Current Research in Biotechnology最新文献

{"title":"Acoustic signatures of microalgal growth: ultrasonic velocity and attenuation as quantitative biomass indicators in Spirulina maxima","authors":"Darmawan Hidayat ,&nbsp;Hilman Sya’ban Sulthoni ,&nbsp;Taufik Taufik ,&nbsp;Septian Ari Kurniawan ,&nbsp;Muhammad Rasyid Ramdhani ,&nbsp;Asri Peni Wulandari","doi":"10.1016/j.crbiot.2026.100380","DOIUrl":"10.1016/j.crbiot.2026.100380","url":null,"abstract":"<div><div>Accurate, real-time measurement of microalgal biomass is vital for optimizing photobioreactor performance and advancing bioprocess monitoring technologies. This study systematically investigated the acoustic signatures of <em>Spirulina maxima</em> (<em>S. maxima</em>) by measuring sound velocity and attenuation at 1 MHz over a 14-day cultivation period and across controlled biomass dilutions (0–100% v/v). Ultrasonic time-of-flight and amplitude measurements were used to determine acoustic parameters, which were subsequently correlated with optical density (OD₆₈₀) to develop predictive models for biomass estimation. Sound velocity increased from approximately 1507 to 1710 m/s during cultivation, exhibiting nonlinear, concentration-dependent behavior (<em>R</em>² = 0.96), while attenuation rose from 0.0035 to 0.0074 dB/cm and exhibited near-linear dependence at early stages, with pronounced nonlinearity at higher biomass levels (<em>R</em>² = 0.93). Concentration-resolved measurements confirmed consistent trends: sound velocity increased steadily across all biomass concentrations, whereas attenuation increased sharply beyond roughly 60% v/v due to greater scattering and viscous–thermal losses. Temporal OD₆₈₀ profiles revealed distinct lag, quasi-stationary, and secondary growth phases, each reflected in characteristic shifts in acoustic response. Strong correlations between ultrasonic parameters and OD₆₈₀ (velocity: <em>r</em> = 0.93; attenuation: <em>r</em> = 0.97) demonstrate the capability of acoustic sensing to detect both mechanical and structural changes in microalgal cultures. Overall, these findings establish low-power ultrasound as a robust, sensitive, and non-invasive technique for real-time biomass monitoring, with significant potential for integration into automated photobioreactors and environmental monitoring systems.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"11 ","pages":"Article 100380"},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147395195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant vs mammal extracellular vesicles: new tools in therapeutic drug delivery","authors":"Elisa Maricchiolo,&nbsp;Pasquale Creanza,&nbsp;Michela Osnato,&nbsp;Mattia Tiboni,&nbsp;Luca Casettari,&nbsp;Annalisa Aluigi,&nbsp;Andrea Pompa","doi":"10.1016/j.crbiot.2025.100352","DOIUrl":"10.1016/j.crbiot.2025.100352","url":null,"abstract":"<div><div>Extracellular vesicles (EVs) are highly promising biological carriers, due to their potential for drug delivery and their involvement in multiple cellular processes. These vesicles, released by cells into the extracellular space, can be classified into different types based on their origin, size, and molecular content. While animal-derived EVs have been extensively studied and characterised, recent research has highlighted the growing interest in plant-derived EVs, which present unique properties that could offer novel advantages in therapeutic applications.</div><div>This review aims to provide an overview of similarities and differences between animal and plant-derived EVs, focusing on their structural and functional characteristics. Additionally, we report various methods used for the isolation and characterisation of these vesicles, to provide a comprehensive summary, highlighting the main challenges and opportunities of each experimental option.</div><div>Moreover, the present work explores the most used techniques for loading bioactive molecules into EVs, transforming them from natural biological entities into innovative drug delivery systems. The ability to encapsulate drugs, small RNA molecules, or proteins within EVs opens up new frontiers for the targeted treatment of diseases, with particular emphasis on overcoming barriers related to drug bioavailability and specificity.</div><div>Finally, this review stresses the importance of ongoing research in the extracellular vesicles field, from both animal and plant origins, given their adaptable properties to multiple pharmaceutical purposes. Plant-derived EVsoffer a sustainable and economic alternative, together with the better characterised mammalian vesicles, showing the potential to strongly improve the drug delivery strategy in the near future.