{"title":"Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species","authors":"Yizhak Hershko , Matan Slutzkin , Daniel Barkan , Amos Adler","doi":"10.1016/j.resmic.2024.104246","DOIUrl":"10.1016/j.resmic.2024.104246","url":null,"abstract":"<div><div>Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic <em>Nocardia</em> species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for <em>N. cyriacigeorgica</em>, <em>N. farcinica</em>, <em>N. brasiliensis</em>, <em>N. wallacei</em>, and <em>N. abscessus</em>. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) <em>N. brasiliensis</em> diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of <em>Nocardia</em> species.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104246"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Lipid lysination by MprF contributes to hemolytic pigment retention in group B Streptococcus","authors":"Elise Caliot , Arnaud Firon , Audrey Solgadi , Patrick Trieu-Cuot , Shaynoor Dramsi","doi":"10.1016/j.resmic.2024.104231","DOIUrl":"10.1016/j.resmic.2024.104231","url":null,"abstract":"<div><div>Group B <em>Streptococcus</em> (GBS) is the leading cause of neonatal sepsis and meningitis. A major virulence factor is a pigmented beta-haemolytic/cyto-lysin (β-h/c) toxin with an ornithine rhamnolipid structure. We initially observed that absence of MprF enzyme altered pigmentation and haemolytic activity in GBS. Next, we showed that MprF-dependent lipid lysination contributes to the retention of the ornithine rhamnolipid within GBS membrane. Furthermore, cationic lipidation by MprF altered membrane properties contributing to resistance to the cyclic lipopeptide daptomycin and to acidic pH. This study highlights the importance of cationic lipids in cell envelope homeostasis and in modulating β-h/c activity.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104231"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142093717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhiwei Huang , Fulong Xiao , Qiao Wang , Xiaojuan Zhang , Yuhu Shen , Yunxia Deng , Ping Shi
{"title":"BSC2 modulates AmB resistance via the maintenance of intracellular sodium/potassium ion homeostasis in Saccharomyces cerevisiae","authors":"Zhiwei Huang , Fulong Xiao , Qiao Wang , Xiaojuan Zhang , Yuhu Shen , Yunxia Deng , Ping Shi","doi":"10.1016/j.resmic.2024.104245","DOIUrl":"10.1016/j.resmic.2024.104245","url":null,"abstract":"<div><div>Previous studies on <em>BSC2</em> have shown that it enhances yeast cell resistance to AmB via antioxidation and induces multidrug resistance by contributing to biofilm formation. Herein, we found that <em>BSC2</em> overexpression could reverse the sensitivity of <em>pmp3</em>Δ to AmB and help the tested strains restore the intracellular sodium/potassium balance under exposure to AmB. Meanwhile, overexpression of the chitin gene <em>CHS2</em> could simulate <em>BSC2</em> to reverse the sensitivity of <em>pmp3</em>Δ and <em>nha1</em>Δ to high salt or AmB. However, <em>BSC2</em> overexpression in <em>flo11</em>Δ failed to induce AmB resistance, form biofilms, and affect cell wall biogenesis, while <em>CHS2</em> overexpression compensated the resistance of <em>flo11</em>Δ to AmB. Additionally, <em>BSC2</em> levels were positively correlated with maintaining cell membrane integrity under exposure to AmB, CAS, or a combination of both. <em>BSC2</em> overexpression in <em>nha1</em>Δ exhibited a similar function of <em>CHS2</em>, which can compensate for the sensitivity of the mutant to high salt. Altogether, the results demonstrate for the first time that <em>BSC2</em> may promote ion equilibrium by strengthening cell walls and inhibiting membrane damage in a FLO path-dependent manner, thus enhancing the resistance of yeast cells to AmB. This study also reveals the possible mechanism of antifungal drugs CAS and AmB combined to inhibit fungi.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104245"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sihem Guesmi , Kais Ghedira , Petar Pujic , Afef Najjari , Guylaine Miotello , Ameur Cherif , Issay Narumi , Jean Armengaud , Philippe Normand , Haïtham Sghaier
