Microbiology spectrum最新文献

{"title":"A stable atypical H₂S-negative, non-motile <i>Salmonella</i> Infantis variant from a human isolate associated with a <i>barA</i> stop-gain mutation.","authors":"Darya Fesina, Nicola Palmieri, Markus Kranzler, Marlene Brandstetter, Christian Kornschober, Ivana Bilic, Michael Hess, Claudia Hess, Victoria Drauch","doi":"10.1128/spectrum.01683-26","DOIUrl":"https://doi.org/10.1128/spectrum.01683-26","url":null,"abstract":"<p><p><i>Salmonella enterica</i> serovar Infantis (<i>S</i>. Infantis) is an increasingly important food-borne pathogen, and detection in broiler flocks via the standardized EN/ISO 6579-1:2017 is of utmost importance. Phenotypic characteristics, such as the production of hydrogen sulfide (H₂S) and swarming behavior, are essential for detection. However, the occurrence of atypical variants lacking such phenotypic characteristics bears a risk to public health. In this study, we characterized an Austrian human-derived <i>S</i>. Infantis strain showing, in addition to the normal colony phenotype (NCP), also an atypical colony variant (ACV) lacking H₂S production and motility. Both phenotypes proved stability, and no differences were found in cell morphology. In comparison to NCP, ACV demonstrated altered biofilm formation on Congo Red agar, and showed lower streptomycin resistance. The genomic analysis revealed a total of 21 mutations specific to ACV, including a stop-gain mutation in <i>barA</i>. Using gene network analysis, a connection between <i>barA</i> and operons relevant for H₂S production, <i>ttr</i>, and <i>phs</i> was found. As <i>barA</i> is a well-known regulator with established roles in motility, the observed truncation provides a plausible regulatory basis for the stable H₂S-negative, non-motile phenotype. Furthermore, mutations in <i>barA</i> have been linked to persistent <i>Salmonella</i> infections in humans, supporting our findings. Importantly, such atypical variants might go undetected in the mandatory control programs.IMPORTANCEPhenotypic characteristics, such as the production of hydrogen sulfide and motility, are essential for culture-based detection of <i>Salmonella</i>. This study shows that <i>Salmonella</i> Infantis can lose these key diagnostic features through regulatory mutations, enabling escape from routine surveillance while maintaining infection potential. As the present mutation is known to contribute to bacterial persistence in the host, our findings highlight a dual clinical concern of diagnostic evasion and possible adaptation to host survival. This work demonstrates a critical limitation of phenotype-dependent diagnostics and underscores the need for surveillance strategies that can detect atypical but clinically relevant <i>Salmonella</i> variants.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0168326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SARS-CoV-2 variant-dependent alterations in nasopharyngeal microbiota and host inflammatory response.","authors":"Mario Maulen, Ignacio Pezoa-Soto, Daniel León, Ela M Dominguez, Alberto J M Martin, Waldo A Díaz-Vásquez","doi":"10.1128/spectrum.00930-26","DOIUrl":"https://doi.org/10.1128/spectrum.00930-26","url":null,"abstract":"<p><p>The SARS-CoV-2 pandemic saw multiple outbreaks occur over short periods. This was linked to the virus's high infectivity and rapid mutation rate, which hindered the development of effective treatments and a comprehensive understanding of COVID-19 pathophysiology. The nasopharyngeal tract, the main entry site of SARS-CoV-2, interacts with angiotensin-converting enzyme 2 receptors via the viral spike glycoprotein, triggering pro-inflammatory responses that affect both tissue integrity and the resident microbiota. Viral infection induces dysbiosis by modulating microbiome diversity. Although distinct variants produce independent symptoms and viral loads, their impact on the nasopharyngeal microbiota and host inflammatory profile remains poorly understood. To address this, we analyzed nasopharyngeal samples from Chilean individuals collected during different phases of the pandemic. The microbiota was characterized by 16S rRNA gene sequencing (V3-V4 region), and cytokine expression was quantified