{"title":"Kocuria rosea LAT6 enhances wheat salt tolerance via modulation of rhizosphere microbial function and nitrogen cycling.","authors":"Weifeng Song, Zhen Wang, Ying Liu, Qian Wang, Mingcong Li, Wenchong Shi, Zheng Gao, Yuan Chen","doi":"10.1038/s41522-026-01103-7","DOIUrl":"https://doi.org/10.1038/s41522-026-01103-7","url":null,"abstract":"<p><p>Pioneer plants in saline-alkali soils support unique rhizosphere microbial communities. Some of these microbes promote plant salt tolerance and growth, although the underlying mechanisms are not yet fully understood. In this study, we isolated Kocuria rosea LAT6 from the rhizosphere of pioneer plants in saline-alkali soils. Genome sequencing revealed genes associated with plant growth promotion and stress adaptation. Inoculation with LAT6 markedly reshaped the rhizosphere microbiota, and metagenomic analysis indicated that specific microbial taxa contributed to enhanced nitrogen-cycling functions. Transcriptome profiling further demonstrated that LAT6 promotes nitrate transport and stimulates phenylpropanoid biosynthesis in wheat. It reveals how microbial reorganization and plant-microbiome interactions enhance nitrogen use under salt stress, highlighting the potential of salt-tolerant consortia for saline-alkaline crops.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148549702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yun-Xuan Guan, Lu Wang, Ling-Xiang Kong, Yan-Yan Sun, Jin-An Zhou, Xiu-Li Wang, Yong-Jing Ma, Li-Ping Guo, Tu-Run Song, Lan Zhu, Si-Jun Wang, Ya-Hui Huang, Ruo-Lin Tao, Wen-Jun Shang, Wen-Zhi Guo, Hui Wang, Jia-Yin Yang, Lin Zhong, Gang Chen, Jie Zhao, Ning-Ning Liu
{"title":"Longitudinal multi-omics analysis identify multi-kingdom microbiome-host interaction dynamics and diagnostic biomarkers of postoperative infection after kidney transplantation.","authors":"Yun-Xuan Guan, Lu Wang, Ling-Xiang Kong, Yan-Yan Sun, Jin-An Zhou, Xiu-Li Wang, Yong-Jing Ma, Li-Ping Guo, Tu-Run Song, Lan Zhu, Si-Jun Wang, Ya-Hui Huang, Ruo-Lin Tao, Wen-Jun Shang, Wen-Zhi Guo, Hui Wang, Jia-Yin Yang, Lin Zhong, Gang Chen, Jie Zhao, Ning-Ning Liu","doi":"10.1038/s41522-026-01099-0","DOIUrl":"https://doi.org/10.1038/s41522-026-01099-0","url":null,"abstract":"<p><p>Despite recent progresses in microbiome and infection, the role of multi-kingdom gut microbiome in kidney transplantation (KT) infection remains unexplored. Here we performed a longitudinal and integrative multi-omics analysis of the gut microbiome, fecal metabolome and plasma metabolome in 169 KT recipients across 5 different transplantation centers, comprising discovery and validation cohorts. We observed KT-specific four kingdom microbiome dysbiosis, including bacteria, fungi, archaea and viruses, with the most pronounced shifts in bacterial and fungal communities. Furthermore, we identified 6 infection-associated co-abundance groups (CAGs) composed of 23 bacterial and 3 fungal species, highlighting extensive bacterial-fungal interactions. Interestingly, infection-associated fecal metabolomic pattern F1, enriched in N-acetylputrescine and hydroxyproline, was positively correlated with Enterococcus-, Citrobacter- and Lactococcus-dominated CAGs, as well as the plasma metabolite signature, represented by phenylacetyl-l-glutamine, indoxyl sulfate and leukotriene. In contrast, cholesterol sulfate and menadione in plasma were aligned with fecal indoleacetic acid and stachyose, a metabolic signature more characteristic of non-infected recipients. Finally, the combinatorial biomarkers of fungal and bacterial species achieved powerful diagnosis ability of KT infection in an independent validation cohort (area under the receiver operating characteristic curve (AUROC) = 0.80) with the fecal metabolites achieving high accuracy (AUROC = 0.83). Collectively, our findings not only uncovered the postoperative infection-specific multi-kingdom microbial network dynamics, but also revealed the microbial and its metabolic biomarkers with powerful diagnostic ability for postoperative infection in kidney transplantation.