Applied and Environmental Microbiology最新文献

{"title":"Adaptation of clinical bacteriology techniques for remote polar research.","authors":"Scott J C Pallett, Bill K Kwok, Stephanie M Y Wong, Luke S P Moore","doi":"10.1128/aem.02147-24","DOIUrl":"10.1128/aem.02147-24","url":null,"abstract":"<p><p>Remote polar regions offer unique opportunities and significant challenges for antimicrobial resistance research in a near-pristine environment. While core microbiology techniques continue to have an important role in supporting environmental research, the severe cold climate presents considerable challenges to laboratory research. We explore adaptations required for core bacteriology investigations in polar regions on an unsupported remote expedition c. 600 km north of the Arctic Circle utilizing the National Collection of Type Culture bacterial strains. Methods of culture, microscopy, biochemical and phenotypic testing, vortex, and centrifuge techniques are explored. Across -21.5 to -41.0°C, culture was satisfactorily enabled using a solar-powered USB incubator and an electricity-free water-bath option utilizing white gas for a variety of standard culture media. Microscopy and biochemical tests supported organism identification. Phenotypic testing for carbapenemase-producing genes using lateral flow devices showed good performance without modification (Carba-5, 20/20 carbapenemase-producing organism tests, 100% sensitivity; 100/100 negative targets, 100% specificity). The modified centrifuge was enabled with a 3D printed disk and Dremel drill and microbial DNA extraction (ZymoBIOMICS) kits were able to extract DNA of suitable quality for analysis. With suitable adaptations, conducting core microbiology techniques (with potential relevance for more advanced techniques) is possible in the remote extreme cold environment.</p><p><strong>Importance: </strong>Antimicrobial resistance (AMR) represents one of the key global public health threats currently facing humanity. The recent UN High-Level Meeting on AMR highlighted the need for greater knowledge generation on its environmental aspects while also considering the potential adverse effects of climate change. The polar regions of the world offer a unique opportunity for AMR research in a near-pristine environment while also holding the potential for novel resistance mechanisms and/or antimicrobial peptide discovery within melting permafrost or glacial ice. Despite considerable technological advances in microbiology, operating in severe cold environments continues to present significant operational challenges. Our report here offers a basis for adaptations to enable both environmental and clinical antimicrobial resistance, microbiome, and discovery research for operating in the harshest of remote environments.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0214724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AAV-based gene delivery of antimicrobial peptides to combat drug-resistant pathogens.","authors":"Piyush Baindara, Dinata Roy, Chandra S Boosani, Santi M Mandal, Jonathan A Green","doi":"10.1128/aem.01702-24","DOIUrl":"10.1128/aem.01702-24","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) have emerged as potential alternatives to conventional antibiotics due to their novelty and multiple mechanisms of action. Because they are peptides, AMPs are amenable to bioengineering and suitable for cloning and expression at large production scales. However, the efficient delivery of AMPs is an unaddressed issue, particularly due to their large size, possible toxicities, and the development of adverse immune responses. Here, we have reviewed the possibilities of adeno-associated virus (AAV)-based localized gene delivery of AMPs for the treatment of infectious diseases with a special focus on respiratory infections. By discussing the gene delivery mechanism of AAV and the accompanying technical and therapeutic challenges with AMPs, we describe a foundation that emphasizes the use of viral vector-based gene delivery of AMPs for disease treatment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0170224"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic investigation of hydrogenases in <i>Thermoanaerobacterium thermosaccharolyticum</i> suggests that redox balance via hydrogen cycling enables high ethanol yield.","authors":"Layse C de Souza, Christopher D Herring, Lee R Lynd","doi":"10.1128/aem.01109-24","DOIUrl":"10.1128/aem.01109-24","url":null,"abstract":"<p><p><i>Thermoanaerobacterium thermosaccharolyticum</i> is an anaerobic and thermophilic bacterium that has been genetically engineered for ethanol production at very high yields. However, the underlying reactions responsible for electron flow, redox equilibrium, and how they relate to ethanol production in this microbe are not fully elucidated. Therefore, we performed a series of genetic manipulations to investigate the contribution of hydrogenase genes to high ethanol yield, generating evidence for the importance of hydrogen-reacting enzymes in ethanol production. Our results indicate that a high ethanol yield, >85% of the theoretical maximum, only occurs when the <i>hfsD, hydAB</i>, and <i>nfnAB</i> genes are all present together, while the <i>hfsB</i> gene is absent. We propose that the products of these three gene clusters facilitate an NADPH-generating reaction via hydrogen cycling, with a stoichiometry comparable with a canonical ferredoxin:NADP⁺ oxidoreductase (FNOR; EC 1.18.1.2) reaction. The hypothesized mechanism provides a balance of nicotinamide cofactors and facilitates ferredoxin recycling, leading to progress in optimizing the energy conversion of biomass-derived sugars to ethanol.