Applied Microbiology and Biotechnology最新文献

{"title":"Study on obtaining bacterial cellulose by Komagataeibacter xylinus in co-culture with lactic acid bacteria in whey","authors":"Justyna Płoska,&nbsp;Monika Garbowska,&nbsp;Iwona Ścibisz,&nbsp;Lidia Stasiak-Różańska","doi":"10.1007/s00253-025-13582-3","DOIUrl":"10.1007/s00253-025-13582-3","url":null,"abstract":"<p>The use of acid whey as a medium is an innovative approach to bacterial cellulose (BC) biosynthesis in co-cultures of acetic acid bacteria with lactic acid bacteria. The aim of this study was to evaluate the possibility of obtaining BC in acid whey by co-culturing <i>K. xylinus</i> with selected strains of lactic acid bacteria and comparing the properties of this biopolymer with BC obtained in <i>K. xylinus</i> monoculture. The <i>K. xylinus</i> + <i>Lb. acidophilus</i> co-culture yielded 2.19 g·L⁻¹ of BC, which was 125% more than the <i>K. xylinus</i> monoculture. Additionally, <i>K. xylinus</i> in co-culture with <i>Lb. acidophilus</i> increased the degradation temperature of BC to 361 °C compared to 303 °C for BC obtained in monoculture. The BC obtained in the co-cultures showed better mechanical properties. BC obtained in co-culture with <i>Lb. delbrueckii</i> showed more than twice the Young’s modulus than BC from monoculture. Moreover, strain at break BC from co-culture with <i>Lb. acidophilus</i> and stress at break BC from co-culture with <i>Lb. helveticus</i> were 72% and 54% higher, respectively, than BC obtained from monoculture <i>K. xylinus.</i> In this study, it was shown that conducting acetic-lactic co-cultures increased the efficiency of BC biosynthesis and improved its properties. Moreover, this study has shown that acid whey is a sufficient and complete substrate for obtaining BC. Results presented in this paper indicate new possibilities for the management of this side product.</p><p>• <i>The K. xylinus + Lb. acidophilus co-culture produced 125% more cellulose than the monoculture.</i></p><p>• <i>High lactic acid content and low pH of acid whey enhance cellulose biosynthesis.</i></p><p>• <i>Acetic acid-lactic acid co-cultures improved the mechanical properties of cellulose.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13582-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144880753","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":"Genetic basis of transmission of blaNDM-1 among foodborne Vibrio parahaemolyticus strains in China","authors":"Dan Chen,&nbsp;Ruanyang Sun,&nbsp;Jing Wang,&nbsp;Kaichao Chen,&nbsp;Miaomiao Xie,&nbsp;Qinlu Lin,&nbsp;Jinwang Li,&nbsp;Sheng Chen,&nbsp;Xiaobo Liu","doi":"10.1007/s00253-025-13567-2","DOIUrl":"10.1007/s00253-025-13567-2","url":null,"abstract":"<p>Carbapenem-resistant <i>Vibrio parahaemolyticus</i> has emerged and spread extensively in China, posing a substantial threat to food safety and human health. This study investigated the prevalence of carbapenem resistance in <i>V. parahaemolyticus</i> strains recovered from various types of food samples in China, and the underlying mechanisms of transmission of the <i>bla</i>_NDM-1 gene harbored by such strains. In this work, a total of 230 (62.1%) strains were isolated from seafood samples collected in Changsha, Hunan Province; among them, 47 strains were found to be cefotaxime-resistant. These strains were subjected to whole-genome sequencing and found to exhibit significant genetic diversity; among them, 13 strains were found to carry the <i>bla</i>_NDM-1 gene. Nanopore sequencing showed that the <i>bla</i>_NDM-1 gene was located in the chromosome in strain VP288 but was plasmid-borne in the other 12 strains. All <i>bla</i>_NDM-1-bearing plasmids were of the IncC type that harbored a conserved backbone. However, the multidrug resistance regions differed significantly from each other and could be classified into four groups: (1) the plasmid pVP181-NDM was the longest and carried an additional Tn7 transposase gene; (2) both pVP156-NDM and pVP209-NDM contained two structurally different resistance regions; (3) both pVP205-NDM and pVP148-NDM harbored two <i>bla</i>_NDM genes flanked by three copies of IS<i>CR1</i> insertion elements; (4) the plasmids pVP228-NDM and pVP14-NDM contained an MDR region similar to that of pVP181-NDM. The high-level carbapenem resistance phenotype exhibited by foodborne <i>V. parahaemolyticus</i> underscores an urgent need for the development of effective control strategies and surveillance to limit the spread of the carbapenem resistance determinants carried by these strains.