Microbiology spectrum最新文献

{"title":"Correlation between <i>Helicobacter pylori</i> infection and severity of gastritis in children.","authors":"Wei Zheng, Xiaoyu Chen, Yaofeng Yang, Kerong Peng, Fubang Li, Hong Zhao, Weizhong Gu, Mizu Jiang","doi":"10.1128/spectrum.00312-25","DOIUrl":"https://doi.org/10.1128/spectrum.00312-25","url":null,"abstract":"<p><p><i>Helicobacter pylori</i> is widely recognized as the chronic infection that is most commonly observed across all age cohorts worldwide and is closely linked to chronic gastritis. In pediatric <i>H. pylori</i> patients, we aim to examine the endoscopic and histopathological alterations in the gastric mucosa. This was a potential monocentric investigation conducted from January 2018 to August 2018, collecting 120 children who underwent gastroscopy due to symptoms of gastrointestinal distress. Endoscopic procedures were conducted to acquire mucosal biopsies for the purpose of histopathological analysis. The investigation comprised a cohort of 120 patients, 64 of whom were identified as having <i>H. pylori</i> infection. <i>The H. pylori</i>-infected cohort had a greater level of inflammation, activity, and lymphoid follicles than the <i>H. pylori</i>-negative cohort. A significant link was discovered between <i>H. pylori</i> infection and both nodular lesions and active gastritis. There was a significant infection link observed between the degree of inflammation and the abundance level of <i>Helicobacter</i> in the <i>H. pylori</i>-infected cohort. There was a significant link between the infection of <i>H. pylori</i> and histopathological manifestations, including active gastritis.IMPORTANCE<i>H. pylori</i> is a significant concern of infection in the field of public health. In children, the endoscopic observations of <i>H. pylori</i> infection exhibit variation, particularly in highly endemic countries where nodular changes in the gastric mucosa are commonly observed. Nevertheless, there is ongoing debate regarding the connection between the colonization level of <i>H. pylori</i> in the gastric mucosa and the extent of histological parameters of gastritis. We mainly explored the link between the <i>H. pylori</i> colonization density in the gastric mucosa and the severity of histological parameters related to gastritis and found that there was a significant link between the infection of <i>H. pylori</i> and histopathological manifestations, including active gastritis.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0031225"},"PeriodicalIF":3.8,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732328","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":"Reassessment of extracellular and intracellular activity of macrolides, rifampicin, and doxycycline against <i>Rhodococcus equi</i> based on bacterial counts and microscopy.","authors":"Anne-Sophie Huguet, Ophélie Gourbeyre, Alain Bousquet-Mélou, Aude A Ferran, Elodie A Lallemand","doi":"10.1128/spectrum.01205-25","DOIUrl":"https://doi.org/10.1128/spectrum.01205-25","url":null,"abstract":"<p><p><i>Rhodococcus equi</i> is an opportunistic intracellular pathogen responsible for severe respiratory infections in foals, requiring prolonged antibiotic treatment. Despite its <i>in vitro</i> susceptibility to multiple antibiotics, the <i>in vivo</i> eradication of intracellular <i>R. equi</i> remains challenging due to its ability to persist and survive within alveolar macrophages. This study aimed to assess <i>in vitro</i> the extracellular and intracellular activity of rifampicin, doxycycline, and four macrolides against <i>R. equi</i> while assessing current methodologies used to differentiate intracellular and extracellular bacteria. We found that the removal of extracellular <i>R. equi</i> with short times of exposure to bactericidal drugs was challenging. We thus proposed an alternative approach with washing steps to assess intracellular antibiotic activity by combining bacterial counts and optical microscopy. Our results indicated that clarithromycin alone, as well as azithromycin or gamithromycin in combination with doxycycline, dramatically reduced both intracellular and extracellular <i>R. equi</i>. This study also highlighted the need for refined <i>in vitro</i> methodologies to assess antibiotic efficacy against <i>R. equi,</i> ultimately contributing to the development of optimized treatment strategies for <i>R. equi</i> infections in foals.