Frontiers in Microbiology最新文献

{"title":"Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.","authors":"Hannes Decadt, Cristian Díaz-Muñoz, Louise Vermote, Inés Pradal, Luc De Vuyst, Stefan Weckx","doi":"10.3389/fmicb.2025.1543079","DOIUrl":"10.3389/fmicb.2025.1543079","url":null,"abstract":"<p><p>Metagenomic studies of the Gouda cheese microbiota and starter cultures are scarce. During the present study, short-read metagenomic sequencing (Illumina) was applied on 89 Gouda cheese and processed milk samples, which have been investigated before concerning their metabolite and taxonomic composition, the latter applying amplicon-based, high-throughput sequencing (HTS) of the full-length 16S rRNA gene. Selected samples were additionally investigated using long-read metagenomic sequencing (Oxford Nanopore Technologies, ONT). Whereas the species identified by amplicon-based HTS and metagenomic sequencing were identical, the relative abundances of the major species differed significantly. <i>Lactococcus cremoris</i> was more abundant in the metagenomics-based taxonomic analysis compared to the amplicon-based one, whereas the opposite was true for the non-starter lactic acid bacteria (NSLAB). This discrepancy was related to a higher fragmentation of the lactococcal DNA compared with the DNA of other species when applying ONT. Possibly, a higher fragmentation was linked with a higher percentage of dead or metabolically inactive cells, suggesting that full-length 16S rRNA gene amplicon-based HTS might give a more accurate view on active cells. Further, fungi were not abundantly present in the Gouda cheeses examined, whereas about 2% of the metagenomic sequence reads was related to phages, with higher relative abundances in the cheese rinds and long-ripened cheeses. Intraspecies differences found by short-read metagenomic sequencing were in agreement with the amplicon sequence variants obtained previously, confirming the ability of full-length 16S rRNA gene amplicon-based HTS to reach a taxonomic assignment below species level. Metagenome-assembled genomes (MAGs) were retrieved for 15 species, among which the starter cultures <i>Lc. cremoris</i> and <i>Lactococcus lactis</i> and the NSLAB <i>Lacticaseibacillus paracasei</i>, <i>Loigolactobacillus rennini,</i> and <i>Tetragenococcus halophilus</i>, although obtaining MAGs from <i>Lc. cremoris</i> and <i>Lc. lactis</i> was more challenging because of a high intraspecies diversity and high similarity between these species. Long-read metagenomic sequencing could not improve the retrieval of lactococcal MAGs, but, overall, MAGs obtained by long-read metagenomic sequencing solely were superior compared with those obtained by short-read metagenomic sequencing solely, reaching a high-quality draft status of the genomes.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1543079"},"PeriodicalIF":4.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802666","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":"Identifying potential nutrient acquisition mechanisms for long-term survival: adaptive evolution of <i>Halomonas</i> isolated from subseafloor crustal fluids.","authors":"Hans Sebastian, Alberto Robador, Dawson Ray, Angus Angermeyer, Steven D'Hondt, Julie A Huber, Steven E Finkel","doi":"10.3389/fmicb.2025.1511421","DOIUrl":"10.3389/fmicb.2025.1511421","url":null,"abstract":"<p><p>In nature, microbes must often survive for long periods of time under conditions of nutrient and carbon limitation while also facing extremes in temperature, pressure, and competition with other microbes. One low-carbon, cold, and high pressure environment is the subseafloor crustal aquifer, where fluids circulate through old ocean crust. While microbial communities are known to be present in these fluids and contribute to biogeochemical cycling, the survival strategies of microbes in these communities is poorly constrained. In this study, multiple <i>Halomonas</i> strains were isolated from subseafloor crustal fluids of North Pond, a site located on the western flank of the Mid-Atlantic Ridge. These organisms are able to grow under laboratory conditions in minimal medium without the addition of carbon sources, as well as in rich nutrient conditions. We found that these <i>Halomonas</i> strains are highly related to each other in genomic content, but each strain has acquired unique mutations and/or undergone genomic rearrangements, suggesting that