by RT-qPCR. Finally, applied rigorous data processing and machine-learning models, Random Forest and K-Nearest Neighbors, to identify associations between SARS-CoV-2 variants, inflammatory markers, and opportunistic bacterial genera. Our results reveal that SARS-CoV-2 infection is associated with distinct immunomicrobial signatures marked by increased TNF-α expression and the expansion of opportunistic taxa. These variant-dependent alterations indicate that host inflammatory responses and microbial dysbiosis are closely intertwined in the nasopharyngeal environment. This study provides a comprehensive framework integrating microbial and host factors to better understand the mechanisms underlying COVID-19 pathogenesis and highlights the potential of combining microbiome and cytokine profiling with machine-learning approaches to differentiate infection outcomes across viral variants.IMPORTANCEUnderstanding how SARS-CoV-2 infection alters the upper respiratory microbiota and host immune responses is essential to uncover the mechanisms underlying COVID-19 severity. In this study, we integrate bacterial 16S rRNA sequencing, inflammatory markers, and machine learning to identify key descriptors of infection such as TNF-α, <i>Acinetobacter</i>, <i>Prevotella</i>, and <i>Staphylococcus</i>. These markers define a conserved immunomicrobial signature across viral variants, linking inflammatory activation with microbial dysbiosis in the nasopharyngeal environment. Our findings highlight the value of the correct and robust application of machine learning models and nested cross-validation strategies in high-dimensional (wide) data sets to improve variant discrimination, reveal host-microbe interactions, and support the development of therapeutic strategies for respiratory viral infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0093026"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DksA regulates intestinal colonization of <i>Klebsiella pneumoniae</i> through metabolic plasticity.","authors":"Jia Wan, Yixuan Wang, Lin Wang, Yaxin Li, Shun Xiong, Xiakun Chu, Dianrong Zhou, Jiachen Li, Meisong Li, Xue Xia, Wenli Wang, Meiting Yang, Weiqing Liu, Yiwu Wen, Zhilang Qiu, Siyuan Feng, Guo-Bao Tian","doi":"10.1128/spectrum.01949-26","DOIUrl":"https://doi.org/10.1128/spectrum.01949-26","url":null,"abstract":"<p><p>Intestinal colonization by <i>Klebsiella pneumoniae</i> is recognized as a pivotal prerequisite for its systemic dissemination and subsequent invasive infection; however, the metabolic basis and regulatory mechanisms underlying this process remain poorly understood. In this study, we employed transposon insertion sequencing (Tn-seq) to systematically identify metabolic genes associated with intestinal colonization in <i>K. pneumoniae</i>. By integrating high-throughput screening with <i>in vivo</i> phenotypic validation, we identified the global transcriptional regulator DksA as a key factor that markedly enhances <i>K. pneumoniae</i> intestinal colonization. Mechanistically, DksA may contribute to intestinal colonization through modulation of central carbon metabolism. Integrated transcriptomic and metabolomic analyses, together with homology modeling and molecular dynamics simulations, suggested that DksA may contribute to allosteric remodeling of key RNA polymerase structural domains, thereby influencing the expression of metabolic genes, carbon source utilization, and intestinal colonization by <i>K. pneumoniae</i>. Collectively, our findings highlight the important role of metabolic plasticity associated with transcriptional regulation in <i>K. pneumoniae</i> intestinal colonization and provide a theoretical framework and potential targets for developing anti-colonization strategies that exploit pathogen metabolic vulnerabilities.