Frontiers in Microbiology最新文献

{"title":"Galacto-oligosaccharides alleviate experimental lactose intolerance associated with gut microbiota in mice.","authors":"Qianxi Li, Xinlei Wang, Siyu Guo, Tongtong Wang, Heng Cao, Yunhe Cao, Bing Dong","doi":"10.3389/fmicb.2025.1530156","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1530156","url":null,"abstract":"<p><strong>Introduction: </strong>Galacto-oligosaccharides (GOS) are beneficial for alleviating lactose intolerance (LI). GOS have the ability to modify the composition of the intestinal microbiota. The development of intestinal diseases could be influenced by the composition of the gut microbiota. Nevertheless, it remains unclear whether gut microbiota exerts an effect when GOS alleviate LI, whether alterations in composition of the intestinal microbiota influence inflammatory response and lactose digestion.</p><p><strong>Methods: </strong>We first investigated the effects of GOS on mice with established lactose intolerance. Next, we demonstrated that prophylactic supplementation with GOS also conferred similar benefits.</p><p><strong>Results: </strong>The results showed that GOS enhanced anti-inflammatory, antioxidant, and gut barrier function. We observed that GOS mediated a change in the gut microbiome by increasing the abundance of <i>Lactobacillus</i>. GOS pre-supplementation reduced incident LI, enhanced anti-inflammatory, antioxidant, and gut barrier function, and markedly altered the gut microbiome by significantly enriching <i>Bifidobacterium</i>. Collectively, the alleviation of LI by GOS suggests an intimate involvement of probiotics.</p><p><strong>Discussion: </strong>This study demonstrates that GOS ameliorated LI in a gut microbiota-dependent manner. Our findings provide novel evidence that GOS substitute for lactase and serve as a potential modulator of the gut microbiota for the prevention of LI.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1530156"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975899/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of dietary fiber on the composition, function, and symbiotic interactions of intestinal microbiota in pre-weaned calves.","authors":"Wentao Lu, Xia Yi, Yuhan Ge, Xinyue Zhang, Kaidi Shen, Haohua Zhuang, Zhaoju Deng, Dengke Liu, Jie Cao, Chong Ma","doi":"10.3389/fmicb.2025.1554484","DOIUrl":"https://doi.org/10.3389/fmicb.2025.1554484","url":null,"abstract":"<p><strong>Introduction: </strong>Dietary fiber plays a crucial role in maintaining gastrointestinal health. However, its protective effects on the intestinal health of calves remain to be fully elucidated. This study aimed to investigate the impact of dietary fiber supplementation on the intestinal microbiota of pre-weaned calves and its potential role in modulating microbial metabolic pathways.</p><p><strong>Methods: </strong>A randomized controlled trial was conducted, enrolling 135 calves that were randomly assigned into three groups: (1) inulin supplementation, (2) psyllium husk powder (PHP) supplementation, and (3) a control group receiving no dietary fiber. Fecal microbiota samples were collected from calves without diarrhea at five time points (0, 7, 14, 28, and 56 days of age). Metagenomic sequencing was performed to analyze microbial composition and functional pathways. Additionally, a differential analysis of carbohydrate-active enzymes (CAZymes) was performed to evaluate the effect of dietary fiber on carbohydrate metabolism enzyme activity within the intestinal microbiota.</p><p><strong>Results: </strong>Calves supplemented with dietary fiber exhibited a significant increase in the abundance of <i>Bifidobacterium</i> and <i>Prevotella</i> compared to the control group. These bacterial genera contributed to intestinal protection by modulating secondary bile acid metabolism and flavonoid metabolism pathways. CAZymes differential analysis revealed an increased abundance of carbohydrate metabolism enzymes in response to dietary fiber supplementation, with distinct microbial community compositions observed among different fiber treatments. Notably, at 56 days of age, calves fed PHP harbored intergeneric symbiotic clusters comprising <i>Clostridium, Prevotella</i>, and <i>Bacteroides</i>, suggesting a cooperative microbial network that may contribute to intestinal homeostasis.</p><p><strong>Discussion: </strong>The findings of this study highlight the beneficial effects of dietary fiber on calf intestinal microbiota, particularly in enhancing microbial diversity and enzymatic activity related to carbohydrate metabolism. The observed microbial symbiosis in PHP-fed calves suggests a potential role in maintaining intestinal homeostasis. These insights provide a theoretical foundation for optimizing dietary interventions to promote gut health in calves during the transition period. Further research is warranted to explore the mechanistic interactions between dietary fiber, gut microbiota, and host health outcomes.