Applied and Environmental Microbiology最新文献

{"title":"Polysulfides promote protein disulfide bond formation in microorganisms growing under anaerobic conditions.","authors":"Yuping Xin, Qingda Wang, Jianming Yang, Xiaohua Wu, Yongzhen Xia, Luying Xun, Huaiwei Liu","doi":"10.1128/aem.01926-24","DOIUrl":"https://doi.org/10.1128/aem.01926-24","url":null,"abstract":"<p><p>Polysulfides commonly occur in anaerobic, microbial active environments, where they play key roles in sulfur cycling and redox transformations. Anaerobic survival of microorganisms requires the formation of protein disulfide bond (DSB). The relationship between polysulfides and anaerobic DSB formation has not been studied so far. Herein, we discovered that polysulfides can efficiently mediate protein DSB formation of microorganisms under anaerobic conditions. We used polysulfides to treat proteins, including roGFP2, Trx1, and DsbA, under anaerobic conditions and found that all three proteins formed intramolecular DSB <i>in vitro</i>. Under anaerobic conditions, <i>Escherichia coli</i> Δ<i>dsbB</i> displayed reduced growth and decreased intracellular protein DSB levels, but polysulfide treatment restored both growth and DSB content. Similarly, polysulfide treatment of <i>E. coli</i> Δ<i>dsbA</i> promoted periplasmic roGFP2 DSB formation and recovered growth under anaerobic conditions. Furthermore, treating <i>Schizosaccharomyces pombe</i> and <i>Cupriavidus pinatubonensis</i> JMP134 with polysulfides increased their intracellular protein DSB content. Collectively, these findings demonstrate that polysulfides can promote DSB formation independently of known enzymatic DSB-mediated systems and the presence of oxygen, thereby benefiting the survival of microorganisms in anaerobic habitats.IMPORTANCEHow polysulfides enhance the adaption of microorganisms to anaerobic environments remains unclear. Our study reveals that polysulfides efficiently facilitate protein DSB formation under anaerobic conditions. Polysulfides contain zero-valent sulfur atoms (S⁰), which can be transferred to the thiol group of cysteine residue. This S⁰ atom then accepts two electrons from two cysteine residues and is reduced to H₂S, leaving the two cysteines linked by a disulfide bond. Anaerobic growth of microorganisms benefits from the formation of DSB. These findings pave the way for a deeper understanding of the intricate relationship between polysulfides and microorganisms in various environmental contexts.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0192624"},"PeriodicalIF":3.9,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative assessment of a restored and natural wetland using ¹³C-DNA SIP reveals a higher potential for methane production in the restored wetland.","authors":"Nora Hamovit, Taniya RoyChowdhury, Denise M Akob, Xuesong Zhang, Gregory McCarty, Stephanie Yarwood","doi":"10.1128/aem.02161-24","DOIUrl":"https://doi.org/10.1128/aem.02161-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Wetlands are the largest natural source of methane (CH&lt;sub&gt;4&lt;/sub&gt;), a potent greenhouse gas produced by methanogens. Methanogenesis rates are controlled by environmental factors such as redox potential, temperature, and carbon and electron acceptor availability and are presumably dependent on the composition of the active methanogen community. We collected intact soil cores from a restored and natural freshwater depressional wetland on Maryland's Delmarva Peninsula (USA) to assess the effects of wetland restoration and redox shifts on microbial processes. Intact soil cores were incubated under either saturated (anoxic) or unsaturated (oxic) conditions and amended with &lt;sup&gt;13&lt;/sup&gt;C-acetate for quantitative stable isotope probing (qSIP) of the 16S rRNA gene. Restored wetland cores supported a distinct community of methanogens compared to natural cores, and acetoclastic methanogens putatively identified in the genus &lt;i&gt;Methanosarcina&lt;/i&gt; were among the most abundant taxa in restored anoxic and oxic cores. The