</p><p><strong>Importance: </strong>Our study elucidates the crucial role of electron flow and redox balancing mechanisms in improving ethanol yields from renewable biomass. We delve into the mechanism of electron transfer, highlighting the potential of key genes to be leveraged for enhanced ethanol production in anaerobic microbial species. We suggest by genetic investigation the existence of a novel Ferredoxin:NADP+ Oxidoreductase (FNOR) reaction, comprising HfsD, HydAB, and NfnAB enzymes, as a promising avenue for achieving balanced stoichiometry and efficient ethanol synthesis. Our findings not only advance the understanding of microbial metabolism but also offer practical insights for developing strategies to improve bioenergy production and sustainability.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0110924"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837493/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A modified iChip for <i>in situ</i> cultivation of bacteria in arid environments.","authors":"Seven Nazipi Bushi, Marie B Lund, Tobias Sandfeld, Sanne Sadolin Nørskov, Simon Fruergaard, Marianne Glasius, Trine Bilde, Andreas Schramm","doi":"10.1128/aem.01325-24","DOIUrl":"10.1128/aem.01325-24","url":null,"abstract":"<p><p>Antimicrobial resistance is an ever-increasing problem for human health, and with only a few novel antimicrobials discovered in recent decades, an extraordinary effort is needed to circumvent this crisis. A promising source of new microbial-derived antimicrobial compounds resides in the large fraction of microbes that are not readily cultured by standard cultivation. It has previously been shown that nests of the social spider <i>Stegodyphus dumicola</i> contain a diverse bacterial community, where only a small fraction of the microbes could be recovered by standard cultivation. To improve the recovery of the bacterial diversity cultured from nests, we modified the previously described isolation chip (iChip) to fit the natural arid environment of <i>S. dumicola</i> nests. Here we provide a comprehensive analysis of the modified iChip's performance. We found that the modified iChip improved the overall culturability, performed equally or better at recovering the bacterial diversity from individual nests, and improved the recovery of rare isolates compared to standard cultivation. Furthermore, we show that the modified iChip can be used in the field. In addition, we observed that the nests contain volatile organic compounds (VOCs) that could serve as substrate for the selective enrichment of rare and iChip-specific isolates. Our modified iChip can be applied for <i>in situ</i> cultivation in a broad range of arid habitats that can be exploited for future drug discovery.IMPORTANCEThe demand for novel antimicrobial compounds is an ever-increasing problem due to the rapid spread of antibiotic-resistant microbes. Therefore, exploring new habitats for microbial-derived antimicrobial compounds is crucial. The nest microbiome of <i>Stegodyphus dumicola</i> remains largely unexplored and could potentially serve as a new source of antimicrobial compounds. To access the nest's microbial diversity, we designed a modified iChip for <i>in situ</i> cultivation inside spider nests and tested its applications in both field and laboratory settings. Our study shows that the iChip's ability to recover <i>in situ</i> abundant genera was comparable or superior to standard cultivation, while the recovery of rare (low-abundant genera) was higher. We argue that these low-abundant and iChip-specific isolates are enriched from naturally occurring nest volatile organic compounds (VOCs) during iChip incubation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0132524"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-resolved adaptation strategies of <i>Rhodobacterales</i> to changing conditions in the Chesapeake and Delaware Bays.","authors":"Mir Alvee Ahmed, Barbara J Campbell","doi":"10.1128/aem.02357-24","DOIUrl":"10.1128/aem.02357-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The abundant and metabolically versatile aquatic bacterial order, &lt;i&gt;Rhodobacterales&lt;/i&gt;, influences marine biogeochemical cycles. We assessed &lt;i&gt;Rhodobacterales&lt;/i&gt; metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed &lt;i&gt;Rhodobacterales&lt;/i&gt; genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. &lt;i&gt;Rhodobacterales&lt;/i&gt; genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. &lt;i&gt;Planktomarina&lt;/i&gt; genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These &lt;i&gt;Rhodobacterales&lt;/i&gt; also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine &lt;i&gt;Rhodobacterales&lt;/i&gt; within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;In the complex web of global biogeochemical nutrient cycling, the &lt;i&gt;Rhodobacterales&lt;/i&gt; emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of &lt;i&gt;Rhodobacterales&lt;/i&gt; genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine &lt;i&gt;Rhodobacterales&lt;/i&gt;, revealing their various energy production pathways and diverse resource management, especially duri","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0235724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837527/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142943252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precision engineering of the probiotic <i>Escherichia coli</i> Nissle 1917 with prime editing.","authors":"Pei-Ru Chen, Ying Wei, Xin Li, Hai-Yan Yu, Shu-Guang Wang, Xian-Zheng Yuan, Peng-Fei Xia","doi":"10.1128/aem.00031-25","DOIUrl":"10.1128/aem.00031-25","url":null,"abstract":"<p><p>CRISPR-Cas systems are transforming precision medicine with engineered probiotics as next-generation diagnostics and therapeutics. To promote human health and treat disease, engineering probiotic bacteria demands maximal versatility to enable non-natural functionalities while minimizing undesired genomic interferences. Here, we present a streamlined prime editing approach tailored for probiotic <i>Escherichia coli</i> Nissle 1917 utilizing only essential genetic modules, including Cas9 nickase from <i>Streptococcus pyogenes</i>, a codon-optimized reverse transcriptase, and a prime editing guide RNA, and an optimized workflow with longer induction. As a result, we achieved all types of prime editing in every individual round of experiments with efficiencies of 25.0%, 52.0%, and 66.7% for DNA deletion, insertion, and substitution, respectively. A comprehensive evaluation of off-target effects revealed a significant reduction in unintended mutations, particularly in comparison to two different base editing methods. Leveraging the prime editing system, we inserted a unique DNA sequence to barcode the edited strain and established an antibiotic-resistance-gene-free platform to enable non-natural functionalities. Our prime editing strategy presents a CRISPR-Cas system that can be readily implemented in any laboratories with the basic CRISPR setups, paving the way for future innovations in engineered probiotics.IMPORTANCEOne ultimate goal of gene editing is to introduce designed DNA variations at specific loci in living organisms with minimal unintended interferences in the genome. Achieving this goal is especially critical for creating engineered probiotics as living diagnostics and therapeutics to promote human health and treat diseases. In this endeavor, we report a customized prime editing system for precision engineering of probiotic <i>Escherichia coli</i> Nissle 1917. With such a system, we developed a barcoding system for tracking engineered strains, and we built an antibiotic-resistance-gene-free platform to enable non-natural functionalities. We provide not only a powerful gene editing approach for probiotic bacteria but also new insights into the advancement of innovative CRISPR-Cas systems.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0003125"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum for Huang et al., \"Insights into the regulatory mechanisms and application prospects of the transcription factor Cra\".","authors":"Ying Huang, Kai-Zhi Jia, Wei Zhao, Li-Wen Zhu","doi":"10.1128/aem.00047-25","DOIUrl":"10.1128/aem.00047-25","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0004725"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of vitamin B₁₂ supply on cellular processes of the facultative vitamin B₁₂ consumer <i>Vibrio campbellii</i>.","authors":"Luna-Agrippina Groon, Stefan Bruns, Leon Dlugosch, Heinz Wilkes, Gerrit Wienhausen","doi":"10.1128/aem.01422-24","DOIUrl":"10.1128/aem.01422-24","url":null,"abstract":"<p><p>Vitamin B₁₂ (cobalamin, herein B₁₂) is a key cofactor for most organisms being involved in essential metabolic processes. In microbial communities, B₁₂ is often scarce, largely because only few prokaryotes can synthesize B₁₂ <i>de novo</i> and are thus considered B₁₂-prototrophs. B₁₂-auxotrophy is mostly manifested by the absence of the B₁₂-independent methionine synthase, MetE. Here, we focus on bacteria that we classified as facultative B₁₂ consumers as they encode both B₁₂-independent and -dependent (MetH) methionine synthases yet largely cannot synthesize B₁₂ <i>de novo</i>. The genus <i>Vibrio</i> belongs to this group, and our work shows that upon B₁₂ supply growth of <i>Vibrio campbellii</i> is accelerated and autoinducer-2 (AI-2) concentrations are enhanced. We speculate that methionine synthesis efficiency, dependent on B₁₂ availability, is linked to AI-2 synthesis. The precursor for AI-2 synthesis is S-adenosyl-L-homocysteine (SAH), which in turn requires methionine as a precursor. In almost all <i>Vibrio</i> species studied, <i>btuF</i> (B₁₂-binding protein), which is required for B₁₂ uptake, and <i>cobD</i> (Adenosylcobinamide-phosphate synthase), which enables remodeling of B₁₂-like compounds, are encoded on the same operon as <i>pfs</i> (or <i>mtnN</i>, Adenosylhomocysteine nucleosidase), the first enzyme in the two-step AI-2 synthesis reaction. Transcriptomic analyses show that virulence factors, such as toxin synthesis, fimbriae formation, and activation of the type-6 secretion system, which have been shown to be regulated by quorum sensing via AI-2, are significantly upregulated in <i>V. campbellii</i> when