Applied Microbiology and Biotechnology最新文献

{"title":"Defined and refined: development of a minimal medium for Clostridium pasteurianum","authors":"Natalia Nadal Alemany,&nbsp;Daniëlle Catharina Verboon,&nbsp;Robbert Kleerebezem,&nbsp;Rebeca Gonzalez-Cabaleiro","doi":"10.1007/s00253-025-13572-5","DOIUrl":"10.1007/s00253-025-13572-5","url":null,"abstract":"<p>Even though microorganisms can often grow in defined media, they are frequently cultured in rich media containing complex components like yeast extract. A drawback of using rich media is the effect of secondary substrates from complex components on the metabolism, which can change the anabolism and the formation of products, complicating the interpretation of experimental results. Rich media containing yeast extract is generally used to grow <i>Clostridium pasteurianum</i>. In this work, we describe the development of a minimal medium for <i>C. pasteurianum</i> combining rational media design, transfers in batch bottles and continuous bioreactors experiments. The media were designed based on literature, the elements needed in the metabolism, and a general chemical formula for the composition of biomass. The media were tested by cultivations in chemostat and batch bottles. Microbial growth was not sustained in an inorganic medium with glucose over batch bottles transfers. In contrast, a medium with glucose supplemented with para-aminobenzoic acid (PABA), biotin and cysteine, supported growth in chemostat (12 retention times) and in batch bottles transfers. Growth was also maintained in the same medium without cysteine during the 12 retention times of chemostat operation, but at a lower dilution rate, showing that cysteine enhanced the growth rate of <i>C. pasteurianum</i> despite not being essential. Microbial growth was sustained through batch bottle transfers in media with PABA only and with biotin only, apart from glucose and cysteine. Therefore, it was concluded that PABA and biotin are essential for the growth of <i>C. pasteurianum</i> without yeast extract, only one—any—amongst both being needed.</p><p>• <i>Clostridium pasteurianum is auxotrophic on B vitamins.</i></p><p>• <i>Both biotin and PABA suffice to support growth in an otherwise inorganic medium.</i></p><p>• <i>Cysteine was not essential but increased its growth rate.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13572-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145256541","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":"Nasal microbiota dysbiosis and functional alterations in children with adenoid hypertrophy: potential biomarkers and post-surgical microbial recovery","authors":"He Jiang,&nbsp;Ping Ye,&nbsp;Shuai Chen,&nbsp;Juan Zhao,&nbsp;Long Chen,&nbsp;Qian Sun,&nbsp;Wenming Jia,&nbsp;Heng Liu,&nbsp;Xin Feng","doi":"10.1007/s00253-025-13555-6","DOIUrl":"10.1007/s00253-025-13555-6","url":null,"abstract":"<p>Nasal cavity and nasopharynx are habitats for both pathogenic and non-pathogenic bacteria. Adenoid hypertrophy (AH) is the main cause in children, with a high incidence, for the airflow reduction in the upper airways. However, limited research described the differences of nasal microbial compositions in AH patients and healthy children. To determine the association between nasal microbiota and AH, total DNAs were collected and extracted from the nasal cavity and the hypertrophic adenoid of the donors, and the 16S rRNA gene V3–V4 region was sequenced. Microbial diversity was compared between the healthy and AH groups, and the enriched functional pathways were predicted. Although the alpha-diversity of microbial communities did not show statistically significant differences between the groups, principal coordinate analysis (PCoA) revealed that the microbiota component in the nasal cavity as well as in the hypertrophic adenoid tissues of children with AH was significantly different from that of healthy children. Genera <i>Alloiococcus</i>, <i>Moraxella</i>, <i>Streptococcus</i>, and <i>Bacteroides</i> were specifically enriched in the AH group’s samples, among which <i>Moraxella</i> spp. was significantly enriched in both nasal cavity and adenoid tissues, indicating a potential association of it with AH. In addition, Tax4fun prediction revealed disordered microbial functions in AH children. Nutrient metabolism, signaling system, chemotactic reaction, genetic replication, and reproduction-related pathways significantly decreased in the AH group but increased after adenoidectomy treatment. This study revealed a high association between specific microorganisms and AH disease. Future work is needed to investigate the role of <i>Moraxella</i> spp. in AH development.</p><p><i>• Microbiota in the nasal cavity has high specificity in distinguishing patients with adenoidal hypertrophy from healthy individuals, indicating that the homeostasis of microbiota in the nasal cavity is highly associated with the healthy status of adenoid.