Frontiers in Microbiology最新文献

{"title":"CRISPR/Cas12a-based method coupled with isothermal amplification to identify <i>Alternaria</i> spp. isolated from wheat grain samples.","authors":"Aisha Shaizadinova, Meruyert Amanzholova, Irina Rukavitsina, Sailau Abeldenov, Anuar Rysbekovich Zhumakayev","doi":"10.3389/fmicb.2024.1468336","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1468336","url":null,"abstract":"<p><p><i>Alternaria</i> fungal species are considered major plant pathogens, infecting various crops and resulting in significant agricultural losses. Additionally, these species can contaminate grain with multiple mycotoxins that are harmful to humans and animals. Efficient pest management relies on timely detection and identification of phytopathogens in plant and grain samples, facilitating prompt selection of a crop protection strategy. Conventional identification tools, such as morphological characterization and identification based on polymerase chain reaction (PCR)-based methods, are time-consuming and laboratory-bound, limiting their implementation for on-site diagnostics essential in the agricultural industry. Isothermal amplification methods, including nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA), enable nucleic acid amplification at constant temperatures, making them ideal for point-of-care diagnostics without the need for thermal cycling equipment. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a)-based identification, coupled with such isothermal amplification methods, represents an emerging nucleic acid-based technology for detecting plant pathogens at high accuracy and sensitivity. This study aimed to develop a CRISPR/Cas12a-based method integrated with RPA amplification for specific detection of <i>Alternaria</i> spp. isolated from wheat grain samples. The developed method targeted the β-tubulin gene was successfully identified <i>Alternaria</i> strains within a 20-min RPA amplification followed by a 30-min CRISPR/Cas12a reaction and visualization of results. Specificity test included pathogenic fungal species commonly hosted wheat grain, such as <i>Fusarium</i> spp. <i>Bipolaris sorokiniana</i>, and <i>Nigrospora oryzae</i> revealed high specificity of the method for <i>Alternaria</i> species. Furthermore, the method exhibited high sensitivity, detecting <i>Alternaria</i> DNA down to 100 copies, validated by real-time fluorescence readout. A fluorescence assay was employed to visualize the results of RPA and CRISPR/Cas12a reaction, demonstrating substantial implementation potential of the method in point-of-care detection of <i>Alternaria</i> spp. In conclusion, we present the CRISPR/Cas12a-based method as a potentially sustainable approach for the rapid, precise, and specific nucleic-acid-based identification of <i>Alternaria</i> species in grain samples.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1468336"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064678","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":"Innovative antifungal strategies: enhanced biofilm inhibition of <i>Candida albicans</i> by a modified tea tree oil formulation.","authors":"Dang Anh Tuan, Pham Vu Nhat Uyen, Nguyen Van Khuon, Ly An Binh, Jan Masak","doi":"10.3389/fmicb.2024.1518598","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1518598","url":null,"abstract":"<p><strong>Introduction: </strong><i>Candida albicans</i> is a significant human pathogen with the ability to form biofilms, a critical factor in its resistance to antifungal treatments. This study aims to evaluate the antifungal activity and biofilm inhibition potential of Tea Tree Oil (TTO) derived from <i>Melaleuca alternifolia</i> cultivated in Vietnam.</p><p><strong>Methods: </strong>The antifungal activity of TTO was assessed by determining the Minimum Inhibitory Concentration (MIC), Minimum Fungicidal Concentration (MFC), Minimum Biofilm Inhibitory Concentration (MBIC), and Minimum Biofilm Eradication Concentration (MBEC) using broth dilution methods. The experiments were conducted on <i>C. albicans</i> in both planktonic and biofilm states across concentrations ranging from 0.1 μL/mL to 10 μL/mL.</p><p><strong>Results: </strong>TTO demonstrated significant antifungal efficacy, with a MIC of 0.1 μL/mL (∼91.217 μg/mL) and an MFC of 10 μL/mL (∼9121.7 μg/mL). It effectively inhibited biofilm formation with a recorded MBIC of 2 μL/mL (∼1824.34 μg/mL). However, MBEC values were not determinable as the concentrations tested did not achieve the eradication of more than 50% of mature biofilm within the experimental conditions.