Biotechnology Reports最新文献

{"title":"The interplay of serum cations, insulin resistance, and atherogenic indices in predicting depression in hypothyroid patients","authors":"Sahira Qasim Al-Baldawi ,&nbsp;Hussein Kadhem Al-Hakeim ,&nbsp;Habib Hamam ,&nbsp;Ikram Khémiri","doi":"10.1016/j.btre.2025.e00932","DOIUrl":"10.1016/j.btre.2025.e00932","url":null,"abstract":"<div><h3>Background:</h3><div>A significant proportion of people with hypothyroidism (HT) is linked to affective disorders, including depression. The pathophysiology and factors affecting or predicating depression in HT patients is still to be elucidated. The current study intends to investigate serum levels of cations, insulin resistance parameters, trace elements and atherogenic indices, in HT+Dep, HT, and healthy control groups.</div></div><div><h3>Methods:</h3><div>We measured the biomarkers in the blood of sixty HT+Dep patients, sixty HT patients, and healthy controls who participated in the study. Selenium was measured using flameless atomic absorption spectrophotometry. While insulin level was measured using the ELISA technique.</div></div><div><h3>Results:</h3><div>We observed significant insulin resistance (IR) and dyslipidemia in HT patients, which were more pronounced in HT+Dep. Moreover, HT+Dep patients exhibited alterations in the blood concentrations of cations and trace elements. Artificial neural network analysis demonstrated that the atherogenic index of plasma (AIP) is the most precise predictor of depression in HT patients, with a success rate of 100%. This was followed by the distance from Castelli’s risk index-I (CRI-I) (24.7%), ionized calcium (23.1%), the IR index (HOMA2IR) (22.4%), and the insulin sensitivity index (HOMA2S%) (21.8%). Selenium, conversely, was the most reliable biomarker for differentiating the HT group from the control group.</div></div><div><h3>Conclusion:</h3><div>Depression in HT patients is associated with alteration in the serum levels of cations, atherogenic indices, trace elements, and IR. AIP is the best predictor for depression in HT patients. It is essential to correct the amounts of blood biomarkers of HT patients to mitigate the severity of depression.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00932"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473730","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":"Basic assessment of microbial dynamics in large- and small-scale biofilters","authors":"Andreas Otto Wagner ,&nbsp;Julia Wurm ,&nbsp;Mathias Wunderer ,&nbsp;Julia Zöhrer ,&nbsp;Andja Mullaymeri ,&nbsp;Eva-Maria Weinseisen ,&nbsp;Eva Maria Prem","doi":"10.1016/j.btre.2025.e00936","DOIUrl":"10.1016/j.btre.2025.e00936","url":null,"abstract":"<div><div>Treating exhaust gas from biogas plants is commonly done using biofilters composed of different filter materials. Immobilized on these filter materials microbes can convert less desirable exhaust gas components into more wanted ones. The evaluation of the performance of those filters based on microbial data is, however, difficult due to a lack in data regarding microbial colonisation of these filter materials. Thus, in the present study microbial abundance and microbial community composition in large- and small-scale biofilters was evaluated using both, cultivation dependent and independent approaches. Large-scale biofilters showed a similar total abundance of bacteria irrespective of the filter material and the water content of the biofilter. In contrast, fungal and yeast abundance was impacted by both, filter material (bark mulch or coconut fibre) and water content. In small scale biofilters (composed of bark mulch) the water content impacted microbial abundance. While a water content of 90% led to a similar development of bacterial and fungal/yeast abundance, 70% water content caused an asynchronous increase in abundance. Analysis of small-scale biofilters revealed an acidotrophic bacterial community including potential methanotrophs.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00936"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473797","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 genomic analysis of underutilized legumes: insights into evolutionary relationships, genome evolution and stress tolerance","authors":"Omena Bernard Ojuederie ,&nbsp;Ufuoma Lydia Akpojotor ,&nbsp;Adetomiwa Ayodele Adeniji ,&nbsp;Tina Chukwuyem Ojuederie ,&nbsp;Jacob Olagbenro Popoola ,&nbsp;Olubukola Oluranti Babalola","doi":"10.1016/j.btre.2025.e00918","DOIUrl":"10.1016/j.btre.2025.e00918","url":null,"abstract":"<div><div>African yam bean, Mung bean, and Winged bean, which are rich sources of nutrients and bioactive compounds, offer significant potential for food and nutrition security, yet they are underutilized. A comparative genomic analysis of these legumes with cowpea was conducted to unearth