mSphere最新文献

{"title":"The ionophore resistance genes <i>narA</i> and <i>narB</i> are geographically widespread and linked to resistance to medically important antibiotics.","authors":"Asalia Ibrahim, Jason Au, Alex Wong","doi":"10.1128/msphere.00243-25","DOIUrl":"10.1128/msphere.00243-25","url":null,"abstract":"<p><p>Ionophores are a class of antibiotics used widely in animal production as anti-coccidials and for growth promotion. Since ionophores are not used in human medicine, it has largely been assumed that they do not contribute to medically important antimicrobial resistance (AMR). Nonetheless, there is increasing concern that ionophore usage could co-select for clinically relevant AMR, since the ionophore resistance genes <i>narA</i> and <i>narB</i> have been found in linkage with multiple AMR genes. We investigated the global distribution and AMR linkage of <i>narA</i> and <i>narB</i> using publicly available data. These ionophore resistance genes can be found worldwide, with >2,400 <i>narAB</i>-bearing isolates reported from 51 countries. Isolates were derived from a range of host species, including poultry, cattle, and humans. <i>narAB</i> was linked with an average of over 10 resistance determinants for AMR, including many medically important antibiotics. These observations indicate that we cannot assume that ionophore use is risk-free, with clear potential for co-selection for clinically relevant AMR.IMPORTANCEIonophores are a type of antibiotic used to promote growth in cattle and pigs and to treat parasitic infections in poultry. It has been assumed that ionophore use in animals does not pose a risk for humans. However, growing evidence suggests that ionophore use may select for medically relevant antibiotic resistance. Using analyses of public data, we found that ionophore resistance is widespread and that it is usually linked to resistance genes for medically relevant drugs. There is thus clear potential for ionophore use to impact the presence of antibiotic resistance genes in the food supply.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0024325"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317518","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":"Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.","authors":"Julia S Bruno, Vitor Heidrich, Felipe C F Restini, Tatiana M M T Alves, Wanessa Miranda-Silva, Franciele H Knebel, Elisangela M Cóser, Lilian T Inoue, Paula F Asprino, Anamaria A Camargo, Eduardo R Fregnani","doi":"10.1128/msphere.00257-25","DOIUrl":"10.1128/msphere.00257-25","url":null,"abstract":"<p><p>Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.</p><p><strong>Importance: </strong>This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in <i>in vivo</i> irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0025725"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144528956","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":"Human papillomavirus 16 mitigates <i>Sneathia vaginalis</i>-induced damage to cervical keratinocytes.","authors":"Phoebe V Bridy, Jasmine C Cruz, Jada L Covington, Taharah I Islam, Catherine E Hadley, Kayla Tran, Rachel Fry, Bradley A Sheffield, Myrna Serrano, Gregory A Buck, Jinlei Zhao, Katherine Y Tossas, Craig Meyers, Iain M Morgan, Claire D James, Kimberly K Jefferson","doi":"10.1128/msphere.00152-25","DOIUrl":"10.1128/msphere.00152-25","url":null,"abstract":"<p><p><i>Sneathia vaginalis</i> is a bacterial component of the vaginal microbiome that is of clinical interest because of its association with preterm birth and other obstetric complications. It produces a cytotoxin, but little is known about the mechanism through which it kills epithelial cells or the role that cytotoxicity plays in bacterial survival. Recent microbiome studies demonstrate an association between <i>S. vaginalis</i> and human papillomavirus (HPV) within the female reproductive tract, suggesting that HPV and <i>S. vaginalis</i> could interact in some way within this shared niche. We analyzed 16S rRNA survey and HPV typing data from our Vaginal Human Microbiome Project and found, in agreement with other reports, that <i>S. vaginalis</i> was associated with HPV infection. To test the hypothesis that HPV promotes the growth of <i>S. vaginalis</i>, growth and cytotoxicity of <i>S. vaginalis</i> in co-culture with HPV16-positive and HPV-negative human cervical keratinocytes (HCK) were quantitatively assessed. Organotypic HCK rafts expressing HPV16 were more resistant to <i>S. vaginalis</i>-induced damage, as assessed by histology, and supported increased bacterial growth relative to HPV-negative HCK rafts. When <i>S. vaginalis</i> was co-cultured with HPV16-positive and HPV-negative HCK monolayers, cytotoxicity was observed in both HPV16-positive and HPV-negative cells, but HPV16-positive cells were more resistant to the toxic effects of the bacteria and supported bacterial growth for an extended period of time. In conclusion, HPV16 may protect cervical keratinocytes from the cytotoxic effects of <i>S. vaginalis</i>, preventing the eradication of colonized cells and supporting bacterial growth, and this could underlie the association between <i>S. vaginalis</i> and HPV <i>in vivo</i>.IMPORTANCE<i>Sneathia