MicrobiologyOpen最新文献

{"title":"Examining the functional space of gut microbiome-derived peptides","authors":"Ying-Chiang J. Lee","doi":"10.1002/mbo3.1393","DOIUrl":"https://doi.org/10.1002/mbo3.1393","url":null,"abstract":"<p>The human gut microbiome contains thousands of small, novel peptides that could play a role in microbe–microbe and host–microbe interactions, contributing to human health and disease. Although these peptides have not yet been systematically characterized, computational tools can be used to elucidate the bioactivities they may have. This article proposes probing the functional space of gut microbiome-derived peptides (MDPs) using in silico approaches for three bioactivities: antimicrobial, anticancer, and nucleomodulins. Machine learning programs that support peptide and protein queries are provided for each bioactivity. Considering the biases of an activity-centric approach, activity-agnostic tools using structural and chemical similarity and target prediction are also described. Gut MDPs represent a vast functional space that can not only contribute to our understanding of microbiome interactions but potentially even serve as a source of life-changing therapeutics.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138570903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacillus-based probiotic cleansers reduce the formation of dry biofilms on common hospital surfaces","authors":"Richard Wormald,&nbsp;Paul N. Humphreys,&nbsp;Christopher J. Charles,&nbsp;Simon P. Rout","doi":"10.1002/mbo3.1391","DOIUrl":"https://doi.org/10.1002/mbo3.1391","url":null,"abstract":"<p>In the absence of liquid suspension, dry biofilms can form upon hard surfaces within a hospital environment, representing a healthcare-associated infection risk. Probiotic cleansers using generally recognized as safe organisms, such as those of the <i>Bacillus</i> genus, represent a potential strategy for the reduction of dry biofilm bioburden. The mechanisms of action and efficacy of these cleaners are, however, poorly understood. To address this, a preventative dry biofilm assay was developed using steel, melamine, and ceramic surfaces to assess the ability of a commercially available <i>Bacillus</i> spp. based probiotic cleanser to reduce the surface bioburden of <i>Escherichia coli</i> and <i>Staphylococcus aureus</i>. Via this assay, phosphate-buffered saline controls were able to generate dry biofilms within 7 days of incubation, with the application of the probiotic cleanser able to prevent &gt;97.7% of dry biofilm formation across both pathogen analogs and surface types. Further to this, surfaces treated with the probiotic mixture alone also showed a reduction in dry biofilm across both pathogen and surface types. Confocal laser scanning microscopy imaging indicated that the probiotic bacteria were able to germinate and colonize surfaces, likely forming a protective layer upon these hard surfaces.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1391","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138431981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to Concomitant knockout of target and transporter genes in filamentous fungi by genome coediting","authors":"","doi":"10.1002/mbo3.1390","DOIUrl":"10.1002/mbo3.1390","url":null,"abstract":"<p>Tamano, K. (2022). Concomitant knockout of target and transporter genes in filamentous fungi by genome coediting. MicrobiologyOpen, e1280. https://doi.org/10.1002/mbo3.1280</p><p>In the above article, the words “autotrophy” and “autotrophic” should be read as “prototrophy” and “prototrophic,” respectively in all instances.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1390","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135392869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity","authors":"Alisson Gillon,&nbsp;Ola Abdelrahman,&nbsp;Eliane Abou-Mansour,&nbsp;Floriane L'Haridon,&nbsp;Laurent Falquet,&nbsp;Pierre-Marie Allard,&nbsp;Laure Weisskopf","doi":"10.1002/mbo3.1389","DOIUrl":"10.1002/mbo3.1389","url":null,"abstract":"<p>The <i>Streptomyces</i> genus is known to produce many specialized metabolites of value for medicine, but the potential of these metabolites in agronomy remains largely unexplored. In this study, we investigated three phylogenetically closely related <i>Streptomyces</i> strains (B5, B91, and B135) isolated from three distinct soil samples in Sudan. Despite belonging to the same species, these strains exhibited different ranges of <i>Phytophthora infestans</i> inhibition. The objective of this work was to identify the active compound(s) responsible for the inhibition of <i>P. infestans</i> and of other plant pathogens by comparing the genomes and metabolomes of the three strains which showed distinct activity patterns: B5 was the strongest inhibitor of oomycetes, B5 and B91 both inhibited most fungi and B135 was the only strain showing antibacterial activity. Our comparative genomic and metabolomic analysis identified borrelidin as the bioactive compound underlying B5's strong anti-oomycete activity and highlighted a few other metabolites as putative candidates underlying the strains' antifungal and antibacterial activities. This study illustrates the power of comparative genomics and metabolomics on phylogenetically closely related strains of differing activities to highlight bioactive compounds that could contribute to new sustainable crop protection strategies.