Microbiological research最新文献

{"title":"2'-Fucosyllactose enhances indole-3-lactic acid production by Bifidobacterium bifidum DNG-08 and alleviates colitis-associated bone loss: Associations with microbiota remodeling and intestinal AHR-related responses.","authors":"Xinyu Wang, Bohan Zheng, Yike Sun, Libo Liu, Chun Li","doi":"10.1016/j.micres.2026.128781","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128781","url":null,"abstract":"<p><p>Inflammatory bowel disease is frequently associated with an imbalance in bone remodeling and a decline in bone mass, however, there is a lack of systematic research on microbiome-based intervention strategies targeting colitis-associated bone loss. In this study, Bifidobacterium bifidum DNG-08 (DNG-08) was selected from four candidate strains based on its favorable 2'-fucosyllactose (2'-FL) utilization and indole-3-lactic acid (ILA) production. Genomic annotation revealed that DNG-08 harbors functional genes related to fucosylated oligosaccharide utilization and the conversion of tryptophan to ILA. In a dextran sulfate sodium (DSS)-induced mouse model, combined intervention with DNG-08 and 2'-FL significantly alleviated colitis-associated phenotypes, and reduced pro-inflammatory cytokine levels by 13.33%-58.69%, while increasing IL-10-1.23 times that of the DSS group. Simultaneously, the combined intervention improved trabecular bone microstructure, increasing the bone formation marker procollagen type I N-terminal propeptide (PINP) by 14.61%-56.37%, decreasing the bone resorption marker C-terminal telopeptide of type I collagen (CTX-I) by 17.03%-21.77%, and upregulating the expression of Wnt3a, β-catenin, and Runx2. Gut microbiota analysis showed that combined intervention could partially reverse DSS-induced dysbiosis, enriching potentially beneficial bacterial taxa while reducing inflammation-associated genera. Notably, combined treatment group exhibited elevated serum ILA levels, increased colonic aryl hydrocarbon receptor (AHR) fluorescence, and upregulatied CYP1A1 expression. Correlation analysis identified significant associations among serum ILA, AHR-related indicators, selected bacterial genera, and bone remodeling parameters. This study highlights that strain-substrate matching may serve as a precise synbiotic strategy to improve inflammation-related gut-bone axis dysfunction.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"315 ","pages":"128781"},"PeriodicalIF":8.5,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CgFre2 contributes to ferric reductase activity, growth and pathogenicity in Colletotrichum gloeosporioides.","authors":"Longhui Huang, Qianlong Sun, Sizhen Liu, Yilong Man, Yangdan Yuan, Min Kuang, Jiawei Sheng, Xinqiu Tan","doi":"10.1016/j.micres.2026.128783","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128783","url":null,"abstract":"<p><p>Ferric reductases are oxidoreductases that catalyze the reduction of environmental Fe³ ⁺ to bioavailable Fe² ⁺ and mediate cellular iron uptake and metabolism. However, the specific biological functions of ferric reductases in Colletotrichum gloeosporioides have not been fully characterized. In this study, 15 ferric reductase-like proteins were screened from the genome annotation of C. gloeosporioides, and CgFre2 was selected for further functional characterization. Targeted deletion of CgFre2 resulted in reduced mycelial growth and a sharp decrease in conidiation. Further observation of conidial development showed delayed conidial germination and an increased incidence of abnormal appressorium formation, which impaired the proper morphogenesis of infection structures and thereby significantly attenuated the pathogenicity of the strain on chili peppers. Moreover, the expression levels of cell wall-related genes were downregulated in the CgFre2 deletion mutant, which exhibited impaired cell wall integrity and hypersensitivity to oxidative stress. Meanwhile, the expression levels of ferric reductase-like genes CgFre3, CgFre6, CgFre11, CgFre13, and CgFre15 were markedly upregulated in the CgFre2 mutant, whereas ferric reductase activity was reduced to 48% of the WT level. Notably, exogenous Fe³ ⁺ supplementation restored infection structure formation and pathogenicity on pepper leaves. Collectively, these findings reveal the biological function of ferric reductase CgFre2 and provide a theoretical basis for developing iron‑targeted green control strategies against pepper anthracnose.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"315 ","pages":"128783"},"PeriodicalIF":8.