</p><p><strong>Discussion: </strong>These findings highlight TTO as a promising natural antifungal agent with strong biofilm-inhibitory properties. However, its limited efficacy in eradicating mature biofilms underscores the need for further studies, potentially involving higher concentrations or synergistic combinations with conventional antifungal agents.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1518598"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064761","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":"Tracing microbial community across endophyte-to-saprotroph continuum of <i>Cinnamomum camphora</i> (L.) Presl leaves considering priority effect of endophyte on litter decomposition.","authors":"Jiamin Xiao, Zaihua He, Xingbing He, Yonghui Lin, Xiangshi Kong","doi":"10.3389/fmicb.2024.1518569","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1518569","url":null,"abstract":"<p><p>Endophytes typically coexist with plants in symbiosis and transition into the saprobic system as plant tissues senesce, participating in the decomposition process of litter. However, the dynamic changes of endophytic communities during this process and their role in litter decomposition remain unclear. This study tracked the microbial composition across the transition from live leaves to litter in <i>Cinnamomum camphora</i> (L.) Presl <i>(C. camphora)</i>, evaluating the contribution of endophytes to litter decomposition by examining microbial diversity, community assembly, and co-occurrence networks along the endophyte-to-saprotroph spectrum. The results revealed increasing bacterial diversity but stable fungal diversity, and the diversity of endogenous microbes is mirrored this in the saprophytic phase. Bacterial community assembly was characterized by deterministic processes during the symbiotic phase, shifted to stochastic processes during the saprophytic phase. In contrast, fungal community assembly was predominantly driven by stochastic processes throughout the continuum. Out of the 49 keystone taxa identified, only <i>Pseudorhodoplanes sinuspersici</i> demonstrated a significant positive correlation with community assembly. All identified bacterial keystone taxa during the saprophytic phase originated from endophytic sources, and around 80% of the fungal keystone taxa in the initial stages of decomposition were similarly endophytic in origin. Additionally, 60% of the dominant bacterial taxa and 28% of the dominant fungal taxa at the commencement of decomposition were of endophytic descent. This suggests that endogenous microbes possess the potential to evolve into both keystone and dominant taxa during the saprophytic phase. Endogenous keystone and dominant microbes both exhibited significant correlations with microbial network, indicating their substantial ecological presence in microbial community. Both endogenous keystone and dominant taxa exerted significant potential influences on litter decomposition. Overall, during the saprophytic phase, endophytes are likely to influence the assemblage of microbial communities, the network structure, and decomposition-related functions. Specifically, it appears that bacterial endophytes may possess a greater adaptability to the decomposition processes of leaf litter compared to their fungal counterparts.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1518569"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774851/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064860","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":"Superiority of native seed core microbiomes in the suppression of bacterial wilt disease.","authors":"Yanling Dong, Jie Gong, Lei Yang, Qipeng Jiang, Chengzhi Wen, Jidan Zhang, Ruiyu Yang, Yao Wang, Yuhao Dai, Gui Gao, Shili Li, Yi Cao, Wei Ding","doi":"10.3389/fmicb.2024.1506059","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1506059","url":null,"abstract":"<p><strong>Introduction: </strong>Native endophytic microorganisms in tobacco seeds are closely related to their resistance to <i>Ralstonia solanacearum</i> (<i>R. solanacearum</i>) infections. However, the role of the native seed core microbiome in the suppression of bacterial wilt disease (BWD) remains underexplored.</p><p><strong>Methods: </strong>The characteristics of endophytic bacterial communities in both resistant and susceptible tobacco varieties were characterized using high-throughput sequencing technology.