Microorganisms最新文献

{"title":"Fire Severity Drives Long-Term Divergence of Soil Microbial Communities and Functional Traits in an Alpine Forest.","authors":"Xun Li, Wenxi Yang, Yan Zhang, Bin Peng, Xiaolin Li","doi":"10.3390/microorganisms14092115","DOIUrl":"10.3390/microorganisms14092115","url":null,"abstract":"<p><p>Increasing wildfire severity under climate change may alter the trajectory of belowground recovery in alpine forests, yet its long-term effects on soil microbial communities remain poorly understood. Here, we examined soil physicochemical properties and microbial communities eight years after fire across unburned, low-, moderate-, and high-severity fire sites in an alpine forest of western Sichuan, China. Fire severity was associated with persistent divergence at depths of 0-10 cm, with significant changes in soil organic carbon (SOC), soil water content (SWC), available nitrogen (AN), and microbial biomass. High-severity fire strongly reduced AN and available phosphorus (AP), whereas moderate-severity fire maintained the highest SOC and SWC. Bacterial alpha diversity remained relatively stable, whereas fungal richness declined markedly under high-severity fire, indicating greater fungal sensitivity to fire disturbance. Fire severity explained 57.35% and 87.32% of bacterial and fungal community variation, respectively, while structural equation modeling indicated that microbial responses were primarily mediated by changes in nutrient availability, soil moisture, and microbial biomass. Functionally, microbial communities shifted from resource-acquisition strategies under low-severity fire toward potential stress-tolerant and saprotrophic-dominated strategies under high-severity fire. Moderate-severity fire enhanced bacterial network complexity and increased the abundance of specific mycorrhizal taxa (e.g., <i>Russula</i>), whereas high-severity fire promoted saprotrophic and stress-resistant taxa such as Actinobacteriota and <i>Penicillium</i>, while suppressing mycorrhizal groups. Overall, fire severity acted as a persistent environmental filter that reorganized microbial community structure and functional strategies of the topsoil, suggesting that increasing fire severity may delay belowground recovery and weaken ecosystem resilience in alpine forests.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial Colony Image Enhancement Algorithm Based on Composite Adversarial D-DCGAN Neural Network.","authors":"Wangxin Li, Mingfeng Ge, Jing Sun, Dongxin Shi, Chenyu Jiang","doi":"10.3390/microorganisms14092112","DOIUrl":"10.3390/microorganisms14092112","url":null,"abstract":"<p><p>Microbial testing plays a crucial role in medical and biological research, serving as a significant direction in disease prevention and control studies. Traditional manual testing, which involves identifying colonies on Petri dishes is the best method, but it is not only expensive but also time consuming. However, the application and development of deep learning can address these issues. However, a crucial condition is that deep learning models require a large amount of labeled medical imaging data. Obtaining high-resolution images is time consuming and cannot generate a large amount of data in a short time. Therefore, we designed a Double Deep Convolutional Generative Adversarial Networks (D-DCGAN) to construct a dataset. Under the DCGAN adversarial network, synthetic colonies are generated by overlapping small single colonies and composite colonies to establish a random synthetic colony model, and a DCGANB generation model is established for the synthesis of complete colonies. In this study, we first evaluated the D-DCGAN model, obtaining an initial FID score of 38.9, and validated the effectiveness of the generated dataset using Faster R-CNN and YOLOv12. Subsequently, a second-order optimization model based on multiple evaluation metrics was developed to determine the optimal augmentation level, identifying 1320 synthetic images from the original 236 samples. With this optimized dataset, the FID score decreased to 37.1, while the detection accuracy reached 0.975. These results demonstrate the feasibility of the proposed framework for effective dataset augmentation and improved downstream detection performance.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extremophilic Microalgae and Cyanobacteria as Platforms for Climate Resilience, Circular Resource Utilization and Bioprospecting.","authors":"Mixue Wang, Yan Wang, Die Zhou, Yu Xie, Shoukai Guo, Zhongliang Sun","doi":"10.3390/microorganisms14092113","DOIUrl":"10.3390/microorganisms14092113","url":null,"abstract":"<p><p>The untapped genetic diversity of extremophilic microalgae provides distinctive physiological and biochemical traits with potential to support Sustainable Development Goal (SDG) 6 (Clean Water and Sanitation), SDG 7 (Affordable and Clean Energy), and SDG 15 (Life on Land). This review examines the diversity, stress-adaptation mechanisms, and biotechnological potential of extremophilic microalgae, with emphasis on their roles in resource recovery, carbon utilization, and bioproduct generation. Their ability to maintain cellular functions under extreme salinity, pH, temperature, radiation, and nutrient conditions enables their cultivation in environments that may be unsuitable for conventional production systems and facilitates the accumulation of lipids, pigments, carbohydrates, proteins, and other