Pub Date : 2026-01-29DOI: 10.1016/j.mimet.2026.107411
Tong Cai, Yusheng Pei
The Bacterial Endotoxin Test (BET) is a critical quality control measure for parenteral drugs and sterile medical devices worldwide. As the global pharmaceutical industry becomes increasingly integrated, the harmonization of pharmacopoeial methods is an inevitable trend. The Chinese Pharmacopoeia (ChP), China's official national standard, has undergone significant evolution in its BET chapter, transitioning from initially referencing the United States Pharmacopoeia (USP) to progressively aligning with the International Council for Harmonization (ICH) Harmonized Tripartite Guideline:Evaluation and Recommendation of Pharmacopoeial Texts for Use in The ICH Regions on Bacterial Endotoxin Test General Chapter Q4B (ICH Q4B).
This article provides a comprehensive overview of the development of the BET in the ChP, with a special focus on the major revisions in the newly implemented 2025 edition. We detail how the ChP 2025 further converges with the ICH harmonized text in aspects such as method classification, procedural descriptions, and key validation parameters. Concurrently, we elucidate the scientific rationale for retaining specific “Chinese characteristics,” such as stricter requirements for water for BET, a different standard for average body weight in limit calculations, and more stringent retest protocols for the gel-clot method, all of which are rooted in domestic regulatory practices and public health considerations. Furthermore, we discuss China's proactive approach to addressing emerging global challenges like Low Endotoxin Recovery (LER) and its pioneering research into resource-saving micro-methods. This review aims to offer international stakeholders a clear perspective on the scientific rigor, commitment to global standards, and unique risk-based considerations that define the modern BET in China.
{"title":"The bacterial endotoxin test in the Chinese pharmacopoeia: A journey of international harmonization and national consideration","authors":"Tong Cai, Yusheng Pei","doi":"10.1016/j.mimet.2026.107411","DOIUrl":"10.1016/j.mimet.2026.107411","url":null,"abstract":"<div><div>The Bacterial Endotoxin Test (BET) is a critical quality control measure for parenteral drugs and sterile medical devices worldwide. As the global pharmaceutical industry becomes increasingly integrated, the harmonization of pharmacopoeial methods is an inevitable trend. The Chinese Pharmacopoeia (ChP), China's official national standard, has undergone significant evolution in its BET chapter, transitioning from initially referencing the United States Pharmacopoeia (USP) to progressively aligning with the International Council for Harmonization (ICH) Harmonized Tripartite Guideline:Evaluation and Recommendation of Pharmacopoeial Texts for Use in The ICH Regions on Bacterial Endotoxin Test General Chapter Q4B (ICH Q4B).</div><div>This article provides a comprehensive overview of the development of the BET in the ChP, with a special focus on the major revisions in the newly implemented 2025 edition. We detail how the ChP 2025 further converges with the ICH harmonized text in aspects such as method classification, procedural descriptions, and key validation parameters. Concurrently, we elucidate the scientific rationale for retaining specific “Chinese characteristics,” such as stricter requirements for water for BET, a different standard for average body weight in limit calculations, and more stringent retest protocols for the gel-clot method, all of which are rooted in domestic regulatory practices and public health considerations. Furthermore, we discuss China's proactive approach to addressing emerging global challenges like Low Endotoxin Recovery (LER) and its pioneering research into resource-saving micro-methods. This review aims to offer international stakeholders a clear perspective on the scientific rigor, commitment to global standards, and unique risk-based considerations that define the modern BET in China.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107411"},"PeriodicalIF":1.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146080332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-29DOI: 10.1016/j.mimet.2026.107412
Sandeep Antil, Govindhasamay R Varatharajan, Jean Claude Ndayishimiye, Pascaline Nyirabuhoro, Damir Saldaev, Santosh Kumar, Ravi Toteja, Seema Makhija, Antonietta La Terza, Yuri A Mazei
Aquatic ecosystems are increasingly threatened by diverse pollutants that compromise ecological integrity and impair ecosystem functioning. Conventional physicochemical monitoring methods are insufficient to detect early biological responses or cumulative stress. Bioindicators offer a biologically integrative, cost-effective, and ecologically meaningful alternative. This review synthesizes current knowledge on established and emerging bioindicator groups, with a critical appraisal of ciliates (Phylum Ciliophora), whose short generation times, trophic versatility, and suitability for both morphological and molecular assays position them as promising next-generation indicators of freshwater ecosystem health. We identify a clear research gap: although numerous primary studies document dose-dependent cytotoxic, oxidative-stress, and behavioural responses in ciliates, but no comprehensive review has consolidated these findings or outlined how ciliates can be operationalized in biomonitoring frameworks. The objectives of this review are to (i) compile and evaluate ciliate-based assays ranging from microscopy to qRT-PCR and multi-omics approaches, (ii) compare ciliates with other bioindicator taxa, and (iii) introduce a novel, empirically testable Ciliate Community Index (CCI) that integrates community composition, morphological integrity, and fold-change-based molecular biomarker responses into a single, unified assessment framework. Literature synthesis reveals consistent early-warning signals, such as motility impairment, vacuolization, and antioxidant responses, demonstrating the feasibility of multi-tiered monitoring while also underscoring the need for standardized protocols and field validation. We conclude that, with appropriate calibration and methodological harmonization, the CCI has strong potential to serve as a sensitive and scalable tool for assessing metal-impacted freshwater ecosystems.