B₁₂ is available. Our results demonstrate that <i>V. campbellii</i> is a facultative B₁₂ consumer and indicate that B₁₂ availability affects AI-2 levels and thus potentially virulence factor regulation.IMPORTANCEMetabolites play a key role in microbial metabolism and communication. While vitamin B₁₂ is an essential cofactor for important enzymatic reactions, autoinducer-2 mediates interspecies signaling and can regulate the expression of genes that are crucial for virulence and survival. In our study, we hypothesize and present findings how these two important metabolites are linked in <i>Vibrio</i> species. <i>Vibrio campbellii</i> grows without B₁₂ but at an accelerated rate when B₁₂ is present, and we detect higher AI-2 values in cultures with B₁₂ amendment. Transcriptome analyses show how vitamin B₁₂ availability significantly upregulates gene expression of virulence factors such as toxin synthesis, fimbrial formation, and activation of the type-6 secretion system in <i>V. campbellii</i>.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0142224"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.","authors":"Derek G Wu, Cassandra R Harris, Katie M Kalis, Malique Bowen, Jennifer F Biddle, Ibrahim F Farag","doi":"10.1128/aem.02229-24","DOIUrl":"10.1128/aem.02229-24","url":null,"abstract":"<p><p>Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, <i>Paracirrhites arcatus</i>; yellow tang, <i>Zebrasoma flavescens</i>; and triggerfish, <i>Rhinecanthus aculeatus</i>) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with <i>Proteobacteria</i>, <i>Bacteroidota</i>, and <i>Firmicutes</i> being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.</p><p><strong>Importance: </strong>The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0222924"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Gac/Rsm regulatory system activates the biosynthesis of mupirocin by controlling the MupR/I quorum sensing system in <i>Pseudomonas</i> sp. NCIMB 10586.","authors":"Yuyuan Cai, Peng Huang, Vittorio Venturi, Runyao Xiong, Zheng Wang, Wei Wang, Xianqing Huang, Hongbo Hu, Xuehong Zhang","doi":"10.1128/aem.01896-24","DOIUrl":"10.1128/aem.01896-24","url":null,"abstract":"<p><p>The biosynthesis of mupirocin, a clinically significant antibiotic produced by <i>Pseudomonas</i> sp. NCIMB 10586, is activated by the <i>N</i>-acyl homoserine lactone (AHL) MupR/I quorum sensing (QS) system. However, to date, limited research has focused on the influence of global regulators such as the GacS/A two-component system (TCS) on the MupR/I QS system or mupirocin biosynthesis. In this study, we characterized the regulatory components of the Gac/Rsm transduction system in the mupirocin-producing model strain NCIMB 10586 and investigated their interconnection with the MupR/I QS circuit and subsequent mupirocin biosynthesis. The production of mupirocin was hampered by either <i>gacS</i> inactivation, <i>gacA</i> inactivation, or the double-mutant of the sRNAs ( RsmY and RsmZ). Similarly, the expressions of <i>mupR</i> and <i>mupI</i>, and AHL synthesis significantly decreased in <i>gacS, gacA,</i> or <i>rsmY/Z</i> mutants, indicating that the GacS/A system stimulates mupirocin biosynthesis via the MupR/I QS system. Five CsrA family proteins, RsmA/E/I/F/N, were found in strain NCIMB 10586, and the single and multiple mutants of <i>rsmA/E/I/F/N</i> showed different phenotypes with respect to mupirocin production. Our results revealed that mupirocin biosynthesis was likely to be negatively regulated by RsmA/E/I, but positively regulated by RsmF. Additionally, the RsmF protein was shown to interact with the 5' leader of <i>mupR</i> mRNA. In summary, the Gac/Rsm system positively regulates the biosynthesis of mupirocin mainly through the MupR/I QS system, and the model of the regulatory mechanism is proposed. The elucidation of the Gac/Rsm-MupR/I regulatory pathway could help devise ways for improving mupirocin production through genetic engineering.IMPORTANCEThe Gac/Rsm regulatory system plays a global regulatory role in bacterial physiology and metabolism, including secondary metabolism. Mupirocin is a clinically important antibiotic, produced by <i>Pseudomonas</i> sp. NCIMB 10586, whose biosynthesis is activated by the MupR/I quorum sensing system. Global regulators have important impacts on the gene expression of secondary metabolic gene clusters and QS genes, and the GacS/A two-component system is one of the main regulators across <i>Pseudomonas</i> species, which significantly influences antibiotic production. Our study presented that the expressions of QS genes and <i>mup</i> gene cluster were downregulated in <i>gacS, gacA,</i> or <i>rsmY/Z</i> mutants compared to the wild-type. The inactivation of <i>rsmA/E/I/F/N</i> in NCIMB 10586, encoding CsrA family proteins, showed different regulatory traits of mupirocin production, in which the RsmF protein could interact with the 5' UTR region of <i>mupR</i> mRNA. These findings provide the understanding of the regulatory role of Gac/Rsm on mupirocin biosynthesis and <i>mupR/I</i> QS system and lay foundations for further improving mupirocin production.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0189624"},"PeriodicalIF":3.9,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11837529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}