</p><p><strong>Importance: </strong>Intestinal colonization is a critical first step in the pathogenesis and transmission of <i>Klebsiella pneumoniae,</i> yet the bacterial factors that support persistence in the gut remain incompletely understood. In this study, we identified the transcriptional regulator DksA as an important contributor to intestinal colonization through genome-wide genetic screening and <i>in vivo</i> validation. Multi-omics analyses suggest that DksA is associated with the regulation of bacterial carbon metabolism and metabolic adaptation, processes that are likely important for survival in the nutrient-variable intestinal environment. Structural modeling further provides insight into how DksA may influence transcriptional regulation. These findings expand our understanding of the factors that facilitate <i>K. pneumoniae</i> gut colonization and highlight bacterial metabolic adaptation as a potential target for strategies aimed at limiting colonization and subsequent infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0194926"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of a recombinant gC-deleted PRV-XJ variant reveals altered disease outcomes following different inoculation routes in mice.","authors":"Xin Wu, Baoling Liu, Hanyu Li, Tong Xu, Pengfei Yuan, Xianlin Pan, Shuying He, Lei Zhao, Yangming Dai, Zhi-Wen Xu, Ling Zhu","doi":"10.1128/spectrum.02731-26","DOIUrl":"https://doi.org/10.1128/spectrum.02731-26","url":null,"abstract":"<p><p>Pseudorabies virus (PRV) variants continue to threaten swine production and can cause severe neurological disease in non-natural hosts. Although glycoprotein C (gC) contributes to PRV attachment to host cells, its role in the pathogenic characteristics of currently circulating PRV variants remains unclear, particularly under different inoculation routes. In this study, we generated a marker-free gC-deleted recombinant virus, rPRV-XJ-ΔgC, based on the genotype II PRV-XJ variant and compared its pathogenic characteristics with those of parental PRV-XJ in C57BL/6 mice. rPRV-XJ-ΔgC retained the ability to cause lethal infection but, compared with PRV-XJ, showed delayed disease progression, reduced early central nervous system (CNS) viral accumulation, and milder neurological and neuropathological changes, particularly following intranasal inoculation. These differences were less evident after intramuscular inoculation. Intranasal infection with rPRV-XJ-ΔgC was also associated with attenuated disruption of the blood-brain barrier, consistent with reduced CNS injury. Collectively, these findings indicate that gC deletion in the PRV-XJ background is associated with altered infection kinetics and route-dependent CNS disease phenotypes.</p><p><strong>Importance: </strong>Pseudorabies virus (PRV) variants remain important pathogens associated with neurological disease, but the contribution of individual viral genes to the pathogenic characteristics of circulating PRV variants remains poorly understood. Here, we investigated the role of glycoprotein C (gC) in the pathogenic phenotype of the genotype II PRV-XJ variant. gC deletion resulted in route-dependent changes in PRV-XJ-induced disease outcomes, with more evident effects following intranasal than intramuscular inoculation. These findings highlight the importance of viral genetic factors and infection routes in shaping PRV-associated disease phenotypes and provide further insight into PRV neuropathogenesis.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0273126"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved disc diffusion-based detection of extended spectrum β-lactamase production in the <i>Klebsiella oxytoca</i> complex.","authors":"Stefano Mancini, Florian Tribelhorn, Tim Roloff, Helena M B Seth-Smith, Natalia Kolesnik-Goldmann, Ramon M Eichenberger, Chantal Quiblier, Vladimira Hinic, Adrian Egli, Oliver Nolte","doi":"10.1128/spectrum.01327-26","DOIUrl":"https://doi.org/10.1128/spectrum.01327-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Accurate discrimination between extended-spectrum β-lactamase (ESBL) production and hyperproduction of the intrinsic OXY-β-lactamase (hyperOXY) in the &lt;i&gt;Klebsiella oxytoca&lt;/i&gt; complex remains challenging, as both mechanisms can generate overlapping resistance phenotypes and lead to unnecessary confirmatory testing or misclassification. We analyzed a collection of 123 whole-genome-sequenced clinical &lt;i&gt;K. oxytoca&lt;/i&gt; complex isolates (2009-2024), including 33 ESBL producers and multiple species-specific &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXY&lt;/sub&gt; variants, to develop