their molecular architecture and uncover their rich genomic profile. Protein and genomic fasta sequences were retrieved from the GenBank of the NCBI, and orthologous genes investigated, and secondary metabolites determined using OrthoVenn3 and PlantiSMASH programs. A total of 7761 single-copy and 20,250 unique genes were identified, which revealed their genetic diversity and conservation. Phylogenetic analysis showed the closest relationship between Cowpea and Mung bean, with Winged bean diverging significantly. Cowpea and Mung bean had significant gene expansions (+1051), while African yam bean (-864) and Winged bean (-643) had substantial gene losses. GO enrichment revealed the contributions to adaptations in the different legume species to biotic and abiotic stresses, highlighting their potential as climate-resilient crops. The highest protein gene (enzyme) count for saccharide (68) and terpene (18) biosynthesis was obtained in AYB. At the same time, mung bean had the highest gene clusters for alkaloids (10) and polyketides (5), and the highest enzyme count for the biosynthesis of alkaloids (32) and polyketides (17). Underutilized legumes exhibited higher essential amino acid levels compared to cowpea. These findings provide valuable insights for breeding programs and biotechnological interventions to improve the nutritional value and acceptance of these underutilized legumes, ultimately contributing to food and nutrition security.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00918"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925919","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":"A modified hot phenol-based protocol for high-purity Escherichia coli lipopolysaccharide extraction: Biochemical validation, stem cell cytotoxicity, and dose dependent multi-organ inflammation in a rat model","authors":"Edris Vahdani ,&nbsp;Ali Sepehrinezhad ,&nbsp;Elham Hosseini ,&nbsp;Saman Soleimanpour ,&nbsp;Sajad Sahab Negah ,&nbsp;Mohammad Ahanjan","doi":"10.1016/j.btre.2025.e00933","DOIUrl":"10.1016/j.btre.2025.e00933","url":null,"abstract":"<div><div>Gram-negative bacteria contain lipopolysaccharides (LPS) in their outer membrane, which induce strong inflammatory responses. Traditional LPS extraction methods often leave residual protein and nucleic acid contamination. These impurities interfere with downstream analyses and reduce reproducibility in biological studies. This study provides a modified hot phenol method combined with enzymatic treatments using proteinase K, DNase, RNase to extract pure LPS from <em>Escherichia coli</em>. Purity was confirmed by gel electrophoresis using Coomassie blue and silver nitrate staining. The biological activity of isolated LPS was tested on mesenchymal and embryonic neural stem cells, demonstrating decreased viability. In Wistar rats, LPS injection elevated serum IL-6 but not TNFα or IL-1β. Histological examinations indicated liver, kidney, brain, and colon tissue damage post-injection. Our results show that the modified hot phenol method efficiently produces high-purity, biologically active LPS suitable for both in vitro and in vivo inflammation studies, supporting research into inflammatory processes and associated diseases.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00933"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145362597","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":"Prospecting technology and economic potential to produce bio-succinic acid: a review","authors":"Diniz A.S. Silva ,&nbsp;Rafael Luque ,&nbsp;Yaimé Delgado-Arcaño ,&nbsp;Elen A. Perpetuo ,&nbsp;Alisson D. da S. Ruy ,&nbsp;Ana Lucia B. de Souza ,&nbsp;Luiz A.M. Pontes","doi":"10.1016/j.btre.2025.e00920","DOIUrl":"10.1016/j.btre.2025.e00920","url":null,"abstract":"<div><div>Succinic acid (SA) is an organic acid and a key building block with various synthetic applications in the food, pharmaceutical, and chemical industries. Currently produced through petrochemical routes, the use of microorganisms to produce it from biomass waste offers a renewable and sustainable alternative. This study evaluates the main technologies for producing succinic acid via biotechnological routes (BioSA) and its market potential, aiming for commercial production. Research highlights BioSA’s competitive edge and significant capacity to synthesize high-value products, such as 1,4-butanediol and polybutylene succinate (PBS), offering a viable alternative to fossil-derived maleic anhydride. Among BioSA-producing microorganisms, <em>Escherichia coli</em> and <em>Actinobacillus succinogenes</em> are the most promising, achieving titers of 1.10 and 1.23 gg^-1, respectively, and yields of 127.1 and 83.7 gL^-1 under anaerobic conditions at low pH, with genetic modifications to maximize productivity. The market is expected to grow at an annual rate of up to 6.7 % through 2032.