mSphere最新文献

{"title":"Predation by a ciliate community mediates temperature and nutrient effects on a peatland prey prokaryotic community.","authors":"Katrina DeWitt, Alyssa A Carrell, Jennifer D Rocca, Samantha Votzke, Andrea Yammine, Ariane L Peralta, David J Weston, Dale A Pelletier, Jean P Gibert","doi":"10.1128/msphere.00309-25","DOIUrl":"https://doi.org/10.1128/msphere.00309-25","url":null,"abstract":"<p><p>Temperature significantly impacts microbial communities' composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on the total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates.IMPORTANCEWhile the importance of the abiotic environment in microbial communities has long been acknowledged, how prevalent ecological interactions like predation may influence these microbial community responses to shifting abiotic conditions is largely unknown. Our study addresses the complex interplay between temperature, nutrients, predation, and their joint effects on microbial community diversity and function. Our findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly alters these responses. Our study underscores the impact of abiotic factors on microbial communities and the importance of accounting for the biotic context in which these occur to understand, let alone predict, these responses properly.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0030925"},"PeriodicalIF":3.7,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144507080","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":"Correlating the oral swab microbial community with milk production metrics in Holstein dairy cows.","authors":"Joseph H Skarlupka, Madison S Cox, Andrew J Steinberger, Dino L Sbardellati, Andrew J Scheftgen, Ibrahim Zuniga-Chaves, Eric Paget, Charles Skadron, Nithya Attipetty, Jennifer C McClure, Derek M Bickhart, Garret Suen","doi":"10.1128/msphere.00167-25","DOIUrl":"10.1128/msphere.00167-25","url":null,"abstract":"<p><p>Oral swabs of dairy cows have been suggested as a proxy for direct ruminal sampling, and this approach can identify the presence of up to 70% of the rumen microbial community. Here, we further extend the utility of this approach by correlating the bacterial community of swabs collected from 226 dairy cows on a research farm in Wisconsin, USA, with average milk yield and days in milk, two phenotypes previously associated with differences in the ruminal microbiome. We then obtained milk production efficiency data for a subset of these animals (gross feed efficiency [GFE] and residual feed intake [RFI]) and correlated these metrics against their associated microbial data. We found that when using the oral swabs, we could identify correlations between bacterial genera and days in milk (<i>P</i> < 0.05). We further show that the ruminal microbiota was associated with average milk yield and days in milk for animals in their first lactation. Differential abundance testing identified amplicon sequence variants (ASVs) associated with these metrics (<i>P</i> < 0.05). Our comparison of bacterial communities between high and low efficiency groups, as determined by GFE and RFI, identified a significant difference in Shannon's diversity in second lactation cows (<i>P</i> < 0.05). We also found that RFI was significantly correlated with the bacterial community in second lactation animals (<i>P</i> < 0.05). Differential abundance analysis identified multiple oral- and rumen-associated ASVs correlated with GFE and RFI (<i>P</i> < 0.05). This study further establishes the utility of oral swabs as a ruminal proxy.IMPORTANCEImproving milk production efficiency is a key goal in the dairy industry and is traditionally pursued through genetic selection, diet optimization, and herd management practices. The ruminal microbiome, essential for digesting feed, has been linked to milk production efficiency, suggesting that microbiome modulation could improve efficiency. However, the integration of rumen microbiology into current management practices is hampered by the difficulty of large-scale rumen sampling, as proxies like fecal samples do not accurately reflect the ruminal microbiota. Traditional methods, like cannulation and stomach tubing, are labor-intensive and impractical for extensive sampling. Our research demonstrates the potential use of oral swabs as a scalable, effective method for characterizing the microbiome and its associations with milk production metrics, recapitulating established associations obtained through traditional ruminal sampling methods.