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148536436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Lysyl-phosphatidylglycerol promotes cell-to-cell contact and biofilm formation of Staphylococcus aureus as a biofilm matrix component.","authors":"Shinya Sugimoto, Keiichiro Hara, Yoshitaka Taketomi, Yuki Nagasaki, Chikara Sato, Makoto Murakami, Yuki Kinjo","doi":"10.1038/s41522-026-01105-5","DOIUrl":"10.1038/s41522-026-01105-5","url":null,"abstract":"<p><p>Staphylococcus aureus biofilms contribute significantly to persistent infections and antibiotic resistance, supported by a complex extracellular matrix. While their proteins, polysaccharides, and extracellular DNA have been well studied, the role of phospholipids in biofilm architecture remains underexplored. Here, we identify extracellular phospholipids within the biofilm matrix, particularly lysyl-phosphatidylglycerol (Lys-PG), as critical structural elements in S. aureus biofilms. Bacterial phospholipase A<sub>1</sub> (PLA<sub>1</sub>), which hydrolyzes phospholipid acyl ester bonds, effectively dispersed pre-formed biofilms and prevented biofilm formation by hydrolyzing extracellular phospholipids, without affecting bacterial growth or exhibiting cytotoxicity. Microscopic analyses revealed that PLA<sub>1</sub> disrupts membranous nanostructures integral to biofilm stability. Lipidomic analysis demonstrated an enrichment of Lys-PG with specific fatty acid species within the biofilm matrix and confirmed their hydrolysis by PLA<sub>1</sub>. Mechanistically, Lys-PG promotes bacterial aggregation by acting as a molecular glue through electrostatic and hydrophobic interactions. Deletion of mprF, responsible for Lys-PG synthesis, markedly impaired biofilm formation. These findings uncover a previously unrecognized structural role of extracellular phospholipids in biofilm architecture and suggest that targeting Lys-PG and its biosynthetic pathway represents a promising strategy for biofilm control.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13448105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148536548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Lipodystrophy induces gut microbiota dysbiosis and its related glucose dysmetabolism in mice.","authors":"KeKao Long, Zhuohao Liu, Pujie Liu, Weimin Zhang, Ming Gao, Guowu Gan, Xin Cao, Yating Cheng, Baile Wang, Xinyi Yuan, Baomin Wang, Danyue Zhao, Aimin Xu, Jordy Evan Sulaiman, Kenneth King-Yip Cheng","doi":"10.1038/s41522-026-01102-8","DOIUrl":"https://doi.org/10.1038/s41522-026-01102-8","url":null,"abstract":"<p><p>Both excessive white adipose tissue (WAT) in obesity and insufficient WAT in lipodystrophy disrupt metabolic homeostasis. Although a vicious cycle between WAT dysfunction and gut dysbiosis is known to drive insulin resistance in obesity, whether lipodystrophy impairs gut function and contributes to glucose dysregulation remains unclear. Using adipocyte-specific MDM2 knockout (Adipo-MDM2-KO) mice as a model of lipodystrophy, we identified a direct role of WAT in maintaining intestinal and gut microbiota homeostasis. Progressive adipose tissue loss in Adipo-MDM2-KO mice caused multiple intestinal abnormalities, including gut microbiota dysbiosis, altered microbial metabolism, impaired intestinal barrier integrity, defective immunoglobulin A (IgA) responses, and endotoxemia. These defects were largely reversed by transplantation of healthy subcutaneous WAT (sWAT). Moreover, fecal microbiota transplantation from Adipo-MDM2-KO mice into C57BL/6J recipients reproduced intestinal defects and glucose intolerance, whereas microbiota depletion in Adipo-MDM2-KO mice largely rescued intestinal abnormalities and partially restored glucose homeostasis. Furthermore, sWAT-secreted adipokines, including extracellular vesicles, directly modulated the abundance and growth of specific gut bacterial communities. Multi-omics analyses further linked lipodystrophy-induced microbiota and metabolomic alterations to systemic endotoxemia and impaired glucose metabolism. Altogether, our findings reveal a critical WAT-gut-microbiota axis in the regulation of intestinal homeostasis and host glucose metabolism.