active microbial communities in the restored wetland cores were also distinguished by the unique presence of facultatively anaerobic bacteria belonging to the orders &lt;i&gt;Firmicutes&lt;/i&gt; and &lt;i&gt;Bacteroidetes&lt;/i&gt;. In natural wetland incubations, methanogen populations were not among the most abundant taxa, and these communities were instead distinguished by the unique presence of aerobic bacteria in the phyla &lt;i&gt;Acidobacteria&lt;/i&gt;, &lt;i&gt;Actinobacteria&lt;/i&gt;, and class &lt;i&gt;Alphaproteobacteria&lt;/i&gt;. Iron-reducing bacteria, in the genus &lt;i&gt;Geobacter&lt;/i&gt;, were active across all redox conditions in both the restored and the natural cores, except the natural oxic-anoxic condition. These findings suggest an overall higher potential for methanogenesis in the restored wetland site compared to the natural wetland site, even when there is evidence of Fe reduction.IMPORTANCEMethane (CH&lt;sub&gt;4&lt;/sub&gt;) is a potent greenhouse gas with an atmospheric half-life of ~10 years. Wetlands are the largest natural emitters of CH&lt;sub&gt;4&lt;/sub&gt;, but CH&lt;sub&gt;4&lt;/sub&gt; dynamics are difficult to constrain due to high spatial and temporal variability. In the past, wetlands were drained for agriculture. Now, restoration is an important strategy to increase these ecosystems' potential for sequestering carbon. However, the consequences of wetland restoration on carbon biogeochemistry are under-evaluated, and a thorough assessment of the active microbial community as a driver of biogeochemical changes is needed. Particularly, the effects of seasonal flooding/drying cycles in geographically isolated wetlands might have implications for CH&lt;sub&gt;4&lt;/sub&gt; emissions in both natural and restored wetlands. Here, we found that active microbial communities in natural and restored wetlands responded differently to flooding and drying regimes, resulting in differences in CH&lt;sub&gt;4&lt;/sub&gt; production potentials. Restored wetlands had a higher potential for CH&lt;sub&gt;4&lt;/sub&gt; production compared to natural w","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0216124"},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Sup35 overexpression on the formation, morphology, and physiological functions of intracellular Sup35 assemblies.","authors":"Jianhui Feng, Ekaterina Osmekhina, Jaakko V I Timonen, Markus B Linder","doi":"10.1128/aem.01703-24","DOIUrl":"https://doi.org/10.1128/aem.01703-24","url":null,"abstract":"<p><p>The yeast prion protein Sup35 is aggregation-prone at high concentrations. <i>De novo</i> Sup35 prion formation occurs at a significantly increased rate after transient overexpression of Sup35 in the presence of another prion, [<i>PIN</i>⁺], but it is still a rare event. Recent studies uncovered an additional and seemingly more prevalent role of Sup35: at its physiological level, it undergoes phase separation to form reversible condensates in response to transient stress. Stress-induced reversible Sup35 condensation in the [<i>psi</i>^-] strain enhances cellular fitness after stress ceases, whereas irreversible Sup35 aggregates in the [<i>PSI</i>⁺] strain do not confer this advantage. However, how Sup35 overexpression, which could potentially lead to irreversible aggregation, affects its condensation under stress conditions remains unclear. In this study, we used a combinatorial method to examine how different levels of Sup35 overproduction and cellular conditions affect the nature, formation, and physical properties of Sup35 assemblies in yeast cells, as well as their impacts on cellular growth. We observed notable morphological distinctions between irreversible Sup35 aggregates and reversible Sup35 condensates, possibly indicating different formation mechanisms. In addition, Sup35 aggregation caused by a very high overexpression level can strongly inhibit cell growth, diminish the formation of stress-induced condensates when Sup35 is completely aggregated, and impair cellular recovery from stress. Together, this study advances our fundamental understanding of the physical properties and formation mechanism of different Sup35 assemblies and their impacts on cellular growth. We conclude that <i>in vivo</i> studies are sensitive to overexpression and can lead to assembly routes that strongly affect functions.