Microbial Genomics最新文献

{"title":"A microbial mirage: when microbiome metrics may obscure ecological meaning.","authors":"Jake M Robinson, Linda Guentas, Martin F Breed","doi":"10.1099/mgen.0.001777","DOIUrl":"10.1099/mgen.0.001777","url":null,"abstract":"<p><p>Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405182","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":"Performance of mechanically sheared DNA in multiplexed Oxford Nanopore sequencing for <i>Salmonella</i> Typhi genomic surveillance.","authors":"Hsu Thinzar Maung, Masamoto Morita, Su Myat Han, Hiroyuki Mishima, Chisa Koga, Jan Wendzl C Evangelista, Mark John Girasol, Shuichi Suzuki, Koh-Ichiro Yoshiura, Toshio Kodama, Chris Smith, Hirotaka Hiyoshi","doi":"10.1099/mgen.0.001805","DOIUrl":"10.1099/mgen.0.001805","url":null,"abstract":"<p><p>Pathogen genomic surveillance is essential for monitoring high-risk lineages and antimicrobial resistance in <i>Salmonella enterica</i> serovar Typhi (<i>S</i>. Typhi), yet implementing whole-genome sequencing in sentinel hospital laboratories remains challenging. We evaluated whether mechanically sheared DNA, paired with high accuracy or super accuracy (SUP) basecalling, enables reliable Oxford Nanopore Technologies (ONT)-only sequencing for multiplexed <i>S</i>. Typhi genomic surveillance. Genomic DNA from three benchmark strains (Ty2, Ty42 and Ty43) was either mechanically sheared to ~15 kb or left unsheared and sequenced in a controlled 6-plex run. The optimized workflow was subsequently evaluated in a 24-plex field run that included 3 benchmark strains and 21 clinical isolates from a sentinel hospital in Manila, Philippines. Both runs were performed using the ONT Ligation Sequencing Kit with Native Barcoding 24 V14 (SQK-NBD114.24) and R10.4.1 flow cells (FLO-MIN114). Assembly metrics, single-nucleotide variation (SNV) concordance, core-genome MLST and downstream functional outputs were compared across DNA preparations and basecalling modes. In the 6-plex run, sheared libraries consistently achieved >1,000× pre-filtered coverage across all strains, whereas unsheared libraries showed highly variable depths and reduced stability after downsampling. When paired with SUP basecalling, sheared datasets produced assemblies comparable to Illumina and hybrid references across both structural accuracy and functional outputs. In the 24-plex run, all samples achieved >100× coverage, and 18 of the 22 retained <i>S</i>. Typhi genomes (81.8%) yielded fully circularized assemblies after exclusion of 2 non-<i>S</i>. Typhi isolates. Serotype prediction, genotyping and <i>in silico</i> antimicrobial resistance predictions remained concordant with the corresponding 6-plex benchmark results. These findings demonstrate that mechanical DNA shearing improves coverage uniformity under multiplexed conditions and, together with SUP basecalling, supports ONT-only <i>S</i>. Typhi genome reconstruction for routine genomic surveillance and broad phylogenetic contextualization. However, for fine-scale transmission analysis and high-resolution SNV interpretation, short-read or hybrid sequencing remains important. Overall, this approach provides a scalable framework for high-multiplex <i>S</i>. Typhi genomic surveillance in sentinel laboratory settings.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13405487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605148","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":"Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.","authors":"Tara Signorelli, Matthew Walker, James Robertson, Kaye Quizon, Yongxiang Zhang, Aleisha R Reimer, Shannon H C Eagle","doi":"10.1099/mgen.0.001738","DOIUrl":"10.1099/mgen.0.001738","url":null,"abstract":"<p><p>Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148448116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic engineering of <i>Staphylococcus haemolyticus</i>: overcoming restriction-modification barriers and targeting virulence genes.","authors":"Hermoine J Venter, J Pauline Cavanagh, Runa Wolden, Dakota Jones, Richard J Roberts, Martin O Christensen, Martha Zepeda-Rivera, Christopher D Johnston","doi":"10.1099/mgen.0.001780","DOIUrl":"10.1099/mgen.0.001780","url":null,"abstract":"<p><p><i>Staphylococcus