a phenotypic strategy for distinguishing these resistance mechanisms using disc diffusion data. We performed antimicrobial susceptibility testing according to EUCAST guidelines and correlated phenotypic findings with genomic resistance determinants. HyperOXY isolates harbored classical activating mutations in &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXY&lt;/sub&gt; promoter regions and displayed a characteristic resistance pattern marked by high-level resistance to amoxicillin-clavulanic acid and piperacillin-tazobactam, resistance to ceftriaxone and cefpodoxime, preserved or borderline susceptibility to ceftazidime, and variable reductions in cefepime susceptibility. In contrast, ESBL-producing isolates showed reproducible clavulanate synergy and distinct inhibition zone distributions for piperacillin-tazobactam, cefpodoxime, and gentamicin. A cefpodoxime inhibition zone diameter &lt;17 mm identified all ESBL-producing isolates (sensitivity 100%) but showed limited specificity (44%). Combining cefpodoxime &lt;17 mm with additional phenotypic criteria allowed confident ESBL attribution without additional testing (specificity 100%), albeit at reduced sensitivity (72%). EUCAST-recommended combination disc ESBL confirmatory testing using cefotaxime or cefepime with clavulanic acid demonstrated the highest diagnostic performance (sensitivity/specificity ≥ 96%). Thirty-three isolates showed ambiguous phenotypes requiring confirmatory testing. Overall, interpretative reading of routine disc diffusion patterns can reliably classify characteristic hyperOXY and ESBL phenotypes and restrict additional confirmatory testing to ambiguous isolates, thereby improving diagnostic efficiency while maintaining high accuracy.IMPORTANCEMembers of the &lt;i&gt;K. oxytoca&lt;/i&gt; complex possess an intrinsic OXY β-lactamase that can be overexpressed and generate resistance patterns closely resembling those of extended-spectrum β-lactamase (ESBL) producers. This phenotypic overlap complicates routine antimicrobial susceptibility testing and frequently leads to unnecessary ESBL confirmatory testing or misclassification, with potential consequences for patient management and infection control. Using a large, genomically characterized strain collection, this study defines reproducible disc diffusion patterns that distinguish hyperOXY-mediated resistance from true ESBL production and evaluates screening and confirmatory strategies based on routinely tested antibiotics. B","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0132726"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploratory associations of gut microbiota composition with HBeAg and HBsAg status in nucleos(t)ide analog-treated chronic hepatitis B.","authors":"Sisi Yang, Siqi Sun, Jiyang Chen, Yani Zhou, Fangping Jia, Yiran Xie, Yinfeng Lu, Qin Ni, Jianhua Hu, Meifang Yang, Yu Shi, Hongyu Jia, Yida Yang","doi":"10.1128/spectrum.03896-25","DOIUrl":"https://doi.org/10.1128/spectrum.03896-25","url":null,"abstract":"<p><p>HBeAg and HBsAg reflect viral replication and host immune status and are important determinants of treatment responsiveness in chronic hepatitis B (CHB). The gut microbiota, a key component of the gut-liver axis, may influence immune regulation and antiviral outcomes. This study characterized gut microbiota profiles across different HBeAg and HBsAg statuses in CHB patients receiving nucleos(t)ide analog (NA) therapy. Fecal shotgun metagenomic sequencing was performed in 29 healthy controls (HC) and 101 NA-treated CHB patients without cirrhosis or hepatocellular carcinoma, including 30 HBeAg-positive (EP) and 71 HBeAg-negative (EN) individuals. The EN group was further stratified by serum HBsAg levels into an advantageous subgroup (<1,500 IU/mL, <i>n</i> = 57) and a non-advantageous subgroup (≥1,500 IU/mL, <i>n</i> = 14). Alpha and beta diversity did not differ significantly among EP, EN, and HC groups. Species-level analyses identified nominal group-related differences in several Bacteroidales- and Firmicutes-associated anaerobic commensals, including Bacteroides uniformis, Blautia obeum, Eubacterium ventriosum, Anaerobutyricum, and Parabacteroides timonensis; however, none remained significant