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00920"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158222","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":"Improving a photosynthetic bioprocess with a ubiquitous additive: Using clay powder in the cultivation of Rhodopseudomonas palustris","authors":"Sheida Stephens ,&nbsp;Mona Abo-Hashesh ,&nbsp;Radhakrishnan Mahadevan ,&nbsp;D. Grant Allen","doi":"10.1016/j.btre.2025.e00930","DOIUrl":"10.1016/j.btre.2025.e00930","url":null,"abstract":"<div><div>A key challenge in process optimization is reactor performance, particularly in light-dependent bioprocesses. While novel photobioreactor designs exist, adapting established bioreactors with simple media supplementation may provide a more practical and modular alternative to complex mechanical modifications. In this study, we evaluated the effect of supplementing 0.2 % (w/v) clay powder on acetate production by <em>Rhodopseudomonas palustris</em> grown on butyrate. Among the clay types tested, kaolin showed the most pronounced benefits, with acetate accumulation increasing by 45 % relative to controls. These improvements are attributed to a combination of enhanced light distribution and increased cellular aggregation. Photosynthetic photon flux density measurements confirmed that kaolin reduced the extent of cellular shading by increasing light scattering within the culture. Taken together, these findings demonstrate that supplementation with a widely available clay can improve light penetration in suspended phototrophic cultures, offering a novel andaccessible strategy for optimizing photosynthetic bioprocesses.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00930"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332691","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":"Benchmarking long-read assembly tools and preprocessing strategies for bacterial genomes: A case study on E. coli DH5α","authors":"Megha S. Kumar ,&nbsp;Manoj Bhat Krishna ,&nbsp;K.P. Soman ,&nbsp;John Stanley ,&nbsp;Nader Pourmand ,&nbsp;Prashanth Suravajhala ,&nbsp;T.G.Satheesh Babu","doi":"10.1016/j.btre.2025.e00931","DOIUrl":"10.1016/j.btre.2025.e00931","url":null,"abstract":"<div><div>Genome assembly is a crucial step in microbial genomics, significantly impacting downstream applications such as functional annotation and comparative genomics. While long-read sequencing technologies have improved genome reconstruction, the choice of assembler and preprocessing methods substantially influences assembly quality. Genome assembly is a crucial step in microbial genomics, significantly impacting downstream applications such as functional annotation and comparative genomics. While long-read sequencing technologies have improved genome reconstruction, the choice of assembler and preprocessing methods substantially influences assembly quality. Here, we benchmarked eleven long-read assemblers—Canu, Flye, HINGE, Miniasm, NECAT, NextDenovo, Raven, Shasta, SmartDenovo, wtdbg2 (Redbean), and Unicycler—using standardized computational resources. Assemblies were evaluated on runtime, contiguity (N50, total length, contig count), GC content, and completeness using Benchmarking Universal Single-Copy Orthologs (BUSCO).</div><div>Assemblers employing progressive error correction with consensus refinement, notably NextDenovo and NECAT, consistently generated near-complete, single-contig assemblies with low misassemblies and stable performance across preprocessing types. Flye offered a strong balance of accuracy and contiguity, although it was sensitive to corrected input. Canu achieved high accuracy but produced fragmented assemblies (3–5 contigs) and required the longest runtimes. Unicycler reliably produced circular assemblies but with slightly shorter contigs than Flye or NextDenovo. Ultrafast tools such as Miniasm and Shasta provided rapid draft assemblies, yet were highly dependent on preprocessing and required polishing to achieve completeness. HINGE and wtdbg2 underperformed due to structural instability and fragmentation.</div><div>Preprocessing had a marked effect: filtering improved genome fraction and BUSCO completeness, trimming reduced low-quality artifacts, and correction benefited OLC-based assemblers but occasionally increased misassemblies in graph-based tools. Overall, assembler choice and preprocessing jointly determine accuracy, contiguity, and computational efficiency. These results provide a reproducible framework for selecting assembly pipelines in prokaryotic genomics, underscoring that no single assembler is universally optimal.