Our previous study reported that the metabolite of Bacillus subtilis BS-Z15 n-butanol site could reduce body weight gain in mice, showing anti-obesity effects. This study further demonstrated the effects of purified mycosubtilin on the body weight gain and gut microbiota of Kunming mice. 30 male Kunming white mice were randomly selected into three groups at four weeks of age: Control (group A), gavage-administered with saline daily; n-butanol site treated (group B), gavage-administered with n-butanol site metabolites (90 mg/kg); and mycosubtilin treated (group C), gavage-administered with mycosubtilin (6 mg/kg). Different groups’ gut microbiota compositions were analyzed using high-throughput sequencing technology. The results showed that the effects of mycosubtilin and n-butanol sites were consistent; the treatment groups showed a significant reduction in body weight gain as well as triglyceride and low-density lipoprotein contents as compared to the control group (P <0.05). Moreover, the size and contents of epididymal adipocytes were also significantly reduced (P <0.05), and the gavage administration of mycosubtilin could significantly increase the expression levels of lipolysis gene adipose triglyceride lipase (ATGL) in the mice liver. Mycosubtilin and n-butanol site treatments could significantly alter the composition of the gut microbiota as compared to the physiologic saline treatment. B. subtilis BS-Z15 metabolites may regulate weight gain primarily by mycosubtilin, according to these findings. The mycosubtilin might reduce weight gain in mice by regulating lipid metabolism, thereby reducing fat accumulation and altering the composition of gut microbiota.
{"title":"Effect of Bacillus subtilis BS-Z15 metabolite mycosubtilin on body weight gain in mice","authors":"Jun Yang, Jingjing Zhao, Jun-Qi Yue, Ming-Yue Ma, Huan Liu, Jia-Yi Chen, Xi-Yuan Cao, Hao-Ran Li, Heping Zhao, Yi Yang, Huixin Zhao","doi":"10.3389/frmbi.2024.1301857","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1301857","url":null,"abstract":"Our previous study reported that the metabolite of Bacillus subtilis BS-Z15 n-butanol site could reduce body weight gain in mice, showing anti-obesity effects. This study further demonstrated the effects of purified mycosubtilin on the body weight gain and gut microbiota of Kunming mice. 30 male Kunming white mice were randomly selected into three groups at four weeks of age: Control (group A), gavage-administered with saline daily; n-butanol site treated (group B), gavage-administered with n-butanol site metabolites (90 mg/kg); and mycosubtilin treated (group C), gavage-administered with mycosubtilin (6 mg/kg). Different groups’ gut microbiota compositions were analyzed using high-throughput sequencing technology. The results showed that the effects of mycosubtilin and n-butanol sites were consistent; the treatment groups showed a significant reduction in body weight gain as well as triglyceride and low-density lipoprotein contents as compared to the control group (P <0.05). Moreover, the size and contents of epididymal adipocytes were also significantly reduced (P <0.05), and the gavage administration of mycosubtilin could significantly increase the expression levels of lipolysis gene adipose triglyceride lipase (ATGL) in the mice liver. Mycosubtilin and n-butanol site treatments could significantly alter the composition of the gut microbiota as compared to the physiologic saline treatment. B. subtilis BS-Z15 metabolites may regulate weight gain primarily by mycosubtilin, according to these findings. The mycosubtilin might reduce weight gain in mice by regulating lipid metabolism, thereby reducing fat accumulation and altering the composition of gut microbiota.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140245312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-13DOI: 10.3389/frmbi.2024.1277645
Madelyn R. Kirsch, Sierra N. Smith, Daniel J. Becker, J. L. Watters, Katharine A. Marske, C. D. Siler, Hayley C. Lanier
Given the role of microbiomes in promoting host health and homeostasis, understanding the factors shaping skin microbial communities in wild vertebrates has become increasingly important in conservation. This goal is even more pressing for amphibians, for which the skin has multiple critical functions, and pathogens currently decimating populations are linked to significant changes in skin microbiomes. However, because microbiomes are also shaped by environmental and ecological influences, as well as by host phylogeny, it is important to quantify these contributions to microbiome structure in the presence of infection.To understand the joint influence of these diverse factors shaping microbiomes, we used 16S rRNA sequencing to characterize the skin microbial communities of six salamander species (families Plethodontidae and Salamandridae) found in Oklahoma and contrasted the effects of infection status, phylogeny, host ecology, and host environment (i.e., climate) on skin microbiomes.Differences at the level of host family were the main factor influencing microbiome diversity; however, we did not detect a substantial phylogenetic signal. Instead, host ecology and environment were more important in driving microbiome differences among species and genera. Salamanders that tested positive for the skin fungal parasite Batrachochytrium dendrobatidis (Bd) also had slightly less diverse microbiomes than Bd-free animals, but no such differences were associated with the systemic pathogen ranavirus (RV).Together, these results indicate a nuanced relationship between the number and type of microbes present on salamander skin and the factors influencing them. By developing a baseline assessment of the microbiome diversity and richness present on the skin of these focal species, this work also provides a foundation for monitoring and evaluating changes in skin microbiomes as populations continue to experience stressors and diseases.