</p><p><strong>Results: </strong>This study found <i>Paenibacillus</i> as a potential microbial antagonist against BWD based on its significantly greater presence in BWD-resistant tobacco varieties, with a relative abundance that was 83.10% greater in the seeds of resistant tobacco than in those of susceptible varieties. Furthermore, a <i>Paenibacillus</i> strain identified as <i>Paenibacillus odorifer</i> 6036-R2A-26 (<i>P. odorifer</i> 26) was isolated from the seeds of the resistant variety. Following irrigation treatment with <i>P. odorifer</i> 26, the BWD index was reduced by 51.08%. Additionally, this strain exhibited significant growth-promoting effects on tobacco. It significantly increased the fresh weight of the tobacco plants by 30.26% in terms of aboveground weight, 37.75% in terms of underground weight, and 33.97% in terms of aboveground dry weight. This study highlights the critical role of <i>Paenibacillus</i> in tobacco seeds in the suppression of BWD, which may result from its antagonistic and growth-promoting properties.</p><p><strong>Discussion: </strong>The results of this study revealed differences in the structural characteristics of endophytic bacterial communities between resistant and susceptible tobacco varieties, with groups such as <i>Paenibacillus</i> potentially playing significant roles in resisting BWD. These findings highlight the superiority of seed endophytic microorganisms. In the context of declining plant disease resistance and the spread of bacterial wilt, core endophytic microorganisms in seeds may emerge as a viable option for enhancing the productivity of agricultural ecosystems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1506059"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064799","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":"Transcriptional activity of ammonia oxidisers in response to soil temperature, moisture and nitrogen amendment.","authors":"Chris Chisholm, Hong Di, Keith Cameron, Andriy Podolyan, Jupei Shen, Limei Zhang, Kosala Sirisena, Xueying Che","doi":"10.3389/fmicb.2024.1466991","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1466991","url":null,"abstract":"<p><p>The contrasting response of AOA, AOB, and comammox <i>Nitrospira amoA</i> transcript abundance to temperature, moisture, and nitrogen was investigated using soil microcosms. The moisture, temperature, and nitrogen treatments were selected to represent conditions typically found in a New Zealand (NZ) dairy farm. AOB dominated all synthetic urine treated soils. Peak AOB <i>amoA</i> transcript abundance was positively correlated with estimated soil ammonia availability. While AOB gDNA abundance and nitrification rate trends were similar. AOA were strongly influenced by soil temperature. At 20°C, AOA <i>amoA</i> peak transcript abundance averaged over 1 order of magnitude higher than at 8°C. Within the AOA community a member of the <i>Nitrosocosmicus</i> clade was positively correlated with ammonium and estimated ammonia concentrations. The presence and relative increase of an AOA community member in a high nitrogen environment poses an interesting contrast to current scientific opinion in NZ. Comammox <i>Nitrospira</i> abundance showed no correlation with soil moisture. This suggests that previously found associations are more complex than originally thought. Further research is required to determine the drivers of comammox <i>Nitrospira</i> abundance in a high moisture environment. Overall, these results indicate that AOB are the main drivers of nitrification in New Zealand dairy farm soils.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1466991"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064875","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":"Interaction between nitrate and trichloroethene bioreduction in mixed anaerobic cultures.","authors":"Dong-Mei Yang, Fen-Li Min, Ying Li, Jia-Lu Ling, Hui-Xian Zhong, Yu-Chun Xia, Ying Feng, Li-Ya Zhao, Zhao-Hua Li, Li-Lian Wen","doi":"10.3389/fmicb.2024.1504235","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1504235","url":null,"abstract":"<p><p>Bioremediation of trichloroethene (TCE)-contaminated sites often leads to groundwater acidification, while nitrate-polluted sites tend to generate alkalization. TCE and nitrate often coexist at contaminated sites; however, the pH variation caused by nitrate self-alkalization and TCE