</p><p><strong>Importance: </strong><i>Rhodococcus equi</i> is a major cause of pneumonia in foals and represents a serious challenge for the equine sector due to the need for prolonged and sometimes ineffective antibiotic treatments. This study highlights the limitations of current <i>in vitro</i> methods used to evaluate antibiotic activity against <i>R. equi</i>, by demonstrating that widely used bactericidal antibiotics like gentamicin may not eliminate extracellular bacteria as effectively as previously assumed, and we emphasize the risk of overestimating intracellular bacterial survival in experimental models. We therefore propose a new method that allows more accurate assessment of antibiotic efficacy within host cells. Our findings help refine <i>in vitro</i> testing strategies and support the identification of antibiotic combinations with effective intracellular activity, offering new perspectives for improving treatment protocols against <i>R. equi</i> infections in foals.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0120525"},"PeriodicalIF":3.8,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732333","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":"Insights on pathoadaptation of sequential <i>Pseudomonas aeruginosa</i> isolates to the urinary tract.","authors":"Caroline Martin-Duval, Sandrine Dahyot, Inès Coquisart, Benoit Bernay, Martine Pestel-Caron, Jean-Christophe Giard","doi":"10.1128/spectrum.00456-25","DOIUrl":"https://doi.org/10.1128/spectrum.00456-25","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is an opportunistic pathogen responsible for 10% of nosocomial urinary tract infections (UTIs). Its large genome and adaptability enable it to cause a wide variety of infections, from respiratory disorders in cystic fibrosis patients to recurrent UTIs. While genomic and phenotypic adaptations of <i>P. aeruginosa</i> have been well-studied in respiratory infections, few studies have investigated pathoadaptation in recurrent UTIs. Here, we investigated the impact of genomic alterations of sequential urinary isolates collected from three patients on phenotypic responses to environmental stresses, virulence, and motility. In addition, to gain insight on adaptive mechanisms of <i>P. aeruginosa</i> in urine, proteomic analyses were conducted using pooled human urine compared to a standard Trypticase Soy (TS) medium. Late isolates showed significantly impaired growth and reduced responses to acid and osmotic stresses compared to early isolates, although responses to oxidative stress remained unchanged. Furthermore, the late isolates were significantly less virulent in the <i>Galleria mellonella</i> infection model. Finally, proteomic analyses revealed the accumulation of proteins associated with flagellum and chemotaxis only in early isolates of two out of three patients, regardless of the culture medium. Motility assays confirmed these results, with late isolates being less motile than early ones. Moreover, siderophore-related proteins were significantly less abundant in late isolates when cultured in human urine, a result not observed in TS medium, suggesting a convergent adaptation trajectory in urine. Our results provide an initial insight into the adaptive mechanisms of <i>P. aeruginosa</i> in the urinary tract.IMPORTANCE<i>P. aeruginosa</i> is the third most common pathogen causing healthcare-associated UTIs. Its ability to form biofilms and develop antibiotic resistance often leads to relapses. Here, we investigated the phenotypic characteristics of longitudinal urinary isolates under specific stress conditions and used an <i>in vivo</i> model to evaluate the virulence of these isolates. Integrating proteomic analysis into this approach allowed us to identify the metabolic and regulatory pathways involved in bacterial adaptation and to establish innovative correlations between genomic, phenotypic, and proteomic data. Altogether, these data enabled us to map the adaptation mechanisms of <i>P. aeruginosa</i> in the urinary environment. These findings provide putative new therapeutic targets and contribute to our understanding of recurrent UTIs caused by this pathogen.