Pub Date : 2024-08-11DOI: 10.1016/j.micres.2024.127872
Antimicrobial resistance has been an increasingly serious threat to global public health. The contribution of non-antibiotic pharmaceuticals to the development of antibiotic resistance has been overlooked. Our study found that the anti-inflammatory drug phenylbutazone could protect P. aeruginosa against antibiotic mediated killing by binding to the efflux pump regulator MexR. In this study, antibiotic activity against P. aeruginosa alone or in combination with phenylbutazone was evaluated in vitro and in vivo. Resazurin accumulation assay, transcriptomic sequencing, and PISA assay were conducted to explore the underlying mechanism for the reduced antibiotic susceptibility caused by phenylbutazone. Then EMSA, ITC, molecular dynamic simulations, and amino acid substitutions were used to investigate the interactions between phenylbutazone and MexR. We found that phenylbutazone could reduce the susceptibility of P. aeruginosa to multiple antibiotics, including parts of β-lactams, fluoroquinolones, tetracyclines, and macrolides. Phenylbutazone could directly bind to MexR, then promote MexR dissociating from the mexA-mexR intergenic region and de-repress the expression of MexAB-OprM efflux pump. The overexpressed MexAB-OprM pump resulted in the reduced antibiotic susceptibility. And the His41 and Arg21 residues of MexR were involved in the phenylbutazone-MexR interaction. We hope this study would imply the potential risk of antibiotic resistance caused by non-antibiotic pharmaceuticals.
{"title":"Non-antibiotic pharmaceutical phenylbutazone binding to MexR reduces the antibiotic susceptibility of Pseudomonas aeruginosa","authors":"","doi":"10.1016/j.micres.2024.127872","DOIUrl":"10.1016/j.micres.2024.127872","url":null,"abstract":"<div><p>Antimicrobial resistance has been an increasingly serious threat to global public health. The contribution of non-antibiotic pharmaceuticals to the development of antibiotic resistance has been overlooked. Our study found that the anti-inflammatory drug phenylbutazone could protect <em>P. aeruginosa</em> against antibiotic mediated killing by binding to the efflux pump regulator MexR. In this study, antibiotic activity against <em>P. aeruginosa</em> alone or in combination with phenylbutazone was evaluated <em>in vitro</em> and <em>in vivo</em>. Resazurin accumulation assay, transcriptomic sequencing, and PISA assay were conducted to explore the underlying mechanism for the reduced antibiotic susceptibility caused by phenylbutazone. Then EMSA, ITC, molecular dynamic simulations, and amino acid substitutions were used to investigate the interactions between phenylbutazone and MexR. We found that phenylbutazone could reduce the susceptibility of <em>P. aeruginosa</em> to multiple antibiotics, including parts of β-lactams, fluoroquinolones, tetracyclines, and macrolides. Phenylbutazone could directly bind to MexR, then promote MexR dissociating from the <em>mexA</em>-<em>mexR</em> intergenic region and de-repress the expression of MexAB-OprM efflux pump. The overexpressed MexAB-OprM pump resulted in the reduced antibiotic susceptibility. And the His41 and Arg21 residues of MexR were involved in the phenylbutazone-MexR interaction. We hope this study would imply the potential risk of antibiotic resistance caused by non-antibiotic pharmaceuticals.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002738/pdfft?md5=d387e694ccd025c86c3220491672c988&pid=1-s2.0-S0944501324002738-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141985496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-10DOI: 10.1016/j.micres.2024.127870
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
抗菌药耐药性(AMR)是一个复杂的问题,需要采取具体的多部门措施来减缓其蔓延。当人们接触抗菌剂时,会导致耐药细菌增加。这意味着,抗菌剂的使用、滥用和过度使用会对细菌产生选择性压力,从而导致 "沉默 "的抗菌剂耐药性基因库的形成。这些基因随后会被调动到致病细菌中,导致 AMR 的传播。许多社会经济和环境因素都会影响抗药性基因的传播和扩散,如医疗保健系统的质量、水质卫生、卫生基础设施和污染等。孢子生物群是肠道微生物群的重要组成部分,在维持肠道平衡方面发挥作用。然而,由于孢子具有很强的传播性,并且很容易扩散,因此可以成为 AMR 的载体。孢子生物群耐药性基因组,尤其是移动耐药性基因组,对于跟踪、管理和限制抗菌药耐药性基因在病原菌和共生菌之间的传播非常重要。
{"title":"Is there a role for intestinal sporobiota in the antimicrobial resistance crisis?","authors":"","doi":"10.1016/j.micres.2024.127870","DOIUrl":"10.1016/j.micres.2024.127870","url":null,"abstract":"<div><p>Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of \"silent\" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002714/pdfft?md5=44fd0108bb79c30d56d204af9b92bebb&pid=1-s2.0-S0944501324002714-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-10DOI: 10.1016/j.micres.2024.127869
Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5–22 % [w/v]) were Methanobacteriota (formerly “Euryarchaeota”), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36–39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.
