microLife最新文献

{"title":"Accessing microbial natural products of the past.","authors":"Martin Klapper, Pierre Stallforth","doi":"10.1093/femsml/uqae023","DOIUrl":"10.1093/femsml/uqae023","url":null,"abstract":"<p><p>Microbial natural products-low molecular weight compounds biosynthesized by microorganisms-form the foundation of important modern therapeutics, including antibiotics, immunomodulators, and anti-cancer agents. This perspective discusses and contrasts two emerging approaches for uncovering natural products of the past. On the one hand, ancestral sequence reconstruction allows recreating biosynthetic pathways that date back hundreds of millions of years. On the other hand, sequencing and <i>de novo</i> assembly of ancient DNA reveals the biosynthetic potential of ancient microbial communities up to 100 000 years. Together, these approaches unveil an otherwise hidden reservoir of functional and structural molecular diversity. They also offer new opportunities to study the biological function and evolution of these molecules within an archaeological context.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae023"},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tracking the uptake of labelled host-derived extracellular vesicles by the human fungal pathogen <i>Aspergillus fumigatus</i>.","authors":"Corissa Visser, Flora Rivieccio, Thomas Krüger, Franziska Schmidt, Zoltán Cseresnyés, Manfred Rohde, Marc Thilo Figge, Olaf Kniemeyer, Matthew G Blango, Axel A Brakhage","doi":"10.1093/femsml/uqae022","DOIUrl":"10.1093/femsml/uqae022","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) have gained attention as facilitators of intercellular as well as interkingdom communication during host-microbe interactions. Recently we showed that upon infection, host polymorphonuclear leukocytes produce antifungal EVs targeting the clinically important fungal pathogen <i>Aspergillus fumigatus</i>; however, the small size of EVs (<1 µm) complicates their functional analysis. Here, we employed a more tractable, reporter-based system to label host alveolar epithelial cell-derived EVs and enable their visualization during <i>in vitro A. fumigatus</i> interaction. Fusion of EV marker proteins (CD63, CD9, and CD81) with a Nanoluciferase (NLuc) and a green fluorescent protein (GFP) facilitated their relative quantification by luminescence and visualization by a fluorescence signal. The use of an NLuc fused with a GFP is advantageous as it allows for quantification and visualization of EVs simultaneously without additional external manipulation and to distinguish subpopulations of EVs. Using this system, visualization and tracking of EVs was possible using confocal laser scanning microscopy and advanced imaging analysis. These experiments revealed the propensity of host cell-derived EVs to associate with the fungal cell wall and ultimately colocalize with the cell membrane of <i>A. fumigatus</i> hyphae in large numbers. In conclusion, we have created a series of tools to better define the complex interplay of host-derived EVs with microbial pathogens.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae022"},"PeriodicalIF":0.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pyoverdine-antibiotic combination treatment: its efficacy and effects on resistance evolution in <i>Escherichia coli</i>.","authors":"Vera Vollenweider, Flavie Roncoroni, Rolf Kümmerli","doi":"10.1093/femsml/uqae021","DOIUrl":"10.1093/femsml/uqae021","url":null,"abstract":"<p><p>Antibiotic resistance is a growing concern for global health, demanding innovative and effective strategies to combat pathogenic bacteria. Pyoverdines, iron-chelating siderophores produced by environmental <i>Pseudomonas</i> spp., present a novel class of promising compounds to induce growth arrest in pathogens through iron starvation. While we previously demonstrated the efficacy of pyoverdines as antibacterials, our understanding of how these molecules interact with antibiotics and impact resistance evolution remains unknown. Here, we investigated the propensity of three <i>Escherichia coli</i> strains to evolve resistance against pyoverdine, the cephalosporin antibiotic ceftazidime, and their combination. We used a naive <i>E. coli</i> wildtype strain and two isogenic variants carrying the <i>bla</i> _TEM-1 β-lactamase gene on either the chromosome or a costly multicopy plasmid to explore the influence of genetic background on selection for resistance. We found that strong resistance against ceftazidime and weak resistance against pyoverdine evolved in all <i>E. coli</i> variants under single treatment. Ceftazidime resistance was linked to mutations in outer membrane porin genes (<i>envZ</i> and <i>ompF</i>), whereas pyoverdine resistance was associated with mutations in the oligopeptide permease (<i>opp</i>) operon. In contrast, ceftazidime resistance phenotypes were attenuated under combination treatment, especially for the <i>E. coli</i> variant carrying <i>bla</i> _TEM-1 on the multicopy plasmid. Altogether, our results show that ceftazidime and pyoverdine interact neutrally and that pyoverdine as an antibacterial is particularly potent against plasmid-carrying <i>E. coli</i> strains, presumably because iron starvation compromises both cellular metabolism and plasmid replication.