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"11 ","pages":"Article 100352"},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145618631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative evaluation of chromium methionine chelate and Nano chromium in alleviating Zearalenone-Induced oxidative stress","authors":"Mohammad Alizadeh ,&nbsp;Arash Abolhassani ,&nbsp;Amirhosein Zanjani Tabasi ,&nbsp;Golnoush Shirkhani ,&nbsp;Asal Ghahreman ,&nbsp;Negin Shafaei ,&nbsp;Ehsan Oskoueian ,&nbsp;Ehsan Karimi","doi":"10.1016/j.crbiot.2026.100388","DOIUrl":"10.1016/j.crbiot.2026.100388","url":null,"abstract":"<div><div>Zearalenone, a mycotoxin from Fusarium fungi found in contaminated feed, poses toxicity risks to livestock. The administration of antioxidant compounds has emerged as a potential approach for mitigating zearalenone-induced toxicity. This study evaluated the effectiveness of chromium-methionine chelate (Cr-Met) and nano-chromium (Nano-Cr) in alleviating zearalenone toxicity in mice. Forty male Balb/c mice were divided into four groups for a 30-day trial: control, zearalenone diet (10 mg/kg), zearalenone + Cr-Met (0.5 mg/kg), and zearalenone + Nano-Cr (0.5 mg/kg). Zearalenone exposure significantly impaired weight gain, feed intake, liver enzyme activity, serum redox potential, and jejunal morphology, while also inducing hepatic inflammation. However, both Cr-Met and Nano-Cr supplementation improved these parameters, with Cr-Met showing superior efficacy due to greater intestinal bioavailability. These results suggest Cr-Met as a promising dietary intervention to mitigate zearalenone-induced toxicity.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"11 ","pages":"Article 100388"},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147797632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Affinity-based recovery of metabolically active microbial cells using BioOrthogonal Non-Canonical amino acid tagging","authors":"Yumechris Amekan ,&nbsp;Sarah Forrester ,&nbsp;Annabel Cansdale ,&nbsp;Marjan W. van der Woude ,&nbsp;Kelly R. Redeker ,&nbsp;James P.J. Chong","doi":"10.1016/j.crbiot.2026.100390","DOIUrl":"10.1016/j.crbiot.2026.100390","url":null,"abstract":"<div><div>Selective identification of translationally active cells remains a key challenge in linking microbial function to population dynamics. Bioorthogonal non-canonical amino acid tagging (BONCAT) enables pulse-labelling of newly synthesized proteins in live cells, providing a time-resolved of translational activity. While BONCAT is typically combined with fluorescent tagging and fluorescence-activated cell sorting (FACS), the reliance on high-end instrumentation and transparent matrices limits its use. Here, we present a fully benchtop workflow by coupling BONCAT with magnetic affinity-based cell separation (BONCAT–ABCS) to enable enrichment of translationally active <em>Escherichia coli</em> subpopulations from a mixed culture without specialised instrumentation. Using a diauxic growth model with glucose and lactose as carbon source and two near-isogenic strains (MV1300 (Lac-) and MV1717 (Lac+)), we quantified BONCAT-labelled and unlabelled fractions across five timepoints using AHA pulse labelling, click chemistry, and absolute qPCR targeting strain-specific chromosomal markers. BONCAT-labelled fractions exhibited significantly higher gene copy numbers and enrichment factors (up to 6.9-fold; <em>p</em> &lt; 0.001, ANOVA with Tukey’s HSD) compared to non-labelled controls, with recovery efficiencies ranging from 12 to 21% and background capture &lt; 4%. BONCAT-ABCS resolved physiological divergence during the diauxic shift, selectively enriching Lac+ cells during lactose metabolism while Lac- cells remained translationally inactive. Importantly, enrichment reflected activity-weighted population shifts rather than rare-cell amplification, highlighting the suitability of BONCAT–ABCS for bulk metabolic profiling. These results support BONCAT–ABCS as an accessible affinity-based enrichment strategy for quantifying translationally active subpopulations and highlight its potential application in bulk metabolic profiling, engineered microbial systems, microbiome analyses, and bioprocess monitoring.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"11 ","pages":"Article 100390"},"PeriodicalIF":4.