Microbiology spectrum最新文献

{"title":"Functional convergence despite taxonomic turnover across coral-associated microbiomes.","authors":"Xiaobin Wen, Shuo Han, Mengjie Wu, Pau Loke Show, Baolin Liao, Zhonghua Cai, Jin Zhou","doi":"10.1128/spectrum.02401-26","DOIUrl":"https://doi.org/10.1128/spectrum.02401-26","url":null,"abstract":"<p><p>Coral-associated microbiomes are fundamental to holobiont health and resilience, yet their community structures often demonstrate high taxonomic variability across host species. Whether such variability results in functional instability or reflects pervasive metabolic redundancy remains unclear. Here, we investigated microbial taxonomic structure, functional potential, and community assembly mechanisms across 15 coral species using 16S rRNA gene sequencing and shotgun metagenomics. These communities exhibited extreme taxonomic heterogeneity, high beta-diversity, and the absence of a universally shared core genus, indicating strong host-specific filtering that dictates microbial membership. In contrast, Kyoto Encyclopedia of Genes and Genomes pathway-based functional profiles exhibited striking convergence across hosts, revealing a conserved metabolic landscape despite extensive taxonomic turnover. Mantel and Procrustes analyses identified a weak but significant correspondence between taxonomic composition and functional potential, a pattern consistent with functional redundancy across coral-associated microbiomes. Null model-based assembly analyses further revealed a decoupling between taxonomic and functional organization. Taxonomic structure was shaped by a host-dependent balance of stochastic and deterministic processes, whereas functional profiles were predominantly assembled through stochastic processes, maintaining consistently high functional redundancy across hosts. Metagenomic profiling uncovered a two-tier functional architecture underlying this stability: a conserved, high-abundance metabolic core enriched in carbon and phosphorus cycling and stress response functions that support microbial persistence in the coral microenvironment, together with lower-abundance host-specific metabolic modules involved in nitrogen and sulfur transformations that enable niche adaptation. Thus, functional requirements primarily govern the coral-associated microbiome rather than taxonomic identity. This synergy between conserved survival traits and flexible metabolic capacities maintains holobiont homeostasis despite extensive taxonomic turnover.IMPORTANCECoral reefs rely on complex partnerships between corals and their associated microorganisms to maintain health and withstand environmental stress. However, it remains unclear whether changes in microbial communities across different coral species lead to loss of important functions. In this study, we examined microorganisms associated with 15 coral species from the South China Sea and found that coral species hosted highly different microbial communities, while maintaining similar microbial functions. Our findings reveal that different microbial groups can perform similar ecological roles, allowing coral-associated communities to remain functionally stable despite changes in microbial membership. This functional flexibility may help corals maintain biological balance under changing environmental co","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0240126"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238826","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":"Host filtering overrides simulated climate change: plant species identity shapes phyllosphere fungal communities and putative pathogen proportions in an alpine meadow.","authors":"Fengzhen Yang, Xiaojian Pu, Jianqiang Huo, Xinrong Li, Zhibiao Nan","doi":"10.1128/spectrum.00294-26","DOIUrl":"https://doi.org/10.1128/spectrum.00294-26","url":null,"abstract":"<p><p>Phyllosphere fungal communities play critical ecological roles in plant fitness and nutrient cycling in terrestrial ecosystems. However, the influences of multifactorial climate change on foliar mycobiomes across distinct plant functional groups remain poorly understood. To elucidate this, we used an 11-year field manipulation experiment to assess the impacts of simulated warming (+2.0°C) and altered precipitation (-50%, ambient, and +50%) on foliar fungal α-diversity, β-diversity, and functional guilds across four co-occurring alpine host plants: a forb (<i>Aster