after global FDR correction across all detected species. Within the EN group, selected taxa showed directionally consistent associations with HBsAg strata in downsampling, leave-one-out, and CLR-based sensitivity analyses, but these subgroup findings also did not remain significant after FDR correction. NA-treated CHB was associated with exploratory taxonomic differences without detectable loss of microbial diversity. The observed associations with HBeAg status and HBsAg burden were hypothesis-generating and require validation in larger longitudinal cohorts incorporating absolute microbial quantification, targeted metabolomics, host immune profiling, and more complete dietary, anthropometric, and other relevant clinical covariates.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0389625"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary stability studies of a β-SARS-CoV-2 virus-like particle vaccine.","authors":"Melissa A Edeling, Linda Earnest, Ashley Huey Yiing Yap, Julio Carrera Montoya, Dhiraj Hans, Joseph Torresi","doi":"10.1128/spectrum.01169-26","DOIUrl":"https://doi.org/10.1128/spectrum.01169-26","url":null,"abstract":"<p><p>We aimed to study the stability of a Beta (β)-SARS-CoV-2 virus-like particle (VLP) vaccine in a series of preliminary experiments using selective stabilizing excipients. β-SARS-CoV-2 VLPs were produced and purified using established methodologies. The thermostability of VLPs was tested at 4°C and -30°C in the presence or absence of stabilizers polysorbate 80, sorbitol, or L-histidine in the presence of a physiological NaCl concentration of 137 mM. The integrity of VLPs was assessed using ELISA, Western immunoblot, and dynamic light scatter (DLS). β-SARS-CoV-2 VLPs were stable at 4°C for 14 days, and the addition of stabilizing excipients improved stability compared to VLPs in PBS alone. Storage of VLPs at -80°C maintained particle integrity by DLS analysis for up to 2 years. Excipients helped to maintain the antigenicity of the VLPs by ELISA and Western immunoblot, and DLS analysis revealed that VLPs retained their particulate structure.<b>IMPORTANCE</b>SARS-CoV-2 continues to circulate globally and cause significant illness. The problem of waning immunity to mRNA/LNPs has necessitated frequent boosters to keep pace with emerging variants. The development of alternative vaccines, therefore, remains a priority. Protein- based vaccines, like VLPs, offer a safe alternative able to produce longer-lasting immune responses. In this preliminary stability analysis, the β-SARS-CoV-2 VLPs were found to be stable at 4°C, and the addition of excipients improved VLP stability. Storage of VLPs at -30°C and -80°C also showed that the VLPs are stable for extended periods. Our findings will be of importance for the ongoing development of a SARS-CoV-2 VLP-based vaccine.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0116926"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic, untargeted metabolomic, and gut microbiota studies on the anticoccidial activity of the combination formula in broilers.","authors":"Tiantian Geng, Hongjun Yang, Yuanxiang Liu, Junlong Zhao, Yanqin Zhou","doi":"10.1128/spectrum.03410-24","DOIUrl":"https://doi.org/10.1128/spectrum.03410-24","url":null,"abstract":"<p><p>Coccidiosis, a devastating intracellular parasitic disease, poses a significant threat to the poultry industry. Traditional control methods, which involve the inclusion of anticoccidial drugs in feed, have raised concerns over veterinary drug residues. Consequently, there is a pressing need to identify suitable alternatives or complementary strategies to anticoccidial drugs, with plant-derived natural products emerging as a promising candidate. Our laboratory has previously identified a combination formula that demonstrates good anticoccidial activity. However, the underlying mechanisms remain elusive. This study aims to elucidate the mechanism of action of this formula using a multi-omics approach, including transcriptomics, untargeted metabolomics, and gut microbiota analysis. Cecal transcriptomic analysis revealed significant enrichment in pathways, such as lysosomes, ribosomes, oxidative phosphorylation, and sphingolipid metabolism following