the strains were all derived from a single ancestral <i>Halomonas</i> progenitor. After serial passage of isolates from this <i>Halomonas</i> population under rich nutrient conditions in the laboratory, we identified mutants that can no longer scavenge scarce nutrients in minimal medium with no added carbon. Genomic analysis identified several genes that appear to be essential for survival under extremely low-nutrient condition, including several hypothetical proteins predicted to function as lipases, peptidases, or nutrient transporters. One of these genes was mutated in six out of the eight lineages studied, indicating that this hypothetical lipase protein is selected against during growth in rich medium, but may be required for growth under low-nutrient conditions. The application of an adaptive evolution platform selecting for survival and growth under one environmental condition that simultaneously selects against survival in different environments may prove to be a very useful tool for identifying genes and metabolic pathways in a wide variety of complex environments.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1511421"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795032","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":"Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers.","authors":"Betzabe Atencio, Stas Malavin, Maxim Rubin-Blum, Roi Ram, Eilon Adar, Zeev Ronen","doi":"10.3389/fmicb.2025.1533115","DOIUrl":"10.3389/fmicb.2025.1533115","url":null,"abstract":"<p><p>Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling. However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition. This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1533115"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795056","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":"A comprehensive analysis of <i>Ardisia crenata</i> Sims from endophytes and rhizosphere soil microorganisms.","authors":"Chang Liu, Jiangli Luo, Demei Yang, Xiongwei Liu, Sixuan Zhou, Ying Zhou","doi":"10.3389/fmicb.2025.1570230","DOIUrl":"10.3389/fmicb.2025.1570230","url":null,"abstract":"<p><strong>Introduction: </strong>Endophytic and rhizosphere microorganisms play crucial roles in influencing the quality and secondary metabolite accumulation of traditional Chinese medicinal.</p><p><strong>Methods: </strong>Endophytic and rhizosphere microorganisms play crucial roles in influencing the quality and secondary metabolite accumulation of traditional Chinese medicinal.</p><p><strong>Results and discussion: </strong>A total of 8,514,557 highquality reads were generated from 140 plant and soil sample in <i>A. crenata</i> Sims based on high-throughput sequencing. The fungal species composition within the endophytic and rhizosphere soil samples of <i>A. crenata</i> Sims is rich and varied, exhibiting notable disparities across different geographical regions of the plant. The alpha diversity and beta diversity indicated significant differences in microbial diversity and community structure between soil and plants. As for endophytic fungi, the dominant phyla in both plants and soil were Ascomycota and Basidiomycota, with different dominant genera between the two compartments. LEfSe analysis at the genus level identified 80 and 124 fungal indicator taxa associated with plants and soil, respectively, including <i>Aspergillus</i>, <i>Acremonium</i>, <i>Fusarium</i>, among others. Co-occurrence network analysis demonstrated intimate interactions among soil fungal microorganisms. Examination of soil physicochemical factors and the primary active constituent (bergenin) across different regions of <i>A. crenata</i> Sims indicated that the highest bergenin concentration is found in the Guangxi region, whereas the Guizhou region boasts relatively abundant soil nutrient components. Correlation analysis revealed that <i>Aspergillus</i>, <i>Fusarium</i>, <i>Penicillium</i>, <i>Tausonia</i>, and <i>Trichoderma</i> are correlated with soil physicochemistry or active compounds. These findings hint at a potential role for endophytic and rhizosphere microorganisms in the accumulation of active compounds within medicinal plants, thereby furnishing a scientific rationale for guiding the cultivation practices of <i>A. crenata</i> Sims.