Applied Microbiology and Biotechnology最新文献

{"title":"First experimentally characterised Proteus phage endolysins have distinct metal cofactor dependencies","authors":"Akash Shambharkar,&nbsp;Thomas P. Thompson,&nbsp;Laura A. McClenaghan,&nbsp;Katie J. J. Brown,&nbsp;Stephen A. Kelly,&nbsp;Brendan F. Gilmore,&nbsp;Timofey Skvortsov","doi":"10.1007/s00253-026-13891-1","DOIUrl":"10.1007/s00253-026-13891-1","url":null,"abstract":"<p><i>Proteus mirabilis</i> is a Gram-negative uropathogenic bacterial species responsible for many catheter-associated urinary tract infections (CAUTIs). Due to the growing rates of antimicrobial resistance among CAUTI pathogens, novel antimicrobial solutions are urgently needed. Bacteriophage endolysins are an emerging class of antimicrobial agents, but no endolysins from <i>P. mirabilis</i> phages have been reported to date. Here, we describe two new <i>Proteus</i> phage endolysins, LysPM1 and LysPM2, containing Peptidase_M15_3 and CHAP domains, respectively. We experimentally confirmed their antibacterial activity against several <i>Proteus</i> spp. when used in combination with outer membrane permeabilizers, including EDTA, citric acid, and chloroform, as well as against frozen bacteria. Both enzymes have optimum activity at pH 7–8 and retain activity at temperatures up to 60 °C. Both endolysins completely lost their lytic activity upon treatment with EDTA, suggesting that divalent cations participate in the catalytic mechanism; the addition of Ca2⁺ and Zn2⁺ to LysPM1, and Ca2⁺ and Mn2⁺ to LysPM2 partially restored the activity. Our study confirms LysPM1 and LysPM2 as the first experimentally characterized <i>Proteus</i> phage endolysins, with LysPM2 also being the first experimentally characterized Gram-negative endolysin with a single CHAP domain. These findings could guide further development of phage-derived lytic enzymes for treatment of <i>Proteus</i> infections.</p><p>• <i>LysPM1 &amp; LysPM2 are the first experimentally characterized Proteus phage endolysins.</i></p><p>• <i>Both are single-domain endolysins: Peptidase_M15_3 in LysPM1 and CHAP in LysPM2.</i></p><p>• <i>Metal cofactors are required for their activity: Zn2⁺ for LysPM1, Ca2⁺ for LysPM2.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-026-13891-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148175092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: The combination of mupirocin and Kayvirus broadens the decolonization effect against Staphylococcus aureus","authors":"Alena Siváková,&nbsp;Eliška Figallová,&nbsp;Tibor Botka,&nbsp;Lukáš Vacek,&nbsp;Jan Tkadlec,&nbsp;Jan Vrbský,&nbsp;Martin Osowski,&nbsp;Petr Petráš,&nbsp;Dominika Polaštík Kleknerová,&nbsp;Milada Dvořáčková,&nbsp;Pavlína Urbanová,&nbsp;Roman Pantůček,&nbsp;Filip Růžička","doi":"10.1007/s00253-026-13900-3","DOIUrl":"10.1007/s00253-026-13900-3","url":null,"abstract":"","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-026-13900-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering of ω-transaminases for advanced applications","authors":"Uwe Wegner,&nbsp;Nicolaus von Wirén,&nbsp;Gotthard Kunze","doi":"10.1007/s00253-026-13888-w","DOIUrl":"10.1007/s00253-026-13888-w","url":null,"abstract":"<p>ω-Transaminases (ω-TAs) are well-established biocatalysts for the asymmetric synthesis of chiral amines, yet their broader application remains limited by challenges related to activity, substrate scope, equilibrium constraints in asymmetric synthesis, and process compatibility e.g. solvent tolerance. In recent years, research has shifted from enzyme discovery toward targeted development strategies aimed at addressing these limitations. This review summarizes recent advances in ω-transaminase development, with a focus on protein engineering and process-level optimization. Structure-guided and semi-rational mutagenesis approaches continue to provide robust, incremental improvements, while multi-site, activity-driven engineering has proven effective for challenging substrates such as β- and γ-amino acids or bulky amines. Emerging AI- and AlphaFold-assisted workflows increasingly support rational enzyme design by reducing experimental efforts. Beyond enzyme sequence optimization, reaction engineering, multienzyme cascades, and process intensification strategies play a crucial role in improving overall performance and scalability. Genome mining and discovery efforts are briefly discussed as supporting tools for expanding the ω-transaminase toolbox. Overall, studies in the last years show that successful ω-transaminase development relies more and more on integrated approaches combining enzyme engineering with intelligent process design, rather than on isolated optimization strategies.