Frontiers in microbiomes最新文献

{"title":"Cercozoan diversity of spring barley grown in the field is strongly plant compartment specific","authors":"Julia Sacharow, S. Ratering, Santiago Quiroga, Rita Geissler-Plaum, Bellinda Schneider, Alessandra Österreicher Cunha-Dupont, Sylvia Schnell","doi":"10.3389/frmbi.2024.1352566","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1352566","url":null,"abstract":"Protists are an important part of the plant holobiome and influence plant growth and pathogenic pressure as consumers. Hordeum vulgare is one of the most economically important crops worldwide, and its yield depends on optimal environmental plant-growth conditions and pathogen defense. This study aimed to analyse the natural compositions of the cercozoan diversity, one of the most important and dominant protist phyla, of spring barley at different developmental stages, from different plant compartments over two years. Hordeum vulgare bulk soil samples were taken before seeding and after harvest on an organic farming field. Bulk soil, rhizosphere soil, roots and leaves were sampled at the flowering and ripening stages, and analysed with cercozoan-specific primers. Results showed a clear dominance of the families Sandonidae, Allapsidae, Cercomonadidae, Rhogostomidae and the order Glissomonadida in all sample types. Separated analyses of root, leaf and soil samples showed that members of the family Sandonidae were strongly enriched in leaf samples, while members of the Allapsidae family were enriched in the roots. No compositional differences were detected between the different plant developmental stages, except for the beta diversity of the leaf samples at the flowering and ripening stages. It can be concluded that the cercozoan diversity of spring barley is primarily affected by the plant compartment and not by the plant developmental stage. Further studies are needed to analyze the cercozoan community in greater taxonomic depth and to target their ecological function.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"129 1-2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139854035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cercozoan diversity of spring barley grown in the field is strongly plant compartment specific","authors":"Julia Sacharow, S. Ratering, Santiago Quiroga, Rita Geissler-Plaum, Bellinda Schneider, Alessandra Österreicher Cunha-Dupont, Sylvia Schnell","doi":"10.3389/frmbi.2024.1352566","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1352566","url":null,"abstract":"Protists are an important part of the plant holobiome and influence plant growth and pathogenic pressure as consumers. Hordeum vulgare is one of the most economically important crops worldwide, and its yield depends on optimal environmental plant-growth conditions and pathogen defense. This study aimed to analyse the natural compositions of the cercozoan diversity, one of the most important and dominant protist phyla, of spring barley at different developmental stages, from different plant compartments over two years. Hordeum vulgare bulk soil samples were taken before seeding and after harvest on an organic farming field. Bulk soil, rhizosphere soil, roots and leaves were sampled at the flowering and ripening stages, and analysed with cercozoan-specific primers. Results showed a clear dominance of the families Sandonidae, Allapsidae, Cercomonadidae, Rhogostomidae and the order Glissomonadida in all sample types. Separated analyses of root, leaf and soil samples showed that members of the family Sandonidae were strongly enriched in leaf samples, while members of the Allapsidae family were enriched in the roots. No compositional differences were detected between the different plant developmental stages, except for the beta diversity of the leaf samples at the flowering and ripening stages. It can be concluded that the cercozoan diversity of spring barley is primarily affected by the plant compartment and not by the plant developmental stage. Further studies are needed to analyze the cercozoan community in greater taxonomic depth and to target their ecological function.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"125 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139794185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial community succession of cow manure and tobacco straw composting","authors":"Songqing Liu, Juan Zhao, Wen-Long Feng, Zong-Jin Zhang, Yun-Fu Gu, Yan-Ping Wang","doi":"10.3389/frmbi.2024.1301156","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1301156","url":null,"abstract":"Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"56 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139850696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial community succession of cow manure and tobacco straw composting","authors":"Songqing Liu, Juan Zhao, Wen-Long Feng, Zong-Jin Zhang, Yun-Fu Gu, Yan-Ping Wang","doi":"10.3389/frmbi.2024.1301156","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1301156","url":null,"abstract":"Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":" 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139791040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kombucha polysaccharide alleviates DSS-induced colitis in mice by modulating the gut microbiota and remodeling metabolism pathways","authors":"Zhong-Hao Ji, Wen-Yin Xie, Pei-Sen Zhao, W. Ren, Hong-Juan Jin, Bao Yuan","doi":"10.3389/frmbi.2024.1341824","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1341824","url":null,"abstract":"Ulcerative colitis (UC) is incurable, and rational dietary interventions are important in preventing UC. Kombucha is a fermented beverage that originated in China and has a variety of activities, including antioxidant, antibacterial and hypoglycemic activities. The aim of this study was to analyze the protective effect of Kombucha polysaccharide (KP) against UC and determine its mechanism of action. The results showed that KP intervention was effective in alleviating dextran sulfate sodium salt (DSS)-induced colitis symptoms and inhibiting DSS-induced inflammation and oxidative stress. Moreover, KP was able to reduce intestinal permeability, promote the expression of tight junction proteins, and help maintain thrush cell numbers and promote mucus secretion. The 16S rDNA results indicated that KP intervention increased the abundance of Rikenellaceae_RC9_gut_group and Clostridiales_unclassified. Untargeted metabolomics techniques revealed that KP can reverse DSS-induced disorders in intestinal metabolism. This study demonstrated that KP alleviated DSS-induced colitis by helping maintain intestinal barrier integrity, regulating the gut microbiota and remodeling metabolism pathways. The findings provide a theoretical basis for the application of KP as a dietary supplement for the prevention of UC.