vaginalis</i> (<i>S. vaginalis</i>) is a bacterial species that lives in the human vagina and can cause complications during pregnancy if it invades the uterus. It is capable of killing cervical epithelial cells. Human papillomaviruses (HPV) are sexually transmitted viruses that can cause genital lesions and cervical cancer. Recently, multiple reports describe an association between <i>S. vaginalis</i> and HPV. This study used cultured cervical epithelial cells expressing the high-risk HPV type, HPV16, and HPV-negative cells to determine whether HPV promotes the growth of <i>S. vaginalis</i>. We found that HPV16 promotes the survival of cervical epithelial cells that are exposed to <i>S. vaginalis</i>. Survival of cervical epithelial cells may benefit the growth of <i>S. vaginalis</i>, which adhere to and feed off of these cells to survive in the female reproductive tract.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0015225"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540968","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":"Straining to define a healthy microbiome.","authors":"Anna M Seekatz","doi":"10.1128/msphere.00797-24","DOIUrl":"10.1128/msphere.00797-24","url":null,"abstract":"<p><p>In 2020, I wrote an mSphere of Influence commentary on two studies that shaped my research perspective on the human gut microbiome (McNulty et al., Sci Transl Med 3:106ra106, 2011, https://doi.org/10.1126/scitranslmed.3002701; Hamilton et al., Gut Microbes 4:125, 2013, https://doi.org/10.4161/gmic.23571). The microbiome field has continued to progress since the publication of these studies over 10 years ago, emerging as a considerable factor in almost all areas focused on disease development. My previous commentary highlighted two areas that piqued my interest early on in my career: (i) that the extant microbial community should be considered when proposing to manipulate the microbiota, such as via probiotics or fecal microbiota transplantation, and (ii) that realized (i.e., transcribed) functional changes of the microbiota may occur independent of changes in its composition. Since writing that commentary, two microbiota-based therapeutics for the treatment of <i>Clostridioides difficile</i> infection have been approved, highlighting the potential success of using the microbiota to treat or prevent disease. Despite these wins and ever-growing evidence of the importance of the microbiome in managing our health, translating mechanistic studies into therapeutic value has been slower. In this minireview, I expand upon two large questions that would increase our ability to translate the microbiome into therapies, highlighting both historical and recent progress.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0079724"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144608908","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":"Development of blood-brain barrier-penetrating antibodies for neutralizing tick-borne encephalitis virus in the brain.","authors":"Mizuki Fukuta, Sayo Fukano, Naoya Maekawa, Shintaro Kobayashi, Shunsuke Okamoto, Minato Hirano, Junko Nio-Kobayashi, Hiroaki Kariwa, Shigeru Kawakami, Satoru Konnai, Kentaro Yoshii","doi":"10.1128/msphere.00184-25","DOIUrl":"10.1128/msphere.00184-25","url":null,"abstract":"<p><p>Tick-borne encephalitis virus (TBEV) belongs to the genus <i>Flavivirus</i> and causes tick-borne encephalitis (TBE), a disease characterized by severe neurological symptoms with a high mortality rate. Currently, no specific antiviral treatments have been developed for TBE. The blood-brain barrier (BBB) restricts drug delivery to the central nervous system, posing a major challenge in developing effective therapies targeting TBEV in the brain. In this study, we developed recombinant anti-TBEV antibodies fused with BBB-penetrating rabies virus glycoprotein (RVG) peptides to facilitate their transport across the BBB. The fusion of RVG peptides to the C-terminus of the heavy chain of whole antibodies or single-chain variable fragment had minimal impact on their neutralizing ability against TBEV. The RVG fusion enhanced antibody binding to the surface of a human brain endothelial cell line and increased permeability in an <i>in vitro</i> BBB model. The RVG-fused antibodies exhibited a higher transport efficiency to the brain than the non-fused antibodies following peripheral injection in mice. Notably, the peripheral administration of the RVG-fused whole antibody after viral invasion into the brain significantly neutralized TBEV in the brains of infected mice. These findings suggest that RVG-fused antibodies represent a promising therapeutic strategy for treating TBE once the virus has entered the brain.