Fecal microbiota transplantation (FMT) has been tested for the prevention and treatment of various intestinal and extra-intestinal diseases, but its efficacy is not stable, which may be due to the lack of an optimized method for screening high-quality donors. The low efficiency and high cost of donor screening are also obstacles to the clinical application of FMT. In this study, we tested the efficiency of the constitution theory of traditional Chinese medicine (TCM) in screening high-quality FMT donors. College student volunteers were sorted into either the balanced TCM constitution (BC) or unbalanced TCM constitution (UBC) groups, with the latter group comprising eight different constitution types, and the gut microbiota profiles of each UBC were compared with that of BC. Subsequently, the success rates of the qualified donors of BC and UBC volunteers were compared. Finally, the anti-obesity effect of FMT, obtained using the fecal microbiota of BC and UBC donors, was tested on mice with high fat diet-induced obesity. The results showed that the gut microbiota of BC and UBC volunteers were significantly different. There was a higher proportion of qualified FMT donors in the BC volunteer group than in the UBC volunteer group. Moreover, the experiment in mice showed that the fecal microbiota of BC and UBC volunteers conferred different anti-obesity effects. Overall, TCM constitution could be a reference for FMT practice. Our study presents a new idea, namely, using TCM constitution theory to efficiently screen high-quality FMT donors.
粪便微生物群移植（FMT）已被用于预防和治疗各种肠道和肠道外疾病，但其疗效并不稳定，这可能是由于缺乏筛选优质供体的优化方法。供体筛选的低效率和高成本也是 FMT 临床应用的障碍。在本研究中，我们测试了中医体质理论在筛选高质量 FMT 供体中的效率。我们将大学生志愿者分为中医体质平衡组（BC）和中医体质不平衡组（UBC），后者包括八种不同的体质类型，并比较了每种 UBC 与 BC 的肠道微生物群谱。随后，比较了 BC 和 UBC 志愿者合格供体的成功率。最后，利用 BC 和 UBC 捐赠者的粪便微生物群，在高脂饮食诱发肥胖的小鼠身上测试了 FMT 的抗肥胖效果。结果显示，BC 和 UBC 志愿者的肠道微生物群存在显著差异。在 BC 志愿者组中，合格的 FMT 捐赠者比例高于 UBC 志愿者组。此外，小鼠实验表明，BC 和 UBC 志愿者的粪便微生物群具有不同的抗肥胖作用。总之，中医体质可作为 FMT 实践的参考。我们的研究提出了一个新思路，即利用中医体质理论有效筛选高质量的 FMT 供体。
{"title":"Comparison of the gut microbiota of college students with the nine balanced and unbalanced traditional Chinese medicine constitutions and its potential application in fecal microbiota transplantation","authors":"Qinhong Huang, Lihui Yang, Guannan Cai, Yongdie Huang, Shian Zhang, Zhenwei Ye, Jing Yang, Chuhui Gao, Jiaxuan Lai, Lyu Lin, Jihui Wang, Ting Liu","doi":"10.3389/frmbi.2023.1292273","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1292273","url":null,"abstract":"Fecal microbiota transplantation (FMT) has been tested for the prevention and treatment of various intestinal and extra-intestinal diseases, but its efficacy is not stable, which may be due to the lack of an optimized method for screening high-quality donors. The low efficiency and high cost of donor screening are also obstacles to the clinical application of FMT. In this study, we tested the efficiency of the constitution theory of traditional Chinese medicine (TCM) in screening high-quality FMT donors. College student volunteers were sorted into either the balanced TCM constitution (BC) or unbalanced TCM constitution (UBC) groups, with the latter group comprising eight different constitution types, and the gut microbiota profiles of each UBC were compared with that of BC. Subsequently, the success rates of the qualified donors of BC and UBC volunteers were compared. Finally, the anti-obesity effect of FMT, obtained using the fecal microbiota of BC and UBC donors, was tested on mice with high fat diet-induced obesity. The results showed that the gut microbiota of BC and UBC volunteers were significantly different. There was a higher proportion of qualified FMT donors in the BC volunteer group than in the UBC volunteer group. Moreover, the experiment in mice showed that the fecal microbiota of BC and UBC volunteers conferred different anti-obesity effects. Overall, TCM constitution could be a reference for FMT practice. Our study presents a new idea, namely, using TCM constitution theory to efficiently screen high-quality FMT donors.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"26 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139169379","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 : 2023-12-20DOI: 10.3389/frmbi.2023.1287336
Lin Chen, Haiyan Ding, Xin Chen, Jiaojiao Wang, Yuan Hu, Hongping Chen, You-ping Liu
The plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.In this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.The main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).This study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.