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"48 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139798207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kombucha polysaccharide alleviates DSS-induced colitis in mice by modulating the gut microbiota and remodeling metabolism pathways","authors":"Zhong-Hao Ji, Wen-Yin Xie, Pei-Sen Zhao, W. Ren, Hong-Juan Jin, Bao Yuan","doi":"10.3389/frmbi.2024.1341824","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1341824","url":null,"abstract":"Ulcerative colitis (UC) is incurable, and rational dietary interventions are important in preventing UC. Kombucha is a fermented beverage that originated in China and has a variety of activities, including antioxidant, antibacterial and hypoglycemic activities. The aim of this study was to analyze the protective effect of Kombucha polysaccharide (KP) against UC and determine its mechanism of action. The results showed that KP intervention was effective in alleviating dextran sulfate sodium salt (DSS)-induced colitis symptoms and inhibiting DSS-induced inflammation and oxidative stress. Moreover, KP was able to reduce intestinal permeability, promote the expression of tight junction proteins, and help maintain thrush cell numbers and promote mucus secretion. The 16S rDNA results indicated that KP intervention increased the abundance of Rikenellaceae_RC9_gut_group and Clostridiales_unclassified. Untargeted metabolomics techniques revealed that KP can reverse DSS-induced disorders in intestinal metabolism. This study demonstrated that KP alleviated DSS-induced colitis by helping maintain intestinal barrier integrity, regulating the gut microbiota and remodeling metabolism pathways. The findings provide a theoretical basis for the application of KP as a dietary supplement for the prevention of UC.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139858121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Akkermansia muciniphila and herbal medicine in immune-related diseases: current evidence and future perspectives","authors":"Xue Ding, Pengfei Meng, Xiu-xia Ma, Jing-Yu Yue, Liang-Ping Li, Li-Ran Xu","doi":"10.3389/frmbi.2024.1276015","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1276015","url":null,"abstract":"Akkermansia muciniphila is considered the “paradigm for next-generation beneficial microorganisms” and has been reported to help alleviat immune-related diseases. Evidence shows that herbal medicine can treat disease by regulating the abundance of A. muciniphila. Recent studies have revealed a link between A. muciniphila and immune-related diseases. Here, we systematically reviewed the association between A. muciniphila, herbal medicine, and immune-related diseases (including inflammatory bowel disease, human immunodeficiency virus, cancer immunotherapy, and immune-related liver injury). We also summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139865273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Akkermansia muciniphila and herbal medicine in immune-related diseases: current evidence and future perspectives","authors":"Xue Ding, Pengfei Meng, Xiu-xia Ma, Jing-Yu Yue, Liang-Ping Li, Li-Ran Xu","doi":"10.3389/frmbi.2024.1276015","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1276015","url":null,"abstract":"Akkermansia muciniphila is considered the “paradigm for next-generation beneficial microorganisms” and has been reported to help alleviat immune-related diseases. Evidence shows that herbal medicine can treat disease by regulating the abundance of A. muciniphila. Recent studies have revealed a link between A. muciniphila and immune-related diseases. Here, we systematically reviewed the association between A. muciniphila, herbal medicine, and immune-related diseases (including inflammatory bowel disease, human immunodeficiency virus, cancer immunotherapy, and immune-related liver injury). We also summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"15 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139805197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat","authors":"Adriana Giongo, Jessica Arnhold, Dennis Grunwald, K. Smalla, Andrea Braun-Kiewnick","doi":"10.3389/frmbi.2024.1335791","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1335791","url":null,"abstract":"The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia, Pseudomonas, Shinella, and Sphingomonas, along with other genera, such as Pedobacter (Bacteroidota), Agromyces and Streptomyces (Actinobacteriota) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"242 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139862438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat","authors":"Adriana Giongo, Jessica Arnhold, Dennis Grunwald, K. Smalla, Andrea Braun-Kiewnick","doi":"10.3389/frmbi.2024.1335791","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1335791","url":null,"abstract":"The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia, Pseudomonas, Shinella, and Sphingomonas, along with other genera, such as Pedobacter (Bacteroidota), Agromyces and Streptomyces (Actinobacteriota) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139802598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}