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148497771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sheep-derived probiotics alleviate weaning-induced oxidative stress in lambs via the gut-liver axis.","authors":"Qicheng Lu, Peng Zhang, Yujie Niu, Chuying Wang, Yayin Qi, Junli Niu, Cheng Chen, Weibin Zeng, Wenju Zhang","doi":"10.1038/s41522-026-01104-6","DOIUrl":"10.1038/s41522-026-01104-6","url":null,"abstract":"<p><p>Weaning is a critical transition in lamb production that can disrupt intestinal homeostasis, promote oxidative stress, and contribute to liver injury. This study investigated whether sheep-derived probiotics could mitigate weaning-associated hepatic injury through the gut-liver axis. Microbiota profiling of six intestinal segments from healthy Hu sheep led to the isolation of nine lactic acid bacterial strains. After in vitro screening for antimicrobial and antioxidant activities, Lactiplantibacillus plantarum M1 and Limosilactobacillus reuteri K4 were selected and administered daily to early-weaned lambs from birth to day 30. Probiotic supplementation partially restored relative organ weights, alleviated hepatic histopathological damage, and reduced biochemical markers of liver injury. It also modulated the colonic mucosal microbiota, enhanced intestinal barrier integrity, and increased colonic acetate and butyrate levels. Liver metabolomics revealed enrichment of the pentose phosphate pathway and glutathione metabolism, accompanied by increased hepatic spermidine abundance and activation of the Nrf2-Keap1 antioxidant pathway. Cell-based validation further showed that spermidine attenuated oxidative stress, at least in part, through modulation of Nrf2-Keap1 signaling. Together, these findings suggest that sheep-derived probiotics may alleviate weaning-induced liver injury in lambs through coordinated microbial, metabolic, and antioxidant regulation along the gut-liver axis.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13601506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148497822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fayez Yassine, Alia Albush, Aya Hanna, Hassan Abbas, Melhem Bilen
{"title":"The gut-heart axis in heart failure: a systematic review and meta-analysis of gut microbiota and metabolites.","authors":"Fayez Yassine, Alia Albush, Aya Hanna, Hassan Abbas, Melhem Bilen","doi":"10.1038/s41522-026-01034-3","DOIUrl":"https://doi.org/10.1038/s41522-026-01034-3","url":null,"abstract":"<p><p>Heart failure remains a major global health challenge. Emerging evidence highlights the gut microbiome's role in its pathogenesis and progression. This systematic review analyzed 32 studies involving 5825 patients to evaluate gut microbiota alterations and microbial metabolites in heart failure. Findings on alpha diversity were inconsistent, but beta diversity showed more agreement. A common pattern included depletion of short-chain fatty acid (SCFA)-producing bacteria and enrichment of pathogenic taxa such as Escherichia and Shigella. Heart failure patients also exhibited elevated levels of harmful metabolites like trimethylamine-N-oxide (TMAO) and phenylacetylglutamine. The dysbiotic profile was marked by increased Proteobacteria and decreased Firmicutes, linked to reduced cardioprotective metabolite production and heightened inflammation. These shifts may worsen heart failure prognosis and contribute to systemic inflammation. The results support the potential of microbiome-targeted therapies, such as probiotics, as adjunctive strategies in heart failure management.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148472063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abel Barré, Véronique Lenoble, Ana Luzia Lacerda, Maria Luiza Pedrotti, Raffaella Casotti, Carola Murano, Vincenzo Donnarumma, Soledad Muniategui-Lorenzo, José M Andrade-Garda, Verónica Fernández-González, Carmen Moscoso-Pérez, Felipe Kessler, Róisín Nash, Fanny Aulanier, Raphaëlle Barry-Martinet, Marc Bouchoucha, João Frias, Jean-François Briand