{"title":"Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10","authors":"Sihem Guesmi , Kais Ghedira , Petar Pujic , Afef Najjari , Guylaine Miotello , Ameur Cherif , Issay Narumi , Jean Armengaud , Philippe Normand , Haïtham Sghaier","doi":"10.1016/j.resmic.2024.104230","DOIUrl":"10.1016/j.resmic.2024.104230","url":null,"abstract":"<div><div>The effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, <em>Kocuria rhizophila</em> PT10, isolated from the rhizosphere of the desert plant <em>Panicum turgidum</em> were investigated using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry. Overall, 1487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids. Also, one of the more significant findings to emerge from this study is the SOS response of stressed PT10. Moreover, a comparison of top hits radio-modulated proteins of cold-acclimated PT10 with proteomics data from gamma-irradiated <em>Deinococcus deserti</em> showed that stressed PT10 has a specific response characterised by a high over-abundance of NemA, GatD, and UdgB.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104230"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141875819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Muhammad Fazle Rabbee , Md. Sarafat Ali , Md. Nurul Islam , Mohammed M. Rahman , Md. Mohidul Hasan , Kwang-Hyun Baek
{"title":"Endophyte mediated biocontrol mechanisms of phytopathogens in agriculture","authors":"Muhammad Fazle Rabbee , Md. Sarafat Ali , Md. Nurul Islam , Mohammed M. Rahman , Md. Mohidul Hasan , Kwang-Hyun Baek","doi":"10.1016/j.resmic.2024.104229","DOIUrl":"10.1016/j.resmic.2024.104229","url":null,"abstract":"<div><div><span>The global human population is growing and demand for food is increasing. Global agriculture<span> faces numerous challenges, including excessive application of synthetic pesticides, emergence of herbicide-and pesticide-resistant </span></span>pathogenic microbes<span><span>, and more frequent natural disasters associated with global warming. Searches for valuable endophytes have increased, with the aim of making agriculture more sustainable and environmentally friendly. Endophytic microbes are known to have a variety of beneficial effects on plants. They can effectively transfer nutrients from the soil into plants, promote plant growth and development<span>, increase disease resistance, increase </span></span>stress tolerance<span><span><span>, prevent herbivore feeding, reduce the virulence of pathogens, and inhibit the growth of rival plant species. Endophytic microbes can considerably minimize the need for agrochemicals, such as fertilizers, fungicides, </span>bactericides, insecticides, and herbicides in the cultivation of crop plants. This review summarizes current knowledge on the roles of endophytes focusing on their mechanisms of disease control against </span>phytopathogens<span><span> through the secretion of antimicrobial substances and volatile organic compounds, and the induction of systemic resistance in plants. Additionally, the beneficial roles of these endophytes and their metabolites in the control of </span>postharvest diseases in plants have been summarized.</span></span></span></div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104229"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141591208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterisation of a new virulent phage isolated from Hainan Island with potential against multidrug-resistant Pseudomonas aeruginosa infections.","authors":"Anyang Li, Chen Chen, Yanmei Li, Yanshuang Wang, Xuemiao Li, Qiao Zhu, Yue Zhang, Shen Tian, Qianfeng Xia","doi":"10.1016/j.resmic.2024.104250","DOIUrl":"10.1016/j.resmic.2024.104250","url":null,"abstract":"<p><p>Multidrug-resistant (MDR) Pseudomonas aeruginosa is a serious life-threatening pathogen. The rise in P. aeruginosa resistance rates has renewed interest in phages as an alternative therapeutic approach for treating bacterial infections. In this study, we investigated the characteristics of the first Pseudomonas phage, vB_PaP_HN01, isolated from Hainan, the only tropical island in China. The lytic rate of this phage against P. aeruginosa reached 64.3 % (27/42). Under the optimal multiplicity of infection (MOI) of 0.1, more than 90 % of phage particles absorb onto the host cell within 10 min, with an eclipse period of around 15 min, and a high titer phage production (10<sup>11</sup> PFU/ml) within 90 min was demonstrated. vB_PaP_HN01 maintains a robust titer after 1 h exposure to pH values and temperatures (up to 50 °C). Genome annotation revealed that vB_PaP_HN01 did not contain drug-resistance or lysogeny-associated genes. It can effectively inhibit the formation of biofilms of MDR P. aeruginosa and eliminated aggressive biofilms (removal rate about 70 %). In the in vivo infection models, it was demonstrated that the survival rate and lifespan of Galleria mellonella larvae were increased alongside the injection of vB_PaP_HN01. These data revealed the potential of vB_PaP_HN01 against P. aeruginosa in clinic.