植物微生物组是植物的第二基因组，对植物的生长和健康非常重要。铁皮石斛是兰科附生草本植物，常附着在树干或岩石上，有不同的栽培模式。对不同栽培模式下的石斛（Dendrobium denneanum Kerr）进行微生物和代谢物研究，可以揭示石斛属植物之间的重要关系、本研究选择了石斛在同一环境中的三种栽培模式：活体树上附生（LT）、石上附生（SE）和盆栽（PO），并采用超高效液相色谱-四极杆飞行时间质谱（UPLC-Q-TOF-MS）对其代谢物进行了测定。D.denneanum根圈和根内圈的主要微生物类群包括属于变形菌门（Proteobacteria）、放线菌门（Actinobacteria）和放线菌门（Actinobacteria）的细菌，以及真菌门（Basidiomycota）和子囊菌门（Ascomycota），它们的丰度在不同的栽培模式下有所不同。土壤特性会影响 D. denneanum 代谢产物和根微生物群的组成，其中土壤全磷（TP）和 pH 值尤其是土壤微生物的重要因素。对根系微生物群落的研究表明，根系内圈真菌与根圈真菌相似，从外部环境到内部结构都有微生物富集。根系微生物群落和代谢物相关性分析表明，根圈微生物以及内生菌和代谢物之间存在显著的相关性。本研究从微生物和代谢物的角度阐明了不同栽培模式对丹顶鹤的影响，并研究了根系微生物对代谢物的影响。研究结果加深了人们对兰科植物根部微生物的认识，为以石斛为代表的石斛属植物的栽培提供了理论依据。
{"title":"Cultivation modes impacting root microbiomes and metabolites in medicinal orchid Dendrobium denneanum","authors":"Lin Chen, Haiyan Ding, Xin Chen, Jiaojiao Wang, Yuan Hu, Hongping Chen, You-ping Liu","doi":"10.3389/frmbi.2023.1287336","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1287336","url":null,"abstract":"The plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.In this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.The main microbial taxa in the rhizosphere and root endosphere of D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).This study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"13 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138955024","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 : 2023-12-14DOI: 10.3389/frmbi.2023.1270352
Z. G. Griffiths, Andrew D. Putt, J. I. Miller, M. F. Campa, D. Joyner, O. Pelz, Nargiz Garajayeva, M. Ceccopieri, P. Gardinali, Terry C. Hazen
The Caspian Sea is the world’s largest landlocked saline lake which lies between Europe and Asia. This region is particularly known for its large-scale oil reserves, pipelines, and drilling activities, which have contributed to the environmental decline of this lake. In addition to pollution from the petroleum industry, drainage from various river basins brings an influx of residential, industrial, and agricultural effluents that induce eutrophication and hypoxic conditions in deeper, colder waters, creating an oxygen gradient. The temperature and oxygen stratification in this environment has presented a unique opportunity to investigate the potential of the biodegradative processes carried out by the indigenous microbial community. We believe these indigenous microbes possess different metabolic capabilities to degrade oil as they adapted to declining oxygen concentrations and temperatures with increasing depths over a prolonged period. Hence, community structure and composition will vary with depth.Microcosms were set up to observe the indigenous microbial reaction after a 60 ppm native crude oil amendment over 115 days. Surface water microcosms were incubated at 28ºC and aerated while deep water microcosms were incubated at 8ºC under anaerobic conditions. These two environmental conditions represent the temperature and oxygen extremes along the gradient and were selected as we try to simulate the indigenous community’s response to this oil contamination. DNA was extracted and amplified from these microcosms and sequenced. Bioinformatic analysis was performed to track changes in the abundance of taxa present and biodiversity over different time points to show the progression of community structure.All microcosms showed the presence of hydrocarbon-degrading phyla, whose presence is consistent with other reports from oil-enriched environments. However, distinct communities were observed in oxic versus hypoxic microcosms.Orders of Bacteria related to sulfate and nitrogen cycling were found in hypoxic microcosms, indicating a possible mechanism for the anaerobic biodegradation of crude oil. GC-MS analysis of initial and final microcosms also provided evidence of degradation of hydrocarbon fractions in both warm, oxic and cold, hypoxic conditions.