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0016725"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983286","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":"Unique dermal bacterial signature differentiates atopic dermatitis skin from healthy.","authors":"Lene Bay, Christopher James Barnes, Blaine Gabriel Fritz, Nanna Ravnborg, Iben Frier Ruge, Anne-Sofie Halling-Sønderby, Sif Ravn Søeborg, Kathrine Hald Langhoff, Claus Lex, Anders Johannes Hansen, Jacob P Thyssen, Thomas Bjarnsholt","doi":"10.1128/msphere.00156-25","DOIUrl":"10.1128/msphere.00156-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Gaining a deeper understanding of the variation in skin microbiota across habitats and layers provides critical insights into the complex host-microbial interactions that drive inflammatory skin diseases. Our study investigated dermal versus epidermal microbiota in lesional and non-lesional skin of 37 adult atopic dermatitis (AD) patients and 37 healthy controls. Skin biopsies were partitioned into epidermal and dermal compartments, while serial tape strips collected the superficial epidermis. Bacterial communities were analyzed by cultivation, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confocal laser scanning microscopy, and metagenomic sequencing. We found that the effects of AD were evident across skin layers. The natural variation between skin layers and habitats diminishes in AD-affected skin, intensifying the impact of the microenvironment and host factors. A remarkably distinct dermal bacterial community was discovered among AD patients, being more conserved and providing a clearer difference between skin habitats, while the epidermis varied substantially. Importantly, comparisons between AD patients and controls revealed more genera differed when studying the dermal samples than the epidermal ones. &lt;i&gt;Staphylococcus&lt;/i&gt;, &lt;i&gt;Corynebacterium,&lt;/i&gt; and &lt;i&gt;Cutibacterium&lt;/i&gt; genera differed with AD status across all samples, but &lt;i&gt;Prevotella&lt;/i&gt; and &lt;i&gt;Mitsuokella&lt;/i&gt; only differed in the dermis. In the dry and moist dermis, this translated into 14 and 61 gene pathways significantly varying with AD status, including many related to the biosynthesis of menaquinones (vitamin K2). These results suggest dermal sampling would allow for the role of the skin microbiome within AD pathogenesis to be better resolved since these communities are simpler and less prone to environmental contamination.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;This study sheds light on the profound impact of skin microbiota's complex composition and distribution in atopic dermatitis (AD). The distinctive bacterial profile and activity, especially within the dermal skin compartment, vividly mirrored the cutaneous conditions in this inflamed microenvironment. The striking similarity in bacterial communities across different skin habitats in atopic skin underscores the high influence of atopic dermatitis-the genetic predisposition to an amplified immune response. This finding suggests that the dermal bacterial profile could be a valuable tool for longitudinally monitoring changes during the disease's relapsing phases, allowing for a precise categorization of patients into specific AD endotypes. Broadening the focus throughout the entire eczema-affected skin paves the way for treatments capable of modulating dermal biological factors, offering more effective management of AD. By further centering the interest in host-microbial interactions, we can refine personalized treatments, ultimately improving the lives of millions suffering from atopic de","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0015625"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008492","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 framework for utilizing leaf-associated microbes to achieve conservation and restoration goals.","authors":"Jacob A Heil, Jessica R Bernardin, Stephanie J Galla, Leonora S Bittleston","doi":"10.1128/msphere.01082-24","DOIUrl":"10.1128/msphere.01082-24","url":null,"abstract":"<p><p>Plant-associated microbiomes have profound effects on ecosystem functioning and play a role in the success of plants at both small and large scales. As key components of healthy plants and ecosystems, plant microbiomes should be considered in conservation and ecosystem management strategies. Many knowledge gaps and logistical barriers exist that increase the difficulty of employing microbes in conservation; however, some success has been achieved by manipulating the root microbiome and in agricultural contexts. In contrast with the root microbiome, the role of the leaf microbiome in conservation remains largely unexplored. In this perspective, we posit that the leaf microbiome plays an essential role in plant and ecosystem health and should be considered in conservation strategies. We include a framework for approaching leaf microbiome management, including identification of sources of disturbance, identifying mechanisms to address resulting plant stress, types of microbial inoculation to achieve desired outcomes, and co-producing plans of management with interest groups and rights holders.