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1570230"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795070","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":"Response of foxtail millet yield, soil chemical property and bacterial community to different green manure-foxtail millet rotation models in North China.","authors":"Guohong Yu, Ya Han, Pengcheng Liu, Hongbo Hao, Mingzhe Li","doi":"10.3389/fmicb.2025.1558354","DOIUrl":"10.3389/fmicb.2025.1558354","url":null,"abstract":"<p><p>China is a largely agricultural country, while the drought climate in northern of China is more and more severe, which influences on the agriculture production seriously. The over-exploitation of groundwater is a critical issue in the low plains of Hebei Province. To address this challenge, the government has implemented winter fallow and rain-fed crop planting policies. In alignment with these policies and ensure the sustainable utilization and protection of cultivated land, this study conducted long-term field experiments using three green manure with foxtail millet rotation models at Shenzhou District experimental base, Hengshui City, Hebei Province. Thefoxtail millet yield, soil bacterial community characteristicsc, and soil physicochemical properties were analyzed to identify an optimal green planting model for promoting sustainable agricultural development. The results revealed that three green manure-foxtail millet rotation models significantly increased millet yield compared to millet-rallow rotation. The foxtail millet-Triticum secale rotation model achieved the highest yield increase, with a 12.47% average improvement in thousand-seed weight in 2021 and 2022 compared to millet-fallow rotation. This rotation model also led to the largest increase in available phosphorus content, which rose by 46.16 and 37.56% in 2021 and 2022, respectively. Furthermore, the diversity and richness of the soil rhizosphere bacterial community were highest under this model. Beneficial bacterial genera, including those in the Phyla Bacteroidetes and Proteobacteria, were more abundant, while the relative abundance of Acidobacteria was lowest. Correlation analysis showed that soil organic matter, available phosphorus, and millet yield were positively correlated with multiple genera of <i>Bacteroidetes</i> and <i>Proteobacteria</i> but negatively correlated with <i>Acidobacteria</i>. In conclusion, the foxtail millet-<i>Triticum secale</i> rotation model effectively improved the soil environment and supported stable, high millet yields. These findings provide a theoretical basis for advancing crop rotation strategies and offer technical support for sustainable agricultural development.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1558354"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795041","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":"Machine learning methods for predicting human-adaptive influenza A virus reassortment based on intersegment constraint.","authors":"Dan-Dan Zeng, Yu-Rong Cai, Sen Zhang, Fang Yan, Tao Jiang, Jing Li","doi":"10.3389/fmicb.2025.1546536","DOIUrl":"10.3389/fmicb.2025.1546536","url":null,"abstract":"<p><strong>Introduction: </strong>It is not clear about mechanisms underlining the inter-segment reassortment of Influenza A viruses (IAVs).We analyzed the viral nucleotide composition (NC) in coding sequences,examined the intersegment NC correlation, and predicted the IAV reassortment using machine learning (ML) approaches based on viral NC features.</p><p><strong>Methods: </strong>Unsupervised ML methods were used to examine the NC difference between human-adapted and zoonotic IAVs. Supervised ML models of random forest classifier (rfc) and multiple-layer preceptor (mlp) were developed to predict the human adaption to IAVs.</p><p><strong>Results: </strong>Our results demonstrated that the frequencies of thymine, cytosine, adenine,and guanine (t, c, a, and g), as well as the content of gc/at were consistently high or low for the segments of <i>PB2</i>, <i>PB1</i>, <i>PA</i>, <i>NP</i>, <i>M1</i>, and <i>NS1</i> (ribonucleoprotein plus [RNPplus]), between mammalian and avian IAVs or between influenza B viruses (IBVs) and IAVs.RNPplus NC negatively correlated with the NC for <i>HA</i>, <i>NA</i>, and <i>M1</i> (envelope protein plus [EPplus]). The human-adapted NC accurately discriminated between human IAVs and avian IAVs. A total of 221,184 simulated IAVs with pd09H1N1 EPplus and with RNPplus from other IAV subtypes indicated a high adaption of the RNPplus, from H6N6, H13N2, and H13N8 and other IAVs.