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 6","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1389","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136069536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata","authors":"Nadim Ahmad,&nbsp;Manfred Ritz,&nbsp;Anjuli Calchera,&nbsp;Jürgen Otte,&nbsp;Imke Schmitt,&nbsp;Thomas Brueck,&nbsp;Norbert Mehlmer","doi":"10.1002/mbo3.1386","DOIUrl":"https://doi.org/10.1002/mbo3.1386","url":null,"abstract":"<p>Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from <i>Hypogymnia physodes, Hypogymnia tubulosa</i>, and <i>Parmelia sulcata</i>. In addition, we present a high-quality PacBio metagenome of <i>Parmelia sulcata</i>, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1386","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50136271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, characterization, and fibroblast uptake of bacterial extracellular vesicles from Porphyromonas gingivalis strains","authors":"Helene R. Haugsten,&nbsp;Anne K. Kristoffersen,&nbsp;Trude M. Haug,&nbsp;Tine M. Søland,&nbsp;Reidun Øvstebø,&nbsp;Hans C. D. Aass,&nbsp;Morten Enersen,&nbsp;Hilde K. Galtung","doi":"10.1002/mbo3.1388","DOIUrl":"https://doi.org/10.1002/mbo3.1388","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 <p>Periodontitis is an inflammatory condition caused by bacteria and represents a serious health problem worldwide as the inflammation damages the supporting tissues of the teeth and may predispose to systemic diseases. <i>Porphyromonas gingivalis</i> is considered a keystone periodontal pathogen that releases bacterial extracellular vesicles (bEVs) containing virulence factors, such as gingipains, that may contribute to the pathogenesis of periodontitis. This study aimed to isolate and characterize bEVs from three strains of <i>P. gingivalis</i>, investigate putative bEV uptake into human oral fibroblasts, and determine the gingipain activity of the bEVs. bEVs from three bacterial strains, ATCC 33277, A7A1-28, and W83, were isolated through ultrafiltration and size-exclusion chromatography. Vesicle size distribution was measured by nano-tracking analysis (NTA). Transmission electron microscopy was used for bEV visualization. Flow cytometry was used to detect bEVs and gingipain activity was measured with an enzyme assay using a substrate specific for arg-gingipain. The uptake of bEVs into oral fibroblasts was visualized using confocal microscopy. NTA showed bEV concentrations from 10⁸ to 10¹¹ particles/mL and bEV diameters from 42 to 356 nm. TEM pictures demonstrated vesicle-like structures. bEV-gingipains were detected both by flow cytometry and enzyme assay. Fibroblasts incubated with bEVs labeled with fluorescent dye displayed intracellular localization consistent with bEV internalization. In conclusion, bEVs from <i>P. gingivalis</i> were successfully isolated and characterized, and their uptake into human oral fibroblasts was documented. The bEVs displayed active gingipains demonstrating their origin from <i>P. gingivalis</i> and the potential role of bEVs in periodontitis.</p>\u0000 </section>\u0000 </div>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1388","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50135494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1","authors":"Kristy S. Syhapanha,&nbsp;David A. Russo,&nbsp;Yun Deng,&nbsp;Nils Meyer,&nbsp;Remington X. Poulin,&nbsp;Georg Pohnert","doi":"10.1002/mbo3.1387","DOIUrl":"https://doi.org/10.1002/mbo3.1387","url":null,"abstract":"<p>In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. <i>Kordia algicida</i> strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom <i>Skeletonema costatum</i>. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene <i>KAOT1_RS09515</i>, hereby named <i>alpA1</i> as a key element in the algicidal activity of <i>K. algicida</i>. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that <i>K. algicida</i> is the only algicidal species within a group of four members of the <i>Kordia</i> genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1387","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50148209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Relationship between the Rod complex and peptidoglycan structure in Escherichia coli","authors":"Risa Ago,&nbsp;Yuhei O. Tahara,&nbsp;Honoka Yamaguchi,&nbsp;Motoya Saito,&nbsp;Wakana Ito,&nbsp;Kaito Yamasaki,&nbsp;Taishi Kasai,&nbsp;Sho Okamoto,&nbsp;Taiki Chikada,&nbsp;Taku Oshima,&nbsp;Issey Osaka,&nbsp;Makoto Miyata,&nbsp;Hironori Niki,&nbsp;Daisuke Shiomi","doi":"10.1002/mbo3.1385","DOIUrl":"https://doi.org/10.1002/mbo3.1385","url":null,"abstract":"<p>Peptidoglycan for elongation in <i>Escherichia coli</i> is synthesized by the Rod complex, which includes RodZ. Although various mutant strains of the Rod complex have been isolated, the relationship between the activity of the Rod complex and the overall