</p>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":" ","pages":"104250"},"PeriodicalIF":2.5,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chien-Jui Huang, Ellen Pauwelyn, Marc Ongena, Peter Bleyaert, Monica Höfte
{"title":"Both GacS-regulated lipopeptides and the type three secretion system contribute to Pseudomonas cichorii induced necrosis in lettuce and chicory.","authors":"Chien-Jui Huang, Ellen Pauwelyn, Marc Ongena, Peter Bleyaert, Monica Höfte","doi":"10.1016/j.resmic.2024.104249","DOIUrl":"https://doi.org/10.1016/j.resmic.2024.104249","url":null,"abstract":"<p><p>Pseudomonas cichorii SF1-54, the causal agent of lettuce midrib rot disease, produces lipopeptides cichofactins and cichopeptins which are important virulence factors. The GacS/GacA two-component system is well known to regulate production of lipopeptides in pseudomonads. Additionally, the functions of the type three secretion system (T3SS) in P. cichorii-plant interactions are not clarified. In this study, we investigated the role of the GacS-regulated lipopeptides and the T3SS in pathogenicity of P. cichorii SF1-54 on two host plants, chicory and lettuce, by constructing mutants in hrpL, which encodes the key sigma factor to control T3SS expression, and gacS. Compared with the wildtype, the hrpL mutant produced lipopeptides at a similar level but the gacS mutant was strongly impaired in lipopeptide production. The mutant deficient in hrpL did not significantly differ from the wildtype in virulence on chicory and lettuce. The gacS mutant exhibited significantly less symptoms on both host plants compared to the wildtype and the hrpL mutant. Intriguingly, the gacS hrpL-double mutant no longer produced lipopeptides, lost virulence and showed impaired colonization on chicory, but was still weakly virulent on lettuce. Thus, contribution of both the GacS-regulated lipopeptides and T3SS to virulence of P. cichorii SF1-54 is host plant dependent.</p>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":" ","pages":"104249"},"PeriodicalIF":2.5,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laura Ripe-Jaime, Erika Díaz, Ángel G Franco, Catherine Keim, Daniela Burgos, Valeria Pizarro, Luis F Cadavid, Anny Cárdenas, Catalina Arévalo-Ferro
{"title":"Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral.","authors":"Laura Ripe-Jaime, Erika Díaz, Ángel G Franco, Catherine Keim, Daniela Burgos, Valeria Pizarro, Luis F Cadavid, Anny Cárdenas, Catalina Arévalo-Ferro","doi":"10.1016/j.resmic.2024.104248","DOIUrl":"https://doi.org/10.1016/j.resmic.2024.104248","url":null,"abstract":"<p><p>Coral diseases contribute to the worldwide loss of coral reefs, with the Black Band Disease (BBD) being a prominent example. BBD is an infectious condition with lesions with a pigmented mat composed of cyanobacteria, sulphate-reducing, sulphide-oxidizing, and heterotrophic bacteria. We compared the heterotrophic bacterial communities of healthy and BBD-affected colonies of the Caribbean coral Orbicella faveolata using culture-dependent and -independent techniques. Twenty and 23 bacterial isolates were identified from healthy and diseased tissues, respectively, which differed in their capacities to metabolize carbohydrates and citrate, either anaerobically or aerobically. They also differed in their quorum-sensing (QS) activity, as QS signaling molecules were found exclusively, and QS-inhibition was found primarily, in isolates from diseased tissues. Screening of bacterial diversity by 16SrDNA metabarcoding showed that members of the bacterial genera Muricauda and Maritimimonas were dominant in healthy tissues whereas members of the cyanobacterial genus Roseofilum were dominant in diseased tissues. These results suggest that bacterial dysbiosis can be linked with altered bacterial communication, likely leading to diachrony and imbalance that may participate in the progression of BBD. Investigating physiological traits and QS-based communication offers insights into the onset and progression of coral infections, paving the way for novel strategies to mitigate their impact.