{"title":"From the Atlantic to the Mediterranean: what factors shape diatom diversity in the plastisphere.","authors":"Abel Barré, Véronique Lenoble, Ana Luzia Lacerda, Maria Luiza Pedrotti, Raffaella Casotti, Carola Murano, Vincenzo Donnarumma, Soledad Muniategui-Lorenzo, José M Andrade-Garda, Verónica Fernández-González, Carmen Moscoso-Pérez, Felipe Kessler, Róisín Nash, Fanny Aulanier, Raphaëlle Barry-Martinet, Marc Bouchoucha, João Frias, Jean-François Briand","doi":"10.1038/s41522-026-01060-1","DOIUrl":"https://doi.org/10.1038/s41522-026-01060-1","url":null,"abstract":"<p><p>Plastic substrates are ubiquitously colonized by complex microbiomes, referred to as the plastisphere. Diatoms, despite being considered the main autotrophic taxa and key early colonizers involved in biofilms, currently remain poorly studied compared to other microbes plastic pieces were immersed in coastal systems at six locations across five countries in the Atlantic Ocean and the Mediterranean Sea. Spatial and seasonal dynamics of plastic-attached diatom communities were investigated by incubating polyethylene (HDPE) at all sites for 84 days. Temporal dynamics at each season were also investigated using HDPE, polypropylene, and polystyrene in Toulon only (North-Western Mediterranean Sea). Using amplicon sequencing of the rbcL gene, geographic location appears to be the primary driver of diatom diversity, followed by season and incubation time, with intra-site variations always smaller than those between sites. Intra-site variations were mostly due to relative abundance changes, while inter-site variations corresponded to shifts between species. Biofilms from the Atlantic shared neither species nor ASVs, whereas biofilms from the Mediterranean shared 5 species and 5% of reads. Pioneer taxa changed depending on the season, while mature taxa tended to converge irrespective of the season. Finally, the nature of conventional plastics plays a minor role in shaping the diatom community, as shown previously for heterotrophs in the plastisphere. Overall, the shaping of diatom communities in biofilms could be observed at different taxonomic levels, down to the genetic variant, highlighting the extent to which genetic divergence occurs. Finally, potential ecological consequences of diatom presence and diversity in the plastisphere are discussed.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Joint contributions of host genetics and heritable gut microbiota to semen quality variation in Duroc boars.","authors":"Liangliang Guo, Xinran Meng, Quan Zhang, Jiajian Tan, Haiqing Sun, Siwen Jiang, Hongkui Wei, Jian Peng","doi":"10.1038/s41522-026-01073-w","DOIUrl":"https://doi.org/10.1038/s41522-026-01073-w","url":null,"abstract":"<p><p>Host genetics and gut microbiota jointly influence host phenotypes. To investigate the genetic and microbial factors affecting boar semen quality, we analyzed whole-genome resequencing and fecal 16S rRNA sequencing data from 1128 Duroc boars. Gut microbiota profiling showed that Firmicutes, Bacteroidetes, and Proteobacteria were dominant phyla, while farm type, herd type, strain, and age significantly affected microbial composition. Genome-wide association analysis identified 32 significant SNPs associated with semen traits, and microbiome-wide association analysis detected 251 genus-level associations. Variance component analysis indicated that host genetics, gut microbiota, and their interactions contributed substantially to semen quality variation. Heritability analysis identified 73 heritable genera, and microbial GWAS further detected 242 SNPs associated with 18 heritable genera. Mendelian randomization analysis further supported a significant association between the heritable genus Intestinibacter and sperm motility. Notably, overlapping genomic regions on chromosome 10 were associated with both Intestinibacter abundance and sperm motility, suggesting that host genetic variation may influence semen quality directly or indirectly through modulation of heritable gut microbiota. These findings provide new insights into host genetics-microbiota interactions underlying boar semen quality.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julian R Garneau, Aline Altenried, Youzheng Teo, Xiaobing Wu, Sarah C McHugh, Michael Taschner, Carla Hernández-Cabanyero, Johann Mignolet, Pénélope Gomes, Hugues de Villiers de la Noue, Grégory Resch, Pascale Vonaesch