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary diversification of respiratory chain composition and the Cyo bo₃-type terminal oxidase regulation across the genus Pseudomonas.","authors":"Bárbara Pérez-Arroyo, Zulema Udaondo, Rubén Delicado-Mateo, Luis Yuste, Renata Moreno, Fernando Rojo","doi":"10.1016/j.micres.2026.128784","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128784","url":null,"abstract":"<p><p>The aerobic electron transport chain (ETC) is a major determinant of metabolic flexibility and ecological success in Pseudomonas, yet the evolutionary dynamics shaping its regulatory architecture remain poorly understood. Here we combine phylogenomics, promoter analysis, and functional assays across 249 Pseudomonas species to reveal extensive diversification in ETC composition and in the regulatory control of a key aerobic terminal oxidase, the Cyo ubiquinol oxidase. Cyo was detected in 83.5% of strains, and the regulatory regions controlling its expression displayed remarkable divergence. Promoter sequences upstream of cyoA segregated into five major classes with low or no similarity between groups. Reporter assays demonstrated that this promoter diversification translates into distinct regulatory behaviours. When cultured in a rich medium, Pseudomonas putida KT2440 exhibited a sharp early-exponential induction of cyoA, whereas Pseudomonas fluorescens, Pseudomonas syringae, Pseudomonas rhizosphaerae, and Pseudomonas aeruginosa showed a much lower induction. In a defined growth medium, Cyo activation varied strongly depending on the carbon source. These species-specific patterns were independent of growth rate, highlighting that regulatory evolution, rather than metabolic demand alone, drives Cyo expression dynamics. Loss of Cyo in P. putida reduced growth rate up to 37% and triggered broad transcriptional reprogramming involving respiration, carbon assimilation, and stress responses. Notably, lack of Cyo led to a > 13-fold increase in the expression of the CIO ubiquinol oxidase. Together, these results show that both the composition and regulatory control have undergone extensive evolutionary diversification in Pseudomonas. This regulatory rewiring enables lineage-specific respiratory behaviours that likely contribute to ecological adaptation.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"315 ","pages":"128784"},"PeriodicalIF":8.5,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simplified Hda1 HDAC complex globally regulates development, colonization and secondary metabolism in the postharvest fungus Aspergillus westerdijkiae.","authors":"Yibing Liu, Xinglu Zhang, Yafan Hu, Qiuhan Zhuo, Gang Wang, Yanhua Fan, Fuguo Xing","doi":"10.1016/j.micres.2026.128765","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128765","url":null,"abstract":"<p><p>Aspergillus westerdijkiae is a major postharvest fungus and an important producer of ochratoxin A (OTA), yet the roles of histone deacetylase (HDAC) complexes in its development, colonization, and OTA biosynthesis remain unclear. Here, our analyses support a simplified Hda1 class II HDAC complex comprising the catalytic subunit AwHda1 and the auxiliary subunit AwHda2-3. Deletion of AwHda1 caused pronounced impairments in vegetative growth, conidiation, and sclerotial formation, whereas deletion of AwHda2-3 left basal growth largely intact but reduced conidiation and sclerotial formation, with an approximately 87% reduction in sclerotial number. Both mutants showed markedly reduced OTA biosynthesis, by up to 99.35%, and significantly reduced colonization capacity on pear (Pyrus bretschneideri 'Huangguan'). Multi-omics profiling revealed broad transcriptional and metabolic remodeling, particularly in ΔAwHda1, including repression of ribosomal genes, decreased cellular ATP, reduced abscisic acid (ABA) levels, and downregulation of LaeA and components of the FluG/Flb-BrlA developmental cascade. Collectively, these findings support a simplified AwHda1-AwHda2-3 complex in A. westerdijkiae and reveal distinct but overlapping contributions of its catalytic and auxiliary subunits to fungal development, postharvest colonization, and OTA biosynthesis, accompanied by broad transcriptional and metabolic changes.