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0108224"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079206","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":"Genomic and transcriptomic insights into vertebrate host-specific <i>Lactobacillus johnsonii</i> adaptation in the gastrointestinal tract.","authors":"Keerthikka Ravi, Nicole R Falkowski, Gary B Huffnagle","doi":"10.1128/msphere.00052-25","DOIUrl":"10.1128/msphere.00052-25","url":null,"abstract":"<p><p>We conducted a comparative genomic analysis of <i>Lactobacillus johnsonii</i> strains isolated from the gastrointestinal tract of diverse vertebrate hosts to explore the genetic basis of host specificity. We then utilized transcriptomics analysis to investigate the expression profile of identified rodent-specific genes in mouse isolate MR1 during <i>in vitro</i> and <i>in vivo</i> growth conditions. There was significant heterogeneity among strains, in both genome sequence and content, with phylogenetic clustering of strains into distinct clades associated with rodent or avian sources. There were not sufficient genomes to identify whether porcine isolates formed their own genetic clade. However, human isolates did not form a distinct clade. Functional enrichment analysis revealed significant enrichment of several genes, including surface proteins and accessory secretory pathway-related genes, as well as tyrosine decarboxylase genes in rodent isolates compared to avian isolates, including in mouse isolate MR1. A total of 40 genes were identified as rodent-associated, and all were transcriptionally active in <i>L. johnsonii</i> MR1. The global transcriptomic analysis of <i>L. johnsonii</i> MR1 was done using cells grown anaerobically, at 37˚C, under both the late-exponential phase and stationary phase, as well as during <i>in vivo</i> growth in the cecum of mono-colonized germ-free mice. Several of these genes were uniquely regulated during late exponential vs stationary phase growth and <i>in vivo</i> colonization in mice, highlighting their potential role in nutrient adaptation and host-microbe interactions.IMPORTANCE<i>Lactobacillus johnsonii</i> is a well-known probiotic species with health-beneficial properties, including host immunomodulation and pathogen inhibition. Its growing relevance in the medical industry highlights the need to understand its biology, particularly how it adapts to different host environments. In bacteria, niche adaptation is often accompanied by the loss or gain of coding sequences along with changes in the genome size. In this study, we explored the genetic diversity of <i>L. johnsonii</i> strains from the gastrointestinal tracts of various vertebrates such as rodents, birds, swine, and humans. We found associations between genome content and host species of origin and could conceptually demonstrate that these genes are being differentially transcribed under varying conditions. Several functions were associated with specific host groups, suggesting that <i>L. johnsonii</i> strains have adapted to their hosts over time.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0005225"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009046","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 novel silver-ruthenium-based antimicrobial kills Gram-negative bacteria through oxidative stress-induced macromolecular damage.","authors":"Patrick Ofori Tawiah, Luca Finn Gaessler, Greg M Anderson, Emmanuel Parkay Oladokun, Jan-Ulrik Dahl","doi":"10.1128/msphere.00017-25","DOIUrl":"10.1128/msphere.00017-25","url":null,"abstract":"<p><p>Amplified by the decline in antibiotic discovery, the rise of antibiotic resistance has become a significant global challenge in infectious disease control. Extraintestinal <i>Escherichia coli</i> (ExPEC), known to be the most common instigators of urinary tract infections (UTIs), represents such a global threat. Novel strategies for more efficient treatments are therefore desperately needed. These include silver nanoparticles, which have been used as antimicrobial surface coatings on catheters to eliminate biofilm-forming uropathogens and reduce the risk of nosocomial infections. AGXX is a promising silver-ruthenium coating that presumably kills bacteria through the generation of reactive oxygen species (ROS). However, neither AGXX's mode of action is fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms toward AGXX been studied in detail. Here, we report that the bactericidal effects of AGXX are primarily based on ROS formation, as supplementation of the media with a ROS scavenger completely abolished AGXX-induced killing. We further show that AGXX impairs the integrity of the bacterial cell envelope and causes substantial protein aggregation and DNA damage already at sublethal concentrations. ExPEC strains appear to be more resistant to the proteotoxic effects of AGXX compared to non-pathogenic <i>E. coli,</i> indicating improved defense capabilities of the uropathogen. Global transcriptomic studies of AGXX-stressed ExPEC revealed a strong oxidative stress response, perturbations in metal homeostasis, as well as the activation of heat shock and DNA damage responses. Finally, we present evidence that ExPEC counteracts AGXX damage through the production of the chaperone polyphosphate, protecting cells from protein aggregation.IMPORTANCEThe rise in drug-resistant bacteria, together with the decline in antibiotic development, requires new strategies for infectious disease control. Gram-negative pathogens are particularly challenging to combat due to their outer membrane. This study highlights the effectiveness of the silver-containing antimicrobial AGXX against the Gram-negative bacterium <i>Escherichia coli</i>. AGXX effectively reduces bacterial survival by interfering with the membrane integrity and causing DNA damage and protein aggregation, which is likely a consequence of uncontrolled generation of oxidative stress. Our findings emphasize AGXX's potential as an antimicrobial surface coating and shed light on potential targets to reduce bacterial resistance to AGXX.