</i></p><p><i>• Several bacterial taxa, including Alloiococcus, Moraxella, Streptococcus, and Bacteroides, are bio-markers for adenoidal hypertrophy, which enriches specifically in both nasal cavities and hypertrophied adenoid tissues of patients.</i></p><p><i>• In the nasal cavity of patients with adenoidal hypertrophy, microbial functions related to pathogenicity were enriched, indicating an association between adenoidal hypertrophy and disorder of microbiota in the nasal cavity.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13555-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145256530","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":"Lytic properties and genomic analysis of bacteriophage Brt_Psa3, targeting Pseudomonas syringae pv. actinidiae","authors":"Emil Gimranov,&nbsp;Hugo Oliveira,&nbsp;Conceição Santos,&nbsp;Luísa Moura,&nbsp;Joana Azeredo","doi":"10.1007/s00253-025-13613-z","DOIUrl":"10.1007/s00253-025-13613-z","url":null,"abstract":"<div><p><i>Pseudomonas syringae</i> pv. <i>actinidiae</i> (Psa) is the causative agent of bacterial canker in kiwifruit (<i>Actinidia</i> spp.). Psa biovar 3 is the most prevalent and virulent, causing frequent and severe outbreaks worldwide. While current treatments have low efficacy, bacteriophages emerge as possible environmentally safe alternative biocontrol agents. In this study, bacteriophage Brt_Psa3 was isolated from the soil of a kiwifruit orchard in Portugal. Morphologically, Brt_Psa3 forms clear plaques and has a Podoviral morphotype. The bacteriophage exhibited broad lytic activity against several plant-pathogenic <i>Pseudomonas</i> strains, including Psa isolates. The isolated bacteriophage has a latent period of 100 min, a burst size of 143 particles/cell, and demonstrates stability at different temperatures and pH values found in kiwifruit orchards. In addition, Brt_Psa3 exhibited tolerance to UVA irradiation during 120 min of incubation. Brt_Psa3 belongs to the <i>Autographiviridae</i> family and <i>Ghunavirus</i> genus, based on full-genome nucleotide alignment and supported by phylogenetic analysis of structural proteins. The phage contains 51 open reading frames with no antibiotic resistance genes identified, within a genome of 40.509 base pairs. In vitro experiments with kiwifruit leaves demonstrated significant reduction of Psa levels (40%) on leaf surfaces, highlighting the bacteriophage’s therapeutic potential in managing bacterial canker in kiwifruits.</p></div>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13613-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145256531","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":"Bidirectional interactions between circadian rhythms and the gut microbiome","authors":"Jhommara Bautista,&nbsp;Sofía Ojeda-Mosquera,&nbsp;Adriana Altamirano-Colina,&nbsp;Camila Hidalgo-Tinoco,&nbsp;Miranda Di Capua Delgado,&nbsp;Andrés López-Cortés","doi":"10.1007/s00253-025-13570-7","DOIUrl":"10.1007/s00253-025-13570-7","url":null,"abstract":"<p>Circadian rhythms are endogenous, near-24-h cycles that synchronize physiological and behavioral functions with environmental cues such as light/dark cycles and food intake. While the central pacemaker in the suprachiasmatic nucleus orchestrates these rhythms, peripheral clocks distributed across organs, including the gastrointestinal tract, exhibit autonomous oscillations that are crucial for local homeostasis. Concurrently, the gut microbiota undergoes diurnal fluctuations in composition and metabolic activity that are tightly coupled to host circadian mechanisms. Recent discoveries reveal a bidirectional relationship: host clocks influence microbial dynamics through feeding behavior, immune signaling, and epithelial renewal, whereas microbial metabolites such as short-chain fatty acids (SCFAs) and bile acids modulate circadian gene expression in peripheral tissues. Disruptions in circadian alignment, whether due to genetic mutations, lifestyle factors like shift work and irregular eating, or environmental perturbations, lead to microbial dysbiosis, metabolic dysfunction, inflammation, and heightened disease susceptibility. Conversely, altered microbiota rhythms can feed back into host systems, impairing metabolic control, immune responses, and neuroendocrine signaling. This reciprocal regulation extends to disease contexts, where circadian-microbiota misalignment contributes to obesity, type 2 diabetes, inflammatory bowel disease, and even neuropsychiatric disorders. This review synthesizes current insights into the molecular and physiological cross-talk between host circadian clocks and the gut microbiota. We discuss how temporal dynamics at the cellular, systemic, and microbial levels are integrated and how their disruption underlies pathogenesis. We further explore the potential of chronobiotics and chrononutrition, including time-restricted feeding (TRF) and bioactive dietary compounds, as emerging strategies to restore circadian-microbial synchrony and improve metabolic health. Understanding this intricate dialogue between host and microbiome may pave the way for personalized, time-based interventions to enhance healthspan and prevent disease occurrence or progression.