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147849820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a high-throughput assay for monitoring adipogenesis in vitro","authors":"Rachel Giles,&nbsp;Chrisna Durandt,&nbsp;Melvin A. Ambele,&nbsp;Michael S. Pepper","doi":"10.1016/j.crbiot.2026.100419","DOIUrl":"10.1016/j.crbiot.2026.100419","url":null,"abstract":"<div><div>The obesity pandemic is listed as a chronic disease by the World Health Organization, and is underpinned by an increase in fat cell formation (adipogenesis). This study aims to develop high-throughput screening assays [flow cytometry, spectrophotometry and real-time reverse transcription polymerase chain reaction (RT-qPCR)] for cost-effective and rapid monitoring of adipogenesis using a human adipose-derived stem cell differentiation model. Adipogenesis was successfully upscaled from 6- to 96-well plates. We found that the most efficient well size differs between the assays investigated. Adipogenic differentiation could best be assessed in a 48-well plate (flow cytometry and spectrophotometry), while a 12-well plate was more efficient for obtaining reliable RT-qPCR results. The cost associated with hypothetically screening 100 compounds (in a high-throughput setting) using the method with the lowest degree of variability and the highest degree of cost-effectiveness was spectrophotometry (48-well plate), followed by flow cytometry (48-well plate) and RT-qPCR (12-well plate). This study provides valuable information for designing and selecting the most efficient high-throughput adipogenesis assays to screen for potential drug candidates in the continuous search of novel and more effective pharmacological agents to combatting obesity and its related comorbidities.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"12 ","pages":"Article 100419"},"PeriodicalIF":6.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149140605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial mycotoxin mitigation across the microbe–matrix–host continuum: mechanisms, fermented-food applications, and gastrointestinal translation","authors":"Imane EL HOUSSNI,&nbsp;Ahmed ZAHIDI,&nbsp;Sihame EL FAKIR,&nbsp;Wissal JAIMA,&nbsp;Rachida HASSIKOU","doi":"10.1016/j.crbiot.2026.100421","DOIUrl":"10.1016/j.crbiot.2026.100421","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Mycotoxin contamination in agricultural commodities is a pervasive global challenge, posing a significant threat to both public health and food security. As conventional mitigation methods are often limited by efficacy, safety, and cost, biological strategies utilizing beneficial microorganisms are emerging as a promising and sustainable alternative. This review provides a comprehensive and critical synthesis of current research on the application of exogenous beneficial microbes – including probiotic strains, functional starter cultures, inactivated cells (paraprobiotics), and engineered agents – for mycotoxin decontamination, with a specific emphasis on their functional role within the fermented food chain and at the gastrointestinal interface. Analysis of peer-reviewed literature confirms two primary mechanisms of microbial-mediated mycotoxin detoxification. The first, physical sequestration, occurs through the non-covalent binding of mycotoxins to cell wall components (e.g., peptidoglycans and β-D-glucans) of specific viable or inactivated microbial strains. Although this mechanism is highly strain-dependent and potentially reversible, it facilitates immediate and substantial mycotoxin reduction without requiring metabolic viability. The second mechanism, enzymatic biotransformation, involves the catalytic modification or cleavage of functional groups within mycotoxin structures. This results in detoxification when the resulting metabolites are structurally confirmed to be non-toxic or significantly less toxic than the parent compound. This review evaluates the efficacy of these processes both &lt;em&gt;in situ&lt;/em&gt;, where probiotics and starter cultures are applied during food fermentation to mitigate toxins, and &lt;em&gt;in vivo&lt;/em&gt;, where administered strains attenuate mycotoxin bioavailability, preserve intestinal epithelial barrier integrity, and support mucosal health. Despite promising results, the field faces significant challenges. Strain specificity remains a major hurdle, as detoxifying capabilities are not ubiquitous among microbial strains. The matrix stability, survival, and activity of administered microbes within diverse food matrices and the dynamic gastrointestinal tract also require further optimization. Future perspectives to advance this technology include the application of multi-omics technologies (e.g., genomics, proteomics, metabolomics), which offer immense potential for identifying novel, highly efficient strains and elucidating the precise molecular pathways of detoxification. Additionally, genetic engineering and synthetic biology strategies can be employed to develop enhanced microbial strains with superior binding affinities or enzymatic degradation activities. In conclusion, microbial-mediated decontamination offers a sustainable and effective strategy to enhance the safety and quality of the fermented food supply chain while protecting host intestinal health. Continued research focused on a mechanistic underst","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"12 ","pages":"Article 100421"},"PeriodicalIF":6.