{"title":"Family shapes microbiome differences in Oklahoma salamanders","authors":"Madelyn R. Kirsch, Sierra N. Smith, Daniel J. Becker, J. L. Watters, Katharine A. Marske, C. D. Siler, Hayley C. Lanier","doi":"10.3389/frmbi.2024.1277645","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1277645","url":null,"abstract":"Given the role of microbiomes in promoting host health and homeostasis, understanding the factors shaping skin microbial communities in wild vertebrates has become increasingly important in conservation. This goal is even more pressing for amphibians, for which the skin has multiple critical functions, and pathogens currently decimating populations are linked to significant changes in skin microbiomes. However, because microbiomes are also shaped by environmental and ecological influences, as well as by host phylogeny, it is important to quantify these contributions to microbiome structure in the presence of infection.To understand the joint influence of these diverse factors shaping microbiomes, we used 16S rRNA sequencing to characterize the skin microbial communities of six salamander species (families Plethodontidae and Salamandridae) found in Oklahoma and contrasted the effects of infection status, phylogeny, host ecology, and host environment (i.e., climate) on skin microbiomes.Differences at the level of host family were the main factor influencing microbiome diversity; however, we did not detect a substantial phylogenetic signal. Instead, host ecology and environment were more important in driving microbiome differences among species and genera. Salamanders that tested positive for the skin fungal parasite Batrachochytrium dendrobatidis (Bd) also had slightly less diverse microbiomes than Bd-free animals, but no such differences were associated with the systemic pathogen ranavirus (RV).Together, these results indicate a nuanced relationship between the number and type of microbes present on salamander skin and the factors influencing them. By developing a baseline assessment of the microbiome diversity and richness present on the skin of these focal species, this work also provides a foundation for monitoring and evaluating changes in skin microbiomes as populations continue to experience stressors and diseases.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"258 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140247355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-08DOI: 10.3389/frmbi.2024.1324476
Alice Rolland, Véronique Douard, Nicolas Lapaque
Obesity is associated with activation of low-grade inflammation in tissues metabolically relevant for the regulation glucose homeostasis. The gut microbiota has been extensively linked to the inflammatory responses observed during obesity emphasizing the interconnection between host immunity and metabolism during obesity. Gut microbiota together with alteration of the gut barrier functions provide a myriad of circulating ligands for the pattern recognition receptors (PRRs) expressed in innate immune cells and nonimmune cells. PRR-dependent signalling drives the expression of a wide range of genes beyond the inflammatory response depending on the specific functions of the targeted cells and on the physiological context. PRRs activation can have opposite effects on host metabolic inflammation. Nucleotide-binding oligomerization domain 1 (NOD1) or NOD-like Receptor pyrin domain containing 3 (NLRP3) activation promote metabolic inflammation and insulin resistance while NOD2 activation improves insulin sensitivity and glucose homeostasis during obesity. Toll-like receptors (TLRs) 2, 4 and 5 also display specific effects on metabolic tissues. TLR5 deficient mice are prone to obesity and inflammation in response to high fat diet, while injection of TLR5 ligand, flagellin, has a protective effect toward diet-induced obesity. To the opposite TLR2 and 4 activations are associated with deleterious metabolic outcome during obesity. TLR4 activation enhances metabolic inflammation and insulin resistance and TLR2 via its activation by molecules derived from the gut microbiota favours the onset of obesity. It is now clear that activation of PRRs by bacterial derived molecules plays a key role in the host metabolic regulation. PRRs are expressed in various cell types complicating the understanding of the mechanisms underlying the relationship between PRRs activation/silencing and metabolic inflammation in obesity context. This review presents an overview of the current understanding of the interrelationship between the gut microbiota and PRRs, with a focus on its consequences for obesity and related metabolic diseases.
