions of LPZ. Meanwhile, we observed that liquid LPZ significantly reduces the production of xanthine in vivo, indicating its potential to lower uric acid. In light of the aforementioned findings, we herein propose the concept of "probiotikinetics." These results provide new insights into the intake of LPZ, along with important evidence for its application in healthy populations.

SlyA, a key transcriptional regulator in Yersinia pestis, is involved in stress adaptation and virulence, yet its regulatory mechanisms remain poorly understood. Here, we investigate the role of the conserved hypothetical protein YhcN and its regulation by SlyA in Y. pestis. We demonstrate that deletion of yhcN impairs bacterial viability under low-temperature and anaerobic conditions and growth. Intriguingly, both deletion and overexpression of slyA lead to upregulation of yhcN transcription, suggesting a complex regulatory interplay. Bioinformatics identified two SlyA-binding sites upstream of the predicted -35 box of the yhcN promoter. We propose that SlyA may mediate a complex regulation of yhcN, wherein basal SlyA level could repress the transcription of the yhcN, while elevated SlyA could activate it. This regulatory switch may enable Y. pestis to fine-tune YhcN expression under fluctuating environmental pressures. Taken together, our findings propose a novel and complex regulatory circuit involving SlyA and YhcN, advancing the understanding of transcriptional networks that govern stress adaptation in Y. pestis.

Yersinia pestis, the etiologic agent of plague, is a genetically monomorphic pathogen. By screening 1085 published Y. pestis genomes, we identified an unusual mutation hotspot within codon 363 of the aspartate ammonia-lyase gene aspA with at least six alleles in the population. Our investigation delves into the significance of the polymorphism at the aspA codon 363 and its impact on the fitness of Y. pestis strains. Notably, we found that the dominating TTG allele (L363), resulting in AspA inactivation, confers a fitness advantage to Y. pestis when competing with other bacteria inhabiting a similar niche, due to elevated expression of pesticin. However, the TTG strain exhibits fitness deficits under various stress conditions compared to the GTG strain (V363), which expresses an active AspA. Drawing from these observations, we propose an evolutionary hypothesis for Y. pestis at the aspA codon 363 locus. It is inferred that GTG represented the ancestral state at this locus. However, the TTG strain swiftly dominated populations in the early evolutionary stage of Y. pestis, likely owing to the V363L substitution that conferred a competitive advantage to Y. pestis over other bacteria. Subsequently, spontaneous mutations emerged, reinstating AspA activity, thereby offering fitness advantages across diverse environments and get fixed within the population. Our findings portraited a scenario of inactivating-restoring mutations relay in Y. pestis microevolution, shedding new lights on the evolutional dynamics of pathogens.

The terms “inflammatome” (holistic inflammation networks) and “inflammatomics” (a novel omics field) were proposed to decode dysbiosis-driven chronic inflammation and its disease links. Inflammatomics explores microbiota–immune crosstalk, particularly innate immune interactions, revealing how dysregulated microbial communities trigger chronic inflammation underlying disorders like inflammatory bowel disease, metabolic diseases, and neurodegeneration. This discipline transcends traditional inflammation paradigms by dissecting molecular pathways connecting dysbiosis to systemic inflammation, enabling early detection and precision interventions. It integrates evolutionary perspectives on host–microbe interactions, emphasizing the human body as a stress-sensitive “organ”. Challenges include standardizing inflammatome profiling, translating findings into clinical tools, and advancing multiomics technologies. By bridging microbial ecology, immunology, and systems medicine, inflammatomics holds a transformative potential to shift health care from reactive treatment to proactive, personalized prevention, targeting disease origins shaped by chronic inflammatome dysregulation.