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149140717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploiting the bacterial type III secretion system of Pseudomonas aeruginosa to impact genomic recombination in murine lungs","authors":"Amanda N. Tuckey,&nbsp;Jennifer Clark,&nbsp;Rasha Q. Al-Rahahleh,&nbsp;Aisha H. Siddiqui,&nbsp;Steven A. DeFreitas,&nbsp;Wynand P. Roos,&nbsp;Mike T. Lin,&nbsp;Jonathon P. Audia,&nbsp;Robert W. Sobol","doi":"10.1016/j.crbiot.2026.100420","DOIUrl":"10.1016/j.crbiot.2026.100420","url":null,"abstract":"<div><div>The Gram-negative bacterium <em>Pseudomonas aeruginosa</em> encodes a Type III Secretion System (T3SS), a molecular syringe that injects bacterially-synthesized effector proteins directly into a target mammalian host cell. While classically studied in the context of bacterial pathogenesis, the T3SS has been repurposed as a powerful tool to deliver novel recombinant proteins that alter cell biology rather than causing disease. Importantly, the direct injection of recombinant protein bypasses the need for delivery of DNA to cells, allowing for transient effects with minimal risk of foreign DNA-induced secondary transformation events. This DNA-independent mode of delivery positions T3SS-based systems as an attractive platform for protein delivery, where transient, non-integrating effects are the therapeutic end goal compared to conventional gene therapy vectors. The primary goal of this proof-of-principle study is to demonstrate the technical feasibility of engineering <em>P. aeruginosa</em> as a recombinant protein delivery system capable of transferring a functional, site-specific, DNA recombinase (Cre) to mammalian cells and thereby inducing a genetically tractable nuclear recombination event. We first confirmed that Cre expression can readily induce recombination in mammalian cells, as expected. We then repurposed the <em>P. aeruginosa</em> T3SS by engineering bacteria to target Cre for T3 secretion and demonstrate successful Cre delivery to lung cells in Cre-reporter mice. <em>P. aeruginosa</em> is an attractive model for therapeutic protein delivery, as attenuated mutants can be engineered with minimal lung pathogenicity and are eventually cleared by the host immune system. Given the genetic tractability of <em>P. aeruginosa</em>, future engineering efforts could extend this platform to deliver proteins that modulate tumor cell survival or enhance therapeutic efficacy, building toward microbial-based strategies for cancer treatment.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"12 ","pages":"Article 100420"},"PeriodicalIF":6.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148995390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative multi-omics and biotechnology for climate resilience and micronutrient biofortification in millets: from trait discovery to precision crop improvement","authors":"Stanislaus Antony Ceasar,&nbsp;A.R. Sree Rathna,&nbsp;Gholamreza Abdi","doi":"10.1016/j.crbiot.2026.100426","DOIUrl":"10.1016/j.crbiot.2026.100426","url":null,"abstract":"<div><div>Millets are small-seeded cereals of the family Poaceae that tolerate drought, heat and poor soils. Their grains are rich in iron, zinc, calcium and phenolic antioxidants. Finger millet is exceptionally rich in calcium, and pearl millet is a good source of iron and zinc. These properties make millet crops useful for tackling climate change and micronutrient malnutrition. This review brings together recent progress in genomics, transcriptomics, proteomics, metabolomics, ionomics, epigenomics, phenomics and genome editing in these crops. Foxtail millet, pearl millet and finger millet now have chromosome-scale reference genomes and multi-omics databases, and pan-genome assemblies are available for foxtail millet, pearl millet and proso millet. In these three species, the stress-signaling network is built around abscisic acid (ABA) signaling, several transcription factor families, reactive oxygen species (ROS) scavenging and osmolyte metabolism. Genetic transformation was long the main bottleneck, but this is now changing. Foxtail millet supports a set of validated genome edits, including base editing and edits that improve grain amino acid quality. High-throughput and simplified protocols are extending transformation to pearl millet and finger millet and genome editing to pearl millet. Research on proso millet, little millet, kodo millet and barnyard millet lags behind. One major gap remains. The molecular machinery that controls micronutrient loading, including metal transporters, chelators and storage proteins, is still poorly understood. We suggest three priorities: biofortification based on mechanism; a transformation and editing platform that works across millet species; and precision breeding that links genomic prediction with digital phenomics and artificial intelligence.