Pub Date : 2024-02-13DOI: 10.3389/frmbi.2024.1274277
Samuel B Pannoni, W. Holben
Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.
{"title":"Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment","authors":"Samuel B Pannoni, W. Holben","doi":"10.3389/frmbi.2024.1274277","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1274277","url":null,"abstract":"Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"109 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139781162","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}
Pub Date : 2024-02-08DOI: 10.3389/frmbi.2024.1352566
Julia Sacharow, S. Ratering, Santiago Quiroga, Rita Geissler-Plaum, Bellinda Schneider, Alessandra Österreicher Cunha-Dupont, Sylvia Schnell
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.
{"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}
Pub Date : 2024-02-08DOI: 10.3389/frmbi.2024.1352566
Julia Sacharow, S. Ratering, Santiago Quiroga, Rita Geissler-Plaum, Bellinda Schneider, Alessandra Österreicher Cunha-Dupont, Sylvia Schnell
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.
{"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}
Pub Date : 2024-02-08DOI: 10.3389/frmbi.2024.1301156
Songqing Liu, Juan Zhao, Wen-Long Feng, Zong-Jin Zhang, Yun-Fu Gu, Yan-Ping Wang
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.
{"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}
Pub Date : 2024-02-08DOI: 10.3389/frmbi.2024.1301156
Songqing Liu, Juan Zhao, Wen-Long Feng, Zong-Jin Zhang, Yun-Fu Gu, Yan-Ping Wang
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.
{"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}
Pub Date : 2024-02-07DOI: 10.3389/frmbi.2024.1341824
Zhong-Hao Ji, Wen-Yin Xie, Pei-Sen Zhao, W. Ren, Hong-Juan Jin, Bao Yuan
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.
{"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}
Pub Date : 2024-02-07DOI: 10.3389/frmbi.2024.1341824
Zhong-Hao Ji, Wen-Yin Xie, Pei-Sen Zhao, W. Ren, Hong-Juan Jin, Bao Yuan
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.
{"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}
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.
Akkermansia muciniphila 被认为是 "下一代有益微生物的典范"，据报道有助于缓解与免疫有关的疾病。有证据表明，中草药可以通过调节粘液虹彩菌的数量来治疗疾病。最近的研究揭示了粘菌与免疫相关疾病之间的联系。在此，我们系统回顾了粘菌素、中药和免疫相关疾病（包括炎症性肠病、人类免疫缺陷病毒、癌症免疫治疗和免疫相关肝损伤）之间的联系。我们还总结了 A. muciniphila 的潜在作用机制，并为未来的研究提供了展望。
{"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}
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.
Akkermansia muciniphila 被认为是 "下一代有益微生物的典范"，据报道有助于缓解与免疫有关的疾病。有证据表明，中草药可以通过调节粘液虹彩菌的数量来治疗疾病。最近的研究揭示了粘菌与免疫相关疾病之间的联系。在此，我们系统回顾了粘菌素、中药和免疫相关疾病（包括炎症性肠病、人类免疫缺陷病毒、癌症免疫治疗和免疫相关肝损伤）之间的联系。我们还总结了 A. muciniphila 的潜在作用机制，并为未来的研究提供了展望。
{"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}
Pub Date : 2024-02-05DOI: 10.3389/frmbi.2024.1335791
Adriana Giongo, Jessica Arnhold, Dennis Grunwald, K. Smalla, Andrea Braun-Kiewnick
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.
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