{"title":"Phage endolysin enables targeted manipulation of the small intestinal microbiota and uncovers niche overlap between oral and butyrate-producing taxa.","authors":"Julian R Garneau, Aline Altenried, Youzheng Teo, Xiaobing Wu, Sarah C McHugh, Michael Taschner, Carla Hernández-Cabanyero, Johann Mignolet, Pénélope Gomes, Hugues de Villiers de la Noue, Grégory Resch, Pascale Vonaesch","doi":"10.1038/s41522-026-01087-4","DOIUrl":"https://doi.org/10.1038/s41522-026-01087-4","url":null,"abstract":"<p><p>Small intestinal oral bacterial overgrowth (SIOBO) is associated with impaired nutrient absorption and is a key contributor to environmental enteric disorder (EED) and stunted child growth. Here, we explore the use of a phage-derived lysin as a precision antimicrobial to selectively target Streptococcus salivarius within complex microbial communities. Using a newly developed bioinformatic and wet-lab pipeline, we identified, cloned, and produced a prophage-encoded lysin from S. salivarius and demonstrated its potent and specific lytic activity against 49 S. salivarius strains isolated from stunted children, while sparing related species such as S. mitis, S. parasanguinis, and S. thermophilus. Application of the lysin to human stool-derived in vitro communities and to mice colonized with S. salivarius led to an approximate 2-3 log reduction in S. salivarius abundance while preserving overall bacterial community. We observed a negative correlation between S. salivarius and Coprococcus (now Allocoprococcus) comes in vitro, and Eubacterium xylanophilum, Akkermansia, Lactobacillus and Ruminococcus in vivo. Spent-medium assays confirmed niche overlap between 10 clinical strains of S. salivarius and 28 taxa commonly recognized as butyrate producers. These results suggest that phage-derived lysins offer multiple benefits by selectively removing ectopically colonized oral taxa and indirectly promoting beneficial anaerobes.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Silvia Cometta, Maria de Los Reyes Becerra Perez, Inbar Shmuely, Flavia Medeiros Savi, Liraz Chai, Dietmar W Hutmacher
{"title":"Long-term spatiotemporal biological and mechanobiological dynamics of Staphylococcus aureus biofilms.","authors":"Silvia Cometta, Maria de Los Reyes Becerra Perez, Inbar Shmuely, Flavia Medeiros Savi, Liraz Chai, Dietmar W Hutmacher","doi":"10.1038/s41522-026-01097-2","DOIUrl":"https://doi.org/10.1038/s41522-026-01097-2","url":null,"abstract":"<p><p>In the context of implanted medical devices, biofilm formation transforms otherwise inert biomaterials into persistent sources of infection that are highly resistant to antimicrobial therapy and immune clearance. This persistent problem demands a critical re-examination of how biofilms are conceptualized, studied, and modeled. Using tissue-mimicking gelatin methacryloyl hydrogels, we show that Staphylococcus aureus spatiotemporal biofilm dynamics are strongly regulated by matrix mechanics and nutrient availability. Nutrient-rich conditions promote hyperproliferative, eDNA-rich microcolonies that actively degrade polymer networks, whereas serum-supplemented conditions produce compact aggregates enriched with vesicle-like structures and serum-derived matrix components. Notably, 3D confinement revealed a previously unrecognized 'budding' dispersal mechanism unique to embedded biofilms. Integrating 3D-printed polycaprolactone implants shows that while implant surfaces promote bacterial adhesion, the surrounding microenvironment exerts primary regulatory control. Longitudinal tracking over 3 weeks recapitulates key biofilm hallmarks and challenges surface-centric paradigms of implant infections, providing a framework for dissecting infection mechanisms and guiding therapeutic strategies.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148437543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}