{"title":"‘Altruistic’ cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics","authors":"","doi":"10.1016/j.micres.2024.127869","DOIUrl":"10.1016/j.micres.2024.127869","url":null,"abstract":"<div><p>Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5–22 % [w/v]) were <em>Methanobacteriota</em> (formerly <em>“Euryarchaeota”</em>), <em>Pseudomonadota</em> and <em>Bacteroidota</em>, followed by <em>Balneolota</em> and <em>Actinomycetota</em> and <em>Uroviricota</em> in smaller proportions, while at high salinities (36–39 % [w/v]) the most abundant phylum was <em>Methanobacteriota,</em> followed by <em>Bacteroidota</em>. The most abundant genera at intermediate salinities were <em>Halorubrum</em> and the bacterial genus <em>Spiribacter</em>, while the haloarchaeal genera <em>Halorubrum</em>, <em>Halonotius</em>, and <em>Haloquadratum</em> were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002702/pdfft?md5=87f6de3422c645ff0bb9d832c328008e&pid=1-s2.0-S0944501324002702-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141998319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1016/j.micres.2024.127871
The gut microbiota plays a critical role in numerous biochemical processes essential for human health, such as metabolic regulation and immune system modulation. An increasing number of research suggests a strong association between the gut microbiota and carcinogenesis. The diverse metabolites produced by gut microbiota can modulate cellular gene expression, cell cycle dynamics, apoptosis, and immune system functions, thereby exerting a profound influence on cancer development and progression. A healthy gut microbiota promotes substance metabolism, stimulates immune responses, and thereby maintains the long-term homeostasis of the intestinal microenvironment. When the gut microbiota becomes imbalanced and disrupts the homeostasis of the intestinal microenvironment, the risk of various diseases increases. This review aims to elucidate the impact of gut microbial metabolites on cancer initiation and progression, focusing on short-chain fatty acids (SCFAs), polyamines (PAs), hydrogen sulfide (H2S), secondary bile acids (SBAs), and microbial tryptophan catabolites (MTCs). By detailing the roles and molecular mechanisms of these metabolites in cancer pathogenesis and therapy, this article sheds light on dual effects on the host at different concentrations of metabolites and offers new insights into cancer research.
{"title":"Exploring gut microbial metabolites as key players in inhibition of cancer progression: Mechanisms and therapeutic implications","authors":"","doi":"10.1016/j.micres.2024.127871","DOIUrl":"10.1016/j.micres.2024.127871","url":null,"abstract":"<div><p>The gut microbiota plays a critical role in numerous biochemical processes essential for human health, such as metabolic regulation and immune system modulation. An increasing number of research suggests a strong association between the gut microbiota and carcinogenesis. The diverse metabolites produced by gut microbiota can modulate cellular gene expression, cell cycle dynamics, apoptosis, and immune system functions, thereby exerting a profound influence on cancer development and progression. A healthy gut microbiota promotes substance metabolism, stimulates immune responses, and thereby maintains the long-term homeostasis of the intestinal microenvironment. When the gut microbiota becomes imbalanced and disrupts the homeostasis of the intestinal microenvironment, the risk of various diseases increases. This review aims to elucidate the impact of gut microbial metabolites on cancer initiation and progression, focusing on short-chain fatty acids (SCFAs), polyamines (PAs), hydrogen sulfide (H<sub>2</sub>S), secondary bile acids (SBAs), and microbial tryptophan catabolites (MTCs). By detailing the roles and molecular mechanisms of these metabolites in cancer pathogenesis and therapy, this article sheds light on dual effects on the host at different concentrations of metabolites and offers new insights into cancer research.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1016/j.micres.2024.127868