bioactive metabolites. These characteristics create opportunities to couple wastewater treatment, carbon capture and utilization, and biomass valorization within circular bioprocesses. However, laboratory-scale demonstrations should not be equated with established environmental or commercial benefits, as strain-specific physiological requirements, energy demand, process control, harvesting, downstream processing, and resource inputs can constrain scale-up. The review therefore emphasizes the need to evaluate extremophilic microalgal systems using integrated techno-economic and life-cycle approaches rather than biological productivity alone. Future advances will depend on combining multi-omics, metabolic engineering, adaptive cultivation, process optimization, and predictive modeling to identify robust strains and cultivation strategies. Such integration could accelerate the translation of extremophile-based bioprocesses into resource-efficient and economically credible applications for environmental sustainability.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Subtype Stratification Reveals Gut Microbial Alterations, Candidate Markers, and Co-Occurrence Network Remodeling in Coronary Artery Disease.","authors":"Peiqi Yan, Chen Tian, Lei Zhu, Zhigang Zhang","doi":"10.3390/microorganisms14092117","DOIUrl":"10.3390/microorganisms14092117","url":null,"abstract":"<p><p>Although gut microbiota dysbiosis is associated with coronary artery disease (CAD), its dynamic alterations across distinct clinical stages remain largely unexplored. This study aimed to identify stage-specific microbial biomarkers across the CAD spectrum. We analyzed 16S rRNA sequencing data from 306 subjects, including non-CAD controls and patients with mild coronary stenosis (MCS), stable angina (SA), unstable angina (UA), and acute myocardial infarction (AMI). Diversity analyses, machine learning, and SPIEC-EASI network modeling were applied to evaluate microbial community shifts and identify core diagnostic markers. Significant structural remodeling of the gut microbiota was observed, particularly during the AMI stage. <i>Veillonella</i>, <i>Intestinimonas</i>, and <i>Streptococcus</i> were identified as the core biomarkers for the MCS, SA, and UA/AMI stages, respectively. From the MCS to the UA stage, ecological network connectivity continuously declined, highlighting critical barrier vulnerability, before transitioning into an antagonism-dominated network in the AMI stage. Machine learning models effectively discriminated among the various disease stages, and key microbial markers remained statistically robust after adjusting for major clinical confounders. The gut microbiota exhibits dynamic, stage-specific dysbiosis throughout CAD progression, providing promising non-invasive biomarkers for precise disease staging and diagnosis.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Genome Sequencing Analysis of ST1, ST11, ST17, and ST37 <i>Clostridioides</i><i>difficile</i> Lineages from a Korean Hospital.","authors":"Seongjin Cho, Young Kyung Lee, Kibum Jeon, Jae-Seok Kim","doi":"10.3390/microorganisms14092122","DOIUrl":"10.3390/microorganisms14092122","url":null,"abstract":"<p><p><i>Clostridioides difficile</i> infection (CDI) is a major cause of antibiotic-associated diarrhea and pseudomembranous colitis and remains one of the most common healthcare-associated infections. <i>Clostridioides difficile</i> sequence types 1 and 11 (ST1 and ST11), which belong to multilocus sequence typing (MLST) clades 2 and 5, respectively, are widely recognized as epidemic-associated lineages. Both lineages harbor virulence-associated genetic features, including truncating variants in <i>tcdC</i> and carriage of the binary toxin locus (CdtLoc). ST37 (clade 4) has been an epidemic lineage in East Asia, whereas ST17 (clade 1) has been reported as a predominant lineage in the Republic of Korea and Japan. We performed short-read whole-genome sequencing (WGS) on 61 clinical isolates collected at a university-affiliated hospital in the Republic of Korea between February 2016 and April 2019. Long-read sequencing was additionally performed for 24 isolates, generating complete genomes by hybrid assembly. ST17 was the most prevalent sequence type (<i>n</i> = 16, 26.2%), followed by ST1 (<i>n</i> = 10, 16.4%). ST1 and ST11 isolates harbored the genetic features reported for these lineages, including truncating variants in <i>tcdC</i>. Genomic profiling further identified virulence-associated genes and antimicrobial resistance (AMR) determinants in diverse lineages. These findings characterize the genomic features of co-circulating <i>C. difficile</i> lineages and reveal the local presence of epidemic-associated strains.