Frontiers in microbiomes最新文献

{"title":"Dynamic interplay between soil microbial communities, enzyme activities, and pear quality across planting years","authors":"X. Pang, Miao Jia, Ying Zhang, Meihui Chen, Pengyao Miao, Weiting Cheng, Zewei Zhou, Qi Zhang, J. Ye, Jiayu Li, Haibin Wang, Xiaoli Jia","doi":"10.3389/frmbi.2024.1381270","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1381270","url":null,"abstract":"Few studies have been reported on the effect of planting years on fruit quality and soil of pear trees. In this study, four planting years (T5, T20, T30, and T40) of Cuiguan pears were used to analyze fruit quality, rhizosphere soil enzymes, and microbial diversity of pear trees, and their correlations. The results showed that the content of sucrose, reducing sugar and ascorbic acid in Cuiguan Pear showed a tendency of increasing and then decreasing with the increase of planting years, in which the highest content was found in 20- and 30-year-old fruits, and the highest content of total acid was found in 5-year-old fruits. Rhizosphere soil enzyme activities varied with planting year, with the highest protease activity in 20-year-old soil, phosphatase and urease in 30-year-old soil, polyphenol oxidase in 5-year-old soil, and sucrase in 40-year-old soil. The microbial diversity index and the number of OTUs showed an increasing and decreasing trend with the increase of planting years. Among the top 11 bacteria in pear rhizosphere soil average relative abundance, with Bradyrhizobium decreasing in relative abundance at the peak pear fruiting stages (T20 and T30), while Acidothermus showed an increasing trend in relative abundance with increasing planting years. RDA analysis showed that there were differences in the microbial community structure of pear trees at different planting years, and that both sucrose and reducing sugar contents in pears were positively correlated with T20 and T30, ascorbic acid content was positively correlated with T40, whereas the total acid content was positively correlated with T5, and that T20 was positively correlated with soil protease and phosphate mono esterase activities, and that T30 was positively correlated with polyphenol oxidase and urease activities, whereas T40 was positively correlated with sucrase activity. In summary, with the increase of planting years, changes in soil microbial community structure and soil enzyme activity have a significant impact on pear quality formation, and the results of the study provide a theoretical basis for scientific management of pear orchards.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140992816","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":"Influences of Ruminococcus bromii and Peptostreptococcaceae on voluntary exercise behavior in a rodent model","authors":"Matthew Rusling, Anisha Karim, A. Kaye, C. Lee, Lauren Wegman−Points, Victoria Mathis, Thomas Lampeter, Li-Lian Yuan","doi":"10.3389/frmbi.2024.1389103","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1389103","url":null,"abstract":"This study investigates the relationship between the gut microbiome and voluntary exercise, focusing on wheel running activity in a rat model. The gut microbiome plays a crucial role in host physiology, homeostasis, and behavior. Alterations in the gut microbiome have been linked to various pathological states and health conditions, including obesity.Given the strong association between physical inactivity and obesity development, our study aimed to identify microbiome factors associated with elevated levels of voluntary exercise. Male Sprague Dawley rats were used in the 4-week exercise paradigm in which voluntary wheel running behavior was monitored alongside weekly microbiome sampling from fecal pellets.We observed individual differences in running activity among the cohort. Significant positive correlations in running distance were identified across the 4-week time course, suggesting that running activity ranking was largely preserved. Furthermore, earlier running activity emerged as a potential predictor for subsequent running behaviors. Analysis of gut microbiome revealed that alpha diversity was positively correlated with daily running distances, with significant differences in beta diversity observed between high and low running groups. Taxonomic analysis showed distinct abundance differences between running and sedentary conditions, particularly in the Ruminococcaceae and Peptostreptococcaceae families.Our results suggest that the microbiome composition changes significantly early in exercise exposure, potentially influencing exercise behavior. Ruminococcaceae, particularly R. bromii, was identified as a significant contributor to exercise adaptation, while Peptostreptococcaceae was inversely related to running performance as well as alpha diversity. This study underscores the potential of the gut microbiome as a modulator of exercise behavior. Future research should focus on