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae021"},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compiling a versatile toolbox for inducible gene expression in <i>Methanosarcina mazei</i>.","authors":"Johanna Hüttermann, Ruth Schmitz","doi":"10.1093/femsml/uqae019","DOIUrl":"10.1093/femsml/uqae019","url":null,"abstract":"<p><p><i>Methanosarcina mazei</i> is a model organism, providing a platform to explore methanoarchaeal regulation mechanisms on the transcriptional and translational level. This study investigates and evaluates various molecular tools to allow inducible gene expression in <i>M. mazei</i>. (i) The TetR/TetO system was utilized to induce expression of a designed antisense RNA directed against sRNA₁₅₄ allowing to increase transcripts of asRNA₁₅₄ (500-fold), resulting in a significant decrease of sRNA₁₅₄ levels (tetracycline-induced knockdown mutant). Strong reduction of sRNA₁₅₄ was further confirmed in the knockdown mutant by up to 50-fold decreased transcript levels of the genes <i>nifH, glnK₁</i> , and <i>glnA₁</i> , the stability of which is increased by sRNA₁₅₄. (ii) For translational regulation, an RNA thermometer was designed and first-ever utilized in an archaeon, inserted into the 5'-untranslated region of a reporter gene, which showed enhanced protein expression upon a temperature shift from 30°C to 40°C. (iii) The long 5'-UTR of a trimethylamine (TMA)-inducible polycistronic mRNA was evaluated and studied as a potential genetic tool for induced gene expression on the translational level. However, we discovered TMA-dependent regulation occurs most likely on the transcript level. (iv) A new selection marker (nourseothricin resistance) was established for <i>M. mazei</i> using the streptothricin acetyltransferase gene. Taken together, our findings provide a foundation for future exploration of genetic regulation and inducible gene expression in <i>M. mazei</i> and other methanoarchaea, advancing genetic studies in these organisms and enhancing their potential for biotechnology applications.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae019"},"PeriodicalIF":0.0,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferring bacterial interspecific interactions from microcolony growth expansion.","authors":"Tania Miguel Trabajo, Isaline Guex, Manupriyam Dubey, Elvire Sarton-Lohéac, Helena Todorov, Xavier Richard, Christian Mazza, Jan Roelof van der Meer","doi":"10.1093/femsml/uqae020","DOIUrl":"10.1093/femsml/uqae020","url":null,"abstract":"<p><p>Bacterial species interactions significantly shape growth and behavior in communities, determining the emergence of community functions. Typically, these interactions are studied through bulk population measurements, overlooking the role of cell-to-cell variability and spatial context. This study uses real-time surface growth measurements of thousands of sparsely positioned microcolonies to investigate interactions and kinetic variations in monocultures and cocultures of <i>Pseudomonas putida</i> and <i>P. veronii</i> under substrate competition (succinate) or substrate independence (d-mannitol and putrescine). In monoculture, microcolonies exhibited expected substrate-dependent expansion rates, but individual colony sizes were affected by founder cell density, spatial positioning, growth rates, and lag times. In coculture, substrate competition favored <i>P. putida</i>, but unexpectedly, reduced the maximum growth rates of both species. In contrast, 10% of <i>P. veronii</i> microcolonies under competition grew larger than expected, likely due to founder cell phenotypic variation and stochastic spatial positioning. These effects were alleviated under substrate independence. A linear relationship between founder cell ratios and final colony area ratios in local neighborhoods (6.5-65 µm radius) was observed in coculture, with its slope reflecting interaction type and strength. Measured slopes in the <i>P. putida</i> to <i>P. veronii</i> biomass ratio under competition were one-third reduced compared to kinetic predictions using a cell-agent growth model, which exometabolite analysis and simulations suggested may be due to metabolite cross-feeding or inhibitory compound production. This indicates additional factors beyond inherent monoculture growth kinetics driving spatial interactions. Overall, the study demonstrates how microcolony growth experiments offer valuable insights into bacterial interactions, from local to community-level dynamics.