Pseudomonas protegens can generally produce multiple antibiotics including pyoluteorin (Plt), 2,4-diacetylphloroglucinol (DAPG), and pyrrolnitrin (Prn). In this study, we discovered and characterized a quorum sensing (QS) system, PpqI/R, in P. protegens H78. PpqI/R, encoded by two open reading frames (ORFs) (H78_01960/01961) in P. protegens H78 genome, is a LuxI/R-type QS system. Four long-chain acyl homoserine lactone (AHL) signaling molecules, 3-OH-C10-HSL, 3-OH-C12-HSL, C12-HSL, and 3-OH-C14-HSL, are produced by H78. Biosynthesis of these AHLs is catalyzed by PpqI synthase and activated by the PpqR regulator in H78 and in Escherichia coli when heterologously expressed. PpqR activates ppqI expression by targeting the lux box upstream of the ppqI promoter in cooperation with corresponding AHLs. The four aforementioned AHLs exhibited different capabilities to induce ppqI promoter expression, with 3-OH-C12-HSL showing the highest induction activity. In H78 cells, ppqI/R expression is activated by the two-component system GacS/A and the RNA chaperone Hfq. Differential regulation of the PpqI/R system in secondary metabolism has a negative effect on DAPG biosynthesis and ped operon (involved in volatile organic compound biosynthesis) expression. In contrast, Plt biosynthesis and prn operon expression were positively regulated by PpqI/R. In summary, PpqI/R, the first characterized QS system in P. protegens, is activated by GacS/A and Hfq and controls the expression of secondary metabolites, including antibiotics.
{"title":"Discovery and characterization of the PpqI/R quorum sensing system activated by GacS/A and Hfq in Pseudomonas protegens H78","authors":"","doi":"10.1016/j.micres.2024.127868","DOIUrl":"10.1016/j.micres.2024.127868","url":null,"abstract":"<div><p><em>Pseudomonas protegens</em> can generally produce multiple antibiotics including pyoluteorin (Plt), 2,4-diacetylphloroglucinol (DAPG), and pyrrolnitrin (Prn). In this study, we discovered and characterized a quorum sensing (QS) system, PpqI/R, in <em>P. protegens</em> H78. PpqI/R, encoded by two open reading frames (ORFs) (H78_01960/01961) in <em>P. protegens</em> H78 genome, is a LuxI/R-type QS system. Four long-chain acyl homoserine lactone (AHL) signaling molecules, 3-OH-C<sub>10</sub>-HSL, 3-OH-C<sub>12</sub>-HSL, C<sub>12</sub>-HSL, and 3-OH-C<sub>14</sub>-HSL, are produced by H78. Biosynthesis of these AHLs is catalyzed by PpqI synthase and activated by the PpqR regulator in H78 and in <em>Escherichia coli</em> when heterologously expressed. PpqR activates <em>ppqI</em> expression by targeting the <em>lux</em> box upstream of the <em>ppqI</em> promoter in cooperation with corresponding AHLs. The four aforementioned AHLs exhibited different capabilities to induce <em>ppqI</em> promoter expression, with 3-OH-C<sub>12</sub>-HSL showing the highest induction activity. In H78 cells, <em>ppqI/R</em> expression is activated by the two-component system GacS/A and the RNA chaperone Hfq. Differential regulation of the PpqI/R system in secondary metabolism has a negative effect on DAPG biosynthesis and <em>ped</em> operon (involved in volatile organic compound biosynthesis) expression. In contrast, Plt biosynthesis and <em>prn</em> operon expression were positively regulated by PpqI/R. In summary, PpqI/R, the first characterized QS system in <em>P. protegens,</em> is activated by GacS/A and Hfq and controls the expression of secondary metabolites, including antibiotics.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141913288","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-05DOI: 10.1016/j.micres.2024.127865
The gut microbiota, mainly resides in the colon, possesses a remarkable ability to metabolize different substrates to create bioactive substances, including short-chain fatty acids, indole-3-propionic acid, and secondary bile acids. In the liver, bile acids are synthesized from cholesterol and then undergo modification by the gut microbiota. Beyond those reclaimed by the enterohepatic circulation, small percentage of bile acids escaped reabsorption, entering the systemic circulation to bind to several receptors, such as farnesoid X receptor (FXR), thereby exert their biological effects. Gut microbiota interplays with bile acids by affecting their synthesis and determining the production of secondary bile acids. Reciprocally, bile acids shape out the structure of gut microbiota. The interplay of bile acids and FXR is involved in the development of multisystemic conditions, encompassing metabolic diseases, hepatobiliary diseases, immune associated disorders. In the review, we aim to provide a thorough review of the intricate crosstalk between the gut microbiota and bile acids, the physiological roles of bile acids and FXR in mammals’ health and disease, and the clinical translational considerations of gut microbiota-bile acids-FXR in the treatment of the diseases.