</p><p><strong>Importance: </strong>The role of condensates in living cells is often studied by overexpression. For understanding their physiological role, this can be problematic. Overexpression can shift cellular functions, thereby changing the system under study, and overexpression can also affect the phase behavior of condensates by shifting the position of the system in the underlying phase diagram. Our detailed study of overexpression of Sup35 in <i>S. cerevisiae</i> shows the interplay between these factors and highlights basic features of intracellular condensation such as the balance between condensation and aggregation as well as how cellular localization and responsiveness depend on protein levels. We also apply super-resolution microscopy to highlight details within the cells.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0170324"},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of novel prebiotic oligosaccharide pools from fiber drives biological insight in bacterial glycan metabolism.","authors":"Chad Masarweh, Maria Maldonado-Gomez, Bruna Paviani, Mrittika Bhattacharya, Cheng-Yu Weng, Christopher Suarez, Shawn Ehlers-Cheang, Aaron Stacy, Juan Castillo, Nithya Krishnakumar, Karen A Kalanetra, Daniela Barile, J Bruce German, Carlito B Lebrilla, David A Mills","doi":"10.1128/aem.02077-24","DOIUrl":"https://doi.org/10.1128/aem.02077-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Prebiotic oligosaccharides are dietary supplements that modulate the intestinal gut microbiome by selectively nourishing subsets of the microbial community with a goal to enhance host health. To date, the diversity of polysaccharide compositions in the fiber consumed by humans is not well represented by the limited scope of oligosaccharide compositions present in current commercial prebiotics. Recently, our UC Davis group developed a novel method to generate oligosaccharides from any polysaccharide fiber, termed &lt;u&gt;F&lt;/u&gt;enton's &lt;u&gt;I&lt;/u&gt;nitiation &lt;u&gt;T&lt;/u&gt;oward &lt;u&gt;D&lt;/u&gt;efined &lt;u&gt;O&lt;/u&gt;ligosaccharide &lt;u&gt;G&lt;/u&gt;roups (FITDOG). Using this method, sugar beet pulp (SBP) was transformed into sugar beet oligosaccharides (SBOs) composed of arabinose- and galactose-containing oligosaccharides. Fecal fermentations of SBO and SBP produced similar shifts in donor-specific bacterial communities and acid metabolite profiles with a general enrichment of &lt;i&gt;Bacteroides&lt;/i&gt; and &lt;i&gt;Bifidobacterium&lt;/i&gt;. However, &lt;i&gt;in vitro&lt;/i&gt; tests revealed more &lt;i&gt;Bifidobacterium&lt;/i&gt; strains could consume SBO than sugar beet arabinan, and specific strains showed differential consumption of arabinofuranooligosaccharides or galactooligosaccharide (GOS) portions of the SBO pool. Genomic and glycomic comparisons suggest that previously characterized, arabinan-specific, extracellular arabinofuranosidases from &lt;i&gt;Bifidobacterium&lt;/i&gt; are not necessary to metabolize the arabino-oligosaccharides within SBO. Synbiotic application of SBO with an SBO-consuming strain &lt;i&gt;Bifidobacterium longum&lt;/i&gt; subsp. &lt;i&gt;longum&lt;/i&gt; SC596 in serial fecal enrichments resulted in enhanced persistence among 9 of 10 donor feces. This work demonstrates a novel workflow whereby FITDOG creates novel oligosaccharide pools that can provide insight into how compositional differences in fiber drive differential gut fermentation behaviors as well as their downstream health impacts. Moreover, these oligosaccharides may be useful in new prebiotic and synbiotic applications.