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0045625"},"PeriodicalIF":3.8,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732331","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":"A tool of the trade for a newly identified filovirus: pseudovirus-based system for Dehong virus entry and neutralization.","authors":"Banhi Biswas","doi":"10.1128/spectrum.01035-25","DOIUrl":"https://doi.org/10.1128/spectrum.01035-25","url":null,"abstract":"<p><p>Pseudovirus-based assays are efficient and accessible platforms for measuring neutralizing antibody titers and screening antiviral drugs against enveloped viruses. They typically employ two types of packaging systems, retroviral-based or vesicular stomatitis virus (VSV)-based systems. These systems have been validated for several high-risk pathogens, including Ebola, Marburg, Dengue and, more recently, SARS-CoV-2, as they offer a safe alternative for studying high-containment viruses. In a recent study (Wu X, Liu F, Li T, Li D, Shen Y, Zhang X, Liu S, Jiang Q, Zhao C, Nie J, Wang Y, Feng B, Liu W, Huang W, Microbiol Spectr, 13:e01557-24, 2025, https://doi.org/10.1128/spectrum.01557-24), Wu and colleagues developed a pseudovirus system and optimized it for neutralization assays targeting the newly identified Dehong virus (DEHV). The authors also utilized this system to detect bioluminescent signals in mouse models. Importantly, using this pseudovirus platform, they confirmed that Niemann-Pick C1 (NPC1) functions as the entry receptor for DEHV, consistent with prior findings using infectious viruses. This work provides valuable insights into the limited understanding of DEHV biology.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0103525"},"PeriodicalIF":3.8,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732326","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":"O-GlcNAcylation at S659 enhances SARS-CoV-2 spike protein stability and pseudoparticle packaging efficiency.","authors":"Ting Xu, Jie Li, Xiaoxuan Lu, Shuai Song, Shengnan Wang, Jing Li, Leiliang Zhang","doi":"10.1128/spectrum.00527-25","DOIUrl":"https://doi.org/10.1128/spectrum.00527-25","url":null,"abstract":"<p><p>The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in viral entry and pathogenesis, making it an important target for therapeutic strategies. In this study, we explore the interaction between the S protein and O-GlcNAc transferase (OGT), revealing a physical association between these proteins using immunoprecipitation and glutathione-S-transferase (GST)-pulldown assays. Our results demonstrate that Serine 659 (S659) is the primary site of O-GlcNAcylation on the S protein, as confirmed by ion mobility mass spectrometry and mutagenesis studies. Notably, the S659A mutation significantly reduces O-GlcNAcylation of the S protein, leading to increased ubiquitination and subsequent degradation of the S protein. Cycloheximide pulse-chase assays further corroborate that the wild-type S protein exhibits greater stability compared with the S659A mutant of S. Despite these stability changes, the S659A mutation does not impair the binding affinity of the S protein to its receptor ACE2. However, we find that the S659A mutation significantly decreases the packaging efficiency of SARS-CoV-2 pseudoparticles. Collectively, our findings highlight the critical role of O-GlcNAcylation at S659 in regulating S protein stability and viral particle assembly, underscoring its potential as a target for therapeutic intervention against SARS-CoV-2.</p><p><strong>Importance: </strong>This study highlights the critical role of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the viral infection process and its potential as a target for therapies and vaccines. By identifying Serine 659 (S659) as a key site for O-GlcNAcylation, the research reveals how modifications at this residue can influence the protein's interactions with host factors, thereby affecting viral replication and pathogenicity. Furthermore, the S659A mutation was shown to lead to a significant increase in ubiquitination and degradation of the S protein, indicating that O-GlcNAcylation is crucial for modulating the protein's stability and, consequently, its efficiency in facilitating viral entry. Understanding these mechanisms is vital for the development of effective interventions against coronavirus disease 2019 (COVID-19). Overall, this research enhances our understanding of how post-translational modifications impact viral behavior, opening avenues for innovative strategies to combat SARS-CoV-2 and future viral threats.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0052725"},"PeriodicalIF":3.