Abstract The convergence of microbiome science with the One Health principle heralds a transformative era in biology, prioritizing the collective well‐being of humans, animals, and the environment. This review delves into the intricate dance between microbiomes and their hosts, revealing their profound impact on health, nutrient cycles, and climate change. Championing a unified approach to health issues across diverse kingdoms of life, One Health emerges as a holistic strategy, underscored by a proposed universal balance theory, “Balance of Dynamic Factors.” This theory spotlights the equilibrium within microbial and human‐animal‐environment interactions, offering a revolutionary pathway to global health and social well‐being. It paves the way for disease prevention, health equity, and sustainability, all of which are purviews of a balanced ecological system. We navigate the challenges and opportunities of this integrative approach, culminating in a call for action for the incorporation of microbiome science into health policies, precision medicine, legislation, eco‐health projects, and education, thereby setting the stage for harmonious coexistence with our planet.

Spaceflight is physically demanding and has negative effects on the health of astronauts. Previous studies demonstrated that the human gut microbiota and immunity were affected by spaceflight and simulated spaceflight. Changes in the abundance of beneficial taxa might influence immunity by disrupting the microbiome network balance. This study investigated the effects of Lactobacillus rhamnosus GG (LGG) on simulated spaceflight-induced helper T cell disorder in hindlimb unloading (HU) mice. Helper T cell ratios in control mice were affected by transplantation of the fecal microbiota from HU mice, and the abundance of LGG in the gut microbiota was affected by both true and simulated spaceflight. The gut microbiota composition, fecal metabolites, and helper T cell ratios were markedly affected by LGG in HU mice, and there was a correlation between helper T cell ratios and gut microbial-derived short-chain fatty acids (SCFAs). Our findings indicate that spaceflight adversely affects helper T cell ratios, and demonstrates that LGG impacts simulated spaceflight-induced helper T cell disorder by modulating microbial-derived SCFAs.

Spaceflight is rigorous and dangerous environment which can negatively affect astronauts’ health and the entire mission. The 60 days of 6° head-down bed rest (HDBR) experiment provided us with an opportunity to trace the change of gut microbiota under simulated microgravity. The gut microbiota of volunteers was analyzed and characterized by 16S rRNA gene sequencing and metagenomic sequencing. Our results showed that the composition and function of the volunteers’ gut microbiota were markedly was affected by 60 days of 6° HDBR. We further confirmed the species and diversity fluctuations. Resistance and virulence genes in the gut microbiota were also affected by 60 days of 6° HDBR, but the species attributions remained stable. The human gut microbiota affected by 60 days of 6° HDBR which was partially consistent with the effect of spaceflight, this implied that HDBR was a simulation of how spaceflight affects the human gut microbiota.

Spaceflight is physically demanding and can negatively affect astronauts' health. It has been shown that the human gut microbiota and cardiac function are affected by spaceflight and simulated spaceflight. This study investigated the effects of the gut microbiota on simulated spaceflight-induced cardiac remodeling using 10 degrees of head-down bed rest (HDBR) in rhesus macaques and 30 degrees of hindlimb unloading (HU) in mice. The gut microbiota, fecal metabolites, and cardiac remodeling were markedly affected by HDBR in macaques and HU in mice, cardiac remodeling in control mice was affected by the gut microbiota of HU mice and that of HU mice was protected by the gut microbiota of control mice, and there was a correlation between cardiac remodeling and the gut microbial-derived metabolite trimethylamine N-oxide. These findings suggest that spaceflight can affect cardiac remodeling by modulating the gut microbiota and fecal metabolites.

Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen’s physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.

Rapid and ultrasensitive microbial detection in actual samples have challenges because of target pathogen diversity and low abundance. In this study, we attempted to capture and concentrate multiple pathogens by combining magnetic beads with polyclonal antibodies against a universal antigen of ompA, LAMOA-1, before further detection. A protein sequence consisting of 241 amino acids with spatial conformation similar to E. coli ompA was identified and expressed as a recombinant protein in prokaryotes according to the results of sequence alignment among 432 sequences of ompA belonging to intestinal bacteria from gram-negative bacteria. Purified from immunized rabbits, the anti-LAMOA-1 antibody was shown to effectively recognize 12 foodborne bacterial species. Antibody-conjugated beads were used to concentrate the bacteria when the bacterial concentration in artificially contaminated samples is between 10 and 100 CFU/mL, which shortens detection duration by 8–24 h. The enrichment strategy is potentially beneficial for detection of foodborne pathogens.