</p><p><i>• The rate of resistance of food-borne V. parahaemolyticus strains to carbapenems was at a concerning level.</i></p><p><i>• The bla</i>_<i>NDM-1</i><i> gene was located in IncC-type plasmids which shared a conserved backbone.</i></p><p><i>• The MDR profiles of bla</i>_<i>NDM-1</i><i>-bearing plasmids varied significantly.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13567-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144880755","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":"A single donor cassette enables site-specific knock-in at either the αAmy3 or αAmy8 locus in rice cells via CRISPR/Cas9","authors":"Desyanti Saulina Sinaga,&nbsp;Po-Yu Huang,&nbsp;Chun‑Kai Huang,&nbsp;Chung-An Lu,&nbsp;Li-Fen Huang","doi":"10.1007/s00253-025-13549-4","DOIUrl":"10.1007/s00253-025-13549-4","url":null,"abstract":"<div><p>CRISPR/Cas9 gene editing is widely used to manipulate gene expression and integrate transgenes into specific target sites, making it a powerful tool for recombinant protein expression. In this study, we generated a single donor cassette for CRISPR/Cas9-mediated knock-in at either the <i>αAmy3</i> or <i>αAmy8</i> locus in rice cells. The transgene was inserted downstream of the promoter and first exon of the rice <i>αAmy3</i> or <i>αAmy8</i> genes, which are highly expressed under sugar-starved conditions in rice suspension cultures. We constructed a simple vector with the homologous intron sequences of the <i>αAmy3</i> and <i>αAmy8</i>, along with rice codon-optimized recombinant receptor binding domain (rcRBD) of the SARS-CoV-2 spike protein, a functional domain responsible for binding to the angiotensin-converting enzyme 2 (ACE2) receptor on host cells. Using this construct, <i>rcRBD</i> was successfully integrated into the intron 1 of either the <i>αAmy3</i> or <i>αAmy8</i> genes. As a result, rcRBD expression was driven by endogenous <i>αAmy3</i> or <i>αAmy8</i> promoter-signal peptide. Under the control of <i>αAmy3</i>-signal peptide, rcRBD proteins was detected in both the soluble cellular protein fraction and culture medium, whereas expression driven by the <i>αAmy8</i> promoter-signal peptide was exclusively detected in the culture medium of rice suspension cells. The highest secreted protein yield of rcRBD in the rice culture medium under the control of <i>αAmy8</i> endogenous promoter reached 20.7 mg/L, demonstrating a production efficiency comparable to that driven by the endogenous <i>αAmy3</i> promoter.</p></div>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13549-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144880754","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":"The rise of Stropharia rugosoannulata industry in China: current state and prospects","authors":"Lei Huang,&nbsp;Can Si,&nbsp;Chun-mei He,&nbsp;Xun-cheng Liu,&nbsp;Jun Duan","doi":"10.1007/s00253-025-13576-1","DOIUrl":"10.1007/s00253-025-13576-1","url":null,"abstract":"<p><i>Stropharia rugosoannulata</i>, commonly known as the wine-cap mushroom or giant <i>Stropharia</i>, is an edible fungus naturally distributed in temperate regions of the Northern Hemisphere. It is characterized by a wine-red cap, a wrinkled-ring-bearing stipe, and a large, thick, and fleshy fruiting body with a crisp and tender texture. This species is rich in nutrients such as proteins, amino acids, and minerals and contains various bioactive compounds including polysaccharides, polyphenols, and flavonoids, thereby providing it with both nutritional and health-promoting properties. <i>S. rugosoannulata</i> can grow on a wide range of agricultural and forestry waste substrates and is highly