{"title":"Ciliates as next-generation bioindicators in pollution-impacted freshwaters: Integrating community signatures with stress-response endpoints.","authors":"Sandeep Antil, Govindhasamay R Varatharajan, Jean Claude Ndayishimiye, Pascaline Nyirabuhoro, Damir Saldaev, Santosh Kumar, Ravi Toteja, Seema Makhija, Antonietta La Terza, Yuri A Mazei","doi":"10.1016/j.mimet.2026.107412","DOIUrl":"10.1016/j.mimet.2026.107412","url":null,"abstract":"<p><p>Aquatic ecosystems are increasingly threatened by diverse pollutants that compromise ecological integrity and impair ecosystem functioning. Conventional physicochemical monitoring methods are insufficient to detect early biological responses or cumulative stress. Bioindicators offer a biologically integrative, cost-effective, and ecologically meaningful alternative. This review synthesizes current knowledge on established and emerging bioindicator groups, with a critical appraisal of ciliates (Phylum Ciliophora), whose short generation times, trophic versatility, and suitability for both morphological and molecular assays position them as promising next-generation indicators of freshwater ecosystem health. We identify a clear research gap: although numerous primary studies document dose-dependent cytotoxic, oxidative-stress, and behavioural responses in ciliates, but no comprehensive review has consolidated these findings or outlined how ciliates can be operationalized in biomonitoring frameworks. The objectives of this review are to (i) compile and evaluate ciliate-based assays ranging from microscopy to qRT-PCR and multi-omics approaches, (ii) compare ciliates with other bioindicator taxa, and (iii) introduce a novel, empirically testable Ciliate Community Index (CCI) that integrates community composition, morphological integrity, and fold-change-based molecular biomarker responses into a single, unified assessment framework. Literature synthesis reveals consistent early-warning signals, such as motility impairment, vacuolization, and antioxidant responses, demonstrating the feasibility of multi-tiered monitoring while also underscoring the need for standardized protocols and field validation. We conclude that, with appropriate calibration and methodological harmonization, the CCI has strong potential to serve as a sensitive and scalable tool for assessing metal-impacted freshwater ecosystems.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107412"},"PeriodicalIF":1.9,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146097179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Traditional foods and beverages represent alternative strategies to counteract bacterial virulence. The fermentation of tea, sugar, supplemented with a symbiotic culture of bacteria and yeast (SCOBY) produces kombucha beverage, which offers several health advantages and is similar to soft drinks. This study investigates the effect of various fermentation factors on the growth levels of Lactobacillus, Lactococcus, total phenolic content and antimicrobial activities of Green Tea, Black Tea and Moringa kombucha beverage (GTBTMK) prepared with a starter SCOBY culture. Formulation of kombucha beverage was optimized using a Simplex-Centroid Mixture Design and Plackett-Burman Design. The best optimized kombucha formulation (18.98 g/L; Dried Apricot was 20 g/L; Dried plum was 10 g/L, Dried Grape was 20 g/L,11.763 g/L Green tea, 0.01238 g/L Black tea and 8.1127 g/L Moringa) contain a high phenolic content of 86.79 mg GAE/mL and exhibited a significant antimicrobial activity against Bacillus cereus ATCC 11778, Micrococcus luteus NCIMB 8166 and Enterococcus faecalis ATCC 29212, Candida albicans ATCC 90028, Cryptococcus neoformans ATCC 14116, Aspergillus brasiliensis ATCC 16404 (Inhibition zone more than 20 mm). This research provides new insights into the development of innovative, functional kombucha beverage potentially expanding the spectrum of health-promoting fermented drinks available to consumers.