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732332","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":"Impact of fluoride varnish and oral health education on caries increment and dental plaque microbiota among children with early mixed dentition: a three-armed 24-month randomized controlled trial.","authors":"Xinyi Zeng, Hai Ming Wong, Qing Zhou, Juan Liu, Ni Zhou","doi":"10.1128/spectrum.00902-25","DOIUrl":"https://doi.org/10.1128/spectrum.00902-25","url":null,"abstract":"<p><p>Dental caries is the most prevalent oral disease globally. A 24-month randomized controlled trial was conducted among 236 children aged between 7 and 8 years (ChiCTR2400084030). They were randomly allocated into three groups and received the following biannual interventions: Group 1: topical fluoride varnish (TFV) using 5% sodium fluoride; Group 2: oral health education (OHE); and Group 3: TFV + OHE. The interventions lasted for 12 months, and a final examination was conducted after 24 months to assess whether the desired effects sustained after the cessation of interventions. After 12-month interventions, when demographic and socioeconomic factors were adjusted, children in Group 1 were more likely to have new caries on their permanent first molars when compared to Group 2 (odds ratio [OR] = 2.86, 95% confidence interval [CI] 1.33, 6.14) or Group 3 (OR = 2.28, 95% CI 1.09, 4.78). There was no significant difference in Shannon diversity index across the three groups. Among the top 10 most abundant genera, <i>Capnocytophaga</i>, <i>Saccaribactetia_(TM7)_[G-1]</i>, <i>Selenomonas</i>, and <i>Porphyromonas</i> differed across the three groups after interventions. The 12-month assessment revealed a lower abundance of <i>Capnocytophaga granulosa</i> among children who did not receive TFV. Although the interventions might have the potential to alter the composition of supragingival dental plaque, the specific mechanisms and clinical significance require further investigation.IMPORTANCEEarly mixed dentition is a critical transition period for children. During this phase, newly erupted permanent first molars (PFMs) with deep fissures are vulnerable to tooth decay. Considering increased independence in diet choices and inconsistent toothbrushing practices among these children, structured oral health education (OHE) is recommended to safeguard their oral health status. The main findings of this 24-month randomized controlled trial revealed that fluoride varnish alone is insufficient to prevent caries on PFMs, underscoring the necessity of reinforcing OHE for this age group. Additionally, dynamic shifts in supragingival plaque composition were observed, including <i>Capnocytophaga</i>, <i>Saccaribactetia_(TM7)_[G-1]</i>, <i>Selenomonas</i>, and <i>Porphyromonas</i>. Notably, <i>Capnocytophaga granulosa</i>, a species previously found among adults with periodontal diseases, was less abundant in children who did not receive fluoride varnish. While these findings highlight the impact of oral health promotion activities on alterations of oral microbiota, further research is needed to clarify the clinical implications of these microbial changes.CLINICAL TRIALSThe study was registered with the Chinese Clinical Trial Registry (ChiCTR2400084030).</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0090225"},"PeriodicalIF":3.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732330","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":"Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.","authors":"Robert Keskey, Stijn Bluiminck, Naseer Sangwan, Rebecca Meltzer, Adam Lam, Renee Thewissen, Alexander Zaborin, Harry van Goor, Olga Zaborina, John Alverdy","doi":"10.1128/spectrum.02766-24","DOIUrl":"https://doi.org/10.1128/spectrum.02766-24","url":null,"abstract":"<p><p>Approximately half of surgical site infections are caused by pathogens resistant to the antibiotics used for prophylaxis. We recently demonstrated that when mice are fed a western diet (WD) that is high in fat and low in fiber, exposed to antibiotics, and undergo an otherwise recoverable surgery, they develop lethal sepsis associated with dissemination of multi-drug-resistant pathogens. Here, we hypothesized that a WD alone can drive the intestinal microbiome to become populated by antibiotic-resistant bacteria independent of exposure to antibiotics. The cecal microbiota response to antibiotics was determined utilizing Biolog Phenotype Microarrays in the presence of 48 different antibiotics. WD-fed mice had a significant increase in antibiotic resistance within their microbiome compared to mice on a standard low-fat, high-fiber