the biological mechanisms linking microbiome changes to exercise adaptation, with R. bromii and Peptostreptococcus as promising candidates for influencing exercise behaviors through future interventional studies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141000078","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":"The microbiome: a link between obesity and breast cancer risk","authors":"Mohamed Gaber, Alana A Arnone, Pierre-Alexandre Vidi, Katherine L Cook","doi":"10.3389/frmbi.2024.1394719","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1394719","url":null,"abstract":"Globally, breast cancer is the leading cause of cancer incidence and mortality among all female cancers. Hereditary factors only account for 5-10% of breast cancers, highlighting the importance of non-hereditary factors, such as obesity. The increasing prevalence of obesity underscores the need to understand its contribution to breast cancer risk. Multiple mechanisms may mediate pro-carcinogenic effects of obesity, including altered adipokine levels, local and systemic inflammation, disruption of insulin and insulin-like growth factor signaling, increased estrogen levels, and alterations of the microbiome. In this review, we focus on the link between gut microbiome alterations and breast cancer risk in the context of obesity. First, we discuss how obesity influences the gut microbiome. Next, we describe the effect of such microbiome alterations on breast carcinogenesis, highlighting underlying molecular mechanisms. Finally, we review preclinical data on the interactions between host and bacteria, current challenges to study the obesity-microbiome connection, and future perspectives in this field.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141017012","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":"Exploring the memory of the gut microbiome: a multifaceted perspective","authors":"Amine Zorgani, Bhaskar C. Das","doi":"10.3389/frmbi.2024.1363961","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1363961","url":null,"abstract":"","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140655653","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":"Transport from the wild rapidly alters the diversity and composition of skin microbial communities and antifungal taxa in spring peeper frogs","authors":"Lauren P. Kane, William G. Van Bonn, F. Oliaro, Christian F. Edwardson, Malissa Smith, Lee J. Pinnell","doi":"10.3389/frmbi.2024.1368538","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1368538","url":null,"abstract":"Amphibians are routinely collected from the wild and added into managed care and public display facilities; however, there is a gap in understanding how these practices might alter the diversity and composition of skin microbial communities on these animals. The aim of this study was to evaluate and compare skin microbial communities of spring peeper frogs (Pseudacris crucifer) from acquisition in the wild through the end of their quarantine period and identify microbial taxa with antifungal properties. From an original group of seventy-six frogs, cohorts of ten were swabbed when acquired in the wild, upon transport from the wild, and swabbed throughout a 9-week quarantine period while under managed care. An immediate loss of microbial richness and diversity was evident upon transfer of the frogs from their original environment and continued throughout subsequent sampling time-points during quarantine. Importantly, antifungal taxa comprised significantly more of the overall skin community after the frogs were moved from the wild, largely due to members of the family Moraxellaceae. Overall, our findings demonstrate that amphibian skin microbiome changes immediately on removal from the wild, and that these changes persist throughout quarantine while being housed under managed care. This may play a pivotal role in the development of dermatological disease and have implications in the health and immune function of amphibians.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140684147","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":"Intestinal bacteria-derived tryptamine and its impact on human gut microbiota","authors":"Nize Otaru, A. Greppi, Serafina Plüss, Janina N. Zünd, Denisa Mujezinovic, Jana Baur, Ekaterina Koleva, Christophe Lacroix, Benoit Pugin","doi":"10.3389/frmbi.2024.1373335","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1373335","url":null,"abstract":"Tryptamine, a neuromodulator derived from tryptophan, has been shown to significantly impact the host gut homeostasis through its production by the gut microbiota. However, the characterization of tryptamine-producing gut bacteria remains limited, the factors regulating tryptamine production largely unexplored, and its effects on the rest of the gut microbial community unknown. In this study, we screened 13 intestinal strains closely related to known tryptamine producers, characterized