&lt;b&gt;IMPORTANCE&lt;/b&gt;Prebiotics seek to selectively alter the host microbiome composition or function, resulting in a concurrent health benefit to the host. However, commercial prebiotics represent a small fraction of the diversity of food polysaccharide compositions. In this work a novel method, &lt;u&gt;F&lt;/u&gt;enton's &lt;u&gt;I&lt;/u&gt;nitiation &lt;u&gt;T&lt;/u&gt;oward &lt;u&gt;D&lt;/u&gt;efined &lt;u&gt;O&lt;/u&gt;ligosaccharide &lt;u&gt;G&lt;/u&gt;roups (FITDOG) was used to generate an oligosaccharide pool from sugar beet pulp (SBP). Sugar beet oligosaccharides (SBOs) resulted in similar changes to SBP in fecal enrichments; however, SBO could be consumed by more beneficial bifidobacterial strains than the cognate polysaccharide. These results demonstrate how the details of glycan structure have a profound influence on how gut bacteria metabolize food carbohydrates. The implications of this work are relevant to understanding how different dietary sources influence the human microbiome and extend to developing nove","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0207724"},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent.","authors":"Michelle Z Hotchkiss, Alexandre J Poulain, Jessica R K Forrest","doi":"10.1128/aem.02036-24","DOIUrl":"https://doi.org/10.1128/aem.02036-24","url":null,"abstract":"<p><p>Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial <i>Bombus impatiens</i> suppliers, wild <i>B. impatiens</i>, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that <i>Apibacter</i> is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial <i>B. impatiens</i> colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0203624"},"PeriodicalIF":3.9,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial peptide DiPGLa-H exhibits the most outstanding anti-infective activity among the PGLa variants based on a systematic comparison.","authors":"Liangjun Zheng, Muhammad Zafir, Ziqian Zhang, Yadong Ma, Fengyi Yang, Xiaokun Wang, Xuemei Xue, Chen Wang, Ping Li, Pilong Liu, Fatma A El-Gohary, Xin Zhao, Huping Xue","doi":"10.1128/aem.02062-24","DOIUrl":"https://doi.org/10.1128/aem.02062-24","url":null,"abstract":"<p><p>The escalating threat of antibiotic-resistant bacteria has heightened global interest in antimicrobial peptides as promising candidates due to their potent broad-spectrum activity and low likelihood of resistance development. Despite this potential, these peptides face challenges, including modest bactericidal efficacy, insufficient safety assessment, and expensive production. In this study, we systematically evaluated a panel of nine AMP variants of PGLa, a natural AMP derived from <i>Xenopus laevis</i>. All peptides retained α-helical structures and exhibited high biocompatibility, with hemolytic concentrations above 128 µg/mL and macrophage survival rates over 80%. Among them, a tandem-repeat variant DiPGLa-H demonstrated the most potent antimicrobial activity, with a therapeutic index of 35.94, against key pathogens such as <i>Escherichia coli, Staphylococcus aureus,</i> and <i>Acinetobacter baumannii</i>. A DAMP4-DiPGLa-H fusion protein was engineered to mitigate potential host toxicity, and we achieved high-purity biosynthesis of DiPGLa-H by employing a combination of acid cleavage and non-chromatographic purification, with yields reaching 21.2 mg/mL. The biosynthesized DiPGLa-H exhibited robust stability across a wide pH range and high temperatures, effectively disrupting biofilms formed by multiple pathogenic species. Mechanistically, DiPGLa-H disrupts both the inner and outer bacterial membranes, causing cell shrinkage, vesiculation, and intracellular leakage. <i>In vivo</i>, DiPGLa-H significantly improved survival rates in mice with induced peritoneal inflammation by 31%-38% while reducing bacterial burdens in key organs by 100-fold to 1,000-fold. These findings unearthed DiPGLa-H as a highly promising AMP. Moreover, the successful development of a cost-effective, high-purity biosynthesis method for DiPGLa-H, utilizing DAMP4 fusion technology, enables its low-cost application in combating multidrug-resistant pathogens.