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00931"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332693","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":"Sustainable fuel and power from biomass: 4E analysis of a solar-assisted DME production system with CO₂ capture","authors":"Atieh Kermani ,&nbsp;Farzin Hosseinifard ,&nbsp;Mohsen Salimi ,&nbsp;Majid Amidpour","doi":"10.1016/j.btre.2025.e00928","DOIUrl":"10.1016/j.btre.2025.e00928","url":null,"abstract":"<div><div>Transitioning to clean energy requires efficient, low-carbon fuel production methods. Traditional biomass-to-fuel approaches are limited by inefficiency, cost, and emissions. This study presents an innovative system based on renewable lignocellulosic biomass to produce dimethyl ether (DME), methanol, and electricity simultaneously. The design integrates thermochemical conversion, solar thermal energy, internal power generation, and post-combustion CO₂ capture. Waste heat and solar energy drive dual electricity-producing loops, enabling internal energy sufficiency and surplus sale. Simulations indicate 50 % total energy efficiency and 49 % exergy efficiency, with hourly production of 2.7 tons DME and 0.56 tons methanol. Economic analysis shows baseline feasibility with an NPV of ∼$530 M and payback period ∼5.5 years; sensitivity to biomass price, capital cost, and discount rate is noted, highlighting potential uncertainty ranges. This integrated pathway offers a scalable, low-carbon, and economically viable solution for sustainable bioenergy.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"48 ","pages":"Article e00928"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219780","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":"An iterative approach to statistical optimization of exopolysaccharide produced by fermentation of Aureobasidium pullulans","authors":"Venessa Dsouza ,&nbsp;Goldee Thoidingjam ,&nbsp;Abdelrahman Saleh ,&nbsp;Michael Zavrel","doi":"10.1016/j.btre.2025.e00914","DOIUrl":"10.1016/j.btre.2025.e00914","url":null,"abstract":"<div><div>Exopolysaccharides are biopolymers with wide-ranging industrial applications. To substitute fossil-based by bio-based, biodegradable polymers, exopolysaccharide production needs to become much more efficient. Pullulan, produced by <em>Aureobasidium pullulans</em>, is popular for its unique properties like film-formation, adhesiveness, biodegradability, etc. This study aims at demonstrating the optimization strategy on pullulan production using statistical optimization iteratively. The process followed a systematic approach including One Factor at A Time (OFAT) and Design Of Experiments (DOE). OFAT confirmed sucrose as carbon source, pH 6 and 4 days of incubation were optimum. Iterative Plackett-Burman Design (PBD) and Response Surface Methodology (RSM) further demonstrated interactions between significant media components and incubation conditions. The final pullulan titer was increased 6.34-fold to 113.5 ± 3.5 g/L of EPS, the highest titer achieved for this strain in shake flasks. Future investigations into fed-batch strategies and scale-up studies can be explored to further improve titers and reduce overall production costs.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"47 ","pages":"Article e00914"},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144878410","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":"Cyclodextrins in action: Modulating candida albicans biofilm formation and morphology","authors":"Rita Márton ,&nbsp;Hanna Hermann ,&nbsp;Virág Tünde Kiss ,&nbsp;Éva Fenyvesi ,&nbsp;Lajos Szente ,&nbsp;Mónika Molnár","doi":"10.1016/j.btre.2025.e00912","DOIUrl":"10.1016/j.btre.2025.e00912","url":null,"abstract":"<div><div>The primary objective of this research was to explore the bioactive potential of cyclodextrins in attenuating biofilm formation in <em>C. albicans</em>. The concentration-dependent effects of both native cyclodextrins and specific derivatives were studied at concentrations ranging from 0.1 to 12.5 mM, to determine the mechanisms by which the extent of biofilm formation can be reduced. Besides, the efficiency of various combinations of cyclodextrins and farnesol, as an antifungal substance, were examined.</div><div>The present study revealed both stimulatory and inhibitory effects of cyclodextrins on biofilm formation, depending on the structure and concentration. The bioactive potential of randomly methylated α- and γ-CD showed significant antifungal properties, as evidenced by a reduction in the biofilm formation. In addition, randomly methylated cyclodextrins were found to significantly enhance the antifungal activity of farnesol against <em>C. albicans</em>. Consequently, their synergistic effect may provide an excellent opportunity to produce a lower dose but more effective anticandidal formulation.</div></div>","PeriodicalId":38117,"journal":{"name":"Biotechnology Reports","volume":"47 ","pages":"Article e00912"},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886013","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}