{"title":"Comparing the response of the indigenous microbial community to crude oil amendment in oxic versus hypoxic conditions","authors":"Z. G. Griffiths, Andrew D. Putt, J. I. Miller, M. F. Campa, D. Joyner, O. Pelz, Nargiz Garajayeva, M. Ceccopieri, P. Gardinali, Terry C. Hazen","doi":"10.3389/frmbi.2023.1270352","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1270352","url":null,"abstract":"The Caspian Sea is the world’s largest landlocked saline lake which lies between Europe and Asia. This region is particularly known for its large-scale oil reserves, pipelines, and drilling activities, which have contributed to the environmental decline of this lake. In addition to pollution from the petroleum industry, drainage from various river basins brings an influx of residential, industrial, and agricultural effluents that induce eutrophication and hypoxic conditions in deeper, colder waters, creating an oxygen gradient. The temperature and oxygen stratification in this environment has presented a unique opportunity to investigate the potential of the biodegradative processes carried out by the indigenous microbial community. We believe these indigenous microbes possess different metabolic capabilities to degrade oil as they adapted to declining oxygen concentrations and temperatures with increasing depths over a prolonged period. Hence, community structure and composition will vary with depth.Microcosms were set up to observe the indigenous microbial reaction after a 60 ppm native crude oil amendment over 115 days. Surface water microcosms were incubated at 28ºC and aerated while deep water microcosms were incubated at 8ºC under anaerobic conditions. These two environmental conditions represent the temperature and oxygen extremes along the gradient and were selected as we try to simulate the indigenous community’s response to this oil contamination. DNA was extracted and amplified from these microcosms and sequenced. Bioinformatic analysis was performed to track changes in the abundance of taxa present and biodiversity over different time points to show the progression of community structure.All microcosms showed the presence of hydrocarbon-degrading phyla, whose presence is consistent with other reports from oil-enriched environments. However, distinct communities were observed in oxic versus hypoxic microcosms.Orders of Bacteria related to sulfate and nitrogen cycling were found in hypoxic microcosms, indicating a possible mechanism for the anaerobic biodegradation of crude oil. GC-MS analysis of initial and final microcosms also provided evidence of degradation of hydrocarbon fractions in both warm, oxic and cold, hypoxic conditions.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"10 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138972187","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 : 2023-12-04DOI: 10.3389/frmbi.2023.1301609
Melanie C. Hay, A. Hinsu, P. Koringa, Ramesh J. Pandit, Po-Yu Liu, M. J. Parekh, S. Jakhesara, Xiaoxai Dai, M. Crotta, Bruno Fosso, G. Limon, Javier Guitian, Fiona M. Tomley, Dong Xia, A. Psifidi, Chaitanya G. Joshi, D. Blake
Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.
{"title":"Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices","authors":"Melanie C. Hay, A. Hinsu, P. Koringa, Ramesh J. Pandit, Po-Yu Liu, M. J. Parekh, S. Jakhesara, Xiaoxai Dai, M. Crotta, Bruno Fosso, G. Limon, Javier Guitian, Fiona M. Tomley, Dong Xia, A. Psifidi, Chaitanya G. Joshi, D. Blake","doi":"10.3389/frmbi.2023.1301609","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1301609","url":null,"abstract":"Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"30 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138604019","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 : 2023-11-13DOI: 10.3389/frmbi.2023.1232571
Helen Tammert, Carmen Kivistik, Veljo Kisand, Kairi Käiro, Daniel P. R. Herlemann
The impact of salinization on freshwater ecosystems became apparent during the 2022 ecological disaster in the Oder River, located in Poland and Germany, which was caused by salt discharge from mining activities. How bacterial communities respond to salinization caused by industrial salt discharge, or climate change-driven events, depends on the sensitivity of these complex bacterial communities. To investigate the sensitivity of bacterial communities to pulse salinization, we performed an experiment in the salinity range from 0.2 to 6.0. In addition, we sampled similar salinities in the littoral zone of the Baltic Sea where the bacterial communities are permanently exposed to the aforementioned salinities. To simulate a major disturbance, we included an ampicillin/streptomycin treatment in the experiment. Although the addition of antibiotics and increase in salinity had a significant impact on the water bacterial richness and community composition, only antibiotics affected the sediment bacterial community in the experiment. In contrast, sediment bacterial communities from the Baltic Sea littoral zone clustered according to salinity. Hence, sediment bacterial communities are more resistant to pulse changes in salinity than water bacteria but are able to adapt to a permanent change without loss in species richness. Our results indicate that moderate pulse salinization events such as industrial salt discharge or heavy storms will cause changes in the water bacterial communities with unknown consequences for ecosystem functioning. Sediment bacterial communities, however, will probably be unaffected in their ecosystem functions depending on the disturbance strength. Long-term disturbances, such as sea level rise or constant salt discharge, will cause permanent changes in the sediment bacterial community composition.