amenable to artificial cultivation. It has been recommended by the Food and Agriculture Organization (FAO) of the United Nations for cultivation in developing countries. Originally cultivated in Germany, this mushroom later spread to other European countries and the USA and was introduced to China in the 1980s. Due to its cultivation characteristics being highly compatible with China’s agricultural conditions, the species has rapidly expanded in the country. Since the implementation of China’s Rural Revitalization and Targeted Poverty Alleviation strategies in 2013, large-scale cultivation projects of <i>S. rugosoannulata</i> have been actively promoted, establishing China as the world’s leading producers and greatly stimulating industrial development. This review summarizes the current state of the <i>S. rugosoannulata</i> industry in China and explores potential directions for the extension of its industrial chain, aiming to provide a reference for its sustainable development and international promotion.</p><p><i>• S. rugosoannulata exhibits high nutritional, medicinal, and ecological value.</i></p><p><i>• China has become the world’s leading producers of S. rugosoannulata.</i></p><p><i>• The development of S. rugosoannulata industry in China provides a model for the world.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13576-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144868654","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":"Eumycetoma: pathogenesis, current treatments, and the search for new drugs","authors":"Dounia El Yachioui,&nbsp;Tim Baltussen,&nbsp;Wendy W. J. van de Sande","doi":"10.1007/s00253-025-13580-5","DOIUrl":"10.1007/s00253-025-13580-5","url":null,"abstract":"<p>Eumycetoma is a neglected tropical disease which can be caused by 69 different fungal species. In 2024, eumycetoma was listed as a high priority fungal infection on the fungal priority list of the World Health Organization. Eumycetoma is characterized by chronic subcutaneous swelling, the formation of grains, and progressive tissue destruction. If left untreated, it can lead to severe complications such as bone destruction and permanent disability. Current antifungal treatments, such as itraconazole and terbinafine, are lengthy and often ineffective without surgical intervention. The search for novel treatments is challenging due to limited interest and return of investment. Drug repurposing has emerged as a promising strategy for discovering new effective therapies against eumycetoma. Additionally, the MycetOS initiative focuses on developing novel antifungal compounds that are tested in vitro and in vivo.</p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13580-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144868631","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":"Signature of oral microbial dysbiosis in different periodontitis risk levels","authors":"Yanan Xu,&nbsp;Yali Liu,&nbsp;Ying Leng,&nbsp;Jinrun Qian,&nbsp;Qiao Yang,&nbsp;Jing Zhu,&nbsp;Guiding Li,&nbsp;Yi Peng","doi":"10.1007/s00253-025-13574-3","DOIUrl":"10.1007/s00253-025-13574-3","url":null,"abstract":"<p>Individuals categorized into distinct periodontitis risk levels often demonstrate substantial disparities not only in the likelihood of developing periodontitis but also in the rate at which the disease progresses. However, the oral microbial communities and their functional characteristics corresponding to different periodontitis risk levels remain to be further explored. Therefore, 52 subjects with periodontitis were selected and categorized into different periodontitis risk groups based on the periodontal risk calculator (PRC). Unstimulated saliva was collected, and metagenomics sequencing was performed to compare microbial diversity, taxonomy, and functional annotation among groups. There was no significant difference in species richness and evenness between the very high risk group and the high risk group, but beta diversity increased in the former group. A higher abundance of <i>Filifactor alocis</i>, <i>Streptococcus cristatus</i>, <i>Klebsiella