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae020"},"PeriodicalIF":0.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acetylomics reveals an extensive acetylation diversity within <i>Pseudomonas aeruginosa</i>.","authors":"Nand Broeckaert, Hannelore Longin, Hanne Hendrix, Jeroen De Smet, Mirita Franz-Wachtel, Boris Maček, Vera van Noort, Rob Lavigne","doi":"10.1093/femsml/uqae018","DOIUrl":"10.1093/femsml/uqae018","url":null,"abstract":"<p><p>Bacteria employ a myriad of regulatory mechanisms to adapt to the continuously changing environments that they face. They can, for example, use post-translational modifications, such as Nε-lysine acetylation, to alter enzyme activity. Although a lot of progress has been made, the extent and role of lysine acetylation in many bacterial strains remains uncharted. Here, we applied stable isotope labeling by amino acids in cell culture (SILAC) in combination with the immunoprecipitation of acetylated peptides and LC-MS/MS to measure the first <i>Pseudomonas aeruginosa</i> PAO1 acetylome, revealing 1076 unique acetylation sites in 508 proteins. Next, we assessed interstrain acetylome differences within <i>P. aeruginosa</i> by comparing our PAO1 acetylome with two publicly available PA14 acetylomes, and postulate that the overall acetylation patterns are not driven by strain-specific factors. In addition, the comparison of the <i>P. aeruginosa</i> acetylome to 30 other bacterial acetylomes revealed that a high percentage of transcription related proteins are acetylated in the majority of bacterial species. This conservation could help prioritize the characterization of functional consequences of individual acetylation sites.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae018"},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11512479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142514267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial hub signaling compounds: natural products disproportionally shape microbiome composition and structure.","authors":"Axel A Brakhage","doi":"10.1093/femsml/uqae017","DOIUrl":"10.1093/femsml/uqae017","url":null,"abstract":"<p><p>Microbiomes are shaped by abiotic factors like nutrients, oxygen availability, pH, temperature, and so on, but also by biotic factors including low molecular weight organic compounds referred to as natural products (NPs). Based on genome analyses, millions of these compounds are predicted to exist in nature, some of them have found important applications e.g. as antibiotics. Based on recent data I propose a model that some of these compounds function as microbial hub signaling compounds, i.e. they have a higher hierarchical influence on microbiomes. These compounds have direct effects e.g. by inhibiting microorganisms and thereby exclude them from a microbiome (excluded). Some microorganisms do not respond at all (nonresponder), others respond by producing themselves NPs like a second wave of information molecules (message responder) influencing other microorganisms, but conceivably a more limited spectrum. Some microorganisms may respond to the hub compounds with their chemical modification (message modifiers). This way, the modified NPs may have themselves signaling function for a subset of microorganisms. Finally, it is also likely that NPs act as food source (C- and/or N-source) for microorganisms specialized on their degradation. As a consequence, such specialized microorganisms are selectively recruited to the microbiota.