self-acidification and how these processes affect nitrate reduction and reductive dichlorination, have not been studied. This study investigated the interaction between nitrate and TCE, two common groundwater co-contaminants, during bioreduction in serum bottles containing synthetic mineral salt media and microbial consortia. Our results showed that TCE concentrations up to 0.3 mM stimulated nitrate reduction, while the effect of nitrate on TCE reductive dechlorination was more complex. Nitrate primarily inhibited the reduction of TCE to dichloroethene (DCE) but enhanced the reduction of vinyl chloride (VC) to ethene. Mechanistic analysis suggested that this inhibition was due to the thermodynamic favorability of nitrate reduction over TCE reduction, while the promotion of VC reduction was linked to pH stabilization via self-alkalization. As the initial nitrate concentration increased from 0 to 3 mM, the relative abundance of putatively denitrifying genera, such as <i>Petrimonas</i> and <i>Trichlorobacter</i>, increased. However, the abundance of fermentative <i>Clostridium</i> sharply declined from 31.11 to 1.51%, indicating strong nitrate inhibition. Additionally, the relative abundance of <i>Dehalococcoides</i>, a genus capable of reducing TCE to ethene, slightly increased from 23.91 to 24.26% at nitrate concentrations up to 0.3 mM but decreased to 18.65% as the nitrate concentration increased to 3 mM, suggesting that <i>Dehalococcoides</i> exhibits a degree of tolerance to high nitrate concentrations under specific conditions. Overall, our findings highlight the potential for simultaneous reduction of TCE and nitrate, even at elevated concentrations, facilitated by self-regulating pH control in anaerobic mixed dechlorinating consortia. This study provides novel insights into bioremediation strategies for addressing co-contaminated sites.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1504235"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064762","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 a colloidal gold immunochromatographic assay utilizing dual-antibody sandwich method for detecting <i>Orientia tsutsugamushi</i>.","authors":"Qingyu Lu, Shiyin Yu, Sibo Wang, Min Cao, Liuxin Li, Miao Xin, Weilong Tan, Yong Qi, Yichen Lu, Xiaohui Xiong","doi":"10.3389/fmicb.2024.1521015","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1521015","url":null,"abstract":"<p><p>A colloidal gold immunochromatographic assay (ICA) based on a dual-antibody sandwich method was developed for the rapid and convenient detection of <i>Orientia tsutsugamushi</i> (<i>O. tsutsugamushi</i>) antigens in the early stages of infection. Monoclonal antibodies designed as 5B3 targeting the conserved region of 56 kDa outer membrane protein in various strains of <i>O. tsutsugamushi</i> were generated through cell fusion and screening techniques and combined with previously prepared polyclonal antibodies as detection antibodies to establish the ICA. Colloidal gold and polyclonal antibody-colloidal gold complexes were synthesized under optimized conditions. The nitrocellulose membrane was treated with 5B3 monoclonal antibody and goat anti-mouse antibody as the test and control lines, respectively. The ICA demonstrated robust sensitivity, with a minimum detection limit of 70.5 ng for the 56 kDa recombinant of the Gilliam strain. Furthermore, a detection limit of 1 × 10⁶ copies/μL DNA of <i>O. tsutsugamushi</i> was determined for both PT and SJ infected cell strains by constructing a relationship between cell number and copy number of the pathogen using a quantitative PCR-based standard curve. The assay also exhibited exceptional specificity, with no false positives observed against other bacterial species, including <i>Escherichia coli</i>, <i>Salmonella</i>, <i>Staphylococcus aureus</i>, and <i>Listeria monocytogenes</i>. In summary, an ICA which is sensitive, specific, and easy to operate was successfully established for the detection of <i>O. tsutsugamushi</i> in scrub typhus, potentially enabling early rapid point-of-care diagnosis of scrub typhus.