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"12 ","pages":"Article 100426"},"PeriodicalIF":6.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149199508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The landscape of LncRNAs in diabetic kidney disease: a meta-analysis of transcriptomics data","authors":"Raziyeh Rezaei ,&nbsp;Basireh Bahrami ,&nbsp;Yousof Gheisari","doi":"10.1016/j.crbiot.2025.100322","DOIUrl":"10.1016/j.crbiot.2025.100322","url":null,"abstract":"<div><div>Non-coding regions of the genome are known to influence complex disorders, yet the role of long non-coding RNAs (lncRNAs) in Diabetic Kidney Disease (DKD) remains underexplored. This study conducts a meta-analysis of RNA-sequencing data from murine kidney samples of type 1 (T1DM) and type 2 diabetes mellitus (T2DM) to identify lncRNAs associated with DKD. DKD-associated datasets were harvested, and after data pre-processing and quality assessment, 6 T1DM and 4 T2DM datasets were included. Data integration, batch correction, and normalization were performed, followed by the identification of differentially expressed lncRNAs (meta-DELs) and mRNAs (meta-DEMs). A DKD mouse model was developed to validate the expression of selected meta-DELs using qRT-PCR. The meta-analysis identified 188 meta-DELs in T1DM and 68 in T2DM. Notably, a small set of lncRNAs have dense mRNA interactions, including <em>Dancer</em>, <em>Gm7628</em>, <em>C4a</em>, and <em>Gm17300</em> in T1DM and <em>Malat1</em>, <em>C4a</em>, <em>Gm17300</em>, and <em>Eif4a2</em> in T2DM. Expression analysis confirmed the up-regulation of seven selected meta-DELs in the DKD model, with Trp53cor1, Gm15462, and Gm42664 reaching statistical significance. This systematic analysis of high-quality expression profiles identified meta-DELs consistently associated with DKD, distinguishing actual lncRNA changes from those influenced by experimental conditions or gene expression noise.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100322"},"PeriodicalIF":4.0,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145003841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of microbial source tracking markers through PCR-based molecular analysis and microbial genome database","authors":"Rifat Zubair Ahmed ,&nbsp;Ashraful Islam ,&nbsp;Tiantian Tian ,&nbsp;Zhe Tian ,&nbsp;Yu Zhang ,&nbsp;Min Yang","doi":"10.1016/j.crbiot.2025.100304","DOIUrl":"10.1016/j.crbiot.2025.100304","url":null,"abstract":"<div><div>Microbial Source Tracking (MST) uses molecular markers targeting host-associated gut microorganisms to identify fecal pollution. However, MST faces significant challenges in fecal source identification, particularly due to the markers’ poor specificity and shared genomic areas among microorganisms from different host sources. This study addresses these challenges by using host-specific <em>Escherichia coli</em> genetic markers, originally developed through a novel, library-independent approach, to detect sources of fecal pollution. A total of 563 <em>E.coli</em> isolates from chicken, cow, and pig feces were isolated and assessed by nine reported host-associated <em>E. coli</em> genetic markers (Chicken: CH7, CH9, CH12, CH13; Cow: CO2, CO3; Pig: P1, P3, P4) through PCR. Marker possession patterns, sensitivity, specificity, and accuracy were calculated. The NCBI Microbial Genome database was searched for sequences homologous to genome regions of studied genetic markers and evaluated by finding the percentage of host sources and sequence location in the genome. Homology evaluation with binary PCR results was used to predict the best-performing marker. PCR results exhibited that the most effective markers were chicken CH7 (67% sensitivity, 77.9% specificity, 74.4% accuracy) and CH9 (55% sensitivity, 99.4% specificity, 84.7% accuracy). However, a homology search in the database narrowed the selection of the top-performing marker to CH7, which showed homology with <em>E.coli</em> from chicken hosts, while other markers exhibited higher homology with <em>E.coli</em> from Humans. Furthermore, sequences from the database homologous to the CH9 and CO2 markers were found on a plasmid, while those for CH12, CO3, P1, and P4 were on the chromosome, and CH7, CH13, and P3 were on both. This study highlights the critical need for integrated approaches to assess molecular markers in MST assays, emphasizing their significance in advancing research within the field.</div></div>","PeriodicalId":52676,"journal":{"name":"Current Research in Biotechnology","volume":"10 ","pages":"Article 100304"},"PeriodicalIF":3.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144212018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}