</p><p><strong>Importance: </strong>AMPs are innate defense molecules in animals, plants, and microorganisms. Notably, one-third of these peptides in databases originate from amphibians. We discovered that naturally weak AMPs from this source can be enhanced through artificial design. Specifically, variant DiPGLa-H showed superior germicidal efficacy and cell selectivity both <i>in vivo</i> and <i>in vitro</i> and can be biosynthesized and purified by combining DAMP4 fusion protein strategy and a simple non-chromatographic method that facilitates large-scale production. Our focus is on understanding the structure-activity relationships of PGLa. Furthermore, the development of a non-chromatographic purification technique for AMPs offers a viable pathway for the large-scale production of these essential compounds.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0206224"},"PeriodicalIF":3.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Arginine accumulation suppresses heat production during fermentation of the biocontrol fungus <i>Beauveria bassiana</i>.","authors":"Tong Wu, Fangfang Zhan, Liqiong Zeng, Yanli Sun, Shihui Fu, Yu Fang, Xiaochun Lin, Haoyu Lin, Jun Su, Shouping Cai","doi":"10.1128/aem.02134-24","DOIUrl":"https://doi.org/10.1128/aem.02134-24","url":null,"abstract":"<p><p><i>Beauveria bassiana</i> (<i>Bb</i>) is one of the most widely used biocontrol agents, and its products constitute more than one-third of the global market share of fungal insecticides. Solid-state fermentation (SSF) is widely used in the production of <i>Beauveria bassiana</i> (<i>Bb</i>) because of its economic practicality and high production efficiency. However, the heat generated during fermentation can sharply reduce both the yield and quality of <i>Bb</i>, and current industrial methods to mitigate high temperatures during fermentation are inadequate, leading to increased production costs. Thus, exploring the underlying mechanism of how heat is produced by <i>Bb</i> is crucial for improving the SSF procedure and yield. This study employed multiomics data analysis of <i>Bb</i> during SSF to explore the relationships between fungal fermentation and environmental factors. We found that the heat production period for SSF was 12 hours to 48 hours post-inoculation. To further explore the underlying mechanism during this heating period, we identified 454 temperature-correlated metabolites (TCMs) and 1,994 temperature-correlated genes (TCGs). Annotations of the above TCMs and TCGs revealed significant enrichment in the arginine biosynthesis pathway; specifically, the expression level of glutamine synthetase, a TCG, decreased with fermentation time, whereas the expression levels of the TCGs L-arginine and L-glutamine increased with fermentation time, and glutamine synthetase and L-glutamine in the arginine biosynthesis pathway cycle produced the end product L-arginine. Furthermore, when the substrates of the SSF were treated with exogenous arginine, the temperature peak of the SSF significantly decreased with increasing concentration of exogenously added arginine.IMPORTANCEA large amount of experimental evidence from the field has shown that <i>Bb</i> is an irreplaceable mature product that protects the health of our agriculture and ecosystem. In addition to high efficiency and host extensiveness, low cost is a critical merit that makes <i>Bb</i> products frequently used in the field. However, the growing cost of power and labor in the <i>Bb</i> industry, especially the SSF procedure, has significantly increased the price of its products, thus restricting the use of <i>Bb</i> in the field. This study not only fills the theoretical knowledge gaps concerning the molecular basis of the interrelationship between <i>Bb</i> and the fermentation environment during SSF but also provides an economical and applicable strategy (the addition of arginine to the fermentation media) to further lower the cost and increase the yield of <i>Bb</i> during SSF at the industrial level.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0213424"},"PeriodicalIF":3.