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1554484"},"PeriodicalIF":4.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of extended-spectrum <i>β</i>-lactamase producing bacteria in feces of shelter dogs as a biomarker for altered gut microbial taxa and functional profiles.","authors":"Reta Abdi, Srinka Datta, Akshaykumar Zawar, Pratap Kafle","doi":"10.3389/fmicb.2025.1556442","DOIUrl":"10.3389/fmicb.2025.1556442","url":null,"abstract":"<p><strong>Background: </strong>The USA is home to 83-88 million dogs, with 3-7 million living in shelters. Shelter dogs move through the supply chain from their geographical origin to adoptive homes, with possible exposure to pathogens and shift in their gut microbiota. However, research in this area is limited. This study examined the effects of intestinal colonization by ESBL bacteria on gut taxa abundance, diversity, and functions in 52 shelter dogs of various ages, sexes, and fertility statuses.</p><p><strong>Methodology: </strong>We isolated fecal DNA, sequenced their 16S, processed the sequences using DADA2, identified taxa profiles in each dog by Phyloseq, and analyzed Chao1, Shannon, and Simpson alpha diversity by ggplot2 and Wilcoxon test. We analyzed beta diversity using Bray-Curtis dissimilarity matrix from the vegan package. Differential abundance of taxa, gut microbiome functions, and differential abundance of microbiome functions were analyzed using DESeq2, PICRUSt2, and ALDEx2, respectively, with Wilcoxon rank and Kruskal-Wallis tests for comparisons between dog groups.</p><p><strong>Results: </strong>Firmicutes (69.3%), Bacteroidota (13.5%), Actinobacteriota (6.77%), Proteobacteria (5.54%), and Fusobacteriota (4.75%) were the major phyla in the gut of shelter dogs. ESBL bacteria colonized dogs had reduced gut microbiota alpha diversity than non-colonized dogs. The abundance levels of the following phyla (Proteobacteria, Deferribacterota, Bacteroidota, Fusobacteriota, and Spirochaetota), class (Gammaproteobacteria, Bacteroidia, Deferribacteres, Brachyspirae, and Fusobacteria), and families (<i>Enterobacteriaceae</i>, <i>Peptostreptococcaceae</i>, <i>Lactobacillaceae</i>, <i>Lachnospiraceae</i>, <i>Prevotellaceae</i>, and <i>Peptostreptococcaceae</i>) were significantly (<i>p</i> < 0.05) varied between the two dog groups. Further stratified analysis by age, sex, and spaying/neutering status influenced the abundance of taxa in ESBL bacteria colonized dogs, indicating these covariates act as effect modifiers. Most gut metabolic and biosynthetic pathways were downregulated in ESBL bacteria colonized dogs compared to non-colonized dogs. However, alpha-linolenic acid metabolism and shigellosis, fluorobenzoate degradation, allantoin degradation, toluene degradation, glycol degradation, fatty acid and beta-oxidation, and glyoxylate metabolism bypass pathways were increased in dogs colonized by ESBL bacteria.</p><p><strong>Conclusion: </strong>Colonization by ESBL bacteria marks altered gut microbiota. Dog's demography and fertility status modify the alterations, indicating host factors and ESBL bacteria interplay to shape gut microbiota. ESBL bacteria or other factors reprogram gut microbiome functions through down and upregulating multiple metabolic and biosynthesis pathways to promote ESBL bacteria colonization.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1556442"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of the TLR9 signaling pathway on acyclovir infection with herpes simplex virus type 2 in HaCaT cells.","authors":"Jialing Shi, Lin Kuang, Li Qi, Ruoyu Li, Yangfan Wu","doi":"10.3389/fmicb.2025.1560340","DOIUrl":"10.3389/fmicb.2025.1560340","url":null,"abstract":"<p><strong>Introduction: </strong>The objective of this study was to investigate the effect of acyclovir (ACV) on the TLR9 signaling pathway after human immortalized epidermal (HaCaT) cell infection with herpes simplex virus type 2 (HSV-2).</p><p><strong>Methods: </strong>In this study, an <i>in vitro</i> cell model of HSV-2 infection was successfully constructed by infecting HaCaT with HSV-2 virus. In order to explore the antiviral mechanism of acyclovir (ACV), high-throughput transcriptome sequencing (RNA-seq) was used to analyze the genome-wide expression profiling of infected cells before and after ACV treatment, and to systematically compare the change characteristics of differentially expressed genes (DEGs). Based on the sequencing results, the study further focused on Toll-like receptor (TLR) 9 signaling, using quantitative real-time reverse transcriptase chain reaction (qRT-PCR) to quantitatively detect the effect of ACV intervention on the mRNA expression level of key molecules of TLR 9 signaling pathway in HSV-2 infected HaCaT cells.