{"title":"Role of pattern recognition receptors and microbiota-derived ligands in obesity","authors":"Alice Rolland, Véronique Douard, Nicolas Lapaque","doi":"10.3389/frmbi.2024.1324476","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1324476","url":null,"abstract":"Obesity is associated with activation of low-grade inflammation in tissues metabolically relevant for the regulation glucose homeostasis. The gut microbiota has been extensively linked to the inflammatory responses observed during obesity emphasizing the interconnection between host immunity and metabolism during obesity. Gut microbiota together with alteration of the gut barrier functions provide a myriad of circulating ligands for the pattern recognition receptors (PRRs) expressed in innate immune cells and nonimmune cells. PRR-dependent signalling drives the expression of a wide range of genes beyond the inflammatory response depending on the specific functions of the targeted cells and on the physiological context. PRRs activation can have opposite effects on host metabolic inflammation. Nucleotide-binding oligomerization domain 1 (NOD1) or NOD-like Receptor pyrin domain containing 3 (NLRP3) activation promote metabolic inflammation and insulin resistance while NOD2 activation improves insulin sensitivity and glucose homeostasis during obesity. Toll-like receptors (TLRs) 2, 4 and 5 also display specific effects on metabolic tissues. TLR5 deficient mice are prone to obesity and inflammation in response to high fat diet, while injection of TLR5 ligand, flagellin, has a protective effect toward diet-induced obesity. To the opposite TLR2 and 4 activations are associated with deleterious metabolic outcome during obesity. TLR4 activation enhances metabolic inflammation and insulin resistance and TLR2 via its activation by molecules derived from the gut microbiota favours the onset of obesity. It is now clear that activation of PRRs by bacterial derived molecules plays a key role in the host metabolic regulation. PRRs are expressed in various cell types complicating the understanding of the mechanisms underlying the relationship between PRRs activation/silencing and metabolic inflammation in obesity context. This review presents an overview of the current understanding of the interrelationship between the gut microbiota and PRRs, with a focus on its consequences for obesity and related metabolic diseases.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"51 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140077109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-07DOI: 10.3389/frmbi.2024.1324967
Sebastian Beilig, M. Pannekens, L. Voskuhl, Rainer U. Meckenstock
Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m−2 OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.
{"title":"Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis","authors":"Sebastian Beilig, M. Pannekens, L. Voskuhl, Rainer U. Meckenstock","doi":"10.3389/frmbi.2024.1324967","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1324967","url":null,"abstract":"Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m−2 OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"16 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140261121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-01DOI: 10.3389/frmbi.2024.1342464
Lynn Ferro, Kyle Bittinger, Sabrina P Trudo, K. Beane, Shawn W. Polson, Jae Kyeom Kim, Jillian C. Trabulsi
The complementary diet influences the gastrointestinal (gut) microbiota composition and, in turn, host health and, potentially, microRNA (miRNA) expression. This study aimed to assess the feasibility of altering the gut microbial communities with short-term food introduction and to determine the effects of different vegetables on the gut microbiota and miRNA expression in infants. A total of 11 infants were randomized to one of the following intervention arms: control, broccoli, or carrot. The control group maintained the milk diet only, while the other groups consumed either a broccoli puree or a carrot puree on days 1–3 along with their milk diet (human milk or infant formula). Genomic DNA and total RNA were extracted from fecal samples to determine the microbiota composition and miRNA expression. Short-term feeding of both broccoli and carrots resulted in changes in the microbiota and miRNA expression. Compared to the control, a trend toward a decrease in Shannon index was observed in the carrot group on days 2 and 4. The carrot and broccoli groups differed by weighted UniFrac. Streptococcus was increased on day 4 in the carrot group compared to the control. The expression of two miRNAs (i.e., miR-217 and miR-590-5p) trended towards decrease in both the broccoli and carrot groups compared to the control, whereas increases in eight and two different miRNAs were observed in the carrot and broccoli groups, respectively. Vegetable interventions differentially impacted the gut microbiota and miRNA expression, which may be a mechanism by which total vegetable intake and variety are associated with reduced disease risk.