haemolyticus</i> is an emerging multidrug-resistant nosocomial pathogen noted for robust biofilm formation and complex restriction-modification (RM) systems that hinder genetic manipulation. These barriers have severely limited mechanistic studies into its pathogenesis and immune evasion. Here, we report the development of a molecular toolbox that enables precise genomic engineering of clinical <i>S. haemolyticus</i> isolates. Using PacBio Single-Molecule Real-Time and bisulfite sequencing, we defined the complete genomes and methylomes of nine isolates, generating a functional readout of the active RM defences present in each strain. Among the RM systems identified, a Type II (PDLC03279) and a Type III (PDL3649/PDLC03643) system were significantly overrepresented in clinical isolates, suggesting a potential role in adaptation to host or hospital-associated environments. To bypass these RM barriers, we implemented a dual strategy: first, applying SyngenicDNA-based approaches to eliminate RM target motifs from genetic tools and second, engineering a surrogate <i>Escherichia coli</i> strain (JMC4) to mimic conserved <i>S. haemolyticus</i> methylation patterns. These tools significantly enhanced transformation efficiency and enabled targeted knockout of four putative virulence genes (<i>sraP, secA2, capA</i> and <i>capI</i>) as well as allelic exchange of the native capsule operon with the corresponding region from a non-encapsulated isolate. To our knowledge, this is the first report of precise genomic modifications in <i>S. haemolyticus</i>. The establishment of robust molecular tools for transformation and genome editing lays a foundation for future functional studies of virulence and host adaptation in this resilient opportunistic pathogen.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 7","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13417997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148605041","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":"Public and patient involvement: exploring public partnership in pathogen whole-genome sequencing research and its data visualisation.","authors":"Suzanne Rotheram, Hannah Trivett, Jane Whitehurst, Caitlin Collins, Jake Carson, Sophie Staniszewska, Xavier Didelot","doi":"10.1099/mgen.0.001763","DOIUrl":"10.1099/mgen.0.001763","url":null,"abstract":"","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13278559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272218","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":"Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.","authors":"Nicole Lerminiaux, Ken Fakharuddin, Heather J Adam, Amrita Bharat, George R Golding, Irene Martin, Michael Mulvey, Laura F Mataseje","doi":"10.1099/mgen.0.001699","DOIUrl":"10.1099/mgen.0.001699","url":null,"abstract":"<p><p>The gold standard for bloodstream infection (BSI) diagnostics involves culturing positive blood cultures (BCs) using phenotypic methods for organism identification and antimicrobial resistance (AMR) testing, which can take up to five days. However, it is crucial to optimize antimicrobial therapy as soon as possible to reduce morbidity and mortality. We present a novel laboratory and bioinformatic workflow to rapidly identify bacterial and fungal organisms and AMR determinants from positive BCs using Oxford Nanopore Technologies long-read sequencing. Using a robust clinical sample size (<i>n</i>=307), after a BC has flagged positive, our average turnaround time from DNA extraction to determination of species identity was 4.4 h for a multiplex run of 12 BCs and 3.7 h for a single sample run. We demonstrated that our pipeline taxonomic species identification results agreed with conventional MALDI-TOF identification for almost all positive BCs (97.7%, 300/307). Most species were accurately identified within the first hour of sequencing (93.7%, 281/300). We explored AMR detection for clinically relevant antimicrobials and observed that assembly-based tools had higher agreement to conventional antimicrobial susceptibility testing (AST) (81.2% after 1 h of sequencing, 89.6% after 5 h of sequencing) than read-based tools. Finally, we developed a publicly available analysis pipeline (venae) that generates a clinician-friendly HTML report, is quick to run and can dynamically update as more sequencing data is acquired. This study demonstrates how applying rapid, real-time genomics to BSI diagnostics can support clinical decision-making and improve patient outcomes by reducing turnaround times.