{"title":"Optimization of physicochemical and antimicrobial properties of functional kombucha beverage sweetened with dried fruits using simplex centroid mixture and Plackett-Burman designs","authors":"Lamia Ayed , Haifa Dhif , Souhir Torjmèn , Kamel Chaieb","doi":"10.1016/j.mimet.2026.107408","DOIUrl":"10.1016/j.mimet.2026.107408","url":null,"abstract":"<div><div>Traditional foods and beverages represent alternative strategies to counteract bacterial virulence. The fermentation of tea, sugar, supplemented with a symbiotic culture of bacteria and yeast (SCOBY) produces kombucha beverage, which offers several health advantages and is similar to soft drinks. This study investigates the effect of various fermentation factors on the growth levels of <em>Lactobacillus</em>, <em>Lactococcus</em>, total phenolic content and antimicrobial activities of Green Tea, Black Tea and Moringa kombucha beverage (GTBTMK) prepared with a starter SCOBY culture. Formulation of kombucha beverage was optimized using a Simplex-Centroid Mixture Design and Plackett-Burman Design. The best optimized kombucha formulation (18.98 g/L; Dried Apricot was 20 g/L; Dried plum was 10 g/L, Dried Grape was 20 g/L,11.763 g/L Green tea, 0.01238 g/L Black tea and 8.1127 g/L Moringa) contain a high phenolic content of 86.79 mg GAE/mL and exhibited a significant antimicrobial activity against <em>Bacillus cereus</em> ATCC 11778, <em>Micrococcus luteus</em> NCIMB 8166 and <em>Enterococcus faecalis</em> ATCC 29212, <em>Candida albicans</em> ATCC 90028, <em>Cryptococcus neoformans</em> ATCC 14116, <em>Aspergillus brasiliensis</em> ATCC 16404 (Inhibition zone more than 20 mm). This research provides new insights into the development of innovative, functional kombucha beverage potentially expanding the spectrum of health-promoting fermented drinks available to consumers.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107408"},"PeriodicalIF":1.9,"publicationDate":"2026-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146064144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In nature, bacteria have two different growth modes: a unicellular life stage, in which the cells are free-moving (planktonic), and a multicellular life stage wherein the cells are immobile and reside within a biofilm structure, composed of a complex network of extracellular polymeric substances (EPS). The EPS contribute to the distinctive characteristics of the biofilm's lifestyle, environmental degradation, as well as virulence and antibiotic resistance. The present review critically analyses the functional significance of extracellular polymeric substances (EPS), characteristics of biofilms and nanoparticle-biofilm interactions for the removal of emerging environmental contaminants. Nanoparticles can also function as emulsifiers, enhancing bioavailability by providing droplet surfaces that facilitate microbial attachment and promote microbial proliferation. The enhancement of certain biofilms through positive interactions with nanoparticles will enable the design of systems that facilitate the development of cost-effective alternatives of interest, including enhanced bioremediation, biodegradation, oil spill mitigation, and improved microbial fuel cell (MFC) performance. Nano-bioremediation is effective across a wide range of emerging environmental contaminants such as PAHs, chlorinated compounds, pHthalates, plastic heavy metals, etc. and provides a sustainable alternative to conventional remediation approaches.