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of wild-boar-derived microbiota transplantation on piglet microbiota, metabolite profile, and gut proinflammatory cytokine production differs from sow-derived microbiota.","authors":"Rajibur Rahman, Janelle M Fouhse, Tingting Ju, Yi Fan, Tulika Bhardwaj, Ryan K Brook, Roman Nosach, John Harding, Benjamin P Willing","doi":"10.1128/aem.02265-24","DOIUrl":"https://doi.org/10.1128/aem.02265-24","url":null,"abstract":"<p><p>Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with <i>Lactobacillus helveticus</i>, <i>Lactobacillus mucosae</i>, and <i>Lactobacillus pontis</i>. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to <i>Lactobacillus</i> abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.IMPORTANCEThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0226524"},"PeriodicalIF":3.9,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance of <i>Vibrio</i> spp. from the coastal California system: discordance between genotypic and phenotypic patterns.","authors":"Peter J Sebastian, Cory Schlesener, Barbara A Byrne, Melissa Miller, Woutrina Smith, Francesca Batac, Caroline E C Goertz, Bart C Weimer, Christine K Johnson","doi":"10.1128/aem.01808-24","DOIUrl":"https://doi.org/10.1128/aem.01808-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antimicrobial resistance in &lt;i&gt;Vibrio&lt;/i&gt; species poses risks to both human and marine mammal health. Whole genome sequencing of &lt;i&gt;Vibrio&lt;/i&gt; spp. can be utilized to screen for antimicrobial resistance genes and allelic variants to provide mechanistic insights in ways that PCR screening and phenotypic interpretation cannot. Our goals were to (i) characterize antimicrobial resistance patterns of &lt;i&gt;Vibrio&lt;/i&gt; spp. pathogens isolated from southern sea otters (&lt;i&gt;Enhydra lutris nereis&lt;/i&gt;), northern sea otters (&lt;i&gt;Enhydra lutris kenyoni&lt;/i&gt;), and environmental samples from the central California coast using whole genome sequencing, and (ii) compare the presence of antimicrobial resistance genes with phenotypic interpretation from antibiotic susceptibility testing. Unexpectedly, genomic classification identified an understudied species, &lt;i&gt;Vibrio diabolicus&lt;/i&gt;, in sea otter and environmental isolates that were previously identified as &lt;i&gt;Vibrio alginolyticus&lt;/i&gt;. A total of 489 &lt;i&gt;Vibrio&lt;/i&gt; spp. isolates were sequenced, and frequently detected antimicrobial resistance genes included multidrug efflux pumps and genes associated with resistance to ß-lactams and tetracyclines. Genes associated with resistance to fluoroquinolones, aminoglycosides, chloramphenicol, and sulfonamides were uncommon. Sea otter isolates were phenotypically susceptible to tetracycline despite carrying genes &lt;i&gt;tet34&lt;/i&gt; and &lt;i&gt;tet35&lt;/i&gt;. Both between- and within-species variations in ampicillin resistance were observed despite the ubiquitous presence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CARB&lt;/sub&gt; genes in &lt;i&gt;V. alginolyticus&lt;/i&gt;, &lt;i&gt;V. diabolicus&lt;/i&gt;, and &lt;i&gt;Vibrio parahaemolyticus&lt;/i&gt;. Discordance between phenotypic and genotypic ampicillin resistance was especially noted for &lt;i&gt;V. parahaemolyticus&lt;/i&gt; and was partially attributed to the allelic variation of the &lt;i&gt;bla&lt;sub&gt;CARB&lt;/sub&gt;&lt;/i&gt; genes. Tetracyclines and fluoroquinolones, but not ß-lactams, are likely to be effective treatments for vibriosis in sea otters.