</p><p><strong>Importance: </strong>Tick-borne encephalitis virus is a neuroinvasive pathogen that causes severe neurologic disease, significantly affecting patients' quality of life. No specific antiviral treatment is available for tick-borne encephalitis caused by virus multiplication in the brain. The delivery of drugs to the brain via peripheral administration is often obstructed by the blood-brain barrier. To develop targeted antiviral therapies for brain infections, we engineered recombinant antibodies capable of crossing the blood-brain barrier via brain-targeted ligands. These antibodies exhibited permeability across the blood-brain barrier in both <i>in vitro</i> and <i>in vivo</i> models and notably effectively neutralized the virus within the brain following peripheral administration. This study is the first to highlight the therapeutic potential of brain-targeted recombinant antibodies after viral entry into the brain, offering a promising pathway for the development of effective antiviral treatments for tick-borne encephalitis.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0018425"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575853","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":"<i>Streptococcus pneumoniae</i> carriage in adults during the COVID-19 pandemic in Portugal: dominance of serotypes included in broader PCVs and of serotype 3.","authors":"Sónia T Almeida, A Cristina Paulo, Alexandra S Simões, Bárbara Ferreira, Raquel Sá-Leão","doi":"10.1128/msphere.00082-25","DOIUrl":"10.1128/msphere.00082-25","url":null,"abstract":"<p><p><i>Streptococcus pneumoniae</i> (pneumococcus) is a leading cause of infections, particularly in infants and the elderly. Recent advances in molecular methods suggest higher pneumococcal carriage rates among adults than previously estimated, raising questions about their role in transmission. This study aimed to estimate pneumococcal carriage prevalence, identify circulating serotypes, and assess risk factors for colonization among adults during the COVID-19 pandemic in Portugal. We conducted a prospective observational study among civil servants aged ≥18 years in Oeiras Municipality from February 2021 to February 2022. Paired nasopharyngeal and oropharyngeal samples were analyzed using qPCR to detect pneumococcal carriage and 66 serotypes/serogroups. This included novel primers and probes for serotypes 4 and 24B/F, overcoming previous concerns associated with false positivity. Risk factors were identified using Bayesian adaptive sampling for variable selection in generalized linear model. Among 3,574 participants, 6.9% were pneumococcal carriers through qPCR without prior culture enrichment. Carriage rates were higher in oropharyngeal than nasopharyngeal samples (5.3% vs 3.7%, <i>P</i> < 0.001). Twenty-six serotypes/serogroups were identified, with the most common being non-encapsulated (NT), 10A, 23B, 3, 11A/D, 33A/F/37, 16F, and 31. Excluding NT, the most frequent serotypes collectively accounted for 45.3% of all carriers. Vaccine coverage estimates were 13.5% for PCV13, 20.4% for PCV15, 40.0% for PCV20, and 64.1% for PCV21. Contact with children < 18 years increased the odds of colonization by 2.73-fold (95% confidence interval [CI], 2.01-3.75), while being male reduced the odds by 54% (odds ratio = 0.46; 95% CI, 0.30-0.69). These findings emphasize the need for ongoing surveillance to clarify adults' role in pneumococcal transmission and support prevention strategies, including adult vaccination and community-level interventions, to mitigate pneumococcal disease.IMPORTANCE<i>Streptococcus pneumoniae</i> is a major pathogen causing significant disease worldwide, yet adult carriage remains underexplored. By evaluating pneumococcal carriage among adults in Portugal during the COVID-19 pandemic, this study provides critical insights into circulating serotypes, including those not targeted by 13-valent pneumococcal conjugate vaccine (PCV13), and highlights key risk factors such as contact with children and sex differences. The findings reveal substantial potential coverage for newer PCVs. This work underscores the importance of adult-focused prevention strategies, including vaccination and ongoing surveillance, to reduce pneumococcal transmission and disease burden in the community.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0008225"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144258520","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":"Tn-seq screens in <i>Candida glabrata</i> treated with echinocandins and ibrexafungerp reveal pathways of antifungal resistance and cross-resistance.","authors":"Timothy J Nickels, Kyle W Cunningham","doi":"10.1128/msphere.00270-25","DOIUrl":"10.1128/msphere.00270-25","url":null,"abstract":"<p><p><i>Candida glabrata</i> (also known as <i>Nakaseomyces glabratus</i>) is the second most common cause of candidiasis, next to <i>Candida albicans,</i> and is rising in prevalence due to intrinsic and acquired mechanisms of antifungal resistance. This study utilizes transposon mutagenesis and deep sequencing (Tn-seq) to explore mechanisms of resistance to four different echinocandins (micafungin, anidulafungin, rezafungin, and caspofungin) and a non-echinocandin inhibitor (ibrexafungerp) of beta-1,3-glucan synthase (GS) in the BG2 strain background. Contrary to the other antifungals, caspofungin susceptibility exhibited high dependence on sphingolipid genes and low dependence on mitochondrial genes. Numerous deficiencies in mitochondrial genes increased fitness in micafungin, anidulafungin, rezafungin, and ibrexafungerp largely through effects on Pdr1, a stress-activated transcription factor known to promote fluconazole resistance. Several targets of Pdr1 (<i>RTA1, LAF1, LAC1, IPT1,</i> and <i>RSB1</i>) altered resistance to one or more of the GS inhibitors when overexpressed individually. Though Gal11 and other subunits of the mediator complex were necessary for the Pdr1 effects, an inhibitor of Gal11 (iKIX1) did not synergize with micafungin due to off-target antagonistic effects. Substantial variation was observed in the genetic resistance spectra for the different GS inhibitors within the BG2 strain background and comparison to the CBS138 strain background. The intra-strain variation was linked to gene deficiencies thought to alter phospholipid and ergosterol composition or asymmetry in cellular membranes. The findings generally support and extend earlier hypotheses that a lipid code governs GS inhibition and antifungal susceptibility in <i>C. glabrata</i>.IMPORTANCEEchinocandins and ibrexafungerp are important antifungals that target the same fungal enzyme. When the fungus acquires resistance to one of these antifungals, it may or may not exhibit cross-resistance to the others. This study investigates how every gene in the pathogenic yeast <i>Candida glabrata</i> contributes to resistance and cross-resistance to all five antifungals of this type. It offers new insights into how each antifungal interacts with the target enzyme and identifies the antifungals where cross-resistance is common or rare, providing guidance on the sequences and combinations that may be most effective in clinical settings.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0027025"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575855","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":"Control of citrate utilization by <i>Candida albicans</i> Adr1.","authors":"Amelia M White, Aaron P Mitchell","doi":"10.1128/msphere.00311-25","DOIUrl":"10.1128/msphere.00311-25","url":null,"abstract":"<p><p><i>Candida albicans</i>, a fungal commensal and pathogen, occupies diverse niches in the human host. Its broad metabolic repertoire is critical for its survival. The model yeast <i>Saccharomyces cerevisiae</i> provides a starting point for analysis of <i>C. albicans</i> physiology and regulatory circuitry, but there are many examples of rewired transcription factors that govern different processes in the two organisms. We focus here on Adr1, which in <i>S. cerevisiae</i> promotes alternative carbon source utilization and in <i>C. albicans</i> promotes ergosterol synthesis. We find that <i>C. albicans</i> Adr1 is also required for growth on citrate and compounds that feed into the citric acid cycle, like glutamate and malate. RNA-sequencing (RNA-seq) shows that predicted citrate metabolic genes, representing both the citric acid cycle and gluconeogenesis, are downregulated in an <i>adr1</i>Δ/Δ mutant. In fact, the three Adr1-dependent genes <i>HGT17, MDH1,</i> and <i>PCK1</i> are required for growth on citrate, as indicated by deletion mutant phenotypes. The hyphal regulator <i>EED1</i> has a negative role in citrate utilization, and an <i>adr1</i>Δ/Δ <i>eed1</i>Δ/Δ double mutant is defective for growth on citrate. This result argues that Adr1 acts downstream or independently of Eed1 to govern citrate utilization. <i>C. albicans</i> Adr1 is rewired compared to its <i>S. cerevisiae</i> ortholog to govern the ability to use citrate, which <i>S. cerevisiae</i> lacks, and potentially to respond to Eed1, for which <i>S. cerevisiae</i> lacks an ortholog.IMPORTANCE<i>Candida albicans</i> is a major fungal pathogen of humans, and its ability to grow on a range of carbon sources is critical for pathogenicity. Here, we find that a known regulator of ergosterol synthesis, Adr1, is also required to use citrate as a carbon source. Adr1 acts downstream or independently of Eed1, a well-known regulator of hypha formation and citrate utilization.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0031125"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306173/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144266808","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":"Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS).","authors":"Pei-Ju Chin, Jaysheel D Bhavsar, Trent J Bosma, Madolyn L MacDonald, Shawn W Polson, Arifa S Khan","doi":"10.1128/msphere.00286-25","DOIUrl":"10.1128/msphere.00286-25","url":null,"abstract":"<p><p>All biological products are required to demonstrate the absence of adventitious viruses (AVs), which may be inadvertently introduced at different steps involved in the manufacturing process. The currently recommended <i>in vitro</i> and <i>in vivo</i> virus detection assays have limitations for broad detection and are lengthy and laborious. Additionally, the use of animals is discouraged by the global 3 R's initiative for replacement, reduction, and refinement. High-throughput or next-generation sequencing (HTS/NGS) technologies can rapidly detect known and novel viruses in biological materials. There are, however, challenges for HTS detection of AVs due to differential abundance of viral sequences in public databases, which led to the creation of a non-redundant, Reference Viral Database (RVDB) containing all viral, viral-like, and viral-related sequences, with a reduced cellular sequence content. In this paper, we describe