</p><p><strong>Discussion: </strong>In summary, there is a distinct human adaption-specific genomic NC between human IAVs and avian IAVs. The intersegment NC correlation constrains segment reassortment. This study presents a novel strategy for predicting IAV reassortment based on viral genetic compatibility.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1546536"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795035","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":"FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals.","authors":"Ze Zhang, Yang Li, Di Zhang, Shuai Chen, Sien Lu, Kang Wang, Miao Zhou, Zehe Song, Qingcui Li, Jie Yin, Xiaoping Liu","doi":"10.3389/fmicb.2025.1557285","DOIUrl":"10.3389/fmicb.2025.1557285","url":null,"abstract":"<p><p>Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray-Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73,571 genes, 11,046 gut microbiota, and 4,540 metabolites. It provides an easy-to-use interface for browsing and searching the association information. Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1557285"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795094","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 relationship between pomegranate root collar rot and the diversity of fungal communities in its rhizosphere.","authors":"Ziqiang Wu, Jianxin Chen, Jie Chen, Yalin Yang, Aiting Zhou, Jianrong Wu","doi":"10.3389/fmicb.2025.1573724","DOIUrl":"10.3389/fmicb.2025.1573724","url":null,"abstract":"<p><strong>Introduction: </strong>The pomegranate (<i>Punica granatum</i>) is a significant economic tree species. In recent years, the root collar rot has severely affected pomegranates in the dry-hot valley regions of Yunnan Province, China. The rhizosphere microbiome plays a crucial role in plant growth, development, and disease resistance.</p><p><strong>Methods: </strong>This study utilized Illumina MiSeq sequencing to analyze the fungal communities in the roots and rhizosphere soils of healthy and diseased pomegranates, focusing on the impact of root collar rot disease on the diversity and structural composition of these communities.</p><p><strong>Results: </strong>The results indicated that in the unique fungal communities of healthy plant roots, the relative abundance of ectomycorrhizal and arbuscular mycorrhizal functional (AMF) groups was 53.77%, including genera such as <i>Glomus</i> and <i>Septoglomus</i>. After infection with root collar rot disease, the rhizosphere fungal communities became more monotonous, with increased differentiation within sample groups. Fungal groups associated with plant diseases and soil nutrient structures underwent significant changes. The disease altered the composition and functional group proportions of rhizosphere fungal communities, a process linked to soil nutrient structures. And the balance between plant-pathogen-related and saprotrophic functional groups in the rhizosphere was disrupted. Through Koch's postulates verification, the pathogen was identified as <i>Lauriomyces bellulus</i>.</p><p><strong>Discussion: </strong>This is the first report of collar rot of pomegranate caused by <i>L. bellulus</i> in China. Studying the differences in rhizosphere fungal community structures and quantities in response to new diseases aids in the rapid prediction of pathogens, effectively saving diagnostic time, and provides theoretical support for disease prediction, diagnosis, and control.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1573724"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795131","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":"A single nucleotide polymorphism produces different transcription profiles in <i>Campylobacter jejuni's cysM</i>.","authors":"Nereus W Gunther Iv, Siddhartha Kanrar, Aisha Abdul-Wakeel, Michael J McAnulty, John Renye, Joseph Uknalis, Gaylen A Uhlich","doi":"10.3389/fmicb.2025.1501331","DOIUrl":"10.3389/fmicb.2025.1501331","url":null,"abstract":"<p><p>A single nucleotide polymorphism (SNP) in the 126 bp untranslated region (UTR) directly upstream of <i>Campylobacter jejuni's cysM</i> (cysteine synthase) results in significant effects on gene transcription. UTR sequences, containing the predicted promoter region of <i>cysM</i>, from 264 different strains were compared, and revealed a SNP twenty nucleotides upstream of the <i>cysM</i> translation start site. In 219 strains the UTR sequence contained