Frontiers in microbiomes最新文献

{"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}

{"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}

{"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}

{"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}

{"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}

{"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= >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}

{"title":"Comparative analysis of microbiota in the ceca of broiler chickens with necrotic enteritis fed a commercial corn diet or with corn high in flavonoids (PennHFD1)","authors":"Katarzyna B. Miska, Monika Proszkowiec-Weglarz, Vinicius Buiatte, Mahmoud Mahmoud, Tyler Lesko, Mark C. Jenkins, Surinder Chopra, Alberto Gino Lorenzoni","doi":"10.3389/frmbi.2023.1212130","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1212130","url":null,"abstract":"Necrotic enteritis (NE) is a disease of the gastrointestinal tract that is common in broiler chickens and causes substantial economic losses to the poultry industry worldwide. The removal of many antimicrobials in poultry diets has driven the search for alternatives. The purpose of this study was to determine the microbiota changes in the cecal luminal (CE-L) and mucosal (CE-M) populations of broiler chickens undergoing clinical NE (co-infected with Eimeria maxima and Clostridium perfringens) while fed a diet containing a flavonoid rich corn (PennHFD1) or control diet using commercial corns. It was previously shown that chickens fed a diet high in flavonoids had improved performance parameters, lower mortality rate, and lower incidence of intestinal lesions. Flavonoids have been shown to have anti-bacterial, immuno-modulatory, and anti-inflammatory activity. The current study included four experimental groups: infected chickens fed commercial corn diet (CTRL-A) or PennHFD1 (CTRL-B) and infected chickens fed commercial corn diet (IF-A) or PennHFD1 (IF-B). We found that most of the microbiota changes were due to infection rather than diet. The alpha diversity in the IF chickens was lower in both CE-L and CE-M. The beta diversity of microbial communities was different between IF and CTRL chickens, as well as between CTRL-A and CTRL-B. The beta diversity of CTRL birds was more homogenous compared to IF samples. Taxonomic analysis showed a decrease in short chain fatty acid producing bacteria in IF birds. An increase in lactic acid producing bacteria, Escherichia coli , and Enterococcus cecorum was also observed in IF birds. It is possible that the effect of the high flavonoid corn on the microbiota was overcome by the effect of NE, or that the positive effects of increased flavonoids in NE-challenged birds are a result of mechanisms which do not involve the microbiota. The effects of high flavonoid corn on NE infections may be further investigated as a possible alternative to antimicrobials.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135168899","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 microbial landscape of the nasopharynx in children: a systematic review of studies using next generation sequencing","authors":"Petra Zimmermann","doi":"10.3389/frmbi.2023.1231271","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1231271","url":null,"abstract":"Introduction The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes. Objectives This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition. Methods MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised. Results The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus , Moraxella , and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome. Conclusion The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135730730","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":"Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities","authors":"Qilin Yang, Jiancheng Wang, Dawei Zhang, Hui Feng, Tohir A. Bozorov, Honglan Yang, Daoyuan Zhang","doi":"10.3389/frmbi.2023.1248384","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1248384","url":null,"abstract":"Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis , in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"155 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135739260","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":"Comparative analysis of intestinal flora at different overwintering periods in wild relict gulls (Larus relictus): first evidence from Northern China","authors":"Hongyu Yao, Zeming Zhang, Nan Wu, Mengping Wang, Qian Wu, Hong Wu, Dapeng Zhao","doi":"10.3389/frmbi.2023.1218281","DOIUrl":"https://doi.org/10.3389/frmbi.2023.1218281","url":null,"abstract":"The migratory bird’s gut microbiome composition and function change during the overwintering period, helping the host to adapt to different environments. Our study investigated the gut microbiome of migratory relict gulls ( Larus relictus ) in the early and late wintering stages from their overwintering grounds in Tianjin, China. We collected 24 and 29 fecal samples at the early and late stages, respectively, and analyzed the samples using high-throughput sequencing technology to find the relationship between diet, living environment, and gut microbiome of migratory birds. The results showed that the diversity and abundance of microbial communities (alpha diversity) increased during the overwintering period and significantly differed between both groups (beta diversity). Based on the gut microbial taxonomic composition, the relative abundance of Firmicutes decreased during the overwintering period, and Proteobacteria increased significantly. Furthermore, Catellicoccus and Breznakia were the main genera in both the early and late stages. Prediction of KEGG functions based on the PICRUSt2 method showed that changes in the gut microbiome resulted in an increased abundance of bacteria associated with amino acid metabolism, metabolism of cofactors and vitamins, energy metabolism, and environmental adaptation in the late stage. Differences in diet and environment at different stages during the overwintering period may have led to the differentiation of microbial communities, and their adaptive mechanisms need to be further investigated. This is the first in-depth study of the gut microbial composition of L. relictus during the overwintering period in northern China. These findings may contribute to the protection of migratory birds.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135828290","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}