</p><p>• <i>Circadian rhythms and microbiota form a bidirectional regulatory feedback loop.</i></p><p>• <i>Disruption of circadian-microbial synchrony drives metabolic and inflammatory disease.</i></p><p>• <i>Chrononutrition offers novel strategies to restore health via circadian–microbiota alignment.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13570-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145256508","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 novel bispecific antibody targeting TNF-α and IL-6 receptor as a potent immunotherapeutic agent for inflammation","authors":"Mansooreh Heravi,&nbsp;Shadi Damough,&nbsp;Ladan Mafakher,&nbsp;Yeganeh Talebkhan,&nbsp;Leila Nematollahi,&nbsp;Leila Ghazizadeh,&nbsp;Soheila Ajdari","doi":"10.1007/s00253-025-13596-x","DOIUrl":"10.1007/s00253-025-13596-x","url":null,"abstract":"<p>Tumor necrosis factor-alpha and interleukin-6 are proinflammatory cytokines involved in several autoimmune diseases, including rheumatoid arthritis. Although monoclonal antibodies targeting these cytokines or their receptors are successful treatment approaches for autoimmune diseases, approximately 30% of treated patients fail to respond. Therefore, the designation of more effective and versatile therapeutics for simultaneously targeting multiple inflammatory pathways is pivotal. This study aimed to design a recombinant bispecific antibody (BisAb) targeting TNF-α and IL-6 receptor based on the complementarity-determining regions (CDRs) of adalimumab and tocilizumab antibodies. The physicochemical properties and tertiary structure of the modeled bispecific antibody proteins were studied through bioinformatics. The interaction of the designed bispecific antibody with human TNF-α and IL-6R was computed by molecular docking and molecular dynamics. The recombinant BisAb (60kDa) was expressed in <i>Escherichia coli.</i> The ELISA results demonstrated that the affinity of BisAb and its Ada-scFv moiety to TNF-α was quite similar with <i>K</i>_aff values of 7.7 and 9.4 × 10^–13 M, respectively. The recombinant BisAb and Toci-scFv also represented similar affinities towards IL-6R (<i>K</i>_aff values of 1.65 and 1.87 × 10^–12 M), closely comparable with the parental tocilizumab antibody. A dose-dependent neutralization of TNF-mediated cytotoxicity was also observed on L929 cells. Decreased phosphorylation of signal transducer and activator of transcription 3 (STAT3) was determined through western blotting with specific antibodies, indicating the blockade of IL-6 receptors before the preincubation with IL-6. The designed BisAb, a minimized biotherapeutic molecule, could successfully target two main ligands (IL-6R and TNF-α) involved in rheumatoid arthritis and many inflammatory/infectious diseases.</p><p>• <i>A new bispecific antibody was designed to target TNF-α and IL-6R.</i></p><p>• <i>In silico studies confirmed the physicochemical and structural properties of BisAb.</i></p><p>• <i>The best-modeled protein was recombinantly expressed in Escherichia coli.</i></p><p>• <i>BisAb significantly inhibited TNF-α-mediated cytotoxicity.</i></p><p>• <i>BisAb could efficiently suppress the IL-6-related phosphorylation of STAT3 protein.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13596-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249441","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, structural, and functional characterization of allomelanin from black yeast Exophiala viscosa, a chassis for fungal melanin production","authors":"Tiffany M. Hennessa,&nbsp;Lauren M. Irie,&nbsp;Hong Dong,&nbsp;Eric S. VanArsdale,&nbsp;Evan R. Glaser,&nbsp;Erin C. Carr,&nbsp;Steven D. Harris,&nbsp;Nathan C. Gianneschi,&nbsp;Zheng Wang","doi":"10.1007/s00253-025-13597-w","DOIUrl":"10.1007/s00253-025-13597-w","url":null,"abstract":"<p>Melanized fungi are known for their remarkable resilience to environmental stress, largely attributed to the protective properties of melanin. In this study, we establish the black yeast <i>Exophiala viscosa</i> as a non-pathogenic, genetically tractable model for the scalable production and functional analysis of DHN-melanin (allomelanin). Cultivation in flasks and bioreactors yielded up to 8.6 g/L of melanin, with the majority tightly incorporated into the cell wall as “melanin ghosts”. Chemical analyses including FTIR, XPS, ssNMR, and EPR confirmed the identity of the pigment as allomelanin and revealed a structural association with chitin. Gene deletions of Pks1, Arp2, and Abr2 validated the DHN-melanin biosynthetic pathway and enabled the generation of pigment-deficient mutants. Functional assays demonstrated that melanin contributes significantly to UV and cold tolerance, while offering limited protection against γ-radiation, suggesting that other pigments,such as carotenoids, may also play a protective role. The unique redox properties, structural integrity, and scalability of melanin production in <i>E. viscosa</i> highlight its potential for bio-derived materials used in radiation shielding, environmental remediation, and thermal regulation. This work establishes <i>E. viscosa</i> as a promising chassis for melanin biomanufacturing and a valuable model for studying fungal melanins in the context of materials science and environmental resilience.