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13256323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218413","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":"Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa.","authors":"Cebile Lekhuleni, Kedibone Ndlangisa, Ana D Sanches Ferreira, Hsueh-Chien R Cheng, Oliver Lorenz, Jackie Kleynhans, Linda de Gouveia, Happy Skosana, Vanessa Quan, Amelieke J H Cremers, Paulina A Hawkins, Sopio Chochua, Lesley McGee, Stephen D Bentley, Susan Meiring, Cheryl Cohen, Stephanie W Lo, Anne von Gottberg, Mignon du Plessis","doi":"10.1099/mgen.0.001737","DOIUrl":"10.1099/mgen.0.001737","url":null,"abstract":"<p><p><b>Background</b>. Serotype 8 has emerged as a common non-vaccine serotype causing invasive pneumococcal disease (IPD) in children and adults globally after the introduction of pneumococcal conjugate vaccines (PCV). We aimed to determine serotype 8 incidence and genomic epidemiology in South Africa.<b>Methods</b>. From national, laboratory-based surveillance for IPD in South Africa, we calculated the incidence of serotype 8 and global pneumococcal sequence cluster 3 (GPSC3) before and after PCV introduction. We performed phylodynamic analysis of genomes from clonal complex (CC) 53 and described South African isolates in the context of a global collection of serotype 8 and GPSC3 genomes.<b>Results.</b> Compared to the pre-PCV period, serotype 8 incidence increased in the late-PCV13 period among children <5 years [incidence rate ratio (IRR) 2.3, 95% confidence interval (CI) 1.3-4.1] and adults >64 years (2.8, 1.1-8.3). Similarly, GPSC3 rates increased among children <5 years (IRR 2.4, 95% CI 1.4-4.3) and individuals of all ages (1.7, 1.3-2.1). Serotype 8 CC53 population dynamics predicted at least five clonal expansions since the most recent common ancestor in 1929 (credible interval 1919-1937), with future predictions showing increases in the effective population size despite remaining largely susceptible to first-line treatment. Serotype 8 CC53 isolates from South Africa had a clonal structure when contextualized within a global collection of serotype 8 and GPSC3 genomes.<b>Conclusion.</b> Serotype 8 invasive disease incidence increased in South Africa after PCV introduction. Predictions showed sustained increases over time. Since South Africa switched to a lower-valency PCV10 (Pneumosil, Serum Institute of India) that does not include serotype 8 in 2024, continued surveillance will be crucial to inform PCV policy-making.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13229004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148143987","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":"Whole-genome analysis of a novel <i>Pandoraea sputorum</i> lineage causing high-mortality bloodstream infections.","authors":"Hua Wu, Lin Liu, Shijia Li, Pei Zhang, Ziling Xing, Qian Huang, Dai Kuang, Wei Liu, Chong Chen, Qianfeng Xia","doi":"10.1099/mgen.0.001663","DOIUrl":"10.1099/mgen.0.001663","url":null,"abstract":"<p><p><b>Background.</b> <i>Pandoraea sputorum</i> is an emerging multidrug-resistant pathogen primarily associated with cystic fibrosis. Bloodstream infections (BSIs) are rare but linked to high mortality. The genomic characteristics and evolutionary history of <i>P. sputorum</i> lineages causing BSIs remain poorly understood.<b>Methods.</b> We performed whole-genome sequencing on 18 <i>P</i>. <i>sputorum</i> isolates recovered from patients with BSIs in China between June 2022 and March 2024. Phylogenetic relationships were determined by core-genome SNP analysis, and the pan-genome was characterized using Roary. Antimicrobial resistance and virulence genes were identified using the CARD and VFDB databases. Evolutionary timescales were estimated using Bayesian molecular clock analysis.<b>Results.