pneumoniae</i>, and <i>Streptococcus anginosus</i> was attributed to the very high risk group, while <i>Pseudopropionibacterium propionicum</i> and <i>Abiotrophia defectiva</i> were found in higher abundance in the high risk group. Functional annotation revealed that biosynthesis of amino acids (lysine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; valine, leucine, and isoleucine biosynthesis), citrate cycle (TCA cycle), carbon fixation pathways in prokaryotes, oxidative phosphorylation, lipopolysaccharide biosynthesis, fatty acid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, pantothenate and CoA biosynthesis, and glutathione metabolism were enriched in the very high risk group. The combined results indicate that the periodontal pathogens associated with a higher risk of periodontitis and the regulation of their related functional pathways increase the risk and likelihood of periodontitis development.</p><p>• <i>There were differences in microbial diversity among different periodontitis risk-level groups.</i></p><p>• <i>Some previously overlooked species and pathogenic pathways were linked to periodontitis risk differences.</i></p><p>• <i>Combining PRC with metagenomic sequencing revealed more potential pathogens.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13574-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144868710","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":"Burst agitation rate promotes sustained semicontinuous cultivation of filamentous fungi in stirred tank reactors","authors":"Conor Ó Lochlainn,&nbsp;Federico Cerrone,&nbsp;Kevin E. O’Connor","doi":"10.1007/s00253-025-13579-y","DOIUrl":"10.1007/s00253-025-13579-y","url":null,"abstract":"<p>Edible filamentous fungi <i>L. edodes</i> (shiitake mushrooms) were cultivated in submerged fermentation in stirred tank bioreactors (STR) both in batch and semicontinuous cultivation in a corn steep liquor (CSL) medium. The adjustment of a combination of constant impeller agitation speed, a short duration of a high-speed agitation (burst), and the frequency of bursts improved biomass (cell dry weight (CDW) titre from 1.75 to 4.95 g/L in a 96-h batch cultivation. These bioreactor process conditions were applied to a semicontinuous culture strategy to produce similar biomass density at a dilution rate of 0.02 h⁻¹ for up to 10 days without washout over the duration of the fermentation. An increase in the dilution rate above 0.02 h⁻¹ resulted in washout of <i>L. edodes</i> over time. Using a richer growth medium through the addition of malt extract, peptone, and molasses allowed <i>L. edodes</i> to grow to 4.7 g/L at a dilution rate of 0.025 h⁻¹ without washout. The maximum biomass productivity (396 mg CDW/h) of the semicontinuous cultivation (<i>D</i> = 0.02 h⁻¹) was 1.9-fold higher than the batch cultivation 206 mg CDW/hour. Use of the richer growth medium at <i>D</i> = 0.025 h⁻¹ improved biomass productivity further to 470 mg/h. Glucans, known bioactives, were present in the fungal biomass at a maximum of 14% of the cell dry weight (CDW) with b-glucans predominating over a-glucans.</p><p>• <i>Short, high-speed impeller bursts homogenise mycelia preventing bioreactor clogging.</i></p><p>• <i>Semicontinuous fermentation at D of 0.02 h−1 generated 5.1 g/L of fungal biomass.</i></p><p>• <i>Cultivation of fungal biomass in STR resulted in biomass with 14% of total glucans.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13579-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144869036","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":"Thermal and shear stress-induced phenotypic changes in Bacillus paralicheniformis TB197 in submerged liquid cultures","authors":"Estefany Chavarria-Quicaño,&nbsp;Miguel A. Hernández-Oñate,&nbsp;Jorge A. Rodríguez-González,&nbsp;Francisco De la Torre-González,&nbsp;Ali Asaff-Torres","doi":"10.1007/s00253-025-13571-6","DOIUrl":"10.1007/s00253-025-13571-6","url":null,"abstract":"<p>Lipopeptides (LPs) are secondary metabolites predominantly produced by <i>Bacillus</i> species and have significant industrial