</p><p>•<i>The state-of-the-art status of ω-TA development is presented.</i></p><p>•<i>The shift from enzyme discovery to substrate-based optimization is highlighted.</i></p><p>•<i>Modern reaction conditions for more environmentally friendly synthesis are reported.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-026-13888-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mechanism underlying biofloc formation of Acidovorax soli Q11 and its application potential","authors":"Yaqi Liu,&nbsp;Na Gao,&nbsp;Jingcheng Dai,&nbsp;Shuangyuan Liu,&nbsp;Ansi Jiang,&nbsp;Yan Huang,&nbsp;Chang Wu,&nbsp;Dongru Qiu","doi":"10.1007/s00253-026-13873-3","DOIUrl":"10.1007/s00253-026-13873-3","url":null,"abstract":"<p>Biofloc technology (BFT) is an emerging microbial-based technology in aquaculture that enhances system productivity by assimilating excessive nitrogenous pollutants, such as ammonia nitrogen and nitrite, into biofloc biomass via the activity of biofloc-forming microbes, rather than relying on conventional nitrification-denitrification or anammox processes. Traditionally, BFT has been implemented by enhancing the carbon/nitrogen ratio (C/N) to stimulate the uptake of ammonia and the biosynthesis of amino acids and proteins of biofloc-forming microbes, whose biomass could be filter-fed and digested by filter-feeding aquatic animals for nutrients. In this study, we isolated a series of biofloc-forming bacteria from multiple aquaculture systems and systematically investigated the molecular mechanisms governing biofloc formation in <i>Acidovorax soli</i> Q11, isolated from a freshwater sturgeon aquaculture pond. Molecular genetic analyses conducted on strain Q11, combined with whole genome sequencing, revealed that biofloc formation is likely regulated by cellulose biosynthesis (<i>bcs</i>) genes. Further characterization of extracellular polymeric substances (EPS) via Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) demonstrated that the secreted EPS exhibited high physicochemical similarity to bacterial cellulose. However, the bioflocs displayed pronounced resistance to cellulase degradation. Notably, the genome of strain Q11 contains two distinct <i>bcs</i> gene clusters, corresponding to Type Ic (harboring <i>bcsD</i>) and Type IIc (harboring <i>bcsE</i> and <i>bcsG</i>), suggesting that this dual <i>bcs</i> operon system may contribute to the enhanced structural stability of the cellulose-like matrix. Furthermore, strain Q11 demonstrated efficient removal of both ammonium (NH₄⁺) and nitrite (NO₂⁻), achieving complete removal of initial NH₄⁺ (39 mg/L) within 36 h and NO₂⁻ (65 mg/L) within 77 h, without detectable accumulation of toxic nitrogenous intermediates. This strain also exhibited versatile carbon source utilization, including effective growth on substrates commonly applied in aquaculture systems, such as glucose, brown sugar, fermentation-derived carbon sources, and rice bran. Collectively, these findings provide new insights into the mechanism of biofloc formation and highlight the potential of <i>Acidovorax soli</i> Q11 as a promising candidate for bioaugmentation in BFT systems, with potential applications in sustainable aquaculture and the treatment of nitrogen-rich wastewater.</p><p>• <i>Biofloc formation mechanism in Acidovorax soli Q11 is mediated by a dual bcs operon system.</i></p><p>• <i>EPS secreted by strain Q11 exhibits high structural stability and cellulase resistance.</i></p><p>• <i>Strain Q11 enables efficient ammonium and nitrite removal, supporting wastewater bioaugmentation.