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"315 ","pages":"128765"},"PeriodicalIF":8.5,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Longitudinal multi-omics pilot study: Small sample size human model of gut microbiota-mitochondrial metabolic dysregulation in primary biliary cholangitis","authors":"Jing Lou ,&nbsp;Xiaoxiang Hu ,&nbsp;Ren Yan ,&nbsp;Jiamin Duan ,&nbsp;Bingbing Du ,&nbsp;Feiyu Wang ,&nbsp;Yini Shao ,&nbsp;Huiyong Jiang ,&nbsp;Lanjuan Li ,&nbsp;Longxian Lv","doi":"10.1016/j.micres.2026.128465","DOIUrl":"10.1016/j.micres.2026.128465","url":null,"abstract":"<div><div>Ursodeoxycholic acid (UDCA) is the first-line therapy for primary biliary cholangitis (PBC), yet a subset of patients responds inadequately, with the underlying mechanisms remaining unclear. In this longitudinal, multi-omics pilot study employing a small-sample human model, we investigated the role of gut microbiota-mitochondrial metabolic dysregulation in influencing the heterogeneity of UDCA treatment response. Our exploratory analysis revealed that UDCA nonresponders exhibit persistent gut dysbiosis, characterized by the depletion of beneficial butyrate-producing bacteria, the expansion of opportunistic fungi such as <em>Candida albicans</em>, and the enrichment of a pro-inflammatory bacterial network centered on <em>Collinsella</em>. Functionally, this dysbiosis in nonresponders is characterized by an enrichment of microbial virulence factors (e.g., flagella) and impaired host energy metabolism, particularly mitochondrial tricarboxylic acid (TCA) cycle dysfunction, as supported by persistently elevated serum pyruvate levels. Conversely, UDCA responders exhibit remodeling of the gut microbiota and improved mitochondrial function, with significant enrichment of serum itaconate. As a proof-of-concept, an integrated microbiota-metabolite predictive model showed potential in identifying nonresponders within our cohort.However, its performance requires validation in independent cohorts, and its clinical utility remains unknown. Overall, this pilot study proposes that UDCA nonresponse may represent a distinct pathological state centered on persistent mitochondrial metabolic dysfunction, offering preliminary insights for developing personalized therapeutic strategies that target the gut-mitochondrion axis.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128465"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-resistance-guided phage cocktail design for effective mitigation of necrotic enteritis in poultry","authors":"Eunbyeol Ahn ,&nbsp;Joonbeom Kim ,&nbsp;Isabel Tobin ,&nbsp;Daeun Shin ,&nbsp;Eunsu Ha ,&nbsp;Guolong Zhang ,&nbsp;Sangryeol Ryu ,&nbsp;Byeonghwa Jeon","doi":"10.1016/j.micres.2026.128473","DOIUrl":"10.1016/j.micres.2026.128473","url":null,"abstract":"<div><div>The withdrawal of antibiotic growth promoters from poultry production has led to the resurgence of <em>Clostridium perfringens</em>-induced necrotic enteritis (NE), resulting in annual global economic losses exceeding $6 billion. With conventional antibiotics becoming less accessible for disease prevention, there is an urgent need for effective non-antibiotic alternatives. Bacteriophage therapy represents a promising approach, although its utility is often constrained by narrow host range and rapid emergence of phage resistance. Here, we present a cross-resistance-guided strategy for rational phage cocktail design that combines phages with complementary and non-overlapping resistance profiles. Through systematic screening of eight <em>C. perfringens</em>-specific phages, we identified two host-range groups exhibiting complementary host ranges and reciprocal cross-resistance. A cocktail comprising CPD4 (siphovirus-like, 52,658 bp) and CPD7 (podovirus-like, 18,958 bp) was formulated based on their potency and divergence. Genomic and morphological analyses confirmed their strictly lytic lifecycle, absence of lysogenic or virulence genes, and high physicochemical stability. Notably, the cocktail demonstrated reciprocal cross-resistance, where resistance to one phage did not confer resistance to the other, thereby ensuring sustained lytic activity and mitigating the emergence of resistant strains. Furthermore, <em>in vivo</em> evaluation demonstrated that the cocktail significantly improved survival, reduced intestinal lesions, and suppressed <em>C. perfringens</em> colonization in NE-challenged chickens. Together, these results establish this cross-resistance-guided phage cocktail design as a practical and cost-effective strategy for NE mitigation in poultry.