</p><p>• <i>Cultivation of E. viscosa in rich medium yielded up to 8.6 g/L of melanin.</i></p><p>• <i>Chemical and genetic analyses identified the pigment as allomelanin.</i></p><p>• <i>Melanin enhanced the tolerance of fungal cells to UV radiation and low temperatures.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13597-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145249432","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":"Revealing the essential role of the lid in mclPHA intracellular depolymerase from Pseudomonas putida KT2440","authors":"Laura Isabel de Eugenio,&nbsp;José Daniel Jiménez,&nbsp;Elena Ramos,&nbsp;Lara Serrano-Aguirre,&nbsp;Jesus M. Sanz,&nbsp;M. Auxiliadora Prieto","doi":"10.1007/s00253-025-13605-z","DOIUrl":"10.1007/s00253-025-13605-z","url":null,"abstract":"<p>Polyhydroxyalkanoates (PHAs) are microbial polyesters that serve as intracellular carbon reserves and represent promising biodegradable alternatives to conventional plastics. However, their large-scale application requires not only cost-effective production but also efficient strategies for recovery and recycling. Unlike short-chain-length PHAs, which are widely degraded by diverse enzymes, the intracellular degradation of medium-chain-length PHAs (mclPHAs) appears to be a genus-specific trait of <i>Pseudomonas</i>. In this context, the PhaZKT depolymerase from <i>Pseudomonas putida</i> KT2440 is considered a model enzyme for intracellular mclPHA mobilization; it is highly substrate-specific, acting almost exclusively on mclPHAs, and consists of an α/β-hydrolase fold with a lid domain, similar to lipases and other enzymes acting on lipid substrates, in contrast to extracellular PHA depolymerases, which generally lack this lid structure. Here, we explored the essential role of this lid structure through site-directed deletions and random mutagenesis. Targeted deletions within or near the lid completely abolished enzyme activity, highlighting its critical structural and functional importance. Random mutagenesis identified two beneficial variants: S184F, located in the lid hinge region, and G286R, situated in a still unmapped region. The S184F mutant exhibited increased esterase activity on <i>p</i>-nitrophenyl esters but significantly reduced depolymerase activity on mclPHA nanoparticles, indicating that lid integrity and dynamics precisely control substrate specificity and access. Molecular dynamics simulations supported these findings, revealing enhanced rigidity near the lid region in the S184F variant. Conversely, G286R showed substantially improved depolymerase activity toward mclPHA, suggesting alternative regions for beneficial mutations without compromising lid functionality. These results underscore the delicate balance between lid integrity and enzyme performance, offering insights into targeted protein engineering for optimized enzymatic recycling of bioplastics.\u0000</p><p>• <i>The lid in PhaZKT is essential for depolymerase activity</i></p><p>• <i>All lid-targeted mutants completely lost enzymatic activity</i></p><p>• <i>Random mutagenesis identified two active distal mutants</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13605-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237774","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":"Microorganisms and enzymes involved in polybutylene adipate terephthalate biodegradation","authors":"Miguel Fernandes,&nbsp;António A. Vicente,&nbsp;Andreia F. Salvador","doi":"10.1007/s00253-025-13565-4","DOIUrl":"10.1007/s00253-025-13565-4","url":null,"abstract":"<p>The European Union aims to achieve climate neutrality, protect the environment, and reduce marine litter, particularly caused by the pollution caused by recalcitrant plastics. The investment in biodegradable solutions as alternatives for conventional plastics is a priority for achieving a circular economy and tackling waste management challenges. However, the introduction of novel plastic blends in the environment must consider their effective biodegradation. Polybutylene adipate terephthalate (PBAT) is one of the most interesting polymers to integrate aliphatic–aromatic copolyesters as alternatives to recalcitrant plastics. Compared to other biodegradable plastics, PBAT offers superior flexibility and thermal stability. PBAT is degradable under industrial composting conditions, at thermophilic temperatures. At lower temperatures in natural environments, biodegradation is very challenging, but recent