{"title":"Microbial biofilms and nanoparticles synergistic interaction: A cutting-edge nano-bioremediation method for environmental cleanup and site restoration","authors":"Manoj Kumar , Meera Goswami , Deepak Pant , Kulamani Parida , Anand Giri","doi":"10.1016/j.mimet.2026.107406","DOIUrl":"10.1016/j.mimet.2026.107406","url":null,"abstract":"<div><div>In nature, bacteria have two different growth modes: a unicellular life stage, in which the cells are free-moving (planktonic), and a multicellular life stage wherein the cells are immobile and reside within a biofilm structure, composed of a complex network of extracellular polymeric substances (EPS). The EPS contribute to the distinctive characteristics of the biofilm's lifestyle, environmental degradation, as well as virulence and antibiotic resistance. The present review critically analyses the functional significance of extracellular polymeric substances (EPS), characteristics of biofilms and nanoparticle-biofilm interactions for the removal of emerging environmental contaminants. Nanoparticles can also function as emulsifiers, enhancing bioavailability by providing droplet surfaces that facilitate microbial attachment and promote microbial proliferation. The enhancement of certain biofilms through positive interactions with nanoparticles will enable the design of systems that facilitate the development of cost-effective alternatives of interest, including enhanced bioremediation, biodegradation, oil spill mitigation, and improved microbial fuel cell (MFC) performance. Nano-bioremediation is effective across a wide range of emerging environmental contaminants such as PAHs, chlorinated compounds, pHthalates, plastic heavy metals, etc. and provides a sustainable alternative to conventional remediation approaches.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107406"},"PeriodicalIF":1.9,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rapid, low-cost strain-level typing is essential for source attribution and microbiological control in clinical and industrial settings. Fourier-transform infrared (FT-IR) spectroscopy using IR Biotyper method was previously optimized to achieve an identification level equivalent to that of whole-genome sequencing (WGS) discrimination of Wickerhamomyces anomalus. However, the species of yeast studied were limited; further, studies that have used the results of WGS as a reference for strain identification in yeast remain limited. Therefore, here, the generalizability of this approach to Candida albicans and Saccharomyces cerevisiae was assessed using publicly available whole-genome datasets as references. Single-nucleotide polymorphisms from 29C. albicans and 27 S. cerevisiae genomes were analyzed to build phylograms and select 5 and 4 mutually distant strains for FT-IR. FT-IR spectra were obtained after a standardized 24-h rotational culture in SD liquid medium, with three independent passages per strain. The same and similar strains clustered tightly, and different strains formed non-overlapping clusters; branches for the same and similar strains were < 0.1 on IR dendrograms, whereas branches for distinct strains were > 0.1. The discriminatory ability of FT-IR fully agreed with the WGS-based same/different classifications. Standardized liquid culture likely reduced cell-state heterogeneity, improving reproducibility. These results extend FT-IR strain typing beyond W. anomalus, providing a rapid, low-cost tool for contamination source attribution.
{"title":"Strain-level typing of Candida albicans and Saccharomyces cerevisiae using Fourier transform infrared spectroscopy and whole-genome sequencing","authors":"Asuka Kashiwaba , Asako Mitani , Takumi Sonoda , Naofumi Shigemune , Hiroki Takahashi","doi":"10.1016/j.mimet.2026.107405","DOIUrl":"10.1016/j.mimet.2026.107405","url":null,"abstract":"<div><div>Rapid, low-cost strain-level typing is essential for source attribution and microbiological control in clinical and industrial settings. Fourier-transform infrared (FT-IR) spectroscopy using IR Biotyper method was previously optimized to achieve an identification level equivalent to that of whole-genome sequencing (WGS) discrimination of <em>Wickerhamomyces anomalus</em>. However, the species of yeast studied were limited; further, studies that have used the results of WGS as a reference for strain identification in yeast remain limited. Therefore, here, the generalizability of this approach to <em>Candida albicans</em> and <em>Saccharomyces cerevisiae</em> was assessed using publicly available whole-genome datasets as references. Single-nucleotide polymorphisms from 29<em>C. albicans</em> and 27 <em>S. cerevisiae</em> genomes were analyzed to build phylograms and select 5 and 4 mutually distant strains for FT-IR. FT-IR spectra were obtained after a standardized 24-h rotational culture in SD liquid medium, with three independent passages per strain. The same and similar strains clustered tightly, and different strains formed non-overlapping clusters; branches for the same and similar strains were < 0.1 on IR dendrograms, whereas branches for distinct strains were > 0.1. The discriminatory ability of FT-IR fully agreed with the WGS-based same/different classifications. Standardized liquid culture likely reduced cell-state heterogeneity, improving reproducibility. These results extend FT-IR strain typing beyond <em>W. anomalus</em>, providing a rapid, low-cost tool for contamination source attribution.