diet (SD) including aminoglycosides, tetracyclines, cephalosporins, fluoroquinolones, and sulfamethoxazole. By metagenomic sequencing, there was an increase in the antibiotic resistance genes (ARGs) within the WD cecal microbiota, including <i>CfxA2</i>, <i>ErmG</i>, <i>TetQ</i>, and <i>LnuC</i>. After just 7 days of WD, the ARGs <i>ErmG</i> and <i>CfxA2</i> were detectable within the stool. WD independent of antibiotic exposure increases the presence of ARGs within the gut microbiota independent of antibiotic exposure.IMPORTANCEAntibiotic resistance is a major challenge in healthcare and results in significant morbidity and mortality. Currently, half of surgical site infections are caused by pathogens resistant to antibiotics used for prophylaxis. In this study, we demonstrate that a western diet alone has the ability to increase the presence of antibiotic resistance genes within the gut microbiome. By understanding dietary influences on the gut resistome, we may improve our understanding of infections with antibiotic-resistant organisms and one day develop personalized antibiotic regimens based on an individual's gut resistome.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0276624"},"PeriodicalIF":3.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732329","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":"A study on the transcriptional characteristics of novel HERV gene in the blood of children with Kawasaki disease and its correlation with the disease.","authors":"Yan Lu, Minli Yuan, Juan Xu, Mengxu Yi, Xingyu Mo, Ying Zhu, Shanjie Wei, Peiting Yang, Chenglin Zhou, Wen Zhang, Hongyan Lu","doi":"10.1128/spectrum.00189-25","DOIUrl":"https://doi.org/10.1128/spectrum.00189-25","url":null,"abstract":"<p><p>Human endogenous retroviruses (HERVs), integral to the human genome, are implicated in autoimmune diseases through superantigen-mediated vascular inflammation. This study examined NCBI next-generation sequencing blood transcriptome data from 62 pairs of children with acute Kawasaki disease (KD) and healthy controls. Bioinformatics analysis identified differentially expressed HERV gene sequences (|Log₂FC| > 0.58, FDR < 0.05), revealing 825 and 5,751 distinct HERV transcriptional variations across two KD data sets (PRJNA271099 and PRJNA739210). Novel HERVs were defined by amino acid sequence similarity of <90%. HERV-K-2177 and HERV-K-3157 demonstrated 70.27% and 56.06% protein-level similarity to known HERVs, respectively. Validation with real-time fluorescence quantitative PCR on blood samples from 18 patients with KD and 10 healthy controls showed significantly elevated expression of HERV-K-2177 and HERV-K18 mRNA in patients with KD (<i>P</i> < 0.05). Phylogenetic analysis placed HERV-K-2177 and HERV-K-3157 within the HERV-K family, though at the peripheral cluster, indicating their potential as novel HERV species. These results suggest a possible association between HERV-K-2177 transcriptional expression and KD.IMPORTANCEHuman endogenous retroviruses (HERVs) are intricate retroviruses passed down through the human genome. This study identified two novel HERVs in the blood transcriptome of children with Kawasaki disease and conducted preliminary experiments to explore the correlation between HERVs and the disease. Phylogenetic analysis indicates that these viruses may represent potential new HERV species. These findings suggest a potential association between HERV transcript expression and Kawasaki disease.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0018925"},"PeriodicalIF":3.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732273","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":"Bidirectional regulation of the brain-gut axis in <i>Macaca mulatta</i>: implications for wildlife conservation and experimentation.","authors":"Zewen Sun, Jun Wang, Ruiping Sun, Baozhen Liu, Keqi Cai, Xinyuan Zhao, Yanfang Wang, Jianguo Zhao, Jingli Yuan","doi":"10.1128/spectrum.01338-25","DOIUrl":"https://doi.org/10.1128/spectrum.01338-25","url":null,"abstract":"<p><p>Although existing research has uncovered the association between psychological stress and gut microbiota dysbiosis, the causal relationship remains unclear. The direct impact of psychological stress on gut microbiota and the potential bidirectional mechanisms remain unclear, including the specific molecular pathways involved. This study investigates the impact of psychological stress on the gut microbiota and associated