{"title":"Resistance of freshwater sediment bacterial communities to salinity disturbance and the implication for industrial salt discharge and climate change-based salinization","authors":"Helen Tammert, Carmen Kivistik, Veljo Kisand, Kairi Käiro, Daniel P. R. Herlemann","doi":"10.3389/frmbi.2023.1232571","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1232571","url":null,"abstract":"The impact of salinization on freshwater ecosystems became apparent during the 2022 ecological disaster in the Oder River, located in Poland and Germany, which was caused by salt discharge from mining activities. How bacterial communities respond to salinization caused by industrial salt discharge, or climate change-driven events, depends on the sensitivity of these complex bacterial communities. To investigate the sensitivity of bacterial communities to pulse salinization, we performed an experiment in the salinity range from 0.2 to 6.0. In addition, we sampled similar salinities in the littoral zone of the Baltic Sea where the bacterial communities are permanently exposed to the aforementioned salinities. To simulate a major disturbance, we included an ampicillin/streptomycin treatment in the experiment. Although the addition of antibiotics and increase in salinity had a significant impact on the water bacterial richness and community composition, only antibiotics affected the sediment bacterial community in the experiment. In contrast, sediment bacterial communities from the Baltic Sea littoral zone clustered according to salinity. Hence, sediment bacterial communities are more resistant to pulse changes in salinity than water bacteria but are able to adapt to a permanent change without loss in species richness. Our results indicate that moderate pulse salinization events such as industrial salt discharge or heavy storms will cause changes in the water bacterial communities with unknown consequences for ecosystem functioning. Sediment bacterial communities, however, will probably be unaffected in their ecosystem functions depending on the disturbance strength. Long-term disturbances, such as sea level rise or constant salt discharge, will cause permanent changes in the sediment bacterial community composition.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136282102","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 : 2023-11-09DOI: 10.3389/frmbi.2023.1287369
Jensen H. C. Yiu, Jieling Cai, Samson W. M. Cheung, Karie Tsz-Ching Chin, Chi Fai Chan, Edward S.C. Ma, Rakesh Sharma, Bernhard Dorweiler, Connie W. Woo
The gut microbiota can be beneficial and harmful to cardiovascular health depending on the mechanisms. The interaction between gut microbiota-derived flagellin and toll-like receptor 5 in hepatocytes, resulting in apolipoprotein A1 (ApoA1) production, brings forth a cardiovascular benefit to the host. Here, the association between flagellated microbiota and high-density lipoprotein-cholesterol (HDL-C) in humans was explored. Through sex-based gut microbiota analysis of two population-based cohorts, the 500 Functional Genomics Project (500FG) and Chinese cohorts, we found positive correlations between the capacity to produce flagellins in the gut microbiota and HDL-C in females of the 500FG and males of Chinese cohorts. Eubacterium rectale, Lachnospira pectinoschiza , Roseburia intestinalis and Roseburia inulinivorans were crucial species for such correlations. Diverse types of flagellins and TLR5, but not NAIP/NLRC4, flagellin-engaging receptors, were detectable by proteomic analysis of the human liver. However, not all flagellated bacteria yield the same degree of such benefit because of differences in the penetration of flagellins where other factors such as geographics and diets may play important roles.