{"title":"A short-term, randomized, controlled, feasibility study of the effects of different vegetables on the gut microbiota and microRNA expression in infants","authors":"Lynn Ferro, Kyle Bittinger, Sabrina P Trudo, K. Beane, Shawn W. Polson, Jae Kyeom Kim, Jillian C. Trabulsi","doi":"10.3389/frmbi.2024.1342464","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1342464","url":null,"abstract":"The complementary diet influences the gastrointestinal (gut) microbiota composition and, in turn, host health and, potentially, microRNA (miRNA) expression. This study aimed to assess the feasibility of altering the gut microbial communities with short-term food introduction and to determine the effects of different vegetables on the gut microbiota and miRNA expression in infants. A total of 11 infants were randomized to one of the following intervention arms: control, broccoli, or carrot. The control group maintained the milk diet only, while the other groups consumed either a broccoli puree or a carrot puree on days 1–3 along with their milk diet (human milk or infant formula). Genomic DNA and total RNA were extracted from fecal samples to determine the microbiota composition and miRNA expression. Short-term feeding of both broccoli and carrots resulted in changes in the microbiota and miRNA expression. Compared to the control, a trend toward a decrease in Shannon index was observed in the carrot group on days 2 and 4. The carrot and broccoli groups differed by weighted UniFrac. Streptococcus was increased on day 4 in the carrot group compared to the control. The expression of two miRNAs (i.e., miR-217 and miR-590-5p) trended towards decrease in both the broccoli and carrot groups compared to the control, whereas increases in eight and two different miRNAs were observed in the carrot and broccoli groups, respectively. Vegetable interventions differentially impacted the gut microbiota and miRNA expression, which may be a mechanism by which total vegetable intake and variety are associated with reduced disease risk.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"71 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140087157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-16DOI: 10.3389/frmbi.2024.1277177
Xi Fu, Aga Shama, D. Norbäck, Qingsong Chen, Yun Xia, Xin Zhang, Yu Sun
Rhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.In this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.The most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).This study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.
{"title":"Exploring the role of indoor microbiome and environmental characteristics in rhinitis symptoms among university students","authors":"Xi Fu, Aga Shama, D. Norbäck, Qingsong Chen, Yun Xia, Xin Zhang, Yu Sun","doi":"10.3389/frmbi.2024.1277177","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1277177","url":null,"abstract":"Rhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.In this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.The most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).This study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"54 48","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139961319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.3389/frmbi.2024.1309947
Gayathri Ilangumaran, S. Subramanian, Donald Lawrence Smith
This study comprehensively analyzed two distinct rhizobacterial strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48, through whole genome de novo sequencing. Isolated from root nodules of Amphicarpaea bracteata, a native legume related to soybean, they were selected to explore beneficial rhizobacteria from native plant relatives. Utilizing Illumina and Nanopore sequencers and MaSuRCA assembly, their complete genetic information was elucidated. Rhizobium sp. SL42 has a 4.06 Mbp circular chromosome and two plasmids with 60% GC content, while Hydrogenophaga sp. SL48 exhibits a 5.43 Mbp circular chromosome with 65% GC content. Genetic analysis identified them as new species, supported by ANI values (77.72% for SL42 and 83.39% for SL48) below the threshold. The genomic analysis unraveled a plethora of genes encoding diverse metabolic functions, secretion systems for substance transport, quorum sensing for coordination, and biosynthetic gene clusters suggesting the production of bioactive compounds. These functional properties contribute to plant growth stimulation, reflecting the symbiotic relationship of rhizobacteria with plants, potentially involving nitrogen fixation and growth-promoting compounds. This research contributes valuable knowledge about plant-microbe interactions and plant growth promotion by these two strains of rhizobacteria.