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609255/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota-Associated Amino Acid Metabolites in Inflammatory Bowel Disease: Emerging Key Players in the Host-Microbe Interface.","authors":"Xianwen Meng, Chunyang Tian, Yijun Zhu, Danping Zheng","doi":"10.3390/microorganisms14092108","DOIUrl":"10.3390/microorganisms14092108","url":null,"abstract":"<p><p>Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic relapsing intestinal inflammatory disorder driven by complex interactions among host genetics, immune dysregulation, and gut microbiota dysbiosis. The functional contribution of microbial metabolites beyond short-chain fatty acids and bile acids remains incompletely understood. A critical and unresolved question is whether microbiota-associated amino acid metabolites are merely passive indicators of dysbiosis or active drivers of intestinal inflammation and tissue repair. In this review, we summarize recent advances in the roles of microbiota-associated amino acid metabolites and their derivatives in IBD, highlighting that amino acid metabolites constitute a functionally distinct class of bioactive signaling molecules that operate through four representative metabolic networks: tryptophan metabolism, aspartate-related metabolism, branched-chain amino acid (BCAA) metabolism, and arginine-polyamine metabolism. We synthesize recent clinical metabolomic data and identify reductions in tryptophan-derived indoles, glutamate, histidine, and selected BCAAs across IBD clinical cohorts and sample matrices, whereas metabolites such as serine, proline, and polyamine degradation products are frequently elevated or associated with disease activity or therapeutic response. Mechanistically, microbiota-associated amino acid metabolites are implicated in intestinal homeostasis and IBD pathogenesis through multifaceted pathways, including modulation of intestinal epithelial barrier integrity (e.g., cell-cell junction, mucus secretion, and stem cell-driven mucosal repair), innate and adaptive immune responses, host-pathogen interactions, and extraintestinal inflammatory signaling (e.g., systemic inflammation, and brain-gut axis communication). Finally, we highlight current challenges and limitations in achieving a causal understanding of microbiota-associated amino acid metabolic alterations in IBD, particularly regarding their origin, spatial distribution, and functional relevance, as well as their potential utility for disease stratification and treatment-response assessment, and discuss how these insights may inform the future development of next-generation biomarkers and precision therapeutic strategies tailored to individual metabolic phenotypes in IBD.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the Processing and Nutrient Digestibility of Defatted <i>Nannochloropsis</i> sp. QH25 Co-Product for Sustainable Rainbow Trout Aquaculture Diets.","authors":"Pallab K Sarker, Benjamin V Schoffstall, Anne R Kapuscinski, Devin Fitzgerald, Anindita Datta, Duncan Gwynne, Connor Greenwood","doi":"10.3390/microorganisms14092104","DOIUrl":"10.3390/microorganisms14092104","url":null,"abstract":"<p><p>The sustainability limitations of fishmeal and fish oil have increased interest in nutrient- rich microalgal co-products for aquafeeds. This study evaluated the effects of processing on the nutritional composition and apparent digestibility of a defatted <i>Nannochloropsis</i> sp. QH25 co-product in rainbow trout (<i>Oncorhynchus mykiss</i>). Experiment 1 assessed the effects of extrusion at 90 °C or 127 °C, with or without precooking, and enzymatic treatment with protease, xylanase, and β-glucanase. Based on nutrient composition, the 90 °C extrusion treatment without precooking was selected for Experiment 2, which compared a reference diet with three diets containing 30% raw, extruded, or enzyme-treated co-product, using four replicate tanks per diet. Extrusion at 127 °C reduced crude protein, gross energy, and methionine concentrations, whereas extrusion at 90 °C largely preserved nutrient composition. Precooking reduced several essential amino acids but increased methionine and did not affect tryptophan. Crude protein digestibility was numerically higher in the extruded co-product than in the raw co-product, although the difference was not statistically significant. Most essential amino acids showed similar digestibility in the raw and extruded treatments, whereas enzymatic processing resulted in lower crude protein and amino acid digestibility. Omega-3 fatty acid digestibility remained high across diets. Overall, the raw co-product showed high nutrient digestibility, while extrusion resulted in only small, generally non-significant numerical differences and enzymatic processing generally resulted in lower nutrient digestibility under the conditions evaluated.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hepatitis E Virus Infection in Pregnant Women.","authors":"Zheng Wang, Yun-Sheng Ge, Min-Ming Wang, Yu-Lin Zhou, Gui-Ping Wen","doi":"10.3390/microorganisms14092105","DOIUrl":"10.3390/microorganisms14092105","url":null,"abstract":"<p><p>Hepatitis E virus (HEV) is a major global public health concern, particularly in resource-limited regions. Approximately 12.5% of individuals worldwide have been exposed to HEV, and 15-110 million individuals have current or recent HEV infection. HEV poses an especially serious threat to pregnant women, in whom infection can progress to severe disease and is associated with a high case fatality rate, particularly during the third trimester. Moreover, maternal HEV infection can lead to various adverse outcomes in fetuses and/or neonates, as documented in both developing and developed countries. No HEV-specific antiviral therapy is approved for use during pregnancy, and pregnancy-specific evidence and recommendations for HEV vaccination remain limited. This narrative review summarizes the diagnosis, prevalence, clinical manifestations, mechanisms underlying severe disease, treatment, and prevention of HEV infection in this high-risk population. It aims to improve clinicians' awareness of the potential impact of HEV infection on pregnant women and their fetuses/neonates, to promote public health literacy, and to accelerate future disease-control efforts.