{"title":"The association between flagellin producers in the gut microbiota and HDL-C level in humans","authors":"Jensen H. C. Yiu, Jieling Cai, Samson W. M. Cheung, Karie Tsz-Ching Chin, Chi Fai Chan, Edward S.C. Ma, Rakesh Sharma, Bernhard Dorweiler, Connie W. Woo","doi":"10.3389/frmbi.2023.1287369","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1287369","url":null,"abstract":"The gut microbiota can be beneficial and harmful to cardiovascular health depending on the mechanisms. The interaction between gut microbiota-derived flagellin and toll-like receptor 5 in hepatocytes, resulting in apolipoprotein A1 (ApoA1) production, brings forth a cardiovascular benefit to the host. Here, the association between flagellated microbiota and high-density lipoprotein-cholesterol (HDL-C) in humans was explored. Through sex-based gut microbiota analysis of two population-based cohorts, the 500 Functional Genomics Project (500FG) and Chinese cohorts, we found positive correlations between the capacity to produce flagellins in the gut microbiota and HDL-C in females of the 500FG and males of Chinese cohorts. Eubacterium rectale, Lachnospira pectinoschiza , Roseburia intestinalis and Roseburia inulinivorans were crucial species for such correlations. Diverse types of flagellins and TLR5, but not NAIP/NLRC4, flagellin-engaging receptors, were detectable by proteomic analysis of the human liver. However, not all flagellated bacteria yield the same degree of such benefit because of differences in the penetration of flagellins where other factors such as geographics and diets may play important roles.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":" 41","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135293606","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 : 2023-11-07DOI: 10.3389/frmbi.2023.1286985
Sierra N. Smith, Jessa L. Watters, Cameron D. Siler
Anurans (frogs and toads) are an ecologically diverse group of vertebrate organisms that display a myriad of reproductive modes and life history traits. To persist in such an expansive array of habitats, these organisms have evolved specialized skin that is used for respiration while also protecting against moisture loss, pathogens, and environmental contaminants. Anuran skin is also colonized by communities of symbiotic microorganisms, and these skin microbiota serve critical roles in numerous processes associated with anuran host health and persistence such as pathogen resistance and immunity. However, gaps remain in our understanding of the environmental and evolutionary processes that shape frog skin microbial communities. Here, we combined existing anuran disease data with 16S rRNA skin microbial inventories to elucidate the roles that geographic location, host evolutionary history, host ecology, and pathogen presence play in the microbial community assemblage of five co-distributed frog host species in Oklahoma. These focal species possess distinct ecological preferences: aquatic, semi-aquatic, and arboreal, and our results indicate that host ecology is the primary driver of frog skin microbial community structure. Additionally, compositional differences were observed among select host species based on geographic location, but this was not consistent among all five frog species. We did not find evidence of phylogenetic signal among our samples and results from the Classification and Regression Tree Analysis revealed that the presence of the amphibian pathogen Batrachochytrium dendrobatidis and the severity of infection were not drivers of skin microbiome differences among our focal host species. Results from this comparative study contribute to our growing understanding of the environmental and host-associated drivers of skin microbial community assemblage and represents one of the first studies on landscape-level variation in skin microbial communities among North American frogs.
{"title":"Host ecology drives frog skin microbiome diversity across ecotone in South-Central North America","authors":"Sierra N. Smith, Jessa L. Watters, Cameron D. Siler","doi":"10.3389/frmbi.2023.1286985","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1286985","url":null,"abstract":"Anurans (frogs and toads) are an ecologically diverse group of vertebrate organisms that display a myriad of reproductive modes and life history traits. To persist in such an expansive array of habitats, these organisms have evolved specialized skin that is used for respiration while also protecting against moisture loss, pathogens, and environmental contaminants. Anuran skin is also colonized by communities of symbiotic microorganisms, and these skin microbiota serve critical roles in numerous processes associated with anuran host health and persistence such as pathogen resistance and immunity. However, gaps remain in our understanding of the environmental and evolutionary processes that shape frog skin microbial communities. Here, we combined existing anuran disease data with 16S rRNA skin microbial inventories to elucidate the roles that geographic location, host evolutionary history, host ecology, and pathogen presence play in the microbial community assemblage of five co-distributed frog host species in Oklahoma. These focal species possess distinct ecological preferences: aquatic, semi-aquatic, and arboreal, and our results indicate that host ecology is the primary driver of frog skin microbial community structure. Additionally, compositional differences were observed among select host species based on geographic location, but this was not consistent among all five frog species. We did not find evidence of phylogenetic signal among our samples and results from the Classification and Regression Tree Analysis revealed that the presence of the amphibian pathogen Batrachochytrium dendrobatidis and the severity of infection were not drivers of skin microbiome differences among our focal host species. Results from this comparative study contribute to our growing understanding of the environmental and host-associated drivers of skin microbial community assemblage and represents one of the first studies on landscape-level variation in skin microbial communities among North American frogs.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"83 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135480280","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 : 2023-11-07DOI: 10.3389/frmbi.2023.1151889
Eric J. de Muinck, Pål Trosvik, Nga Nguyen, Peter J. Fashing, Vetle M. Stigum, Nina Robinson, Johanne U. Hermansen, Monica C. Munthe-Kaas, Lars O. Baumbusch
Background There is an increasing awareness of the importance of the gut microbiome in disease progression and the maintenance of human health. However, links between the microbiome and cancer onset remain relatively unexplored. This is especially the case for childhood cancers, which although rare, are the predominant cause of death among children in Western countries. Methods Fecal samples were collected from patients, before the onset of treatment, by the Norwegian Childhood Cancer Biobank in Oslo and from children attending kindergartens in Oslo, Norway. Using 16S rRNA gene amplicon sequencing, we compared the gut microbiome compositions of the children diagnosed with cancer with children attending kindergarten. Results We observed significant differences in the relative abundances of several taxa, including a striking depletion of Faecalibacterium prausnitzii , an important taxa linked to gut health maintenance. Conclusions Our observations provide evidence that the gut microbiome may play an important role in physiological changes associated with the onset of childhood cancer. However, further studies should be designed in order to validate our findings. Furthermore, these results suggest that variations in the microbial community could potentially be used as an early indicator of childhood cancer.