applications. The synthesis of these compounds is regulated by <i>quorum</i> sensing systems, which are activated in response to abiotic stress. This study examined the impact of heat and shear stresses on the growth, LPs production, and phenotype formation of the <i>Bacillus paralicheniformis</i> TB197 strain in controlled submerged cultures. A differential expression analysis was performed on genes associated with phenotypes, including biofilms (<i>tas</i>A), motility (<i>hag</i>), sporulation (<i>ssp</i>B), and the production of lipopeptides (<i>fen</i>B and <i>lich</i>A). The findings demonstrated that, under conditions of 30 °C, an increase in agitation levels from 300 to 600 rpm resulted in a 1.5-fold enhancement in cell concentration and a 2.8-fold increase in LPs production. At 40 °C, these values were 2.80- and 2.06-fold, respectively. Furthermore, <i>fen</i>B and <i>lich</i>A expression levels increased by 17- and 36-fold, respectively, suggesting that the combined stress of 40 °C and 600 rpm promotes the development of LP-producing phenotypes. However, at 45 °C, although cell concentration showed no difference compared to 40 °C, LPs production decreased 2.49-fold, with reductions in <i>lich</i>A (sixfold) and <i>fen</i>B (65-fold) expression. Under these conditions, a predominance of sporulating and biofilm-forming phenotypes was observed, supported by increased expression of <i>tas</i>A and <i>ssp</i>B genes. These findings show that thermal and mechanical stresses differentially modulate the expression of phenotypes and the production of LPs in <i>B. paralicheniformis</i> TB197.</p><p>• <i>Shear and thermal stress differentially modulate Bacillus paralicheniformis TB197 phenotypes.</i></p><p>• <i>Conditions of 40°C and 600 rpm induce lipopeptide-producing phenotypes, thereby optimizing their biosynthesis.</i></p><p>• <i>Shear and thermal stress suppress flagellate phenotypes while promoting sporulation and biofilm formation.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13571-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858567","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":"The roles of NHEJ and TLS pathways in genomic alterations and phenotypic evolution in the yeast Yarrowia lipolytica","authors":"Cen Yan,&nbsp;Ye-Ke Wang,&nbsp;Yuan-Ru Xiong,&nbsp;Xin-Qiu Zhou,&nbsp;Yuan-Chun Fang,&nbsp;Ruo-Tian Nie,&nbsp;Cunqi Ye,&nbsp;Ke Zhang,&nbsp;Dao-Qiong Zheng","doi":"10.1007/s00253-025-13575-2","DOIUrl":"10.1007/s00253-025-13575-2","url":null,"abstract":"<p>Non-homologous end joining (NHEJ) is a DNA repair pathway that directly ligates broken DNA ends without the need for a homologous template, whereas translesion synthesis (TLS) is a DNA damage tolerance mechanism in which specialized DNA polymerases bypass lesions on the template strand. Although both pathways play critical roles in maintaining genome integrity across organisms, they inherently introduce mutations. Here, we investigate how these two pathways contribute to spontaneous and genotoxic stress–induced genomic alterations in the yeast <i>Yarrowia lipolytica</i>. A NHEJ-deficient mutant (<i>ku70</i>) and three TLS-deficient mutants (<i>rev1</i>, <i>rev3</i>, and <i>rad30</i>) are subjected to mutation accumulation experiments, followed by whole-genome sequencing. Our results show that the deletion of <i>KU70</i> has no significant effect on the rates of spontaneous single-nucleotide variations (SNVs), small insertions and deletions, or chromosomal rearrangements, while the deletion of <i>REV1</i> and <i>REV3</i> leads to significant reductions in spontaneous SNV rates. These findings indicate that TLS but not the NHEJ pathway is a major contributor to spontaneous mutagenesis in <i>Y. lipolytica</i>. Moreover, exposure to 0.02% methyl methanesulfonate and 80 J/m² ultraviolet (UV) radiation resulted in 48- and 107-fold increases in SNV rates, respectively. These induced SNVs were largely dependent on DNA polymerases Rev1 and <i>ζ</i>, further underscoring their central roles in genotoxic stress–induced mutagenesis. We observe that DNA polymerase <i>η</i> can suppress C to T and C to A substitutions while promoting T to C mutations, exhibiting a dual function in regulating mutagenesis under UV treatment. Phenotypic evolution experiments reveal that TLS activity enhances the adaptive potential of <i>Y. lipolytica</i> under oxidative stress, underlying its broader impact on environmental fitness. Together, these findings provide new insights into the distinct roles of the NHEJ and TLS pathways in preserving genome integrity in <i>Y. lipolytica</i>.