a guanine at this locus, and the remaining 45 strains had an adenine at the same position. Strains possessing the guanine SNP showed higher amounts of <i>cysM</i> transcripts compared to adenine SNP strains. When both UTR regions were cloned upstream of the major flagellar subunit (<i>flaA</i>) the guanine SNP UTR resulted in significantly greater levels of <i>flaA</i> transcription compared to the adenine SNP containing UTR. Additionally, when the UTR containing the guanine SNP was fused to <i>flaA</i>, motility was restored for a <i>flaAB</i> null mutant. Motility was not rescued initially when <i>flaA</i> was fused to the UTR containing the adenine SNP UTR. However, when the <i>flaAB</i> null mutant, containing a copy of <i>flaA</i> fused to the adenine-containing UTR, was incubated in Brucella broth for a minimum of two consecutive passages each lasting 48 h, transcription of <i>flaA</i> increased and motility was restored. Additional analysis of the <i>flaA</i> mRNA produced by the strain containing the adenine SNP UTR fused to <i>flaA</i> grown in Brucella broth versus agar suggests that the effects on motility occurred through blocking of full-length mRNA production.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1501331"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795080","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":"Development of extensive growth and growth boundary models for mesophilic and psychrotolerant <i>Bacillus cereus</i> in dairy products (Part 1).","authors":"Maryam Maktabdar, Ellen Wemmenhove, Elissavet Gkogka, Paw Dalgaard","doi":"10.3389/fmicb.2025.1553885","DOIUrl":"10.3389/fmicb.2025.1553885","url":null,"abstract":"<p><p>Guidelines for combinations of product characteristics to prevent unacceptable growth of <i>Bacillus cereus</i> in foods are lacking, and models are therefore valuable for predicting these responses. <i>B. cereus</i> isolates of dairy origin were used to generate a comprehensive dataset to develop two cardinal parameter growth and growth boundary models for mesophilic and psychrotolerant <i>B. cereus</i>, respectively. Each model incorporated the inhibitory effect of 11 environmental factors, i.e., temperature, pH, NaCl/a_w, organic acids (acetic, benzoic, citric, lactic, and sorbic), phosphate salts (orthophosphate, diphosphate, and triphosphate), and the effect of interactions between these factors. Cardinal parameter values for mesophilic and psychrotolerant strain cocktails were estimated using 231 and 203 maximum specific growth rates (<i>μ_max</i> values), respectively, generated in a standard liquid laboratory medium (BHI broth). Furthermore, an additional 113 and 100 <i>μ_max</i> values were generated for the two strain cocktails using a dairy-specific liquid medium (an ultra-filtration permeate from whey) to evaluate growth responses obtained in BHI broth. Cardinal parameter values for the two extensive growth boundary models were selected conservatively using data from BHI broth or UF permeate, such that the widest growth range was obtained for each environmental factor. The studied cocktail of six vegetative mesophilic <i>B. cereus</i> isolates exhibited greater acid tolerance in UF permeate than in BHI broth with lower <i>pH_min</i> (<i>pH_min</i> values of 4.75 versus 4.98), higher minimum inhibitory concentrations (<i>MIC</i>) of undissociated lactic acid (<i>MIC_u,LAC</i> of 2.99 versus 2.34 mM) and total citric acid (<i>MIC_T,CAC</i> of 169.1 versus 82.5 mM). The psychrotolerant <i>B. cereus strain</i> cocktail also had lower <i>pH_min</i> and higher values for <i>MIC_LAC</i> and <i>MIC_T,CAC</i> in UF permeate than in BHI broth. The remaining cardinal parameter values were determined from growth rates in BHI broth. The two new models can predict the combined effect of storage temperature and a wide range of dairy product characteristics, including combinations of organic acids and phosphate melting salts. These growth and growth boundary models can support the evaluation and management of the two <i>B. cereus</i> subgroups in various dairy products. However, product validation of the two predictive models is required to determine their performance and range of applicability.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"16 ","pages":"1553885"},"PeriodicalIF":4.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795087","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}