physical and chemical structures of the peptidoglycan have not been reported. We constructed a RodZ mutant, termed RMR, and analyzed the growth rate, morphology, and other characteristics of cells producing the Rod complexes containing RMR. The growth and morphology of RMR cells were abnormal, and we isolated suppressor mutants from RMR cells. Most of the suppressor mutations were found in components of the Rod complex, suggesting that these suppressor mutations increase the integrity and/or the activity of the Rod complex. We purified peptidoglycan from wild-type, RMR, and suppressor mutant cells and observed their structures in detail. We found that the peptidoglycan purified from RMR cells had many large holes and different compositions of muropeptides from those of WT cells. The Rod complex may be a determinant not only for the whole shape of peptidoglycan but also for its highly dense structure to support the mechanical strength of the cell wall.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1385","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50145344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic interactions between Candida albicans and different streptococcal species in a multispecies oral biofilm","authors":"Tenzin Kunchok Lueyar,&nbsp;Lamprini Karygianni,&nbsp;Thomas Attin,&nbsp;Thomas Thurnheer","doi":"10.1002/mbo3.1381","DOIUrl":"https://doi.org/10.1002/mbo3.1381","url":null,"abstract":"<p>The oral cavity is colonized by a plethora of bacteria, fungi, and archaea, including streptococci of the mitis group (MSG) and the yeast <i>Candida albicans</i>. This study aims to investigate the role of streptococcal species in the development of oral biofilm and the cross-kingdom interactions between some of the members of the commensal MSG and the pathogen yeast <i>C. albicans</i> using a multispecies supragingival biofilm model. A total of nine different in vitro biofilms were grown, quantified with culture analyses, and visually examined with confocal laser scanning microscopy (CLSM). A four-species biofilm without any streptococcal species was used as a basic biofilm. In each subsequent inoculum, one species of MSG was added and afterward combined with <i>Streptococcus mutans</i>. The eight-species biofilm contained all eight strains used in this study. Culture analyses showed that the presence of <i>S. mutans</i> in a four-species biofilm with <i>Streptococcus oralis</i> or <i>S. oralis</i> subsp. <i>tigurinus</i> did not differ significantly in <i>C. albicans</i> colony-forming unit (CFU) counts compared to biofilms without <i>S. mutans</i>. However, compared to other <i>mitis</i> species, <i>Streptococcus gordonii</i> combined with <i>S. mutans</i> resulted in the lowest CFUs of <i>C. albicans</i>. Visual observation by CLSM showed that biofilms containing both <i>S. mutans</i> and one species of MSG seemed to induce the formation of filamentous form of <i>C. albicans</i>. However, when several species of MSG were combined with <i>S. mutans</i>, <i>C. albicans</i> was again found in its yeast form.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1381","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50119393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Similarity in milk microbiota in replicates","authors":"Josef Dahlberg,&nbsp;Erik Pelve,&nbsp;Johan Dicksved","doi":"10.1002/mbo3.1383","DOIUrl":"https://doi.org/10.1002/mbo3.1383","url":null,"abstract":"<p>Receiving the same results from repeated analysis of the same sample is a basic principle in science. The inability to reproduce previously published results has led to discussions of a reproducibility crisis within science. For studies of microbial communities, the problem of reproducibility is more pronounced and has, in some fields, led to a discussion on the very existence of a constantly present microbiota. In this study, DNA from 44 bovine milk samples were extracted twice and the V3–V4 region of the 16S rRNA gene was sequenced in two separate runs. The FASTQ files from the two data sets were run through the same bioinformatics pipeline using the same settings and results from the two data sets were compared. Milk samples collected maximally 2 h apart were used as replicates and permitted comparisons to be made within the same run. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson's diversity was the same. Multivariate analyses of all samples demonstrate that the sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42%–45% depending on whether binary or abundance-based similarity indices were used. Within-run comparisons of milk samples collected maximally 2 h apart showed an average similarity of 39%–47% depending on the similarity index used and that similarity differed significantly between runs. We conclude that repeated DNA extraction and sequencing significantly can affect the results of a low microbial biomass microbiota study.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":"12 5","pages":""},"PeriodicalIF":3.4,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1383","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50155966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}