</p><p><strong>Results: </strong>A total of 896 significant changes in gene expression were identified by the transcriptome analysis, including 314 upregulated genes and 582 downregulated genes. GO enrichment analysis showed that the differentially expressed genes were mainly related to CC includes the ubiquitin ligase complex, mitochondrial protein-containing complex, DNA-binding transcription activator activity, exonuclease activity, catabolic process, nuclear-transcribed mRNA catabolic process nuclear-transcribed mRNA catabolic process; KEGG enrichment analysis showed that the differentially expressed genes were mainly related to Toll-like receptor signaling pathway, herpes simplex virus 1 infection, and TNF signaling pathway. The RT-PCR results were confirmed to be basically consistent with the sequencing results.</p><p><strong>Conclusion: </strong>ACV altered the transcriptome level of HSV-2 infection in HaCaT cells. The RT-PCR results confirmed that ACV intervened in HSV-2 infection through the TLR9 signaling pathway.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1560340"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Surface display of Lys0859, a <i>Streptococcus suis</i> prophage lysin, on <i>Bacillus subtilis</i> spores and its antibacterial activity against <i>Streptococcus suis</i>.","authors":"Linkang Wang, Xiaochao Duan, Mengyuan Zhu, Haiyan Wang, Xinxin Li, Dayue Hu, Xiangmin Li, Ping Qian","doi":"10.3389/fmicb.2025.1519935","DOIUrl":"10.3389/fmicb.2025.1519935","url":null,"abstract":"<p><strong>Introduction: </strong><i>Streptococcus suis</i>, an important zoonotic and opportunistic pathogen in pigs, brings huge economic losses to the pig-raising industry and infects humans with diseases. Phage lysin is regarded as a promising substitute for antibiotics due to its ability to quickly and efficiently kill bacteria without easily developing resistance. However, their clinical applications have been hindered by inherent instability under environmental stressors.</p><p><strong>Methods: </strong>We constructed <i>B. subtilis</i> spores displaying bacteriophage lysin Lys0859 using spore coat protein CotG as an anchoring motif. Environmental tolerance was evaluated through thermal (37-95°C), pH (1.0-8.0), and enzymatic challenges, while antibacterial efficacy against <i>S. suis</i> was assessed using agar diffusion assays and murine infection models with systemic bacterial load quantification.</p><p><strong>Results: </strong>The spore-display system enhanced environmental resistance of Lys0859 while preserving its bactericidal efficacy. In vitro assays demonstrated 1 × 10⁶ CFU rBS^CotG-0859 spores exhibited equivalent bactericidal activity to 39.11 μg free Lys0859 against <i>S. suis</i>. <i>In vivo</i>, spore treatment reduced <i>S. suis</i> SC19 colonization by 0.47-1.96 log units (<i>p</i> < 0.05) across all tissues compared with PBS controls.</p><p><strong>Discussion: </strong>This study achieved functional display of prophage lysin Lys0859 on <i>B. subtilis</i> spores through CotG anchoring, demonstrating potent <i>in vitro</i> anti-streptococcal activity. Crucially, this strategy streamlined bioproduction by eliminating purification demands and lowering costs, lays the foundation for the clinical application of prophage lysin.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1519935"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of the canine gut microbiota of a military dog birth cohort.","authors":"Jae-Uk An, Seung-Hyun Mun, Woo-Hyun Kim, Je Kyung Seong, Kyoungwan Park, Seongbeom Cho","doi":"10.3389/fmicb.2025.1481567","DOIUrl":"10.3389/fmicb.2025.1481567","url":null,"abstract":"<p><strong>Introduction: </strong>We systematically tracked early life stages in a military dog birth cohort to investigate canine gut microbiota dynamics related to environmental exposure during growth. This study utilized 16s rRNA amplicon sequencing-based analysis with molecular epidemiology of <i>Enterococcus faecalis</i> within a controlled environment at a military dog training center.</p><p><strong>Methods: </strong>We examined shifts in gut microbiota diversity and taxonomic composition across four growth stages (lactation, weaning, starter, puppy) in three littermate groups. Additionally, <i>E. faecalis</i> dynamics was analyzed to confirm strain sharing among littermate groups.</p><p><strong>Results: </strong>Gut microbiota changed rapidly during early growth, stabilizing at the puppy stage. This is supported by increased similarity in taxonomic composition among littermate groups, as they experienced an increased shared external environment and consumed the identical diets. <i>E. faecalis</i> strain sharing among littermate groups increased as dogs aged. Nine <i>E. faecalis</i> cluster types were identified; three specific types (type I, II, and IX) dominated in each littermate group during lactation. With greater exposure to the shared external environment, cluster type I gradually assumed dominance across all groups. Despite the dynamic shifts in microbiota, we found five genera within the core microbiota, <i>Bacteroides</i>, <i>Peptoclostridium</i>, <i>Fusobacterium</i>, <i>Lactobacillus</i>, and <i>Blautia</i>.