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107405"},"PeriodicalIF":1.9,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Trichoderma atroviride is well-known biocontrol fungus that plays a crucial role in controlling plant fungal diseases. In this study, the Serine Protease (T. atSp1) gene of T. atroviride was selected as the target gene to investigate the effects of Agrobacterium tumefaciens concentration, conidial concentration, mixing ratio of conidia and Agrobacterium cells, and induction time on transformation efficiency. The optimal knockout system was achieved under conditions that the density of A. tumefaciens was OD600 = 0.5, the concentration of conidia suspension was 106 conidia/mL, the mixture ratio of conidia suspension and A. tumefaciens AGL-1 was 1:1, and the induction time was 0.5 h. The transformation efficiency reached 28.33 to 61.67 transformants per 106 conidia under the optimized conditions. The ΔT. atSp1 was successfully validated by PCR analysis. Additionally, two genes of T. atEDG1 and T. atchi18 were also knocked out and verified, further demonstrating the robustness of this ATMT system. This study provides a stable and efficient genetic manipulation protocol for T. atroviride, facilitating further to understand genes function and biocontrol mechanisms.
{"title":"An efficient targeted gene deletion approach for Trichoderma atroviride using Agrobacterium tumefaciens-mediated transformation.","authors":"Mengke Li, Yihong Li, Xiaoyu Zhang, Hui Zhou, Yusheng Liu, Qiuye Liu, Shuqin Xiao","doi":"10.1016/j.mimet.2026.107407","DOIUrl":"10.1016/j.mimet.2026.107407","url":null,"abstract":"<p><p>Trichoderma atroviride is well-known biocontrol fungus that plays a crucial role in controlling plant fungal diseases. In this study, the Serine Protease (T. atSp1) gene of T. atroviride was selected as the target gene to investigate the effects of Agrobacterium tumefaciens concentration, conidial concentration, mixing ratio of conidia and Agrobacterium cells, and induction time on transformation efficiency. The optimal knockout system was achieved under conditions that the density of A. tumefaciens was OD<sub>600</sub> = 0.5, the concentration of conidia suspension was 10<sup>6</sup> conidia/mL, the mixture ratio of conidia suspension and A. tumefaciens AGL-1 was 1:1, and the induction time was 0.5 h. The transformation efficiency reached 28.33 to 61.67 transformants per 10<sup>6</sup> conidia under the optimized conditions. The ΔT. atSp1 was successfully validated by PCR analysis. Additionally, two genes of T. atEDG1 and T. atchi18 were also knocked out and verified, further demonstrating the robustness of this ATMT system. This study provides a stable and efficient genetic manipulation protocol for T. atroviride, facilitating further to understand genes function and biocontrol mechanisms.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107407"},"PeriodicalIF":1.9,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Phytoplankton are key bioindicators in aquatic ecosystems, where species distribution and cell abundance serve as vital metrics for environmental assessment. Although image-based automated identification has progressed, accurately counting colonial cells remains challenging. This paper proposes a novel method for simultaneous phytoplankton recognition and cell counting. Using ResNet50 as a backbone, deep features are extracted from microscopic images of algal colonies. These features are then fed into two parallel branches for classification and counting, respectively, with model parameters updated through alternating training. Evaluated on 16 common colonial algae species from Lake Chaohu, the proposed method achieved 99.2% identification accuracy, 93.9% average counting accuracy, with mean absolute error and mean squared error of 1.290 and 2.263, respectively. This method effectively overcomes the challenges associated with colonial phytoplankton by integrating both identification and counting into a unified framework, providing a robust tool for automated aquatic algal monitoring.