diplostephioides</i>), a grass (<i>Elymus nutans</i>), a legume (<i>Oxytropis kansuensis</i>), and a sedge (<i>Kobresia humilis</i>), combining ITS1 metabarcoding with compositional bias-corrected modeling (Analysis of Compositions of Microbiomes with Bias Correction 2). We found that host plant species identity acted as the overriding ecological filter, explaining 34.1% of community variation ([Formula: see text]) and predominantly governing putative pathogen proportions ([Formula: see text]; forb > grass > sedge > legume). In contrast, climate manipulation impacts were strictly host-dependent: experimental warming significantly elevated fungal OTU richness solely in the legume <i>O. kansuensis</i> ([Formula: see text]), while restructuring community β-diversity exclusively in <i>O. kansuensis</i> ([Formula: see text], [Formula: see text]) and the sedge <i>K. humilis</i> ([Formula: see text], [Formula: see text]). In addition, while precipitation shifts minimally affected broad-scale diversity, both climate factors induced fine-scale taxonomic turnover in specific lineages (notably <i>Aureobasidium</i>, <i>Cladosporium</i>, <i>Vishniacozyma</i>, and <i>Colletotrichum</i>); crucially, overall guild-level putative pathogen proportions remained resilient against all climate treatments and their interactions ([Formula: see text]). Our findings suggest that host intrinsic filtering and functional buffering outweigh direct short-term climatic pressures, and emphasize that future alpine foliar disease vulnerability will be predominantly mediated by climate-driven shifts in host plant community dominance rather than direct climatic stimulation of potential pathogens.</p><p><strong>Importance: </strong>The phyllosphere represents a vital ecological interface where fungal communities dictate plant fitness and ecosystem functioning, yet their vulnerability to concurrent warming and altered precipitation remains poorly understood in fragile alpine biomes. Here, we demonstrate that host plant species identity serves as the overriding ecological filter structuring foliar fungal communities, overriding direct short-term climatic stressors and effectively buffering potential pathogen burdens. Climate warming and precipitation shifts induced only fine-scale, host-specific adjustments in individual fungal lineages rather than triggering broad functional pathogen outbreaks. These findings provide c","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0029426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238841","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":"Modelling herpes simplex virus type 2 and Zika virus replication in mouse vaginal organoids and human vaginal spheroids.","authors":"Ananya Saraph, Imogen Porter, Grace Bodykevich, Ingrid Barta, May Dang-Lawson, Maria Tokuyama","doi":"10.1128/spectrum.01569-26","DOIUrl":"https://doi.org/10.1128/spectrum.01569-26","url":null,"abstract":"<p><p>Sexually transmitted viral infections disproportionately affect women and have adverse outcomes on maternal and fetal health. Since they are acquired through the vaginal tract, the vaginal epithelium is an important site to study host-viral interactions. An <i>in vitro</i> model of mouse vaginal epithelial organoids that can be infected by herpes simplex virus was recently established. Here, we used multiple vaginal organoid systems and studied their response to infection by herpes simplex virus type 2 (HSV-2) and Zika virus (ZIKV), both of which can be sexually transmitted and result in adverse effects on maternal and fetal health. We showed that mouse vaginal organoids support the replication of HSV-2 and ZIKV and respond to interferon treatment. We also established human vaginal spheroids from VK2/E6E7 cells that contain distinct apical and basal cell layers and are also susceptible to HSV-2 and ZIKV infection. Acyclovir treatment reduced HSV-2 replication in both mouse organoids and VK2 spheroids. However, ZIKV was restricted by remdesivir in VK2 spheroids but not in mouse organoids, indicating differences in antiviral activity depending on the organoid system. Finally, we established apical-out mouse vaginal organoids that were also susceptible to HSV-2 and ZIKV infection. Altogether, our results show that vaginal organoids and spheroids are useful <i>in vitro</i> models to study vaginal viral infections and effects of antiviral drugs.IMPORTANCEThe vaginal epithelium is the site of acquisition of sexually transmitted viral infections in women but has been historically understudied. 