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Vibriosis (infection with non-cholera &lt;i&gt;Vibrio&lt;/i&gt; spp.) is the most common seafood-borne illness globally, with major impacts on public health, food security, and wildlife health. Potential treatments of antimicrobial-resistant &lt;i&gt;Vibrio&lt;/i&gt; spp. in humans, aquaculture, and marine wildlife rehabilitation are complicated by current diagnostic challenges regarding bacterial species identification and interpretation of antimicrobial resistance patterns. Unexpected detection of previously misidentified &lt;i&gt;Vibrio diabolicus&lt;/i&gt; in sea otters suggests that a broader taxonomic group of &lt;i&gt;Vibrio&lt;/i&gt; infect sea otters than previously described. We also determined that the presence of ß-lactamase genes alone in sea otter isolates does not necessarily correlate with an ampicillin-resistant phenotype, likely due to deleterious amino acid substitutions in certain &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CARB&lt;/sub&gt; alleles. Continued monitoring of &lt;i&gt;Vibrio&lt;/i&gt; spp. phenotypes a","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0180824"},"PeriodicalIF":3.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenanthrene degradation by a flavoprotein monooxygenase from <i>Phanerodontia chrysosporium</i>.","authors":"Mika Hayasaka, Link Hamajima, Yuki Yoshida, Reini Mori, Hiroyuki Kato, Hiromitsu Suzuki, Ryoga Tsurigami, Takaaki Kojima, Masashi Kato, Motoyuki Shimizu","doi":"10.1128/aem.01574-24","DOIUrl":"https://doi.org/10.1128/aem.01574-24","url":null,"abstract":"<p><p>Phenanthrene (PHEN), a polycyclic aromatic hydrocarbon (PAH), is degraded by white-rot fungi like <i>Phanerochaete chrysosporium</i> (the fungus has been renamed as <i>Phanerodontia chrysosporium</i>). PHEN is metabolized by <i>P. chrysosporium</i> and transformed into various monohydroxylated and dihydroxylated products. These intermediates are further degraded by cleavage of the aromatic ring. However, the enzymes involved in PHEN conversion in <i>P. chrysosporium</i> remain largely unidentified. We aimed to identify and characterize the <i>P. chrysosporium</i> enzymes involved in the degradation of PHEN and its intermediates. Recombinant <i>P. chrysosporium</i> flavoprotein monooxygenase 11 (FPMO11), a homolog of the salicylate 1-monooxygenase from the naphthalene-degrading bacterium <i>Pseudomonas putida</i> G7, was overexpressed in <i>Escherichia coli</i>. FPMO11 catalyzes the oxidative decarboxylation of 1-hydroxy-2-naphthoate (1H2N) and 2-hydroxy-1-naphthoate (2H1N) to 1,2-dihydroxynaphthalene (1,2DHN). To the best of our knowledge, this is the first study to identify and characterize enzymes with 1H2N and 2H1N monooxygenase activities in members of the FPMO superfamily. Additionally, our search for a dioxygenase with the ability to catalyze the aromatic ring cleavage of 1,2DHN led to the identification of intradiol dioxygenase (IDD) 1 and IDD2 from <i>P. chrysosporium</i>, which catalyzes the ring cleavage of 1,2DHN. Thus, this study also identified, for the first time, intradiol 1,2DHN dioxygenase activity in members of the IDD superfamily. The findings highlight the unique substrate spectra of FPMO11 and IDDs, rendering them attractive candidates for biotechnological applications, especially mitigation of environmental and health risks associated with PAH pollution.IMPORTANCEPhenanthrene (PHEN), a polycyclic aromatic hydrocarbon (PAH), is a widely studied pollutant in environmental science and toxicology due to its presence in fossil fuels, tobacco smoke, and as a byproduct of incomplete combustion processes. White-rot fungi like <i>P. chrysosporium</i> can degrade PHEN through the production of extracellular oxidative enzymes. We investigated the properties of PHEN-degrading enzymes in <i>P. chrysosporium</i>, specifically one flavoprotein monooxygenase (FPMO11) and two intradiol dioxygenases (IDD1 and IDD2). Our findings indicate that the enzymes catalyze the aromatic ring cleavage of PHEN, using the intermediates as substrates, transforming them into less harmful and more biodegradable compounds. This could help reduce environmental pollution and mitigate health risks associated with PAH exposure. The potential of these enzymes for biotechnological applications is also highlighted, emphasizing their critical role in understanding PAH degradation by white-rot fungi.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0157424"},"PeriodicalIF":3.9,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}