肠道微生物群主要存在于结肠中,具有代谢不同底物生成生物活性物质的卓越能力,包括短链脂肪酸、吲哚-3-丙酸和次级胆汁酸。在肝脏中,胆汁酸由胆固醇合成,然后经过肠道微生物群的修饰。除了被肠肝循环回收的胆汁酸外,还有一小部分胆汁酸逃脱了重吸收,进入全身循环,与法尼类固醇 X 受体(FXR)等多种受体结合,从而发挥其生物效应。肠道微生物群与胆汁酸相互作用,影响胆汁酸的合成并决定次级胆汁酸的产生。反过来,胆汁酸也塑造了肠道微生物群的结构。胆汁酸和 FXR 的相互作用涉及多种系统疾病的发展,包括代谢性疾病、肝胆疾病和免疫相关疾病。在这篇综述中,我们旨在全面回顾肠道微生物群与胆汁酸之间错综复杂的相互作用、胆汁酸和 FXR 在哺乳动物健康和疾病中的生理作用,以及肠道微生物群-胆汁酸-FXR 在疾病治疗中的临床转化考虑。
{"title":"Exploring the role of a novel postbiotic bile acid: Interplay with gut microbiota, modulation of the farnesoid X receptor, and prospects for clinical translation","authors":"","doi":"10.1016/j.micres.2024.127865","DOIUrl":"10.1016/j.micres.2024.127865","url":null,"abstract":"<div><p>The gut microbiota, mainly resides in the colon, possesses a remarkable ability to metabolize different substrates to create bioactive substances, including short-chain fatty acids, indole-3-propionic acid, and secondary bile acids. In the liver, bile acids are synthesized from cholesterol and then undergo modification by the gut microbiota. Beyond those reclaimed by the enterohepatic circulation, small percentage of bile acids escaped reabsorption, entering the systemic circulation to bind to several receptors, such as farnesoid X receptor (FXR), thereby exert their biological effects. Gut microbiota interplays with bile acids by affecting their synthesis and determining the production of secondary bile acids. Reciprocally, bile acids shape out the structure of gut microbiota. The interplay of bile acids and FXR is involved in the development of multisystemic conditions, encompassing metabolic diseases, hepatobiliary diseases, immune associated disorders. In the review, we aim to provide a thorough review of the intricate crosstalk between the gut microbiota and bile acids, the physiological roles of bile acids and FXR in mammals’ health and disease, and the clinical translational considerations of gut microbiota-bile acids-FXR in the treatment of the diseases.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141913290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-04DOI: 10.1016/j.micres.2024.127866
Alpine meadows, which are critical for biodiversity and ecosystem services, are increasingly degrading, necessitating effective restoration strategies. This study explored the mechanism by which Kobresia humilis, an alpine meadow-constructive species, modulates the rhizosphere microbiome via root exudates to enhance growth. Field investigations revealed that the plant height of K. humilis in a severely degraded (SD) alpine meadow was significantly higher than that in other K. humilis populations. Consequently, we analysed the differences between this plot and other K. humilis samples with different degrees of degradation to explore the reasons underlying the phenotypic differences in K. humilis. 16 S rRNA amplicon sequencing results showed that the SD plots were significantly enriched with more Bacillus, altering the composition of the rhizosphere microbial community of K. humilis. The collection and analysis of root exudates from various K. humilis locations revealed distinct differences. Procrustes analysis indicated a strong correlation between the root exudates and the rhizosphere microbiome composition of K. humilis. Model-based integration of metabolite observations, species abundance 2 (MIMOSA2), and Spearman's rank correlation coefficient analysis were used to identify the root exudates potentially related to the enrichment and recruitment of Bacillus. Bacillus from SD samples was isolated and screened, and the representative strain D334 was found to be differentially enriched compared to other samples. A series of in vitro experiments with the screened root exudates and strain D334 demonstrated that K. humilis could recruit Bacillus and promote its colonisation by releasing flavonoids, particularly baicalin. Additionally, K. humilis can release sucrose and riboflavin, which promote strain growth. Finally, soil microbiome transplantation experiments confirmed that different K. humilis phenotypes were closely related to the functions of the rhizosphere microbiome, especially in root morphological shaping. Moreover, the effects of Bacillus inoculation and the microbiome on the plant phenotypes were consistent. In summary, this study revealed a new mechanism by which K. humilis recruits rhizosphere growth-promoting bacteria and enhances soil nutrient utilisation, thereby promoting plant growth. These findings provide a theoretical basis for ecological restoration using soil microbial communities and clarify the relationship between plant metabolites and microbial community assembly.