3D vaginal organoids that model the vaginal epithelium can be used to study virus-host interactions and provide novel insights. We demonstrated that vaginal organoids derived from mouse tissues could be infected with herpes simplex virus type 2 (HSV-2) and Zika virus (ZIKV), and these organoids are also capable of expressing immune genes. We then generated \"flipped\" mouse organoids that better represent the natural orientation of the vaginal epithelial lining. We also developed spheroids from human vaginal epithelial cells and showed that they can also be infected with HSV-2 and ZIKV. Finally, we showed that antiviral drugs reduced viral infection in these vaginal organoid and spheroid models. Our findings show that vaginal organoids and spheroids possess characteristics that make them useful models to study viral infections, as well as to test antiviral drugs.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0156926"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238909","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":"Further clinical performance of the First to Know Syphilis Self-Test with a larger sampling of pregnant individuals.","authors":"Jody D Berry, Lisa Nibauer, Maryam Ardakani, Hazim Aljewari, Antony George Joyee","doi":"10.1128/spectrum.02450-26","DOIUrl":"https://doi.org/10.1128/spectrum.02450-26","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0245026"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238828","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":"Clinical interpretation of mixed 23S rRNA genotypes in stool-based <i>Helicobacter pylori</i> resistance testing.","authors":"Toshihiko Kakiuchi","doi":"10.1128/spectrum.02822-26","DOIUrl":"https://doi.org/10.1128/spectrum.02822-26","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0282226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238885","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":"Genomic insights into non-tuberculous mycobacteria isolated from patients in a Chinese hospital.","authors":"Ting Liu, Yunuo Wu, Anqi Tian, Nuo Xu, Dongxin Liu, Shihan Zhou, Shenghai Wu, Wei Lu","doi":"10.1128/spectrum.00544-26","DOIUrl":"https://doi.org/10.1128/spectrum.00544-26","url":null,"abstract":"<p><p>Non-tuberculous mycobacteria (NTM) are increasingly recognized as important opportunistic pathogens, yet the genomic basis of their antimicrobial resistance and virulence in clinical settings remains incompletely understood. We performed whole-genome sequencing on 28 clinical isolates of NTM collected from Chinese patients (primarily bronchoalveolar lavage fluid) between 2022 and 2025, combined with broth microdilution susceptibility testing and comprehensive bioinformatics analysis. The collection comprised diverse species, including <i>Mycobacterium intracellulare</i>, <i>Mycobacterium chimaera</i>, <i>Mycobacterium marseillense</i>, <i>Mycobacterium abscessus</i>, <i>Mycobacterium fortuitum</i>, <i>Mycobacterium lentiflavum</i>, <i>Mycobacterium kansasii</i>, and <i>Mycobacterium colombiense</i>. Phenotypic testing revealed extensive multidrug resistance: 100% of isolates were resistant to rifampicin, erythromycin, imipenem, and doxycycline; 82.1% were resistant to ciprofloxacin; 89.3% were resistant to linezolid; and only amikacin retained substantial activity (50% susceptible). Resistome profiling using the Comprehensive Antibiotic Resistance Database/Resistance Gene Identifier identified heterogeneous distributions of efflux pumps (tap), ribosomal methylases [Erm(39)], β-lactamases (blaF), and other determinants, consistent with both intrinsic and accessory-genome-mediated resistance. Virulence factor annotation against the Virulence Factor Database revealed 531 unique factors, with hierarchical clustering separating isolates into two major clades: (i) rapid-growing species (<i>M. abscessus</i> and <i>M. fortuitum</i>) enriched in secretion systems (ESX/T7SS), polyketide synthases, and lipid biosynthesis genes, and (ii) slow-growing <i>Mycobacterium avium</i> complex species showing lower overall virulence gene abundance. Pangenome analysis indicated a relatively closed pangenome structure, with 1,026 core genes and substantial shell/cloud compartments contributing to strain-specific adaptations. These findings provide genomic insights into the multidrug-resistant and