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0001725"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187428","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":"The GATA-like transcription factor Gat201 determines alkaline-restricted growth in <i>Cryptococcus neoformans</i>.","authors":"Elizabeth S Hughes, Laura R Tuck, Zhenzhen He, Elizabeth R Ballou, Edward W J Wallace","doi":"10.1128/msphere.00191-25","DOIUrl":"10.1128/msphere.00191-25","url":null,"abstract":"<p><p>The fungus <i>Cryptococcus neoformans</i> is an opportunistic human pathogen that causes fatal meningitis through uncontrolled proliferation in host tissues. Evasion of host defenses relies on a protective polysaccharide capsule, regulated, in part, by the GATA-like transcription factor Gat201. Gat201 additionally contributes to virulence through capsule-independent mechanisms. Here, we show that Gat201 affects the proliferation of <i>C. neoformans</i>: in RPMI-1640 cell culture media at an alkaline pH that restricts wild-type cell growth, <i>gat201</i>∆ strains show increased budding, growth, and viability. RNA-seq analysis shows that Gat201 pathway genes, including co-factors <i>GAT204</i> and LIV3, are rapidly activated within minutes of inoculating <i>C. neoformans</i> in RPMI media, and strains mutated for <i>GAT204</i> and, to a lesser extent, <i>LIV3</i> also show improved growth. The effect of Gat201 on growth is pH-dependent: <i>gat201</i>∆ cells grow better than wild-type cells at high pH but worse than wild-type cells at neutral pH, in otherwise identical media. Together, this identifies the Gat201 pathway as an alkaline-responsive regulator of proliferation: Gat201 appears to govern an environment-dependent trade-off between proliferation and production of the defensive capsule. Furthermore, evolutionary analysis shows that Gat201 is in a subfamily of GATA-like transcription factors that is conserved within diverse fungi but absent in model yeasts. Together, our findings urge improved understanding of proliferation in diverse environmental niches in order to understand the mechanistic basis of fungal pathogenesis.IMPORTANCEInfectious microorganisms must adapt to differences between external and host environments in order to colonize and cause disease. <i>Cryptococcus neoformans</i> is an encapsulated fungal pathogen that can infect human airways and travel to the brain to cause life-threatening meningitis. The airway is a dynamic environment characterized by nutrient limitation, high temperature (37°C), CO₂, and transiently high pH (>8.5). In both the lung and brain, fungal proliferation through budding is a major driver of pathogenesis; however, the regulators of <i>Cryptococcus</i> proliferation are poorly understood and distinct from other model yeasts. In this work, we explore how <i>Cryptococcus</i> adapts to shifting environments and identify that the transcription factor Gat201, known to regulate capsule production, negatively regulates proliferation under alkaline conditions. Our findings highlight the need for improved understanding of proliferation/adaptation and its regulation in non-model systems.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0019125"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216332","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":"The antibacterial activity and therapeutic potential of the amphibian-derived peptide TB_KKG6K.","authors":"Cristina Schöpf, Magdalena Knapp, Jakob Scheler, Débora C Coraça-Huber, Alessandra Romanelli, Peter Ladurner, Anna C Seybold, Ulrike Binder, Reinhard Würzner, Florentine Marx","doi":"10.1128/msphere.01016-24","DOIUrl":"10.1128/msphere.01016-24","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) have great potential to be developed as topical treatments for microbial infections of the skin, including those caused by the gram-positive human pathogen <i>Staphylococcus aureus</i>. Among the AMPs, temporin B (TB) is of particular interest. This 13-amino-acid-long cationic peptide is secreted by the granular glands of the European frog <i>Rana temporaria</i> and represents a primary line of defense against invading pathogens. The objective of this study was to investigate the antibacterial efficacy and the mode of action of the synthetic TB analog, TB_KKG6K, in a drug-resistant clinical isolate of <i>S. aureus</i> and assess the peptide's tolerance and curative potential in an <i>in vitro</i> infection model using three-dimensional human epidermis equivalents (HEEs). The results revealed a high bactericidal efficacy of TB_KKG6K at low micromolar concentrations. The peptide perturbed the bacterial cell membrane integrity by permeabilization and depolarization. TB_KKG6K showed