</p><p><strong>Discussion: </strong>This study is the first to explore the dynamic nature of early-life canine gut microbiota, illustrating its transition to stability and its resilience to environmental perturbations within the controlled training environment of a military dog birth cohort.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1481567"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The single-cell transcriptional landscape of lung cells from PCV2d-infected mice.","authors":"Yunlong Chen, Gang Fan, Bin Yang, Xinyi Fan, Haiyan Chen, Zhuoyuan Ma, Jiao Lou, Jingmei Xu, Yan Wang, Shiqiang Zhang","doi":"10.3389/fmicb.2025.1554961","DOIUrl":"10.3389/fmicb.2025.1554961","url":null,"abstract":"<p><strong>Introduction: </strong>Porcine Circovirus (PCV2) infection is prevalent in pig farming and causes significant economic losses. In recent years, the PCV2d subtype has become the most prevalent genotype worldwide, exhibiting higher virulence, leading to more severe viremia and organ damage. Therefore, studying the biological characteristics of the PCV2d subtype is of great significance.</p><p><strong>Methods: </strong>We established a PCV2d infection model using BALB/c mice and employed single-cell RNA sequencing (scRNA-seq) to systematically analyze the transcriptome of 10 cell types in the lung tissues of infected mice. We developed a comprehensive marker gene catalog for these cell types.</p><p><strong>Results: </strong>Compared to uninfected mice, PCV2d infection induced extensive viral replication and immunosuppressive responses in most cell types. Monocyte macrophages with high levels of viral replication, pro-inflammatory cytokines, and various cell population interactions occurring through CD40-CD40L and CXCL14-CXCR4 were identified. These cells predominantly mediate antigen presentation and processing pathways <i>in vivo</i>, contributing to PCV2d-driven inflammatory lung injury.</p><p><strong>Discussion: </strong>Our data uncovered a complex unique immune response scenario in the lung tissue of mice after PCV2d infection, deciphering the potential mechanisms underlying PCV2d-driven inflammatory responses in mice. Furthermore, this study provides a rich database for the molecular basis of different cell types' responses to PCV2d infection.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1554961"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The LAMP-CRISPR-Cas13a technique for detecting the CBASS mechanism of phage resistance in bacteria.","authors":"Concha Ortiz-Cartagena, Patricia Fernández-Grela, Lucia Armán, Lucía Blasco, Daniel Pablo-Marcos, Inés Bleriot, Laura Fernández-García, Clara Ibarguren-Quiles, Felipe Fernández-Cuenca, Antonio Barrio-Pujante, Belén Aracil, Jorge Calvo-Montes, María Tomás","doi":"10.3389/fmicb.2025.1550534","DOIUrl":"10.3389/fmicb.2025.1550534","url":null,"abstract":"<p><strong>Introduction: </strong>Antimicrobial resistance (AMR) is a major public health threat, driving the need for alternative treatments such as phage therapy. However, bacterial defense mechanisms, often regulated by the quorum sensing (QS) network and encoded in genomic islands (GIs), can generate phage-resistant mutants. Understanding these resistance mechanisms is essential for optimizing phage therapy.</p><p><strong>Methods: </strong>This study analyzed 48 <i>Klebsiella pneumoniae</i> strains to identify pathogenicity islands (PAIs) containing anti-phage defense (APD) proteins. We constructed a knockout strain lacking the cyclase gene from the type II CBASS defense systems present in PAIs to investigate QS regulation and its role in cell viability. The LAMP-CRISPR-Cas13a technique was used to confirm gene knockout and to detect the main cyclase in type I CBASS systems, i.e., APECO1.</p><p><strong>Results: </strong>A total of 309 pathogenicity islands (PAIs), containing 22.1% of anti-phage defense (APD) proteins, were identified. Type I and II CBASS APD systems were also detected in the genome of the 48, <i>K. pneumoniae</i> strains, and only two type II CBASS systems were located in PAIs. Alluding to these defense mechanisms, the QS revealed to be involved in the regulation of the type II CBASS systems contained in PAIs. Finally, the LAMP-CRISPR-Cas13a technology successfully detected the main cyclases habored in type I and II CBASS systems, respectively.</p><p><strong>Discussion: </strong>The study findings highlight the regulatory role of the QS network in APD systems. Notably, this is the first study to develop an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 h), thereby helping to optimize phage therapy by detecting bacterial resistance mechanisms and predicting the potential inefficacy of therapeutic phages and thus improving patient prognosis.