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae017"},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial markets: socio-economic perspective in studying microbial communities.","authors":"Fariha Mostafa, Aileen Krüger, Tim Nies, Julia Frunzke, Kerstin Schipper, Anna Matuszyńska","doi":"10.1093/femsml/uqae016","DOIUrl":"10.1093/femsml/uqae016","url":null,"abstract":"<p><p>Studying microbial communities through a socio-economic lens, this paper draws parallels with human economic transactions and microbes' race for resources. Extending the 'Market Economy' concept of social science to microbial ecosystems, the paper aims to contribute to comprehending the collaborative and competitive dynamics among microorganisms. Created by a multidisciplinary team of an economist, microbiologists, and mathematicians, the paper also highlights the risks involved in employing a socio-economic perspective to explain the complexities of natural ecosystems. Navigating through microbial markets offers insights into the implications of these interactions while emphasizing the need for cautious interpretation within the broader ecological context. We hope that this paper will be a fruitful source of inspiration for future studies on microbial communities.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae016"},"PeriodicalIF":0.0,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11421381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resistance against aminoglycoside antibiotics via drug or target modification enables community-wide antiphage defense.","authors":"Larissa Kever, Qian Zhang, Aël Hardy, Philipp Westhoff, Yi Yu, Julia Frunzke","doi":"10.1093/femsml/uqae015","DOIUrl":"10.1093/femsml/uqae015","url":null,"abstract":"<p><p>The ongoing arms race between bacteria and phages has forced bacteria to evolve a sophisticated set of antiphage defense mechanisms that constitute the bacterial immune system. In our previous study, we highlighted the antiphage properties of aminoglycoside antibiotics, which are naturally secreted by <i>Streptomyces</i>. Successful inhibition of phage infection was achieved by addition of pure compounds and supernatants from a natural producer strain emphasizing the potential for community-wide antiphage defense. However, given the dual functionality of these compounds, neighboring bacterial cells require resistance to the antibacterial activity of aminoglycosides to benefit from the protection they confer against phages. In this study, we tested a variety of different aminoglycoside resistance mechanisms acting via drug or target (16S rRNA) modification and demonstrated that they do not interfere with the antiphage properties of the molecules. Furthermore, we confirmed the antiphage impact of aminoglycosides in a community context by coculturing phage-susceptible, apramycin-resistant <i>Streptomyces venezuelae</i> with the apramycin-producing strain <i>Streptoalloteichus tenebrarius</i>. Given the prevalence of aminoglycoside resistance among natural bacterial isolates, this study highlights the ecological relevance of chemical defense via aminoglycosides at the community level.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae015"},"PeriodicalIF":0.0,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11350373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coordinated regulation of osmotic imbalance by c-di-AMP shapes ß-lactam tolerance in Group B <i>Streptococcus</i>.","authors":"Terry Brissac, Cécile Guyonnet, Aymane Sadouni, Ariadna Hernández-Montoya, Elise Jacquemet, Rachel Legendre, Odile Sismeiro, Patrick Trieu-Cuot, Philippe Lanotte, Asmaa Tazi, Arnaud Firon","doi":"10.1093/femsml/uqae014","DOIUrl":"10.1093/femsml/uqae014","url":null,"abstract":"<p><p><i>Streptococcus agalactiae</i> is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is not known whether specific mechanisms constrain the emergence of resistance. In this study, we first report ß-lactam tolerance due to the inactivation of the c-di-AMP phosphodiesterase GdpP. Mechanistically, tolerance depends on antagonistic regulation by the repressor BusR, which is activated by c-di-AMP and negatively regulates ß-lactam susceptibility through the BusAB osmolyte transporter and the AmaP/Asp23/GlsB cell envelope stress complex. The BusR transcriptional response is synergistic with the simultaneous allosteric inhibition of potassium and osmolyte transporters by c-di-AMP, which individually contribute to low-level ß-lactam tolerance. Genome-wide transposon mutagenesis confirms the role of GdpP and highlights functional interactions between a lysozyme-like hydrolase, the KhpAB RNA chaperone and the protein S immunomodulator in the response of GBS to ß-lactam. Overall, we demonstrate that c-di-AMP acts as a turgor pressure rheostat, coordinating an integrated response at the transcriptional and post-translational levels to cell wall weakening caused by ß-lactam activity, and reveal additional mechanisms that could foster resistance.</p>","PeriodicalId":74189,"journal":{"name":"microLife","volume":"5 ","pages":"uqae014"},"PeriodicalIF":0.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11238645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}