{"title":"Automatic colony cell counting method of phytoplankton in microscopic images with multi-task learning","authors":"Renqing Jia , Gaofang Yin , Nanjing Zhao , Min Zhang , Chao Zhu , Tianhong Liang , Jingze Zhang , Changbiao Yuan , Jiamin Tao , Peng Yun","doi":"10.1016/j.mimet.2026.107396","DOIUrl":"10.1016/j.mimet.2026.107396","url":null,"abstract":"<div><div>Phytoplankton are key bioindicators in aquatic ecosystems, where species distribution and cell abundance serve as vital metrics for environmental assessment. Although image-based automated identification has progressed, accurately counting colonial cells remains challenging. This paper proposes a novel method for simultaneous phytoplankton recognition and cell counting. Using ResNet50 as a backbone, deep features are extracted from microscopic images of algal colonies. These features are then fed into two parallel branches for classification and counting, respectively, with model parameters updated through alternating training. Evaluated on 16 common colonial algae species from Lake Chaohu, the proposed method achieved 99.2% identification accuracy, 93.9% average counting accuracy, with mean absolute error and mean squared error of 1.290 and 2.263, respectively. This method effectively overcomes the challenges associated with colonial phytoplankton by integrating both identification and counting into a unified framework, providing a robust tool for automated aquatic algal monitoring.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107396"},"PeriodicalIF":1.9,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-17DOI: 10.1016/j.mimet.2026.107397
Sabina D. Hidat , Joan Masatu , Nelson E. Masota , Rogers Mwakalukwa , Paul Malaba , Joseph Sempombe , Doreen Mloka
Antimicrobial resistance (AMR) remains a significant threat to global health, requiring various mitigation strategies. Soil-dwelling microbes have long been a valuable source of novel antibiotics; however, their low cultivability using standard methods has often led to the discovery of known antibiotics. This bottleneck has been partially overcome by using isolation chips (iChips), which enhance the cultivability (both in terms of number and diversity) of soil bacteria. This has created a need to find new screening methods that allow high-throughput screening, are less resource-intensive, and can screen multiple test organisms.
To address this, soil samples were collected from three different regions of Tanzania, and numerous bacterial soil species colonies were grown in iChips and then transferred to master plates. Replica plates were created using a velvet transfer method and utilized for parallel agar overlay assays against Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Master plates with 33–62 colonies showing variation in size, morphology, and spatial arrangement were produced by cultivating agar plugs from iChips. Three to four replicates, which preserved these characteristics at the transfer efficiencies of 91.3–100% were obtained without contamination. Zones of inhibition -to-colony diameter ratios ranging 1.15–3.27 were obtained following parallel primary screening against test strains, hence enabling the identification of potential antibiotic producers.
This is the first report of the combined iChip and velvet transfer workflow that offers a high-throughput, resource-efficient, and scalable method for primary screening of various soil-derived bacteria for antibacterial Natural Products (NPs), while also maintaining the master plates for downstream investigations.
{"title":"Combining isolation chips with velvet transfer for high-throughput primary screening of antibiotic-producing soil-dwelling bacteria","authors":"Sabina D. Hidat , Joan Masatu , Nelson E. Masota , Rogers Mwakalukwa , Paul Malaba , Joseph Sempombe , Doreen Mloka","doi":"10.1016/j.mimet.2026.107397","DOIUrl":"10.1016/j.mimet.2026.107397","url":null,"abstract":"<div><div>Antimicrobial resistance (AMR) remains a significant threat to global health, requiring various mitigation strategies. Soil-dwelling microbes have long been a valuable source of novel antibiotics; however, their low cultivability using standard methods has often led to the discovery of known antibiotics. This bottleneck has been partially overcome by using isolation chips (iChips), which enhance the cultivability (both in terms of number and diversity) of soil bacteria. This has created a need to find new screening methods that allow high-throughput screening, are less resource-intensive, and can screen multiple test organisms.</div><div>To address this, soil samples were collected from three different regions of Tanzania, and numerous bacterial soil species colonies were grown in iChips and then transferred to master plates. Replica plates were created using a velvet transfer method and utilized for parallel agar overlay assays against <em>Escherichia coli</em>, <em>Klebsiella pneumoniae</em>, and <em>Staphylococcus aureus</em>. Master plates with 33–62 colonies showing variation in size, morphology, and spatial arrangement were produced by cultivating agar plugs from iChips. Three to four replicates, which preserved these characteristics at the transfer efficiencies of 91.3–100% were obtained without contamination. Zones of inhibition -to-colony diameter ratios ranging 1.15–3.27 were obtained following parallel primary screening against test strains, hence enabling the identification of potential antibiotic producers.</div><div>This is the first report of the combined iChip and velvet transfer workflow that offers a high-throughput, resource-efficient, and scalable method for primary screening of various soil-derived bacteria for antibacterial Natural Products (NPs), while also maintaining the master plates for downstream investigations.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107397"},"PeriodicalIF":1.9,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146003742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-15DOI: 10.1016/j.mimet.2026.107395