</p>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":" ","pages":"104248"},"PeriodicalIF":2.5,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Roles of Pseudomonas aeruginosa siderophores in interaction with prokaryotic and eukaryotic organisms","authors":"","doi":"10.1016/j.resmic.2024.104211","DOIUrl":"10.1016/j.resmic.2024.104211","url":null,"abstract":"<div><p><span><span>Pseudomonas aeruginosa</span></span><span> is an opportunistic pathogen that produces two types of siderophores<span>, pyoverdine and pyochelin, that play pivotal roles in iron scavenging from the environment and host cells. </span></span><em>P. aeruginosa</em><span><span> siderophores can serve as </span>virulence factors and perform various functions. Several bacterial and fungal species are likely to interact with </span><em>P. aeruginosa</em> due to its ubiquity in soil and water as well as its potential to cause infections in plants, animals, and humans. Siderophores produced by <em>P. aeruginosa</em> play critical roles in iron scavenging for prokaryotic species (bacteria) and eukaryotic hosts (fungi, animals, insects, invertebrates, and plants) as well. This review provides a comprehensive discussion of the role of <em>P. aeruginosa</em><span> siderophores in interaction with prokaryotes and eukaryotes as well as their underlying mechanisms of action. The evolutionary relationship between </span><em>P. aeruginosa</em> siderophore recognition receptors, such as FpvA, FpvB, and FptA, and those of other bacterial species has also been investigated.</p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 7","pages":"Article 104211"},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140909218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The effect of β-ionone on bacterial cells: the use of specific lux-biosensors","authors":"","doi":"10.1016/j.resmic.2024.104214","DOIUrl":"10.1016/j.resmic.2024.104214","url":null,"abstract":"<div><p><span>The diversity of the biological activity<span><span> of volatile organic compounds (VOCs), including unsaturated </span>ketone<span> β-ionone, promising pharmacological, biotechnological, and agricultural agent, has aroused considerable interest. However, the functional role and mechanisms of action of VOCs remain insufficiently studied. In this work, the response of bacterial cells to the action of β-ionone was studied using specific bioluminescent lux-biosensors containing stress-sensitive promoters. We determined that in </span></span></span><span><em>Escherichia coli</em></span><span> cells, β-ionone induces oxidative stress (P</span><em>katG</em> and P<em>dps</em><span> promoters) through a specific response mediated by the OxyR/OxyS regulon, but not SoxR/SoxS (P</span><em>soxS</em> promoter). It has been shown that β-ionone at high concentrations (50 μM and above) causes a weak induction of the expression from the P<em>ibpA</em> promoter and slightly induces the P<em>colD</em> promoter in the <em>E. coli</em> biosensors; the observed effect is enhanced in the Δ<em>oxy</em><span><span>R mutants. This indicates the presence of some damage to proteins and DNA. β-Ionone was found to inhibit the bichaperone-dependent DnaKJE-ClpB refolding of heat-inactivated bacterial </span>luciferase in </span><em>E. coli</em> wild-type and Δ<em>ibpB</em> mutant strains. In the cells of the Gram-positive bacterium <span><span>Bacillus subtilis</span></span><span><span> 168 pNK-MrgA β-ionone does not cause oxidative stress. Thus, in this work, the specificity of bacterial </span>cell stress responses to the action of β-ionone was shown.</span></p></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 7","pages":"Article 104214"},"PeriodicalIF":2.5,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140916647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}