improvements in RVDB, which include the transition of RVDB production scripts from the original Python 2 to Python 3 codebase, updating the semantic pipeline to remove misannotated non-viral sequences and irrelevant viral sequences, use of taxonomy for the removal of phages, and inclusion of a quality-check step for SARS-CoV-2 genomes to exclude low-quality sequences. Additionally, RVDB website updates include search tools for exploring the database sequences and implementation of an automatic pipeline for providing annotation information to distinguish non-viral and viral sequences in the database. These updates for refining RVDB are expected to enhance HTS bioinformatics by reducing the computational time and increasing the accuracy for virus detection.IMPORTANCEHigh-throughput sequencing (HTS) has emerged as an advanced technology for demonstrating the safety of biological products. HTS can be used as an alternative adventitious virus detection method for replacing the currently recommended <i>in vivo</i> and PCR assays and supplementing or replacing the <i>in vitro</i> cell culture assays. However, HTS bioinformatics analysis for broad virus detection, including both known and novel viruses, depends on using a comprehensive and accurately annotated database. In this study, we have refined our original comprehensive Reference Virus Database (RVDB) for greater accuracy of virus detection with a reduced computational burden. Additionally, the production script for automating the generation of RVDB was updated to facilitate reliable database production and timely availability.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0028625"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144476111","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":"Significant associations between high-risk sexual behaviors and enterotypes of gut microbiome in HIV-negative men who have sex with men.","authors":"Kangjie Li, Xinjing Liu, Xiaohua Zhong, Haijiao Zeng, Tian Liu, Bing Lin, Pinyi Chen, Biao Xie, Xiaoni Zhong","doi":"10.1128/msphere.00232-25","DOIUrl":"10.1128/msphere.00232-25","url":null,"abstract":"<p><p>Gut microbiome of men who have sex with men (MSM) exhibits distinctive characteristics compared with general populations. The dysbiosis of the gut microbiome in MSM is also associated with the onset and evolution of HIV infection. Enterotype is an important feature of the gut microbiome and remains unaffected by demographic factors. However, the enterotypes of gut microbiome in MSM are unclear. The associations between enterotypes and high-risk sexual behaviors in this population also remain to be elucidated. HIV-negative MSM were recruited in this study. Fecal samples of the participants were collected and subjected to 16S rRNA gene sequencing. Enterotype clusters were determined by Jensen-Shannon divergence based on genus-level relative abundance. Microbial function predictions were conducted by PICRUSt2 software. Univariate and multivariate logistic regression approaches were utilized to analyze the associations of enterotypes with sexual behaviors. A three-category random forest machine learning model was performed to further examine the correlation between abundant microbiome in each enterotype cluster and anal sex roles. Two enterotype clusters were identified in our data sets, primarily driven by genera <i>Phocaeicola</i> and <i>Segatella</i>. The alpha diversity was comparable between the two enterotype clusters. Microbial metabolic functions significantly differed, and multivariate logistic regression indicated a significant association between anal sex role and enterotype. The results of the three-category random forest model indicate that the dominant bacterial communities in gut enterotypes can effectively differentiate MSM who engage exclusively in receptive anal intercourse from those who engage in insertive or versatile anal intercourse (AUC: 0.6400, 0.6929, respectively). We identified two enterotype clusters of gut microbiome in HIV-negative MSM. Enterotypes of MSM were significantly associated with anal sex roles. These findings further highlight the close correlation between the gut microbiome and anal intercourse roles.</p><p><strong>Importance: </strong>Our study's discovery that gut microbiome enterotypes are significantly associated with anal sex roles in HIV-negative MSM opens a new frontier in understanding the complex interplay between microbiology and sexual health. This finding underscores the urgency of delving into the mechanistic connections between the gut microbiome, sexual behaviors, and HIV infection. By identifying modifiable factors influencing gut microbiome composition, we have paved the way for developing personalized preventive strategies that could disrupt the transmission dynamics of HIV within this high-risk population. This research contributes to the fundamental understanding of the gut microbiome's role in the sexual health of MSM, making it a pivotal advancement in the fields of gut microbiome research and sexual health.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0023225"},"PeriodicalIF":3.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144485187","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}