no toxicity in the invertebrate mini-host model <i>Galleria mellonella</i> and a high level of tolerance when topically applied in HEEs. Importantly, the therapeutic potential of TB_KKG6K was confirmed in HEEs infected with <i>S. aureus</i>. The topical application of TB_KKG6K significantly reduced the bacterial load and lowered the pro-inflammatory response in the infected HEEs. These findings reinforce the antibacterial potential and therapeutic efficacy of TB_KKG6K against <i>S. aureus</i> infection, particularly in the context of a cutaneous infection.IMPORTANCEThe emergence of multidrug-resistant bacteria has rendered the exploration of novel therapeutic treatment strategies a pivotal area of research. Among the most promising candidates are amphibian-derived antimicrobial peptides (AMPs), which are ideal for the development of novel drugs due to their multifaceted mode of action. Extensive studies have been conducted on these peptides over the last decade, resulting in the development of temporin B (TB) peptide analogs that have undergone modifications to their primary sequence. These modified analogs have demonstrated enhanced antibacterial and antifungal efficacy, while exhibiting reduced hemolytic activity. TB_KKG6K has the potential to be a promising candidate for topical treatments due to its small size and high antimicrobial activity against pathogens of the human skin. In particular, it demonstrated efficacy against <i>Staphylococcus aureus</i>, a skin commensal that can become an opportunistic pathogen, causing a range of infections from minor skin infections to life-threatening diseases such as bacteremia and sepsis.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0101624"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094394","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":"Field expedient stool collection methods for gut microbiome analysis in deployed military environments.","authors":"Car Reen Kok, James B Thissen, Michele Cerroni, David R Tribble, Anthony Cancio, Sophia Tran, Christina Schofield, Rhonda E Colombo, Tom Troth, Christie Joya, Tahaniyat Lalani, Nicholas A Be","doi":"10.1128/msphere.00818-24","DOIUrl":"10.1128/msphere.00818-24","url":null,"abstract":"<p><p>Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that <i>Corynebacterium</i> and <i>Blautia</i> were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0081824"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144079233","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":"Defining neuronal responses to the neurotropic parasite <i>Toxoplasma gondii</i>.","authors":"Hannah J Johnson, Joshua A Kochanowsky, Sambamurthy Chandrasekaran, Christopher A Hunter, Daniel P Beiting, Anita A Koshy","doi":"10.1128/msphere.00216-25","DOIUrl":"10.1128/msphere.00216-25","url":null,"abstract":"<p><p>A select group of pathogens infects neurons in the brain. Prior dogma held that neurons were \"defenseless\" against infecting microbes, but many studies suggest that neurons can mount anti-microbial defenses. However, a knowledge gap in understanding how neurons respond <i>in vitro</i> and <i>in vivo</i> to different classes of microorganisms remains. To address this gap, we compared a transcriptional data set derived from primary neuron cultures (PNCs) infected with the neurotropic intracellular parasite <i>Toxoplasma gondii</i> with a data set derived from neurons injected with <i>T. gondii</i> protein <i>in vivo</i>. These curated responses were then compared to the transcriptional responses of PNCs infected with the single-stranded RNA viruses, West Nile virus or Zika virus. These analyses highlighted a conserved response to infection associated with chemokines (<i>Cxcl10, Ccl2</i>) and cytokines (interferon signaling). However, <i>T. gondii</i> had diminished IFN-α signaling <i>in vitro</i> compared to the viral data sets and was uniquely associated with a decrease in neuron-specific genes (<i>Snap25</i>, <i>Slc17a7</i>, <i>Prkcg</i>). These data underscore that neurons participate in infection-induced neuroinflammation and illustrate that neurons possess both pathogen-specific and pathogen-conserved responses.IMPORTANCEThough neurons are commonly the target of pathogens that infect the central nervous system (CNS), few data sets assess the neuronal response to infection. This paucity of data is likely because neurons are perceived to have diminished immune capabilities. However, to understand the role of neurons in neuroinflammation and their immune capabilities, their responses must be investigated. Here, we analyzed publicly accessible, neuron-specific data sets to compare neuron responses to a eukaryotic pathogen vs two Orthoflaviviruses. A better understanding of neuron responses to different infections will allow us to develop methods for inhibiting pathways that lead to neuron dysfunction, enhancing those that limit pathogen survival, and mitigating infection-induced damage to the CNS.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0021625"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187429","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}