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1521015"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064775","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":"<i>In silico</i> analysis of the effect of HCV genotype-specific polymorphisms in Core, NS3, NS5A, and NS5B proteins on T-cell epitope processing and presentation.","authors":"Samina Baig, Assel Berikkara, Ramsha Khalid, Syed A Subhan, Tanveer Abbas, Syed Hani Abidi","doi":"10.3389/fmicb.2024.1498069","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1498069","url":null,"abstract":"<p><strong>Background: </strong>HCV genotypes are 30-35% polymorphic at the nucleotide level, while subtypes within the same genotype differ by nearly 20%. Although previous studies have shown the immune escape potential of several mutations within the HCV proteins, little is known about the effect of genotype/subtype-specific gene polymorphism on T-cell immunity. Therefore, this study employed several <i>in silico</i> methods to examine the impact of genotype/subtype-specific polymorphisms in Core, NS3, NS5A, and NS5B sequences on T cell epitope processing and HLA-epitope interactions.</p><p><strong>Methods: </strong>For this study, 8,942, 17,700, 14,645, and 3,277 HCV Core, NS3, NS5A, and NS5B sequences, respectively, from eight genotypes and 21 subtypes were retrieved from the Los Alamos HCV Database. Next, the NetCTL tool was employed to predict Cytotoxic T Lymphocyte (CTL) epitopes based on combined proteasomal cleavage, TAP efficacy, and HLA class I receptor binding scores. PEP-FOLD was used to model selected epitopes, followed by peptide-HLA docking using HPEPDOCK. Finally, molecular dynamics simulations were conducted for 200 ns using Desmond software to analyze differences in HLA-epitope (from different HCV genotypes) interaction kinetics and dynamics.</p><p><strong>Results: </strong>A total of 3,410, 8,054, 6,532, and 14,015 CTL epitopes were observed in the HCV Core, NS3, NS5A, and NS5B sequences, respectively. Significant genotype/subtype-specific variations in CTL values and docking scores were observed among NS3, NS5A, and NS5B proteins. <i>In silico</i> results reveal that epitopes from genotype 6b (NS3), 6d/r (NS5B), 6o and 6 k (NS5A) exhibit higher immunogenicity than other genotypes, forming more energetically stable complexes with host receptors. These epitopes, compared to those from the same positions but different genotypes, showed binding energies of -144.24 kcal/mol, -85.30 kcal/mol, and - 43 kcal/mol, respectively. Over a 200 ns MD simulation, GT 6b and 6d/r epitopes displayed up to a 40% stronger binding energy with the HLA receptor. These findings suggest that patients infected with GT 6 may experience enhanced T cell responsiveness and broader immunogenicity.</p><p><strong>Conclusion: </strong>Our study suggests that genotype/subtype-specific polymorphism in HCV may result in altered immune responses by modulating T-cell epitope processing and interaction with HLA receptors. Further experimental studies can be performed to confirm the effect of genotype/subtype-specific polymorphisms on T cell-mediated immune response.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1498069"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064281","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":"16S rRNA and metabolomics reveal the key microbes and key metabolites that regulate diarrhea in Holstein male calves.","authors":"P P Cao, C L Hu, M J Li, Y H An, X Feng, X H Ma, D Z Wang, Z H Song, G S Ji, D Yang, Q Ma, W F Yang, J N Dong, H R Zhang, Y Ma, Y F Ma","doi":"10.3389/fmicb.2024.1521719","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1521719","url":null,"abstract":"<p><strong>Introduction: </strong>Diarrhea is a prevalent disease among calves, which significantly hinders their growth and development, thereby impacting farm productivity and revenue. This study aimed to investigate the impact of diarrhea on calf growth.</p><p><strong>Methods: </strong>Holstein male calves with similar birth weight (39.5 ± 4.2 kg) were included in this study, and key parameters such as fecal score, diarrhea incidence, and growth performance from birth to weaning were measured. Rectal fecal samples from both diarrheic (<i>n</i> = 24) and healthy calves (<i>n</i> = 24) aged 1-4 weeks were analyzed using 16S rRNA gene sequencing and untargeted metabolomics.