their production kinetics, and evaluated whether tryptophan decarboxylation to tryptamine contributes to acid stress tolerance, as shown in other amino acid-dependent acid tolerance systems. We also examined the impact of tryptamine on the composition and function of four healthy human gut microbiota by conducting 48-h ex vivo fecal batch fermentations. To complement the ex vivo experiments, we tested the effect of tryptamine exposure (range: 0.5–8 mM) on the growth of 18 intestinal strains. We identified tryptamine production in five taxa, i.e., Enterocloster asparagiformis, Blautia hansenii, Clostridium nexile, Clostridium sporogenes, and Ruminococcus gnavus, with R. gnavus DSM 108212 accumulating up to 3.4 mM tryptamine after 48 h. An increased tryptophan concentration led to higher tryptamine production. However, tryptamine production was not promoted at low pH and may not protect cells from acid-induced cellular damage. Exposing gut microbial communities to 2.4 mM tryptamine caused mild changes in gut microbiota function and composition. All donors showed reduced carbohydrate consumption after 5 h, leading to donor-specific alterations of short-chain fatty acids (SCFAs) (i.e., propionate, acetate, butyrate) and branched-chain fatty acids (BCFAs) (i.e., isobutyrate and isovalerate) after 48 h. Tryptamine also induced a mild change of community structure, with a consistent reduction in the phylum Bacteroidota as well as amplicon sequence variants (ASVs) related to the genera Bacteroides, Blautia, and Faecalibacterium. We confirmed the sensitivity of Bacteroides and Faecalibacterium strains in vitro at concentrations of 2 mM and above. Multiple gut commensals remained unaffected when exposed to 8 mM tryptamine. Taken together, our findings demonstrated that intestinal bacteria-derived tryptamine is a bioactive molecule that not only alters host homeostasis locally but also modulates the physiology of gut microbial communities. The specific mechanism through which tryptamine exerts its inhibitory effects on specific gut microbes while leaving others unaffected remains to be elucidated.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140750505","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":"Utilizing symbiotic relationships and assisted migration in restoration to cope with multiple stressors, and the legacy of invasive species","authors":"Lisa M. Markovchick, Abril Belgara‐Andrew, Duncan Richard, Tessa Deringer, K. Grady, K. Hultine, G. Allan, T. Whitham, J. Querejeta, C. Gehring","doi":"10.3389/frmbi.2024.1331341","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1331341","url":null,"abstract":"Climate change has increased the need for forest restoration, but low planting success and limited availability of planting materials hamper these efforts. Invasive plants and their soil legacies can further reduce restoration success. Thus, strategies that optimize restoration are crucial. Assisted migration and inoculation with native microbial symbiont communities have great potential to increase restoration success. However, assisted migrants can still show reduced survival compared to local provenances depending on transfer distance. Inoculation with mycorrhizal fungi, effective if well-matched to plants and site conditions, can have neutral to negative results with poor pairings. Few studies have examined the interaction between these two strategies in realistic field environments where native plants experience the combined effects of soil legacies left by invasive plants and the drought conditions that result from a warming, drying climate.We planted two ecotypes (local climate and warmer climate) of Populus fremontii (Fremont cottonwoods), in soils with and without legacies of invasion by Tamarix spp. (tamarisk), and with and without addition of native mycorrhizal fungi and other soil biota from the warmer climate.Four main results emerged. 1) First year survival in soil legacies left behind after tamarisk invasion and removal was less than one tenth of survival in soil without a tamarisk legacy. 2) Actively restoring soil communities after tamarisk removal tripled first year cottonwood survival for both ecotypes, but only improved survival of the warmer, assisted migrant ecotype trees in year two. 3) Actively restoring soil communities in areas without a tamarisk history reduced first year survival for both ecotypes, but improved survival of the warmer, assisted migrant ecotype trees in year two. 4) By the second year, inoculated assisted migrants survived at five times the rate of inoculated trees from the local ecotype.Results emphasize the detrimental effects of soil legacies left after tamarisk invasion and removal, the efficacy of assisted migration and restoring soil communities alongside plants, and the need to thoughtfully optimize pairings between plants, fungi, and site conditions.