virulence-heterogeneous nature of contemporary Chinese clinical isolates of NTM.IMPORTANCEIn this study, we sequenced 28 clinical non-tuberculous mycobacterial strains, performed comprehensive drug susceptibility testing, and analyzed virulence factors to elucidate genomic determinants of resistance and pathogenicity, as well as evolutionary characteristics. These findings aim to bridge existing knowledge gaps, informing improved diagnostic and therapeutic strategies for non-tuberculous mycobacterial infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0054426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238876","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":"Impact of different clarithromycin resistance in <i>Mycobacterium abscessus</i> lung disease: a multicenter cohort study.","authors":"Ting-Wei Kao, Sheng-Wei Pan, Chia-Jung Liu, Ping-Huai Wang, Hsin-Ni Huang, Yu-Tsung Huang, Chin-Chung Shu","doi":"10.1128/spectrum.04232-25","DOIUrl":"https://doi.org/10.1128/spectrum.04232-25","url":null,"abstract":"<p><p>Macrolides remained cornerstone of <i>Mycobacterium abscessus</i> treatment, but emerging resistance patterns compromised therapeutic efficacies. Clarithromycin resistance can manifest as either mutational or inducible, while the clinical impacts of different resistance mechanisms in <i>M. abscessus</i> pulmonary disease (MAB-PD) had been poorly characterized. We conducted a multicenter retrospective cohort study from 2011 to 2023 across four tertiary centers in Taiwan. Adults with clarithromycin-resistant MAB-PD were included and stratified by resistance type: mutational vs inducible. Outcomes included all-cause 3-year mortality, microbiological clearance, and radiographic progression. Among 108 enrolled patients, 16 (14.7%) had mutational resistance and the remaining 92 had inducible type. Isolates comprised 103 <i>M. abscessus</i>, three <i>M. massiliense</i>, and two <i>M. bolletii</i>. Mutational resistance was associated with significantly higher 3-year mortality (18.8% vs 4.3%, <i>P</i> = 0.03) and lower acid-fast smear conversion rates in treated patients (18.2% vs 67.6%, <i>P</i> = 0.004). Multivariable analysis identified mutational clarithromycin resistance as an independent predictor of mortality (adjusted hazard ratio 5.21, 95% confidence interval 1.10-24.6, <i>P</i> = 0.04). Strains with mutational resistance demonstrated higher median minimal inhibitory concentrations to linezolid (24 vs 16 mg/L), cefoxitin (64 vs 32 mg/L), and amikacin (16 vs 8 mg/L). Mutational clarithromycin resistance in MAB-PD is associated with substantially worse clinical outcomes compared to inducible resistance, including higher mortality and poorer treatment responses. These findings suggested that more intensive treatment strategies might be needed for mutational clarithromycin resistance in MAB-PD.</p><p><strong>Importance: </strong>Macrolide resistance critically undermines treatment outcomes in <i>Mycobacterium abscessus</i> lung disease, yet the prognostic impact of distinct resistance mechanisms has remained unclear. This multicenter study demonstrates that mutational clarithromycin resistance, although less common than inducible resistance, is associated with markedly higher mortality, poorer microbiological response, and broader multidrug resistance. These findings provide clinically actionable evidence that not all macrolide resistance is equivalent. Recognizing mutational resistance as a high-risk phenotype has important implications for risk stratification, prognostication, and treatment intensification, supporting a more personalized approach to managing MAB-LD in routine clinical practice.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0423225"},"PeriodicalIF":4.1,"publicationDate":"2026-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149238903","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":"Clinical and genomic features of <i>Chryseobacterium</i> species isolated from clinical cultures.","authors":"Eriko Muramatsu, Masahiro Suzuki, Yukino Inagaki, Tomoki Ayukawa, Jumpei Yamauchi, Ryota Hase, Takehiro Hashimoto, Naoya Itoh, Yasufumi Matsumura, Hideaki Kato, Kohei Uemura, Kayoko Hayakawa, Sho Saito, Yohei Doi, Aki Sakurai","doi":"10.1128/spectrum.01793-26","DOIUrl":"https://doi.org/10.1128/spectrum.01793-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Chryseobacterium&lt;/i&gt; species are environmental bacteria occasionally implicated