research has shown novel insights on PBAT biodegradation in a variety of environments. This review gives an overview of PBAT physical and chemical properties and its application in plastic blends and focuses on PBAT biodegradation. We compiled information about the microorganisms and enzymes involved in PBAT biodegradation and the environmental conditions in which the biodegradation occurs. For the first time, this review comprehensively compares enzymatic systems, microbial strains, and soil biodegradation while also identifying methodological limitations in the literature. The information presented herein is important to understand the opportunities and limitations of using PBAT in alternative plastic formulations and will hopefully guide the development of biotechnological solutions for plastic waste decontamination, contributing to building a greener future.</p><p>• <i>The blend of PBAT with other materials, change their biodegradation potential</i></p><p>• <i>Identification of the PBAT properties affecting biodegradation</i></p><p>• <i>Compilation of the few microorganisms known as PBAT degraders in several environments</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13565-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237779","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":"Biofloc system with synbiotic supplementation improves Penaeus vannamei immunity against AHPND","authors":"Magdalena Lenny Situmorang,&nbsp;Anggie Nur Fadillah,&nbsp;Atian Azizy,&nbsp;Gede Suantika","doi":"10.1007/s00253-025-13587-y","DOIUrl":"10.1007/s00253-025-13587-y","url":null,"abstract":"<p>Mass mortality due to disease emergence has resulted in enormous losses in shrimp production. One of the deadliest shrimp pathogens is the disease-causing <i>Vibrio parahaemolyticus</i> (VP_AHPND), which induces acute hepatopancreatic necrosis and has recently become resistant to various classes of antibiotics. Biofloc systems and synbiotic feed supplementation are potential alternative strategies for overcoming this problem. In this study, a biofloc system was generated by inoculating the probiotic <i>Halomonas alkaliphila</i>, a consortium of nitrifying bacteria, and the microalgae <i>Chaetoceros calcitrans</i> with molasses at a C/N ratio of 15. The synbiotic-supplemented feed contained 0.375% (w/w) of prebiotic red seaweed <i>Kappaphycus alvarezii</i> powder, 0.125% (w/w) <i>Spirulina</i> sp., and freeze-dried <i>H. alkaliphila</i> powder at 10⁹ CFU/kg feed. Over a 84-day culture period, the biofloc system with or without synbiotic supplementation resulted in more stable water quality and significantly increased shrimp total biomass and survival. After a <i>V. parahaemolyticus</i> challenge, the highest survival was found in the biofloc system with or without a synbiotic (70 ± 0%), similar to the semibatch system supplemented with antibiotic enrofloxacin orally at 60 mg/kg body weight after pathogen injection (73 ± 6%). Gene expression analysis revealed enhanced humoral immune responses, with upregulation of antimicrobial peptides (ALF-a, lyz) and melanization (proPO). These findings suggest that the application of a biofloc system with or without synbiotic feed supplementation could be a potential alternative to antibiotics, increasing disease resistance and modulating the immune response against potential AHPND-causing <i>V. parahaemolyticus</i> infection in <i>P. vannamei</i> growout culture.</p><p>• <i>Bioflocs and synbiotics provide additional nutrients, promoting shrimp productivity</i></p><p>• <i>Bioflocs, with or without synbiotics, improve shrimp survival and humoral immunity</i></p><p>• <i>Bioflocs, with or without synbiotics, offer similar survival compared to enrofloxacin</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13587-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145210485","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":"Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression","authors":"Jinping Wu,&nbsp;Jie Zhou,&nbsp;Qinghua Zhao,&nbsp;Chaozhu Yang,&nbsp;Yafan Bai","doi":"10.1007/s00253-025-13600-4","DOIUrl":"10.1007/s00253-025-13600-4","url":null,"abstract":"<p><i>Amorphophallus konjac</i>, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic <i>Rhizopus arrhizus</i> and <i>Rhizopus microsporus</i> were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while <i>Rhizopus</i> spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance.</p><p>• <i>Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria.</i></p><p>• <i>Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links.</i></p><p>• <i>Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.</i></p>","PeriodicalId":8342,"journal":{"name":"Applied Microbiology and Biotechnology","volume":"109 1","pages":""},"PeriodicalIF":4.3,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00253-025-13600-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145210486","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}