treatment with the combination formula. Untargeted metabolomic profiling indicated a pronounced enrichment in the gut IgA generation immune network pathway, with retinoic acid identified as a key differential metabolite. Gut microbiota sequencing analysis suggested that the combination formula modulates the gut microbiota of infected broilers towards a composition resembling that of healthy broilers. Collectively, these results suggest that the combination formula exerts its anticoccidial effects through the regulation of differential gene clusters, metabolites, and microbiota. The results of this study have provided us with a deeper understanding of the good anticoccidial effects of the combination formula.</p><p><strong>Importance: </strong><i>Eimeria tenella</i> is a significant parasitic protozoan that poses a substantial threat to the development of the poultry industry. The combination formula, a synergistic blend of plant-derived natural products, has been identified in our laboratory for its good anticoccidial effects. In this study, we employed non-targeted metabolomics, transcriptomics, and gut microbiome sequencing to elucidate the mechanism of action against coccidiosis. Our results revealed a multitude of differential gene clusters and metabolites. Furthermore, the gut microbiota structure of the cecal content in the treated group more closely resembled that of the healthy control group.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0341024"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlation-based analysis of gene expression in <i>Cardinium</i>, <i>Wolbachia</i>, and <i>Tyrophagus putrescentiae</i> reveals distinct host-symbiont interactions and parallel evolutionary expansion of infection-associated genes.","authors":"Jan Hubert, Eliza Glowska-Patyniak, Jitka Stara, Stefan Green","doi":"10.1128/spectrum.02596-26","DOIUrl":"https://doi.org/10.1128/spectrum.02596-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Cardinium&lt;/i&gt; and &lt;i&gt;Wolbachia&lt;/i&gt; are phylogenetically distinct intracellular symbionts that have convergently evolved mechanisms to infect a wide range of arthropod and nematode hosts. Here, we investigated the interaction dynamics of two basal strains, &lt;i&gt;Cardinium&lt;/i&gt; (cTPut) and &lt;i&gt;Wolbachia&lt;/i&gt; (wTPut), in the stored-product mite &lt;i&gt;Tyrophagus putrescentiae&lt;/i&gt; (Acari: Astigmata). The KEGG-annotated gene expression profiles of mite samples were analyzed in single infections (&lt;i&gt;Cardinium&lt;/i&gt; or &lt;i&gt;Wolbachia&lt;/i&gt;) and mixed infections across three time points (2, 4, and 6 months). Temporal effects on gene expression were marginal; therefore, correlation-based network analyses were used to characterize host-symbiont interactions. The symbionts exhibited distinct host-targeting strategies: &lt;i&gt;Wolbachia&lt;/i&gt; displayed a \"broad\" interaction pattern characterized by numerous weak correlations with host KEGG genes, whereas &lt;i&gt;Cardinium&lt;/i&gt; showed a \"focused\" strategy involving fewer but stronger correlations. These patterns were consistent across global KEGG data sets, immune and regulatory pathways (including AMPK, autophagy, endocytosis, Hippo, lysosome, MAPK, mTOR, and Notch), receptor subsets, and metabolic pathways. Consistent with these interaction patterns, orthologous analyses across &lt;i&gt;Cardinium&lt;/i&gt; and selected &lt;i&gt;Wolbachia&lt;/i&gt; genomes revealed that infection-associated genes are not broadly conserved but are enriched in lineage-specific, duplicated gene families, particularly in &lt;i&gt;T. putrescentiae&lt;/i&gt;-associated symbionts. These findings indicate that infection-related traits evolve primarily through lineage-specific gene family expansion rather than conservation and suggest that basal &lt;i&gt;Cardinium&lt;/i&gt; and &lt;i&gt;Wolbachia&lt;/i&gt; employ fundamentally distinct host interaction strategies.IMPORTANCEThe study provides novel insight into host-symbiont interactions: &lt;i&gt;Cardinium&lt;/i&gt;, &lt;i&gt;Wolbachia&lt;/i&gt; infecting mite &lt;i&gt;Tyrophagus putrescentiae&lt;/i&gt;, an important producer of allergens (i) &lt;i&gt;Cardinium&lt;/i&gt; gene expression