对生物多样性和生态系统服务至关重要的高山草甸正日益退化,需要采取有效的恢复策略。本研究探讨了高山草甸构建物种蒿草(Kobresia humilis)通过根部渗出物调节根瘤微生物群以促进生长的机制。实地调查显示,在严重退化(SD)的高山草甸上,K. humilis的株高明显高于其他K. humilis种群。因此,我们分析了该地块与其他不同退化程度的蒿草样本之间的差异,以探索蒿草表型差异的原因。16 S rRNA 扩增子测序结果显示,降解地块明显富含更多的芽孢杆菌,改变了蒿草根瘤微生物群落的组成。从不同地点收集和分析蒿草根部渗出物发现了明显的差异。Procrustes 分析表明,根部渗出物与蒿草根瘤微生物群组成之间存在很强的相关性。利用基于模型的代谢物观测整合、物种丰度 2(MIMOSA2)和斯皮尔曼等级相关系数分析,确定了可能与芽孢杆菌的富集和招募有关的根外渗物。对 SD 样本中的芽孢杆菌进行了分离和筛选,发现代表性菌株 D334 与其他样本相比富集程度不同。利用筛选出的根部渗出物和菌株 D334 进行的一系列体外实验表明,腐霉菌可以招募芽孢杆菌,并通过释放黄酮类化合物(尤其是黄芩苷)促进芽孢杆菌的定殖。此外,腐霉菌还能释放蔗糖和核黄素,促进菌株生长。最后,土壤微生物组移植实验证实,不同的 K. humilis 表型与根圈微生物组的功能密切相关,尤其是在根系形态塑造方面。此外,芽孢杆菌接种和微生物组对植物表型的影响是一致的。总之,本研究揭示了一种新的机制,通过这种机制,K. humilis可以招募根圈生长促进菌,提高土壤养分利用率,从而促进植物生长。这些发现为利用土壤微生物群落进行生态恢复提供了理论依据,并阐明了植物代谢产物与微生物群落组装之间的关系。
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Pub Date : 2024-08-03DOI: 10.1016/j.micres.2024.127863
High-throughput sequencing studies have shown that diet or antimicrobial treatments impact animal gut microbiota equilibrium. However, properties related to the gut microbial ecosystem stability, such as resilience, resistance, or functional redundancy, must be better understood. To shed light on these ecological processes, we combined advanced statistical methods with 16 S rRNA gene sequencing, functional prediction, and fitness analyses in the gut microbiota of the cockroach Blattella germanica subject to three periodic pulses of the antibiotic (AB) kanamycin (n=512). We first confirmed that AB did not significantly affect cockroaches' biological fitness, and gut microbiota changes were not caused by insect physiology alterations. The sex variable was examined for the first time in this species, and no statistical differences in the gut microbiota diversity or composition were found. The comparison of the gut microbiota dynamics in control and treated populations revealed that (1) AB treatment decreases diversity and completely disrupts the co-occurrence networks between bacteria, significantly altering the gut community structure. (2) Although AB also affected the genetic composition, functional redundancy would explain a smaller effect on the functional potential than on the taxonomic composition. (3) As predicted by Taylor's law, AB generally affected the most abundant taxa to a lesser extent than the less abundant taxa. (4) Taxa follow different trends in response to ABs, highlighting "resistant taxa," which could be critical for community restoration. (5) The gut microbiota recovered faster after the three AB pulses, suggesting that gut microbiota adapts to repeated treatments.