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13453990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developing an oncolytic Newcastle disease virus production process with EB66 cells","authors":"Lennart Jacobtorweihe,&nbsp;Annabelle Saulnier,&nbsp;Arnaud Léon,&nbsp;Yvonne Genzel,&nbsp;Udo Reichl","doi":"10.1007/s00253-026-13889-9","DOIUrl":"10.1007/s00253-026-13889-9","url":null,"abstract":"<div><p>Newcastle disease virus (NDV) has been the subject of extensive research as a potential oncolytic virus for various types of cancer. While clinical studies are ongoing, the manufacturing of high NDV doses on a large scale is challenging. It has previously been documented that Vero cells are capable of producing 2.4 × 10⁸ TCID₅₀/mL in suspension batch production. However, the requirement of higher input doses and the challenging nature of establishing high cell density processes with Vero cells are significant obstacles in the effective utilization of these therapies. In pursuit of enhanced process intensification and the generation of viral vectors at elevated cell densities, EB66 cells have been identified as a highly effective producer cell line. In this study, the characteristics of EB66 cells in regard to NDV production were examined, with particular reference to cell growth and cell-specific virus productivity in batch and semi-perfusion mode. Optimal infection conditions for producing NDV in batch and semi-perfusion modes were identified for cultivation parameters including temperature, protease concentration (TrypLE), and multiplicity of infection. The favorable production conditions were then transferred to different batch processes using a stirred tank bioreactor and an orbital shaken bioreactor. These processes yielded up to 4.2 × 10⁸ TCID₅₀/mL of the NDV LaSota strain with a cell-specific virus yield of 41 TCID₅₀/cell. First semi-perfusion runs resulted in concentrations of 65 × 10⁶ cells/mL and an infectious virus titer of 7.5 × 10⁸ TCID₅₀/mL. Finally, the potency of the produced viruses was evaluated, and a reduction in tumor size in mice after NDV injection was demonstrated. Overall, these results indicate that EB66 cells could be a viable host for producing oncolytic NDV.</p></div>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-026-13889-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rational development of an mRNA antibody cocktail with extended therapeutic window against ricin intoxication","authors":"Mei Wu,&nbsp;Xi Luo,&nbsp;Pei-Yu Jiang,&nbsp;Qian Xu,&nbsp;Fei-Xue Du,&nbsp;Xiang Chen,&nbsp;Feng-Qin Yang,&nbsp;Zi-Jin Cui,&nbsp;Yu-Yan Li,&nbsp;Jie-Yu Chen,&nbsp;Tian-Shu Cao,&nbsp;Jing-Lin Wang,&nbsp;Wen-Wen Xin,&nbsp;Qing Ye,&nbsp;Cheng-Feng Qin","doi":"10.1007/s00253-026-13893-z","DOIUrl":"10.1007/s00253-026-13893-z","url":null,"abstract":"<p>Ricin, a highly toxic protein derived from <i>Ricinus communis</i>, is recognized as a biological threat due to its high toxicity and the absence of approved specific antidotes. Monoclonal antibodies (mAbs) represent an emergency therapeutic for ricin intoxication. However, the short therapeutic window of existing antibody administration significantly limits their effectiveness in post-exposure treatment. To address these limitations, we developed a novel strategy leveraging lipid nanoparticle (LNP) encapsulated-mRNA platform for toxin antibodies delivery in vivo, enabling a time-saving, cost-effective approach that extends the therapeutic window. We designed and characterized two mRNA-encoded antibodies targeting the A chain (RTA) and B chain (RTB) of ricin, termed mRNA-43RCA and mRNA-Sy1H3, respectively. Then, each LNP-encapsulated mRNA antibody was combined to formulate the final mRNA antibody cocktail, termed mRNA-cocktail-LNP. In vivo studies demonstrated that a single administration of mRNA-cocktail-LNP enabled the rapid production of neutralizing antibodies, which conferred protection in mice against a subsequent lethal-dose ricin challenge. Additionally, mRNA-cocktail-LNP exhibited a significantly extended circulating half-life compared to its protein-format antibody in mice, and a single prophylactic dose provided complete protection against lethal ricin challenge for at least 14 days post administration. More importantly, mRNA-cocktail-LNP conferred protection even when administered 10 h after lethal-dose ricin exposure, demonstrating an extended therapeutic window. Taken together, our results indicate that mRNA-cocktail-LNP represents a promising therapeutic candidate against ricin intoxication, highlighting the potential of mRNA-LNP platform as a universal strategy for developing antibody-based countermeasures against ricin and a broad spectrum of other biological threats.</p><p>• <i>An mRNA antibody cocktail (mRNA-cocktail-LNP) was designed to against RT and protect the mice from challenge with ricin both prophylactic and post-exposure treatments</i></p><p>• <i>mRNA-cocktail-LNP with a prolonged half-life compared to its protein format.</i></p><p>• <i>mRNA-cocktail-LNP significantly extended the limited therapeutic window to 10 h for ricin intoxication treatment.