responds to the presence of &lt;i&gt;Wolbachia&lt;/i&gt;, whereas &lt;i&gt;Wolbachia&lt;/i&gt; gene expression shows no reciprocal response; (ii) the two symbionts employ contrasting host interaction strategies with the host, with &lt;i&gt;Cardinium&lt;/i&gt; exhibiting fewer but stronger associations and &lt;i&gt;Wolbachia&lt;/i&gt; showing widespread but weaker correlations; (iii) distinct host pathways are differentially associated with each symbiont; and (iv) we identified 40 of the most correlated bacterial genes to the host that include candidates of viral origin, suggesting a potential role of horizontally acquired elements in the host. Furthermore, evolutionary analyses demonstrate that infection-associated genes are primarily lineage expanded rather than broadly conserved across symbiont genomes. Given the allergenic relevance of &lt;i&gt;T. putrescentiae&lt;/i&gt;, these findings suggest that symbiont-specific interaction strategies can indirectly influence host physiology an","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0259626"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bovine and human serum albumins promote recovery of culturability in diphenyleneiodonium-induced viable but non-culturable <i>Mycobacterium tuberculosis</i>, potentially involving protein kinase activity.","authors":"Yuta Morishige, Yoshiro Murase, Kinuyo Chikamatsu, Hiroyuki Yamada, Akio Aono, Yuriko Igarashi, Keisuke Kamada, Yoshiko Shimomura, Makiko Hosoya, Satoshi Mitarai","doi":"10.1128/spectrum.03541-25","DOIUrl":"https://doi.org/10.1128/spectrum.03541-25","url":null,"abstract":"<p><p>We investigated the mechanisms underlying the fetal bovine serum (FBS)-induced reactivation of diphenyleneiodonium (DPI)-induced viable but non-culturable (VBNC) state of <i>Mycobacterium tuberculosis</i> (Mtb) using the H37Rv strain. We found that bovine serum albumin (BSA), a major component of FBS, was sufficient to promote recovery of culturability in DPI-induced VBNC Mtb cells under our experimental conditions. Human serum albumin also showed a similar effect, whereas mouse serum albumin and egg-white albumin (ovalbumin) did not induce comparable recovery, suggesting that specific structural or biochemical features shared by bovine and human serum albumin may contribute to this process. In addition, antioxidative agents, including N<i>-</i>acetyl-<i>L</i>-cysteine (NAC), did not induce reactivation, suggesting that the antioxidative property alone is insufficient to explain the effect of BSA. Recovery of culturability was suppressed by protein kinase inhibitors, such as H89 and staurosporine, which are known to target multiple kinases, including serine/threonine protein kinases in Mtb. These findings suggest that protein kinase activity may be involved in BSA-induced recovery of culturability from the DPI-induced VBNC Mtb cells. Overall, our study identifies albumin-dependent recovery of culturability in DPI-induced VBNC model of Mtb and highlights the need to compare recovery mechanisms across distinct dormancy models.</p><p><strong>Importance: </strong><i>Mycobacterium tuberculosis</i> (Mtb) cells can enter a viable but non-culturable (VBNC) state under stress, complicating the interpretation of bacterial survival and recovery in experimental dormancy models. However, the factors that restore culturability from defined VBNC populations remain less understood. This study shows that serum albumin promotes recovery of culturability from Mtb cells rendered VBNC state by diphenyleneiodonium (DPI) treatment. The effect was observed with bovine and human serum albumins but not mouse serum albumin or ovalbumin, indicating that albumin-dependent recovery is not a general property of all albumins. The lack of comparable recovery by the antioxidant N-acetyl-<i>L</i>-cysteine (NAC) further suggests that the antioxidative activity alone does not explain this phenomenon. By identifying albumin-dependent recovery in a defined DPI-induced VBNC model, this work provides a basis for testing whether similar or distinct recovery mechanisms operate in other Mtb dormancy models.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0354125"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}