{"title":"Reduced abundance of Faecalibacterium prausnitzii in the gut microbiota of children diagnosed with cancer, a pilot study","authors":"Eric J. de Muinck, Pål Trosvik, Nga Nguyen, Peter J. Fashing, Vetle M. Stigum, Nina Robinson, Johanne U. Hermansen, Monica C. Munthe-Kaas, Lars O. Baumbusch","doi":"10.3389/frmbi.2023.1151889","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1151889","url":null,"abstract":"Background There is an increasing awareness of the importance of the gut microbiome in disease progression and the maintenance of human health. However, links between the microbiome and cancer onset remain relatively unexplored. This is especially the case for childhood cancers, which although rare, are the predominant cause of death among children in Western countries. Methods Fecal samples were collected from patients, before the onset of treatment, by the Norwegian Childhood Cancer Biobank in Oslo and from children attending kindergartens in Oslo, Norway. Using 16S rRNA gene amplicon sequencing, we compared the gut microbiome compositions of the children diagnosed with cancer with children attending kindergarten. Results We observed significant differences in the relative abundances of several taxa, including a striking depletion of Faecalibacterium prausnitzii , an important taxa linked to gut health maintenance. Conclusions Our observations provide evidence that the gut microbiome may play an important role in physiological changes associated with the onset of childhood cancer. However, further studies should be designed in order to validate our findings. Furthermore, these results suggest that variations in the microbial community could potentially be used as an early indicator of childhood cancer.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"206 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135475829","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 : 2023-11-03DOI: 10.3389/frmbi.2023.1258290
Paul M. Campbell, Thomas Willmott, Gavin J. Humphreys, Oana Piscoran, Houda Chea, Angela M. Summers, Joanne E. Konkel, Christopher G. Knight, Titus Augustine, Andrew J. McBain
Introduction Chronic kidney disease (CKD) may affect the human microbiome via increased concentrations of uremic toxins such as urea and creatinine. Methods We have profiled the oral microbiota in patients with CKD before and one week after kidney transplantation. Living kidney donors were also longitudinally tracked over a similar period, allowing direct comparison between a group undergoing transplant surgery alone (donors) (n=13) and a group additionally undergoing the introduction of immunosuppressive agents and the resolution of CKD (recipients) (n=45). Results Transplantation was associated with a similar pattern of decreasing alpha diversity in the oral microbiome in recipients and donors via Kruskal-Wallis testing, within one week of transplantation. Amplicon sequence variants (ASVs) associated with Haemophilus parainfluenzae , Aggregatibacteria segnis , Peptostreptococcus and Actinobacillu s were significantly decreased in recipients within a week of transplantation. Discussion A reduction in ASVs in these genera could influence the risk of bacterial endocarditis, a rare but high-mortality kidney transplantation complication. A range of factors may drive the observed changes in oral microbiome including both factors associated with surgery itself and the decreases in salivary urea, administration of macrolide antibiotic immunosuppressants, and disruption to immune function that characterise kidney transplant.