Yersinia pestis, the causative agent of plague, is a genetically monomorphic bacterial pathogen that evolved from Yersinia pseudotuberculosis approximately 7,400 years ago. We observed unusually frequent mutations in Y. pestis YPO0623, mostly resulting in protein translation termination, which implies a strong natural selection. These mutations were found in all phylogenetic lineages of Y. pestis, and there was no apparent pattern in the spatial distribution of the mutant strains. Based on these findings, we aimed to investigate the biological function of YPO0623 and the reasons for its frequent mutation in Y. pestis. Our in vitro and in vivo assays revealed that the deletion of YPO0623 enhanced the growth of Y. pestis in nutrient-rich environments and led to increased tolerance to heat and cold shocks. With RNA-seq analysis, we also discovered that the deletion of YPO0623 resulted in the upregulation of genes associated with the type VI secretion system (T6SS) at 26°C, which probably plays a crucial role in the response of Y. pestis to environment fluctuations. Furthermore, bioinformatic analysis showed that YPO0623 has high homology with a PLP-dependent aspartate aminotransferase in Salmonella enterica, and the enzyme activity assays confirmed its aspartate aminotransferase activity. However, the enzyme activity of YPO0623 was significantly lower than that in other bacteria. These observations provide some insights into the underlying reasons for the high-frequency nonsense mutations in YPO0623, and further investigations are needed to determine the exact mechanism.

Abstract Background Spaceflight is physically demanding and can negatively affect astronauts’ health. It has been shown that the human gut microbiota and cardiac function are affected by spaceflight and simulated spaceflight. This study investigated the effects of the gut microbiota on simulated spaceflight-induced cardiac remodeling using 10 degrees of head-down bed rest (HDBR) in rhesus macaques and 30 degrees of hindlimb unloading (HU) in mice. Results In macaques, the gut microbiota, fecal metabolites, and cardiac remodeling were markedly affected by HDBR, and there was a correlation between cardiac remodeling and the gut microbial-derived metabolite trimethylamine N-oxide. The gut microbiota and fecal metabolites in mice were also markedly affected by HU and correlated with cardiac remodeling. Cardiac remodeling in control mice was affected by the gut microbiota of HU mice and that of HU mice was protected by the gut microbiota of control mice. Conclusion The gut microbiota, fecal metabolites, and cardiac remodeling were markedly affected by HDBR in macaques and HU in mice. These results are consistent with the known effects of spaceflight and HDBR in humans. Cardiac remodeling was affected by the gut microbiota under simulated spaceflight conditions, and the gut microbial-derived trimethylamine N-oxide was correlated with cardiac remodeling. These findings suggest that spaceflight can affect cardiac remodeling by modulating the gut microbiota and fecal metabolites.

Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.

Yersinia pestis is the etiological agent of plague, a deadly infectious disease that has caused millions of deaths throughout history. Obtaining iron from the host is very important for bacterial pathogenicity. Y. pestis possesses many iron uptake systems. Yersiniabactin (Ybt) plays a major role in iron uptake in vivo and in vitro, and in virulence toward mice as well. FyuA, a β-barrel TonB-dependent outer membrane protein, serves as the receptor for Ybt. In this study, we examined the role of the fyuA gene in Y. pestis virulence using different challenging ways and explored the underlying mechanisms. The BALB/c mouse infection assay showed that the virulence of the mutant strains (ΔfyuA and ΔfyuAGCAdel) was lower when compared with that of the wild-type (WT) strain 201. Furthermore, the attenuation of virulence of the mutant strains via subcutaneous and intraperitoneal challenges was far greater than that via intravenous injection. Iron supplementation restored lethality during subcutaneous challenge with the two mutants. Thus, we speculated that the attenuated virulence of the mutant strains toward the mice may be caused by dysfunctional iron uptake. Moreover, ΔfyuA and ΔfyuAGCAdel strains exhibited lower survival rates in murine RAW264.7 macrophages, which might be another reason for the attenuation. We further explored the transcriptomic differences between the WT and mutant strains at different temperatures and found that the expressions of genes related to Ybt synthesis and its regulation were significantly downregulated in the mutant strains. This finding indicates that fyuA might exert a regulatory effect on Ybt. Additionally, the expressions of the components of the type III secretion system were unexpectedly upregulated in the mutants, which is inconsistent with the conventional view that the upregulation of the virulence genes enhances the virulence of the pathogens.

Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.

With the increase of crewed space missions and the rise of space microbiology, the research of microbes grown under microgravity environment has been attracting more attention. The research scope in space microbiology has been extended beyond pathogens directly related to spaceflight. Y. pestis, the causative agent of plague, is also of interest to researchers. After being cultivated for 40 consecutive passages in either simulated microgravity (SMG) or normal gravity (NG) conditions, the Y. pestis strain 201 cultures were analysed regarding their phenotypic features. By using crystal violet staining assays, increased biofilm amount was detected in Y. pestis grown under SMG condition. Besides that, the damage degrees of Hela cell caused by SMG-grown Y. pestis were found diminished in comparison to those under NG condition. Consistent with this observation, the death course was delayed in mice infected with SMG-grown Y. pestis, suggesting that microgravity condition can contribute the attenuated virulence. RNA-seq-based transcriptomics analysis showed that a total of 218 genes were differentially regulated, of which 91 upregulated and 127 downregulated. We found that dozens of virulence-associated genes were downregulated, which partially explained the reduced virulence of Y. pestis under SMG condition. Our study demonstrated that long-term exposure to SMG influences the pathogenesis and biofilm formation ability of Y. pestis, which provides a novel avenue to study the mechanism of physiology and virulence of this pathogen. Microgravity enhanced the ability of biofilm formation and reduced the virulence and cytotoxicity of Y. pestis. Many virulence-associated genes of Y. pestis were differentially regulated in response to the stimulated microgravity. However, there is no molecular evidence to explain the enhanced biofilm formation ability, which requires further research. Taken together, the phenotype changes of Y. pestis under SMG conditions can provide us a new research direction of its potential pathogenesis.

目的 利用革兰阴性细菌外膜蛋白A高度保守的特性,设计和制备可识别多种食源性革兰阴性细菌的免疫磁珠,并对该免疫磁珠的识别和富集效果进行评价.方法 利用革兰阴性外膜蛋白A序列高度保守的特性,从国际生物基因数据库(NCBI)提取该蛋白的氨基酸序列进行同源比对;使用抗原表位预测工具"BepiPred"预测具有免疫原性的抗原表位;将预测的多肽序列分两组混合免疫大耳白兔制备多克隆抗体,并利用间接ELISA法对抗体进行评价,挑选出优质抗体偶联磁珠捕捉细菌,利用平板培养计数的方法检验抗体的有效性和广谱性.结果 经间接ELISA筛选,制备的多抗可识别阪岐克洛诺杆菌、肠出血性大肠埃希菌O157:H7、弗氏志贺菌、肠炎沙门菌、鼠伤寒沙门菌、小肠结肠炎耶尔森菌6种常见食源性致病菌,识别灵敏度为25μg/ml;使用该抗体制备的500 nm羧基免疫磁珠对6种细菌的捕捉率为0.47％～2.03％.结论 与传统的免疫磁珠相比较,该项目制备的多抗免疫磁珠具有广谱性的特点,可提高检验效率,是一种具有应用前景的检测思路.

Aim:The aim of this study was to access the effect of HmsA, a 65-nt small regulatory RNA encoded by the pPCP1 plasmid, onYersinia pestisvirulence.Materials & methods:Survival and the competition index were determined in mice infected with wild-type Y. pestisand anhmsAdeletion mutant. RNA-seq was used to identify HmsA-regulated genes.Results:HmsA deletion enhancedY. pestisvirulence. However, there was no overlap between 18 upregulated genes associated with pathogenicity and potential direct HmsA targets, based on gene expression screening after HmsA-pulse overexpression.Conclusion:HmsA inhibitsY. pestisvirulence, but this effect may be mediated by indirect effects on pathogenesis, iron homeostasis and/or other cellular processes.