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity and Structural Composition of Bacterial Communities in Mineral Springs of the Andean-Amazonian Transition Zone in Northern Peru.","authors":"Damaris Leiva-Tafur, Liz M Cumpa-Velásquez, Lorenzo Culqui, Carmen N Vigo, Cristian Hurtado Burga, Deisy Iliquin Chavez, Oscar Andrés Gamarra-Torres, Manuel Oliva-Cruz","doi":"10.3390/microorganisms14092106","DOIUrl":"10.3390/microorganisms14092106","url":null,"abstract":"<p><p>Mineral springs in the Andean-Amazonian transition represent poorly explored aquatic ecosystems whose hydrogeochemical heterogeneity may favor the establishment of specialized microbial communities. In this study, bacterial communities in sediments from 19 mineral springs in northern Peru were characterized using 16S rRNA gene sequencing, and their relationships with hydrogeochemical conditions and predicted functional potential were evaluated. The springs exhibited temperatures ranging from 15.1 to 38.2 °C and total dissolved solids (TDS) concentrations ranging from 0.022 to 162.5 mg L^-1, reflecting marked variation in thermal and mineralization conditions. Bacterial communities were dominated by Desulfobacteraceae, Desulfosarcinaceae, Chlorobiaceae, Nitrosomonadaceae, Nitrospiraceae, and Rhodobacteraceae, including representative genera such as <i>Halanaerobium</i>, <i>Chlorobium</i>, <i>Thiothrix</i>, and <i>Sulfurovum</i>. Although alpha diversity did not differ significantly among hydrogeochemical categories, beta diversity analyses indicated compositional differentiation among thermal categories, while RDA revealed a significant multivariate association between bacterial community composition and the combined hydrogeochemical gradient (F = 1.0934, <i>p</i> = 0.035). Co-occurrence network analysis identified <i>Desulfotignum</i>, <i>Roseimarinus</i>, <i>Halanaerobium</i>, and <i>Anaerophaga</i> among the most highly connected taxa. PICRUSt2 predicted functional potential associated with carbon fixation, nitrogen and sulfur transformations, phosphorus acquisition and polyphosphate-related metabolism, and ferrous iron uptake. These findings provide the first integrated characterization of these bacterial communities and establish a baseline for future research on microbial ecology, biogeochemical cycling, and environmental biotechnology in Andean-Amazonian ecosystems of Peru.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental Sources and Tissue-Specific Selection Jointly Shape the Bacterial Community of the Sea Cucumber (<i>Apostichopus japonicus</i>) in Artificial Reef Areas of Laizhou Bay, Bohai Sea.","authors":"Shengkai Lin, Qingchen Zhao, Linlin Ma, Tuo Zhou, Hexiang Yang, Zhongxin Wu, Tao Tian, Qingxia Li","doi":"10.3390/microorganisms14092109","DOIUrl":"10.3390/microorganisms14092109","url":null,"abstract":"<p><p>The sea cucumber <i>Apostichopus japonicus</i> is an important aquaculture species in artificial reef areas. Understanding the bacterial communities in its different tissues and their relationship with the environment is of great ecological significance for reef area management and healthy aquaculture. In this study, environmental samples, including seawater and sediment, as well as tissue samples of <i>A. japonicus</i> gut and respiratory tree, were collected from seven stations in the artificial reef area of Laizhou Bay, Bohai Sea. Total DNA was extracted from each sample, and the bacterial communities were characterized using PacBio full-length 16S rRNA amplicon sequencing technology. The results showed that bacterial diversity was highest in sediments, followed by the gut, whereas seawater and respiratory tree samples showed lower diversity. The gut bacterial community structure closely resembled that of the surrounding sediments, characterized by a substantial enrichment of taxa such as Cyanobacteriota and Planctomycetota. FAPROTAX analysis exhibited relatively high representation of putative functions related to complex organic matter degradation in gut samples. In contrast, the respiratory tree bacterial community structure was more similar to that of seawater, with Alphaproteobacteria as the dominant group. The respiratory tree samples showed relatively high predicted representation of methylotrophy and methanol oxidation, suggesting a putative functional association with one-carbon compound utilization. These results indicate that the bacterial community in <i>A. japonicus</i> tissues is shaped by a combination of environmental sources and tissue-specific selection, with the gut community being more closely associated with sediment and the respiratory tree community with seawater. These findings provide microecological insights into habitat optimization and sea cucumber stock enhancement management in artificial reef areas, specifically indicating that sediment- and seawater-derived microbial sources should be taken into account to support the tissue-specific bacterial communities of <i>A. japonicus</i>.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"14 9","pages":""},"PeriodicalIF":4.7,"publicationDate":"2026-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13609560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149062647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}