{"title":"Transplantation impacts on the oral microbiome of kidney recipients and donors","authors":"Paul M. Campbell, Thomas Willmott, Gavin J. Humphreys, Oana Piscoran, Houda Chea, Angela M. Summers, Joanne E. Konkel, Christopher G. Knight, Titus Augustine, Andrew J. McBain","doi":"10.3389/frmbi.2023.1258290","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1258290","url":null,"abstract":"Introduction Chronic kidney disease (CKD) may affect the human microbiome via increased concentrations of uremic toxins such as urea and creatinine. Methods We have profiled the oral microbiota in patients with CKD before and one week after kidney transplantation. Living kidney donors were also longitudinally tracked over a similar period, allowing direct comparison between a group undergoing transplant surgery alone (donors) (n=13) and a group additionally undergoing the introduction of immunosuppressive agents and the resolution of CKD (recipients) (n=45). Results Transplantation was associated with a similar pattern of decreasing alpha diversity in the oral microbiome in recipients and donors via Kruskal-Wallis testing, within one week of transplantation. Amplicon sequence variants (ASVs) associated with Haemophilus parainfluenzae , Aggregatibacteria segnis , Peptostreptococcus and Actinobacillu s were significantly decreased in recipients within a week of transplantation. Discussion A reduction in ASVs in these genera could influence the risk of bacterial endocarditis, a rare but high-mortality kidney transplantation complication. A range of factors may drive the observed changes in oral microbiome including both factors associated with surgery itself and the decreases in salivary urea, administration of macrolide antibiotic immunosuppressants, and disruption to immune function that characterise kidney transplant.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"27 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135819495","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 : 2023-11-02DOI: 10.3389/frmbi.2023.1292571
Sarah Pitell, Sarah-Jane Haig
Respiratory infections from drinking water-associated pathogens that can cause infections in the immunocompromised (DWPIs) are increasing, yet knowledge of DWPI aerosolization and if dynamics are DWPI-specific is lacking. Although there are several DWPI mitigation strategies, the use of antimicrobial showerheads is one of the easiest and most economical. There are many manufacturers and designs of antimicrobial showerheads that claim to remove microorganisms from shower water, yet all fail to assess efficacy in realistic conditions. In this study, a custom-built shower laboratory housing triplicates of three different showerheads (antimicrobial filter-based, antimicrobial silver-embedded and conventional acrylonitrile butadiene styrene plastic) were used to assess the physiochemical and microbial dynamics in shower water and respirable shower water-associated aerosols (1µm – 5 µm) over the course of 84 days. Collectively, findings from the study suggest that showerheads marketed as antimicrobial produce similar chemical and DWPI water quality to non-antimicrobial showerheads (p= >0.05) when operated under real-world conditions, however marked differences in the rare microbial community were present. In addition, although there were no differences in absolute DWPI abundance between showerhead type, each DWPI peaked in concentration at a different biofilm ages, suggesting that potential DWPI inhalation risk is DWPI- specific and influenced by the number of days of operation of the showerhead.
{"title":"Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols","authors":"Sarah Pitell, Sarah-Jane Haig","doi":"10.3389/frmbi.2023.1292571","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1292571","url":null,"abstract":"Respiratory infections from drinking water-associated pathogens that can cause infections in the immunocompromised (DWPIs) are increasing, yet knowledge of DWPI aerosolization and if dynamics are DWPI-specific is lacking. Although there are several DWPI mitigation strategies, the use of antimicrobial showerheads is one of the easiest and most economical. There are many manufacturers and designs of antimicrobial showerheads that claim to remove microorganisms from shower water, yet all fail to assess efficacy in realistic conditions. In this study, a custom-built shower laboratory housing triplicates of three different showerheads (antimicrobial filter-based, antimicrobial silver-embedded and conventional acrylonitrile butadiene styrene plastic) were used to assess the physiochemical and microbial dynamics in shower water and respirable shower water-associated aerosols (1µm – 5 µm) over the course of 84 days. Collectively, findings from the study suggest that showerheads marketed as antimicrobial produce similar chemical and DWPI water quality to non-antimicrobial showerheads (p= &gt;0.05) when operated under real-world conditions, however marked differences in the rare microbial community were present. In addition, although there were no differences in absolute DWPI abundance between showerhead type, each DWPI peaked in concentration at a different biofilm ages, suggesting that potential DWPI inhalation risk is DWPI- specific and influenced by the number of days of operation of the showerhead.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"30 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135933913","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：