</p><p><strong>Results: </strong>Our findings indicated a high prevalence of diarrhea among calves between 1-4 weeks of age on pasture, which led to a marked decrease in growth performance, including average daily gain. At the genus level, the relative abundance of <i>GCA-900066575</i> in one-week-old diarrheic calves was significantly higher; <i>Escherichia-Shigella</i> and <i>Pseudoflavonifractor</i> were more abundant in two-week-old calves; while <i>Tyzzerella</i> and <i>Lachnospiraceae_UCG-004</i> increased significantly in four-week-old calves, and correlated negatively with average daily gain, suggesting that these bacteria may promote the occurrence of diarrhea. Correlation analysis revealed that fecal metabolites such as arachidonic acid, cis-vaccenic acid, oleic acid, choline, creatinine, and others were significantly negatively correlated with calf growth performance and were significantly increased in diarrheic calves. WGNCA identified that dark magenta module metabolites were significantly associated with diarrhea traits from 1-4 weeks. Thirteen metabolites, including glycerophospholipids (such as 1-stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine), fatty acids (such as dodecanoic acid), and arachidonic acid, were positively correlated with <i>GCA-900066575</i>, <i>Escherichia-shigella</i>, <i>Tyzzerella</i>, and <i>Clostridium_butyricum</i>, but negatively correlated with <i>UBA1819</i>, <i>Lachnoclostridium_sp_YL32</i>, and <i>Clostridium_scindens</i>.</p><p><strong>Discussion: </strong>Therefore, <i>GCA-900066575</i>, <i>Escherichia-shigella</i>, <i>Lachnospiraceae_UCG-004</i>, and <i>Tyzzerella</i> are likely key bacterial genera causing diarrhea in calves, while arachidonic acid, glycerol phospholipids, and fatty acids are critical metabolites associated with this condition. These alterations in the fecal microbiota and metabolite composition were found to be the principal contributors to growth retardation in diarrheic calves.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1521719"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064350","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":"Acute stress triggers sex-dependent rapid alterations in the human small intestine microbiota composition.","authors":"Bruno K Rodiño-Janeiro, Olfat Khannous-Lleiffe, Marc Pigrau, Jesse R Willis, Eloísa Salvo-Romero, Adoración Nieto, Elba Expósito, Marina Fortea, Cristina Pardo-Camacho, Mercé Albert-Bayo, Ana María González-Castro, Danila Guagnozzi, Cristina Martínez, Beatriz Lobo, María Vicario, Javier Santos, Toni Gabaldón, Carmen Alonso-Cotoner","doi":"10.3389/fmicb.2024.1441126","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1441126","url":null,"abstract":"<p><strong>Background/aims: </strong>Digestive disorders of gut-brain interaction (DGBI) are very common, predominant in females, and usually associated with intestinal barrier dysfunction, dysbiosis, and stress. We previously found that females have increased susceptibility to intestinal barrier dysfunction in response to acute stress. However, whether this is associated with changes in the small bowel microbiota remains unknown. We have evaluated changes in the small intestinal microbiota in response to acute stress to better understand stress-induced intestinal barrier dysfunction.</p><p><strong>Methods: </strong>Jejunal biopsies were obtained at baseline and 90 min after cold pain or sham stress. Autonomic (blood pressure and heart rate), hormonal (plasma cortisol and adrenocorticotropic hormone) and psychological (Subjective Stress Rating Scale) responses to cold pain and sham stress were monitored. Microbial DNA from the biopsies was analyzed using a 16S metabarcoding approach before and after cold pain stress and sham stress. Differences in diversity and relative abundance of microbial taxa were examined.</p><p><strong>Results: </strong>Cold pain stress was associated with a significant decrease in alpha diversity (<i>P</i> = 0.015), which was more pronounced in females, along with significant sex differences in the abundance of specific taxa and the overall microbiota composition. Microbiota alterations significantly correlated with changes in psychological responses, hormones, and gene expression in the intestinal mucosal. Cold pain stress was also associated with activation of autonomic, hormonal and psychological response, with no differences between sexes.</p><p><strong>Conclusions: </strong>Acute stress elicits rapid alterations in bacterial composition in the jejunum of healthy subjects and these changes are more pronounced in females. Our results may contribute to the understanding of female predominance in DGBI.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"15 ","pages":"1441126"},"PeriodicalIF":4.0,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11778178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064448","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}