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13453996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fungal signatures in a cadaver and a separated upper limb: insights from a forensic case study","authors":"Klaudyna Spychała,&nbsp;Łukasz Szleszkowski,&nbsp;Agata Thannhäuser,&nbsp;Agata Piecuch,&nbsp;Jakub Suchodolski,&nbsp;Rafał Ogórek","doi":"10.1007/s00253-026-13895-x","DOIUrl":"10.1007/s00253-026-13895-x","url":null,"abstract":"<p>The application of fungi in forensic investigations remains limited, particularly in cases involving dismembered human remains. In this study, we characterized the mycobiome of a decomposing human body and a detached upper limb recovered from different locations using culture-dependent methods. A total of 23 fungal species were identified across four culture media and three incubation temperatures, including 20 species from the body and ten from the upper limb. The dominant taxa included <i>Yarrowia lipolytica</i>, <i>Yarrowia deformans</i>, <i>Mucor hiemalis</i>, and <i>Geotrichum candidum</i>. Notably, seven species were shared between the body and the detached limb, indicating partially preserved fungal signatures despite environmental differences. These findings suggest that fungal community profiles may serve as a complementary tool for associating separated human body parts and for assessing postmortem relocation. Additionally, 11 fungal species were identified on human remains for the first time (<i>Acaulium album</i>, <i>Acaulium caviariforme</i>, <i>Akanthomyces lecanii</i>, <i>Dialonectria ullevolea</i>, <i>Fusarium acuminatum</i>, <i>Fusarium falsibabinda</i>, <i>Fusarium oxysporum</i>, <i>Fusarium redolens</i>, <i>Fusarium sacchari</i>, <i>Linnemannia hyalina</i>, and <i>Penicillium clavigerum</i>), expanding current knowledge of postmortem fungal colonization in temperate climates.</p><p>• <i>The regional postmortem mycobiome of a corpse and a severed upper limb</i></p><p>• <i>Shared fungal species suggest partial preservation of mycobiome signatures</i></p><p>• <i>Fungal profiles as potential indicators for the identification of dismembered body parts</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13454014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adapting prime editing with split prime editors in Escherichia coli and its application to Staphylococcus aureus genome editing","authors":"Seong Hyeok Ma,&nbsp;Goosang Yu,&nbsp;Suyeon Park,&nbsp;Hyuna Sung,&nbsp;Uk Jin Jeong,&nbsp;Hyongbum Henry Kim,&nbsp;Junho Cho,&nbsp;Sang Sun Yoon","doi":"10.1007/s00253-026-13897-9","DOIUrl":"10.1007/s00253-026-13897-9","url":null,"abstract":"<div><p>Prime editing is a precise and rapid genome-editing technique that modifies short DNA sequences using tailored guide RNAs. To implement this technique in bacteria, we used Prime Editor 2 (PE2) with the DeepPrime gRNA design tool and assessed its gene-editing efficiency in <i>Escherichia coli</i> and methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) cells. Our findings indicate that a split PE2, comprising a reverse transcriptase and two Cas9 nickase domains, exhibited gene-editing efficiency comparable to that of the intact PE2. The efficiency observed in <i>E. coli</i> was significantly affected by the target sites, edit type, and the presence of exonucleases. In MRSA, which serves as a model to evaluate the applicability in non-model bacterial species, Streptococcus pyogenes PE2 (SpPE2) exhibited superior performance relative to <i>Staphylococcus aureus</i> PE2 (SaPE2). Furthermore, the split SpPE2 lacking the reverse transcriptase successfully induced the intended mutation in MRSA. This study demonstrates the feasibility of prime editing within bacterial systems.