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140378848","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":"Differential enrichment of bacteria and phages in the vaginal microbiomes in PCOS and obesity: shotgun sequencing analysis","authors":"Senlin Zheng, Huimin Chen, Hongyi Yang, Xulan Zheng, Tengwei Fu, Xiaoyan Qiu, Meiqin Wang","doi":"10.3389/frmbi.2023.1229723","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1229723","url":null,"abstract":"Previous research has linked vaginal bacteria to polycystic ovary syndrome (PCOS) and obesity in women, yet the specific disparities in vaginal microbiota between these conditions remain unclear.In this study, we aimed to elucidate the contribution of dysregulated vaginal microbiota to PCOS and obesity by analyzing the vaginal microbiota in reproductive-aged women with and without PCOS, as well as obese and non-obese women, using shotgun sequencing.Swab specimens were collected from four groups of subjects: PCOS and obese, PCOS and non-obese, non-PCOS and obese, and non-PCOS and non-obese. A total of 333 bacteria and 24 viruses/phages were identified to the species level. Clustering analysis revealed that non-PCOS and non-obese individuals exhibit a similar “healthy” vaginal microbiome, while both obesity and PCOS were associated with microbial dysbiosis. Significant differences in abundance were observed for 26 bacterial species and 6 phages/viruses between groups. Notably, pathobionts such as Streptococcus pyogenes, Leptospira santarosai, Citrobacter amalonaticus, Listeria ivanovii, and Clostridium perfringens were significantly less abundant or absent in the non-PCOS and non-obese group. Furthermore, the abundance of Lactobacillus, Pseudomonas bacteria, and their corresponding phages exhibited positive correlations. Lactobacillus bacteria, lactobacillus phage, and pseudomonas phage/virus were identified as indicators of a healthy vaginal microbiome. Importantly, the differentially enriched bacteria in the PCOS and obesity groups were distinct.This study confirms that PCOS and obesity are associated with differing enrichment of bacteria and viruses/phages, with both conditions linked to microbial dysbiosis. Moreover, our findings suggest that vaginal phage diversity is associated with a healthy vaginal microbiota, while dysbiosis is associated with a decrease in phages alongside increased bacterial diversity.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140379629","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":"Searching for bacterial plastitrophs in modified Winogradsky columns","authors":"Fatai A. Olabemiwo, Claudia Kunney, Rachel Hsu, Chloe De Palo, Thaddeus Bashaw, Kendall Kraut, Savannah Ryan, Yuting Huang, Will Wallentine, Siddhant Kalra, Valerie Nazzaro, Frederick M. Cohan","doi":"10.3389/frmbi.2024.1303112","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1303112","url":null,"abstract":"Plastic pollution has surged due to increased human consumption and disposal of plastic products. Microbial communities capable of utilizing plastic as a carbon source may play a crucial role in degrading and consuming environmental plastic. In this study, we investigated the potential of a modified Winogradsky column (WC) to enrich Connecticut landfill soil for plastic-degrading bacteria and genes.By filling WCs with landfill soil and inorganic Bushnell Haas medium, and incorporating polyethylene (PE) strips at different soil layers, we aimed to identify bacterial taxa capable of degrading PE. We employed high-throughput 16S rRNA sequencing to identify the microbes cultivated on the plastic strips and the intervening landfill soil. We used PICRUSt2 to estimate the functional attributes of each community from 16S rRNA sequences.After 12 months of incubation, distinct colors were observed along the WC layers, indicating successful cultivation. Sequencing revealed significant differences in bacterial communities between the plastic strips and the intervening landfill-soil habitats, including increased abundance of the phyla Verrucomicrobiota and Pseudomonadota (néé Proteobacteria) on the strips. Based on inferred genomic content, the most highly abundant proteins in PE strip communities tended to be associated with plastic degradation pathways. Phylogenetic analysis of 16S rRNA sequences showed novel unclassified phyla and genera enriched on the plastic strips. Our findings suggest PE-supplemented Winogradsky columns can enrich for plastic-degrading microbes, offering insights into bioremediation strategies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140226188","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":"Editorial: Environmental microbiomes, metabolites, and respiratory diseases","authors":"Xi Fu, Dan Norbäck, Yu Sun","doi":"10.3389/frmbi.2024.1388525","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1388525","url":null,"abstract":"","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140247684","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}