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128473"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146166012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactiplantibacillus plantarum BGI-N6 mitigates obesity-linked inflammation and oxidative stress via gut microbiota-mediated metabolites","authors":"Hui Guo ,&nbsp;Wanjie Zhang ,&nbsp;Dongwei Zhang ,&nbsp;Xiaojie Li ,&nbsp;Yan Qin Tan","doi":"10.1016/j.micres.2026.128461","DOIUrl":"10.1016/j.micres.2026.128461","url":null,"abstract":"<div><div>Obesity-driven systemic inflammation is a critical contributor in the progression of metabolic diseases. While lactic acid bacteria (LAB) are recognized for countering diet-induced obesity, their specific role in mitigating the associated inflammatory pathways requires further elucidation. This study investigated the capacity of a novel LAB strain, <em>Lactiplantibacillus plantarum</em> BGI-N6 (N6), to alleviate obesity and its related inflammatory responses in a high-fat diet (HFD)-fed Sprague-Dawley (SD) rat model. N6 supplementation effectively attenuated body weight gain, fat deposition, and liver steatosis, while concurrently improving systemic metrics such as blood lipid profiles. Crucially, the treatment significantly reduced HFD-induced systemic inflammation and oxidative stress. Analysis of the gut microbiota demonstrated that N6 administration modulated gut microbiota composition, enhancing β-diversity and reducing the abundance of pro-inflammatory taxa, including <em>Sutterella wadsworthensis</em>, <em>Bilophila wadsworthia</em>, and <em>Holdemania filiformis</em>. These structural changes were accompanied by metabolic shifts, specifically an increased production of butyric and valeric acids and a decrease in propionic acid. Furthermore, N6 specifically downregulated bacterial biosynthesis pathways for lipopolysaccharide (LPS), an effect attributed to the reduced abundance of key gram-negative species such as <em>Sutterella wadsworthensis</em>, resulting in significantly lower serum LPS levels. Correlation analyses confirmed the strong association of these microbial and metabolic changes with improved metabolic and inflammatory parameters. Collectively, these findings demonstrate that N6 ameliorates obesity-induced inflammation and oxidative stress through a multi-faceted mechanism involving gut microbiota restructuring, SCFA modulation, and LPS reduction, underscoring its potential as a therapeutic probiotic for metabolic disorders.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128461"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146142742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the role of endolysin LysCPD7 harboring C. perfringens spore binding domain","authors":"Eunsu Ha ,&nbsp;Daeun Shin ,&nbsp;Sangryeol Ryu ,&nbsp;Minsuk Kong","doi":"10.1016/j.micres.2026.128474","DOIUrl":"10.1016/j.micres.2026.128474","url":null,"abstract":"<div><div>Due to their potent bactericidal activity, phage-derived endolysins are considered promising alternatives to conventional antibiotics. Although some endolysins from phages infecting spore-forming bacteria contain a spore binding domain (SBD), their biological function remains unclear. LysCPD7, an endolysin from the <em>Clostridium perfringens</em> phage CPD7, showed high antimicrobial activity, effectively reducing <em>C. perfringens</em> contamination in milk and beef broth. Fluorescence assays and immunogold electron microscopy showed that LysCPD7 lacks a C-terminal cell wall binding domain, but contains a SBD that localizes to the spore cortex layer. We found that an E187K mutation in the SBD resulted in reduced spore binding capacity while retaining lytic activity. Infection with the wild-type CPD7 led to a decrease in sporulation efficiency in <em>C. perfringens</em>, whereas the mutant CPD7 carrying the E187K substitution in the SBD had no impact on sporulation, suggesting that the SBD may play a role in the inhibition of sporulation in <em>C. perfringens.</em> Our findings could contribute to the rational design of effective antimicrobials or diagnostic tools for controlling <em>C. perfringens</em> and provide new insights into the interactions between phages and their spore-forming hosts.