</b> The case fatality rate among patients was 27.8% (5 out of 18). Common clinical manifestations included fever (83.3%, 15 out of 18), productive cough (77.8%, 14 out of 18) and dyspnoea (61.1%, 11 out of 18). All isolates formed a distinct monophyletic lineage, genetically distant (>2,000 SNPs) from known <i>P. sputorum</i> strains but with minimal intra-lineage diversity (15-98 SNPs), indicating recent clonal expansion. The pan-genome was highly conserved, with core genes comprising 94.6% of the gene repertoire. All strains harboured core genome-encoded <i>ceoB</i> (efflux pump) and <i>OXA-155</i> (β-lactamase) genes, conferring resistance to multiple antimicrobials but remaining susceptible to imipenem. Bayesian analysis estimated the origin of this lineage in 2004 (95% highest posterior density: 2003.2-2005.8), with major diversification occurring between 2007 and 2018.<b>Conclusion.</b> We identified a novel, recently emerged and highly clonal lineage of <i>P. sputorum</i> associated with high-mortality BSIs. Its stable reservoir of core genome-encoded resistance mechanisms poses a significant therapeutic challenge. This lineage represents an emerging multidrug-resistant threat to public health, necessitating enhanced surveillance and infection control measures.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13229510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148144042","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":"Multi-omic characterization of the sow colostrum and milk microbiome and proteome.","authors":"Devin B Holman, Katherine E Gzyl, Arun Kommadath, Pekka Määttänen","doi":"10.1099/mgen.0.001726","DOIUrl":"10.1099/mgen.0.001726","url":null,"abstract":"<p><p>Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as <i>Sarcina perfringens</i> and <i>Streptococcus suis,</i> and potentially beneficial bacterial species like <i>Lactobacillus amylovorus</i> and <i>Lactiplantibacillus plantarum</i>. The microbial composition and functional potential shifted significantly as the milk matured, with <i>L. amylovorus</i>, <i>Limosilactobacillus reuteri</i> and <i>Rothia spp</i>. among the most relatively abundant taxa. Several antimicrobial resistance genes, including <i>erm</i>(C), <i>tet(K</i>), <i>tet</i>(M), <i>lnu(A</i>), <i>poxtA</i> and <i>fexB</i>, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including <i>Rothia spp</i>. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13279891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome mining and phylogenomics reveal diverse biosynthetic gene clusters in desert Actinobacteria.","authors":"Dina H Amin, Timothy G Barraclough","doi":"10.1099/mgen.0.001764","DOIUrl":"https://doi.org/10.1099/mgen.0.001764","url":null,"abstract":"<p><p>Antimicrobial resistance is a growing global health threat, heightening the need for new bioactive compounds from underexplored microbial niches. Desert ecosystems are increasingly recognized as reservoirs of metabolically versatile Actinobacteria that encode diverse biosynthetic pathways. In this study, we investigated Actinobacteria isolated from the underexplored Sinai Desert in Egypt using phylogenomics and genome-mining approaches. Genomes belonging to <i>Streptomyces</i>, <i>Micromonospora</i> and <i>Actinoplanes</i> were assembled and analysed for biosynthetic potential. Mining of these genomes revealed a broad repertoire of putative non-ribosomal peptide synthetase and polyketide synthase biosynthetic gene clusters (BGCs), including several divergent clusters with low predicted similarity to characterized references. These putatively divergent BGCs are likely to represent biosynthetic pathways with uncharacterized chemical products that could be explored by further experimental and chemical validation. The high diversity and divergence of BGCs in these desert strains could reflect ecological adaptation to harsh conditions and highlight their potential as a source of distinct antimicrobial and antitumour metabolites. Overall, this work underscores desert Actinobacteria as valuable candidates for future natural product discovery and synthetic biology applications.</p>","PeriodicalId":18487,"journal":{"name":"Microbial Genomics","volume":"12 6","pages":""},"PeriodicalIF":4.5,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148352398","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}