</p></div>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-026-13897-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148155152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Glycerol-mediated improvement of heterologous aurachin D production in E. coli","authors":"Jonas Korb,&nbsp;Büsra Demir,&nbsp;Kai Graw,&nbsp;Markus Nett","doi":"10.1007/s00253-026-13890-2","DOIUrl":"10.1007/s00253-026-13890-2","url":null,"abstract":"<p>Neglected tropical diseases and the increasing prevalence of antibiotic resistance in nosocomial infections represent a major challenge in medicine. Intensive research into bioactive compounds has identified the myxobacterial natural product aurachin D as promising drug candidate due to its potent antibiotic and antiprotozoal properties. The biosynthesis of aurachin D from 2-methyl-1<i>H</i>-quinolin-4-one (MQO) is catalyzed by the membrane-bound farnesyltransferase AuaA. Recently, this enzymatic conversion was reconstructed in the heterologous host <i>Escherichia coli</i>, yielding an aurachin D titer of 17 mg L⁻¹. In this study, we investigated the influence of the medium on aurachin D biosynthesis in <i>E. coli</i> in order to improve the product titer. Our analyses revealed that the glycerol concentration has a major impact on both the growth of the production host and the biocatalytic formation of aurachin D. After switching to a glycerol-based minimal medium and adjustment of the MQO precursor concentration, an aurachin D titer of 124 mg L⁻¹ was achieved in a microbioreactor system, highlighting the superior performance of minimal over complex medium as well as the beneficial effect of glycerol compared to glucose. Further studies were conducted to elucidate the mechanism underlying glycerol’s effects. While improved growth and substrate solubilization were found to be insignificant for increasing the product titer, it was demonstrated that glycerol supplementation positively influenced the expression of the enzyme AuaA. Using a folding reporter, we were able to show that the availability of correctly folded AuaA increased until growth defects of the host, presumably resulting from osmotic stress, began to appear.</p><p>• <i>Product toxicity is negligible</i><i> in the production of aurachin D using E. coli</i></p><p>• <i>The media supplement glycerol improves the availability of the enzyme AuaA</i></p><p>• <i>Aurachin D titers increase after switching to a minimal medium</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13222167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a gut microbiota model for the analysis of bacterial modifications of xenobiotics","authors":"Natalie Hager,&nbsp;Jan-Lorenz Weyers,&nbsp;Laura Falk,&nbsp;Maike Passon,&nbsp;Marie-Christine Simon,&nbsp;Waldemar Seel,&nbsp;Jean-Lou Christian Michel Dorne,&nbsp;Uwe Deppenmeier","doi":"10.1007/s00253-026-13861-7","DOIUrl":"10.1007/s00253-026-13861-7","url":null,"abstract":"<p>The human gut microbiota influences host physiology by metabolizing xenobiotics, such as drugs, dietary additives, and environmental contaminants. To enable standardized assessment of microbial xenobiotic metabolism, we established a defined bacterial colon model from pooled human fecal samples, by preparing clean bacterial cell suspensions using density gradient centrifugation. The bacterial cell fraction remained structurally intact, allowing long-term preservation at −70 °C with glycerol as a cryoprotectant. The bacteria were fully reactivated without compromising cellular integrity. Glycerol as a disturbing substrate was removed by washing steps. The system preserved microbial diversity, enzymatic activity, and metabolic functionality over 24 h under anaerobic conditions. Unlike fecal-based models, the model was free from non-cellular contaminants, which could cause unpredictable interactions between test compounds and reactive components within the fecal matrix. Enzymatic assays demonstrated hydrolytic, reductive, and proteolytic activities comparable to native feces. 16S rRNA gene sequencing confirmed taxonomic stability and compositional shifts in response to different substrates. A fiber-rich substrate proved to be optimal for maintaining the bacterial composition over 24 h. We further applied the model to investigate the microbial biotransformation of selected model xenobiotics using high-performance liquid chromatography and mass spectrometry, capturing substrate-specific conversion patterns and formation of expected primary products. A versatile addition of food ingredients, dietary supplements, pharmaceuticals, and environmental chemicals is possible to analyze their effects on the composition of the microbiota, its enzymatic activity, and the excretion of metabolites and end products. Together, this bacterial colon model provides a reproducible, high-throughput capable and ethically viable platform for pharmaco microbiomic studies and next-generation risk assessment.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"110 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13222238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}