in human infections; however, their clinical and genomic features are not fully characterized. This study investigated the clinical, genotypic, and phenotypic characteristics of &lt;i&gt;Chryseobacterium&lt;/i&gt; strains collected through the MultiDrug-Resistant Organisms Clinical Research Network, a multicenter prospective study of patients with carbapenem-resistant gram-negative bacilli isolated at tertiary care hospitals in Japan between April 2019 and March 2024. Among 18 patients with &lt;i&gt;Chryseobacterium&lt;/i&gt; spp. confirmed by whole-genome sequencing (WGS), 5 had infection, and 13 were colonized. Bacteremia and pneumonia were the common types of infection. The isolates comprised five species, with &lt;i&gt;Chryseobacterium indologenes&lt;/i&gt; and &lt;i&gt;Chryseobacterium culicis&lt;/i&gt; being the most frequently detected. Compared with WGS, 16S rRNA gene sequencing demonstrated the highest species-level identification accuracy (93.8%), followed by MALDI Biotyper (50.0%), VITEK-MS (31.3%), and VITEK 2 Blue (31.3%). All systems correctly identified &lt;i&gt;C. indologenes&lt;/i&gt;, but other species were frequently misidentified or remained unidentified because of limited database coverage. All isolates exhibited broad β-lactam resistance, including resistance to carbapenems, which was associated with species-specific combinations of metallo-β-lactamase and extended-spectrum β-lactamase genes. Minocycline, trimethoprim-sulfamethoxazole, and cefiderocol retained activity across all species. These findings highlight that diverse &lt;i&gt;Chryseobacterium&lt;/i&gt; species, including uncommon ones, can be associated with human infections. Incorporating genomic approaches such as WGS or 16S rRNA gene analysis can improve species-level identification, especially for rare or emerging species.IMPORTANCE&lt;i&gt;Chryseobacterium&lt;/i&gt; species are emerging opportunistic pathogens that pose a diagnostic and therapeutic challenge as they are intrinsically resistant to most β-lactams, including carbapenems, and are often misidentified by routine clinical laboratory systems. In this multicenter study, we show that clinical &lt;i&gt;Chryseobacterium&lt;/i&gt; isolates represent greater species diversity than is typically recognized, extending beyond &lt;i&gt;Chryseobacterium indologenes&lt;/i&gt; to include uncommon species associated with both infection and colonization. Whole-genome sequencing clarified species assignments, revealed species-specific β-lactamase profiles, and highlighted the limitations of commonly used identification platforms, particularly for species absent from commercial databases. Despite broad β-lactam resistance, cefiderocol, minocycline, and trimethoprim-sulfamethoxazole retained &lt;i&gt;in vitro&lt;/i&gt; activity across species. These findings emphasize the need for genomic or sequence-based identification to accurately define the clinical spectrum of &lt;i&gt;Chryseobacterium&lt;/i&gt; species, guide interpretation of antimicrobial susceptibility,","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0179326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220543","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":"An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting, and extraction bias in sorted microbial communities.","authors":"Valerie Goethals, Nathan Vanwinsen, Fabian Mermans, Sofie De Gand, Nico Boon, Tom Van de Wiele, Kim De Paepe","doi":"10.1128/spectrum.00712-26","DOIUrl":"https://doi.org/10.1128/spectrum.00712-26","url":null,"abstract":"<p><p>Fluorescence-activated cell sorting (FACS) followed by metataxonomics is commonly used to probe the composition of microbial subpopulations with a functionality of interest. Metataxonomic analysis of sorted low-microbial-biomass samples is prone to contamination and bias introduced during sorting and DNA extraction. To improve metataxonomic accuracy, the DNA yield obtained by the DNeasy PowerSoil Pro kit was first maximized. FACS-sequencing using the optimized DNA extraction method distorted the composition of sorted microbiota by introducing sheath fluid contaminants, termed the FACSome. Since FACSome contaminants were experiment-specific, a standardized, applicable <i>in silico</i> decontamination method was developed to characterize and remove FACSome contamination in PacBio and Illumina metataxonomic sequencing data based on carefully selected controls. The optimized