metabolites in wild Hainan macaques, revealing that stress significantly alters microbial composition and function. Specifically, stress-induced changes in the gut microbiota are linked to shifts in key metabolites, particularly coumarins, which are known to interact with the nervous system. This suggests a feedback loop where stress modulates neurological function via microbiota-derived metabolites. We identified several differential metabolites, including specific C10757, that can serve as biomarkers for detecting stress-induced health risks. These findings highlight the potential of microbiota-based interventions to mitigate stress-related health issues and provide essential data for wildlife health monitoring. The study highlights the role of gut microbiota as a stress biomarker, underscoring the importance of psychological well-being in wildlife conservation and research to guide ethical animal management.</p><p><strong>Importance: </strong>This study uncovers how psychological stress alters gut microbiota in wild animals, enhancing understanding of the gut-brain axis in natural ecosystems. Crucially, it identifies microbial profiles as non-invasive stress biomarkers, enabling early detection of environmental threats in conservation. The findings emphasize the ethical need to incorporate stress assessments (e.g., microbiota and cortisol analyses) into wildlife research to ensure welfare and data validity. Mechanistic parallels with captive species suggest evolutionary conservation of gut-brain pathways, opening avenues for cross-species therapies. By bridging psychobiology and conservation, this work establishes a framework for stress resilience interventions and ethical wildlife management, advancing both ecological health and humane science. Future research should explore microbiota-targeted strategies and cross-species applicability to optimize conservation outcomes.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0133825"},"PeriodicalIF":3.8,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732327","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":"QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.","authors":"Armando G Licata, Marica Zoppi, Chiara Dossena, Federico Rossignoli, Davide Rizzo, Manuela Marra, Giorgio Gargari, Giacomo Mantegazza, Simone Guglielmetti, Luca Bergamaschi, Olga Nigro, Stefano Chiaravalli, Maura Massimino, Loris De Cecco","doi":"10.1128/spectrum.01673-25","DOIUrl":"https://doi.org/10.1128/spectrum.01673-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (&lt;i&gt;R&lt;/i&gt; = 0.99, &lt;i&gt;P&lt;/i&gt; &lt; 0.0001). These findings were further validated using fecal samples. Application of the pipeline to pediatric samples revealed distinct, differentially abundant &lt;i&gt;Bifidobacterium bifidum&lt;/i&gt; and &lt;i&gt;Bifidobacterium adolescentis&lt;/i&gt; variants in children whose microbiota closely resembled that of their caregivers. Overall, this study presents a validated, open-source QIIME2 and R pipeline for multi-amplicon sequencing, providing a standardized and reproducible framework for 16S rRNA gene profiling in clinical and research contexts.IMPORTANCEMulti-amplicon sequencing comprehensively characterizes microbial communities by targeting multiple regions of the 16S rRNA gene. However, analytical workflows and reference databases provided by commercial library preparation kits frequently rely on proprietary primers and closed-source pipelines, which can limit transparency, reproducibility, and adaptability. To address these limitations, we developed and validated an open-source bioinformatics pipeline utilizing QIIME2 and R. Our pipeline integrates data from all targeted 16S regions, generating microbial profiles comparable to those produced by proprietary software. Validation was performed using mock samples and fecal samples collected from pediatric cancer patients and their caregivers, confirming the pipeline's reliability and broad applicability. Furthermore, our pipeline enables detailed analysis of microbial variants, surpassing traditional genus-level restrictions and fully leveraging the enhanced coverage offered by multi-amplicon sequencing. Our findings highlight the necessity of adopting open-source solutions to ensure scientific r","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0167325"},"PeriodicalIF":3.7,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708162","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}