</p><p>• <i>The NHEJ pathway has a limited role in spontaneous genomic alterations in Y. lipolytica.</i></p><p>• <i>DNA polymerases Rev1 and ζ contribute to most UV- and MMS-induced mutations.</i></p><p>• <i>The dual roles of Pol η in UV-induced mutations were revealed.</i></p><p>• <i>NHEJ and TLS pathways are crucial to phenotypic evolution of Y. lipolytica.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13575-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843176","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":"Advanced monolayer and layer-by-layer nanocapsule systems for sustained release of carvacrol and trans-cinnamaldehyde against multidrug-resistant Salmonella in poultry","authors":"Samah Mechmechani,&nbsp;Kosar Zadeh,&nbsp;Neda Zadeh,&nbsp;Adem Gharsallaoui,&nbsp;Nahla O. Eltai,&nbsp;Tareq M. Osaili,&nbsp;Layal Karam","doi":"10.1007/s00253-025-13573-4","DOIUrl":"10.1007/s00253-025-13573-4","url":null,"abstract":"<p>The rise of antibiotic-resistant <i>Salmonella</i> in poultry poses a significant public health challenge. This study assessed the efficacy of carvacrol and <i>trans</i>-cinnamaldehyde, in free and nanoencapsulated forms, as natural alternatives to chlorine for inactivating antibiotic-resistant <i>Salmonella</i> in chicken. While several studies have evaluated free <i>trans</i>-cinnamaldehyde and carvacrol, there is a notable lack of research on encapsulated forms, using different types of capsules for controlled release of these antimicrobials in food applications. Both compounds were encapsulated by spray-drying into monolayer nanocapsules using maltodextrin as the carrier material, and into layer-by-layer nanocapsules with an additional layer of low methoxyl pectin, to enhance their stability and prolong antimicrobial activity. Twelve treatment groups were evaluated, including controls (distilled water), chlorine (50 ppm), and various concentrations of carvacrol and <i>trans</i>-cinnamaldehyde in their free or nanoencapsulated forms. The combination of monolayer and layer-by-layer carvacrol nanocapsules at a total concentration of 4% resulted in the highest <i>Salmonella</i> reduction (3.7 log CFU/g) after 11 days, significantly outperforming all other treatments (<i>p</i> &lt; 0.05). <i>Trans</i>-cinnamaldehyde-based treatments, whether free or encapsulated forms, demonstrated delayed but notable reductions (2.0–2.2 log CFU/g), followed by carvacrol treatments at 2% using layer-by-layer nanocapsules alone or in combination with monolayer nanocapsules (1.5 log CFU/g). Free or monolayer carvacrol at 2% achieved reductions of 1.1–1.3 log CFU/g, while chlorine (50 ppm) was the least effective, with a reduction of 0.9 log CFU/g. These findings underscore the potential of nanoencapsulated carvacrol and <i>trans</i>-cinnamaldehyde as sustainable, eco-friendly, and effective solutions for enhancing poultry safety, mitigating antimicrobial resistance, and meeting consumer preferences for natural food preservation.</p><p>• <i>Carvacrol and trans-cinnamaldehyde treatments effectively reduced Salmonella in poultry</i></p><p>• <i>Combination of monolayer and layer-by-layer carvacrol nanocapsules at 4% achieved the highest reduction (3.7 log CFU/g)</i></p><p>• <i>Trans-cinnamaldehyde showed notable Salmonella reductions of 2.0–2.2 log CFU/g</i></p><p>• <i>Chlorine was the least effective treatment, reducing Salmonella by 0.9 log CFU/g</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13573-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144843217","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}