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1550534"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies.","authors":"Stefanie Wagner, Michael Weber, Lena-Sophie Paul, Angelika Grümpel-Schlüter, Jeannette Kluess, Klaus Neuhaus, Thilo M Fuchs","doi":"10.3389/fmicb.2025.1481197","DOIUrl":"10.3389/fmicb.2025.1481197","url":null,"abstract":"<p><strong>Background: </strong>The intestinal microbiota contributes to the colonization resistance of the gut towards bacterial pathogens. Antibiotic treatment often negatively affects the microbiome composition, rendering the host more susceptible for infections. However, a correct interpretation of such a perturbation requires quantitative microbiome profiling to reflect accurately the direction and magnitude of compositional changes within a microbiota. Standard 16S rRNA gene amplicon sequencing of microbiota samples offers compositional data in relative, but not absolute abundancies, and the presence of multiple copies of 16S rRNA genes in bacterial genomes introduces bias into compositional data. We explored whether improved sequencing data analysis influences the significance of the effect exerted by antibiotics on the faecal microbiota of young pigs using two veterinary antibiotics. Calculation of absolute abundances, either by flow cytometry-based bacterial cell counts or by spike-in of synthetic 16S rRNA genes, was employed and 16S rRNA gene copy numbers (GCN) were corrected.</p><p><strong>Results: </strong>Cell number determination exhibited large interindividual variability in two pig studies, using either tylosin or tulathromycin. Following tylosin application, flow cytometry-based cell counting revealed decreased absolute abundances of five families and ten genera. These results were not detectable by standard 16S analysis based on relative abundances. Here, GCN correction additionally uncovered significant decreases of <i>Lactobacillus</i> and <i>Faecalibacterium</i>. In another experimental setting with tulathromycin treatment, bacterial abundance quantification by flow cytometry and by a spike-in method yielded similar results only on the phylum level. Even though the spike-in method identified the decrease of four genera, analysis by fluorescence-activated cell sorting (FACS) uncovered eight significantly reduced genera, such as <i>Prevotella</i> and <i>Paraprevotella</i> upon antibiotic treatment. In contrast, analysis of relative abundances only showed a decrease of <i>Faecalibacterium</i> and <i>Rikenellaceae</i> RC9 gut group and, thus, a much less detailed antibiotic effect.</p><p><strong>Conclusion: </strong>Flow cytometry is a laborious method, but identified a higher number of significant microbiome changes in comparison to common compositional data analysis and even revealed to be superior to a spike-in method. Calculation of absolute abundances and GCN correction are valuable methods that should be standards in microbiome analyses in veterinary as well as human medicine.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1481197"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Manno-oligosaccharides as a promising antimicrobial strategy: pathogen inhibition and synergistic effects with antibiotics.","authors":"Rachel E Asbury, Bradley A Saville","doi":"10.3389/fmicb.2025.1529081","DOIUrl":"10.3389/fmicb.2025.1529081","url":null,"abstract":"<p><p>Infections caused by pathogenic bacteria pose a significant health challenge to humans and animals, especially given the rising incidence of antimicrobial resistance. Addressing this challenge has resulted in initiatives seeking alternatives to traditional antibiotics. Manno-oligosaccharides (MOS) exhibit pathogen-binding properties, due to their ability to prevent bacterial adhesion to epithelial cells, such as those within the urinary tract and intestinal epithelium. This suggests that MOS could offer a promising alternative to antibiotics. In this study, we explore the ability of various <i>β</i>-MOS products to inhibit the growth of <i>Escherichia coli, Klebsiella pneumoniae, Listeria monocytogenes,</i> and <i>Streptococcus mutans</i>, in addition to their ability to render antibiotics more effective. Inhibition profiles were distinct for each bacterial strain and differed according to <i>β</i>-MOS structure. Antibiotics were significantly potentiated by MOS in some cases, such as ceftazidime against <i>K. pneumoniae</i>. This research shows the role of carbohydrate structure in the anti-bacterial properties of non-digestible oligosaccharides such as MOS and positions MOS as a promising strategy in the treatment of bacterial infections.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1529081"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}