Lauren Remijas , Martine P. Bos , María Miguélez Sánchez , Robin van Houdt , Gernot Rohde , Andries E. Budding
The diagnosis of pleural infection has traditionally relied on microbiological culture, a method often limited by slow bacterial growth and difficulties in culturing fastidious organisms. This study introduces Molecular Culture ID, a rapid and comprehensive molecular technique capable of detecting and identifying a wide range of bacteria down to the species level. By analyzing 440 pleural effusion samples derived from patients suspected of pleural infection and comparing the outcome to routine diagnostics, we demonstrate that Molecular Culture ID significantly outperforms traditional culture. Molecular Culture ID identified 133 positive samples, compared to 55 positive samples identified by traditional culture. The 78 additional positive samples detected by Molecular Culture contained important pathogens including species such as Streptococcus pneumoniae, Escherichia coli, and Staphylococcus aureus. These findings highlight Molecular Culture ID as a promising alternative for the rapid and accurate diagnosis of pleural infections, offering a substantial improvement over conventional methods.
{"title":"Advancing pleural effusion diagnosis: Application of Molecular Culture ID in pathogen detection","authors":"Lauren Remijas , Martine P. Bos , María Miguélez Sánchez , Robin van Houdt , Gernot Rohde , Andries E. Budding","doi":"10.1016/j.mimet.2026.107395","DOIUrl":"10.1016/j.mimet.2026.107395","url":null,"abstract":"<div><div>The diagnosis of pleural infection has traditionally relied on microbiological culture, a method often limited by slow bacterial growth and difficulties in culturing fastidious organisms. This study introduces Molecular Culture ID, a rapid and comprehensive molecular technique capable of detecting and identifying a wide range of bacteria down to the species level. By analyzing 440 pleural effusion samples derived from patients suspected of pleural infection and comparing the outcome to routine diagnostics, we demonstrate that Molecular Culture ID significantly outperforms traditional culture. Molecular Culture ID identified 133 positive samples, compared to 55 positive samples identified by traditional culture. The 78 additional positive samples detected by Molecular Culture contained important pathogens including species such as <em>Streptococcus pneumoniae, Escherichia coli</em>, and <em>Staphylococcus aureus</em>. These findings highlight Molecular Culture ID as a promising alternative for the rapid and accurate diagnosis of pleural infections, offering a substantial improvement over conventional methods.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107395"},"PeriodicalIF":1.9,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1016/j.mimet.2025.107384
Anja Logo , Tabea Koch , Monika Maurhofer , Thomas Oberhänsli , Barbara Thürig , Franco Widmer , Pascale Flury , Johanna Mayerhofer
Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, often vary across studies, challenging comparability. We investigated two aspects of sample preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (<2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0–2 mm) and coarse (2–10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl-affinity-based magnetic method and a silanol-affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and distinct bacterial and fungal community structures compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for Bacillota. Although the effects of particle size and extraction method were small compared to the overall diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses.
{"title":"Microbial community analyses of composts are influenced by particle size fraction and DNA extraction method","authors":"Anja Logo , Tabea Koch , Monika Maurhofer , Thomas Oberhänsli , Barbara Thürig , Franco Widmer , Pascale Flury , Johanna Mayerhofer","doi":"10.1016/j.mimet.2025.107384","DOIUrl":"10.1016/j.mimet.2025.107384","url":null,"abstract":"<div><div>Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, often vary across studies, challenging comparability. We investigated two aspects of sample preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (<2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0–2 mm) and coarse (2–10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl-affinity-based magnetic method and a silanol-affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and distinct bacterial and fungal community structures compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for <em>Bacillota</em>. Although the effects of particle size and extraction method were small compared to the overall diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107384"},"PeriodicalIF":1.9,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145978485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号