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128474"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146172510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The molecular arms race: Xenophagy, pathogen evasion, and emerging host-directed therapies","authors":"Onaiza Ansari ,&nbsp;Farhan Ahmed ,&nbsp;Nilofar Siddiquee ,&nbsp;Anam Mursaleen ,&nbsp;Syeda Rushna ,&nbsp;Javaid Ahmad Sheikh ,&nbsp;Mohd Shariq","doi":"10.1016/j.micres.2026.128460","DOIUrl":"10.1016/j.micres.2026.128460","url":null,"abstract":"<div><div>Xenophagy, a form of selective autophagy targeting intracellular pathogens, constitutes a central arm of cell-autonomous innate immunity. This review synthesizes recent advances in the molecular regulation of xenophagy, emphasizing ubiquitin-dependent and ubiquitin-independent cargo tagging, receptor redundancy and context dependence, and post-translational control of autophagy-related 8/microtubule-associated protein 1 light chain 3 (ATG8/MAP1LC3/LC3) engagement. We discuss how pathogens exploit or evade xenophagic defenses at multiple checkpoints, cargo recognition, receptor recruitment, autophagosome biogenesis, and lysosomal fusion, highlighting mechanistically defined bacterial and viral countermeasures. Attention is given to the distinction between canonical xenophagy and non-canonical LC3-associated phagocytosis (LAP), clarifying their divergent regulatory logic and functional outcomes. We further examine the integration of xenophagy with innate immune signaling, antigen processing and presentation, and intercellular communication via exosomes, thereby linking intracellular pathogen restriction to adaptive immunity. Emerging discovery platforms, including multi-omics and clustered regularly interspaced short palindromic repeats (CRISPR-based) genetic screens, are evaluated for their potential to uncover novel xenophagy regulators. Finally, we critically assess translational opportunities for xenophagy-targeted host-directed therapies, emphasizing pathogen-specific context, tissue-restricted delivery, and the risks of non-selective autophagy modulation. Together, this review provides a mechanistic and translational framework for understanding xenophagy as a dynamic, context-dependent immune defense pathway rather than a uniformly protective degradative process.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128460"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Morphological classification of Schizochytrium and mutagenic selection of high-oil-producing strains based on deep learning","authors":"Yu Qin ,&nbsp;Ying Ou ,&nbsp;Jian Zheng ,&nbsp;Shoushuai Feng ,&nbsp;Li Xie ,&nbsp;Qiong Wang ,&nbsp;Hailing Li ,&nbsp;Ren Gong ,&nbsp;Hailin Yang","doi":"10.1016/j.micres.2026.128464","DOIUrl":"10.1016/j.micres.2026.128464","url":null,"abstract":"<div><div>As a natural producer of omega-3 fatty acids, <em>Schizochytrium</em> demonstrates exceptional cell density and docosahexaenoic acid (DHA) production efficiency, establishing its status as a microbial platform of industrial significance. However, the absence of real-time fermentation monitoring systems constrains production optimization and hinders the sustainable commercialization of omega-3 products. Morphometric analysis offers potential for tracking microbial growth and metabolite accumulation, yet the complex relationships between <em>Schizochytrium</em> morphology, biomass dynamics, and lipid biosynthesis remain unresolved. Conventional morphological characterization relies on labor-intensive microscopic observation by trained personnel, necessitating automated image analysis solutions. We developed a novel 13-class morphotype classification system integrating cellular division characteristics and lipid droplet parameters, coupled with a purpose-built object detection architecture. The enhanced MLC-YOLO framework achieved 84.2 % mean average precision (mAP), representing a 2.2 % improvement over the standard YOLOv8s implementation. Fermentation monitoring identified strong positive correlations (<em>p</em> &lt; 0.001) between Lipid-saturated unicells (G11) and lipid yield, whereas Small lipid droplet tripartite cells (G4) and Small lipid droplet quadripartite cells (G6) inversely correlated with productivity. Application of the G11/(G4 +G6) selection index facilitated the isolation of mutant strain S62, which had a lipid content of 50.46 %, an increase of 1.96 % over the parental strain. This study addresses fundamental knowledge gaps in <em>Schizochytrium</em> morphology, establishes deep learning-enabled cellular phenotyping as a viable strain selection strategy, and propels the development of smart biomanufacturing systems for industrial omega-3 production.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"307 ","pages":"Article 128464"},"PeriodicalIF":6.9,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146157652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}