高通量测序研究表明,饮食或抗菌治疗会影响动物肠道微生物群的平衡。然而,必须更好地了解与肠道微生物生态系统稳定性相关的特性,如恢复力、抵抗力或功能冗余。为了揭示这些生态过程,我们将先进的统计方法与 16 S rRNA 基因测序、功能预测和适应性分析相结合,研究了受到三种周期性抗生素(AB)卡那霉素影响的德国蜚蠊(n=512)的肠道微生物群。我们首先确认,抗生素对蟑螂的生物适应性没有明显影响,肠道微生物群的变化不是由昆虫生理变化引起的。我们首次对该物种的性别变量进行了研究,结果发现肠道微生物群的多样性和组成没有统计学差异。对照种群和处理种群的肠道微生物群动态比较显示:(1)AB 处理降低了多样性,完全破坏了细菌之间的共生网络,显著改变了肠道群落结构。(2)虽然 AB 也影响遗传组成,但功能冗余对功能潜力的影响小于对分类组成的影响。(3) 正如泰勒定律所预测的那样,AB 对数量最多的类群的影响一般小于数量较少的类群。(4) 分类群对 AB 的反应趋势不同,突出了 "抗性分类群",这可能对群落恢复至关重要。(5)肠道微生物群在三次AB脉冲后恢复较快,表明肠道微生物群能适应重复处理。
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Pub Date : 2024-08-02DOI: 10.1016/j.micres.2024.127841
In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described Bacillus nakamurai was selected for its strong in vitro antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced B. nakamurai strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in B. velezensis, greenhouse experiments show that B. nakamurai BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than B. velezensis QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.
{"title":"Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai","authors":"","doi":"10.1016/j.micres.2024.127841","DOIUrl":"10.1016/j.micres.2024.127841","url":null,"abstract":"<div><p>In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described <em>Bacillus nakamurai</em> was selected for its strong <em>in vitro</em> antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced <em>B. nakamurai</em> strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in <em>B. velezensis</em>, greenhouse experiments show that <em>B. nakamurai</em> BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by <em>Alternaria solani</em> and <em>Exserohilum turcicum</em>, respectively, at levels similar to or better than <em>B. velezensis</em> QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that <em>B. nakamurai</em> BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.</p></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0944501324002428/pdfft?md5=fffc26b9c220475bd011d61204b1e754&pid=1-s2.0-S0944501324002428-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141993244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-02DOI: 10.1016/j.micres.2024.127862
Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that Musa plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as Pseudocercospora fijiensis (P. fijiensis), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (in vitro or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria Bacillus subtilis EA-CB0575 (T2 treatment) or infection by P. fijiensis (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas 16 S sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12–41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of P. fijiensis in banana plants and advance the understanding of how plant domestication influences the endosphere.
内生菌是栖息在植物内部组织中的微生物,在植物生长和抗病方面发挥着关键作用。此外,先前的研究已经证实,穆萨植物从其微生物群中获得了疾病保护功能。值得注意的是,香蕉的作物野生近缘种之一加尔各答 4 号(Calcutta 4)表现出对各种植物病原体(如斐济假丝酵母菌(P. fijiensis))的抗性,而威廉姆斯(Williams)商业栽培品种(cv.)则非常易感。因此,本研究的主要目的是表征和比较加尔各答 4 号和威廉姆斯香蕉共生时的内生微生物群组成。同时,研究还考察了不同植物部位(芽或根)、不同生长阶段(离体或温室)和不同适应性因素(如添加促进植物生长的枯草芽孢杆菌 EA-CB0575(T2 处理)或被 P. fijiensis 感染(T3 处理))之间内生微生物群的差异。使用了依赖培养和不依赖培养的技术来评估这些差异,并评估香蕉内生菌在不同条件下的可培养性。在对所有处理进行评估时,微生物培养产生了 331 个分离物,分布在 54 个属中,而 16 S 测序产生了 9510 个 ASV,分布在 1456 个属中。阿尔法和贝塔多样性在不同植株上表现出显著差异,与对照植株(T1)相比,病原体感染植株(T3)的系统发育多样性有所增加。此外,在 T3 植株中还发现了与氮代谢相关的 4 个丰度不同的属,在比较品种时,有 7 个属的丰度出现差异。在对依赖培养和不依赖培养的方法进行比较时,发现分离菌属占不依赖培养方法检测到的菌属的 3.7%,占总数据的 12-41%,具体取决于处理方法。这些结果对于提出源自作物野生近缘种的管理策略,以提高易感商业品种对影响作物生长发育的适应性因素的抗逆性至关重要。此外,这些结果还有助于破译 P. fijiensis 对香蕉植物的致病作用,并促进对植物驯化如何影响内圈的理解。
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