{"title":"Complete genome sequences of Rhizobium sp. strain SL42 and Hydrogenophaga sp. strain SL48, microsymbionts of Amphicarpaea bracteata","authors":"Gayathri Ilangumaran, S. Subramanian, Donald Lawrence Smith","doi":"10.3389/frmbi.2024.1309947","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1309947","url":null,"abstract":"This study comprehensively analyzed two distinct rhizobacterial strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48, through whole genome de novo sequencing. Isolated from root nodules of Amphicarpaea bracteata, a native legume related to soybean, they were selected to explore beneficial rhizobacteria from native plant relatives. Utilizing Illumina and Nanopore sequencers and MaSuRCA assembly, their complete genetic information was elucidated. Rhizobium sp. SL42 has a 4.06 Mbp circular chromosome and two plasmids with 60% GC content, while Hydrogenophaga sp. SL48 exhibits a 5.43 Mbp circular chromosome with 65% GC content. Genetic analysis identified them as new species, supported by ANI values (77.72% for SL42 and 83.39% for SL48) below the threshold. The genomic analysis unraveled a plethora of genes encoding diverse metabolic functions, secretion systems for substance transport, quorum sensing for coordination, and biosynthetic gene clusters suggesting the production of bioactive compounds. These functional properties contribute to plant growth stimulation, reflecting the symbiotic relationship of rhizobacteria with plants, potentially involving nitrogen fixation and growth-promoting compounds. This research contributes valuable knowledge about plant-microbe interactions and plant growth promotion by these two strains of rhizobacteria.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"115 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139840658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.3389/frmbi.2024.1309947
Gayathri Ilangumaran, S. Subramanian, Donald Lawrence Smith
This study comprehensively analyzed two distinct rhizobacterial strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48, through whole genome de novo sequencing. Isolated from root nodules of Amphicarpaea bracteata, a native legume related to soybean, they were selected to explore beneficial rhizobacteria from native plant relatives. Utilizing Illumina and Nanopore sequencers and MaSuRCA assembly, their complete genetic information was elucidated. Rhizobium sp. SL42 has a 4.06 Mbp circular chromosome and two plasmids with 60% GC content, while Hydrogenophaga sp. SL48 exhibits a 5.43 Mbp circular chromosome with 65% GC content. Genetic analysis identified them as new species, supported by ANI values (77.72% for SL42 and 83.39% for SL48) below the threshold. The genomic analysis unraveled a plethora of genes encoding diverse metabolic functions, secretion systems for substance transport, quorum sensing for coordination, and biosynthetic gene clusters suggesting the production of bioactive compounds. These functional properties contribute to plant growth stimulation, reflecting the symbiotic relationship of rhizobacteria with plants, potentially involving nitrogen fixation and growth-promoting compounds. This research contributes valuable knowledge about plant-microbe interactions and plant growth promotion by these two strains of rhizobacteria.
{"title":"Complete genome sequences of Rhizobium sp. strain SL42 and Hydrogenophaga sp. strain SL48, microsymbionts of Amphicarpaea bracteata","authors":"Gayathri Ilangumaran, S. Subramanian, Donald Lawrence Smith","doi":"10.3389/frmbi.2024.1309947","DOIUrl":"https://doi.org/10.3389/frmbi.2024.1309947","url":null,"abstract":"This study comprehensively analyzed two distinct rhizobacterial strains, Rhizobium sp. SL42 and Hydrogenophaga sp. SL48, through whole genome de novo sequencing. Isolated from root nodules of Amphicarpaea bracteata, a native legume related to soybean, they were selected to explore beneficial rhizobacteria from native plant relatives. Utilizing Illumina and Nanopore sequencers and MaSuRCA assembly, their complete genetic information was elucidated. Rhizobium sp. SL42 has a 4.06 Mbp circular chromosome and two plasmids with 60% GC content, while Hydrogenophaga sp. SL48 exhibits a 5.43 Mbp circular chromosome with 65% GC content. Genetic analysis identified them as new species, supported by ANI values (77.72% for SL42 and 83.39% for SL48) below the threshold. The genomic analysis unraveled a plethora of genes encoding diverse metabolic functions, secretion systems for substance transport, quorum sensing for coordination, and biosynthetic gene clusters suggesting the production of bioactive compounds. These functional properties contribute to plant growth stimulation, reflecting the symbiotic relationship of rhizobacteria with plants, potentially involving nitrogen fixation and growth-promoting compounds. This research contributes valuable knowledge about plant-microbe interactions and plant growth promotion by these two strains of rhizobacteria.","PeriodicalId":73089,"journal":{"name":"Frontiers in microbiomes","volume":"127 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139780964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.3389/frmbi.2024.1274277
Samuel B Pannoni, W. Holben
Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.
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Pub Date : 2024-02-13DOI: 10.3389/frmbi.2024.1274277
Samuel B Pannoni, W. Holben
Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.
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