DNA extraction and decontamination methods were validated in soil, water, feces, saliva, gut reactor, and mock microbial communities. Metataxonomic profiles of non-selectively sorted and unsorted samples derived from these ecosystems did not perfectly match due to relic DNA depletion during FACS. Effective (97%) relic DNA depletion was confirmed with a spike-in experiment and is desirable since naturally present relic DNA can interfere with function-driven FACS-sequencing. A nuclease-based digest further enhanced relic DNA depletion. Since FACS depleted relic DNA, the preservation of intact cells prior to sorting is essential for activity- or viability-targeted FACS. Intact cells were best preserved during long-term -80°C storage of fecal samples that were not amended with glycerol-1× Tris-EDTA cryoprotectant.IMPORTANCEBulk meta-omics fail to provide sufficient resolution to gain mechanistic insights in microbial ecosystems. Function-driven microbiome research requires high-throughput profiling of active microbial subpopulations. These can be singled out through fluorescence-activated cell sorting (FACS) combined with function-, activity-, or viability-based labeling. The resulting low-biomass sorted samples present a currently overlooked challenge for accurate 16S rRNA gene profiling. We systematically identified all potential sources of interference to enable decontamination of 16S rRNA gene sequences from sorted microbiota. While this study focused on metataxonomic read-outs, our optimized extraction and decontamination workflow can advance other sequencing-based omics analyses of sorted microbial communities. Our optimized FACS-sequencing workflow is thus imperative to unlock the full potential of single-cell labeling and FACS, in turn enabling mode-of-action studies that will broaden our understanding of microbe-environment interactions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0071226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220550","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":"Alternative respiratory electron transport pathways drive differential aminoglycoside susceptibility.","authors":"Stuti Srivastav, L Karvannan, Amitesh Anand","doi":"10.1128/spectrum.01775-26","DOIUrl":"https://doi.org/10.1128/spectrum.01775-26","url":null,"abstract":"<p><p>Bacterial bioenergetics is increasingly recognized as a central determinant of antibiotic tolerance and resistance. Here, we define how architectural variation within the aerobic electron transport system (ETS) modulates proton motive force (PMF) and governs antibiotic susceptibility. We constructed four <i>Escherichia coli</i> strains with unbranched respiratory pathways differing in proton-translocation efficiencies. A low-PMF ETS variant exhibited selective tolerance to aminoglycosides, while susceptibility to β-lactams and tetracycline remained unchanged. Using fluorescent gentamicin, we demonstrate that reduced PMF directly limits drug uptake. Interestingly, wild-type <i>E. coli</i> was as susceptible as the high-PMF variant. These results establish respiratory energy transduction as a mechanistic bottleneck for aminoglycoside efficacy and position ETS remodeling as a bioenergetic route to antibiotic tolerance.IMPORTANCEInfectious diseases remain a major global health challenge, and the failure of antibiotics to effectively treat them is compounding the threat. This study shows that the way bacteria produce energy can strongly influence how well certain antibiotics work. By engineering bacteria with different respiratory pathways, we demonstrate that bacteria in a low-energy state became specifically more tolerant to aminoglycoside antibiotics such as gentamicin and tobramycin. Importantly, this tolerance was linked to reduced drug entry into the cell rather than resistance gained due to acquisition of adaptive genetic change. The findings reveal that bacterial energy metabolism is not simply a housekeeping process, but a major factor determining antibiotic effectiveness. This work helps explain why some bacteria survive antibiotic treatment despite lacking resistance mutations and highlights bacterial respiration as a promising target for developing strategies to restore antibiotic sensitivity and combat persistent infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0177526"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220595","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}