Current Research in Microbial Sciences最新文献_第5页

Mercury-driven fungal endophytic community and the role of endophytes in rice grain mercury accumulation 汞驱动的真菌内生群落及其在水稻籽粒汞积累中的作用

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-12-03 DOI: 10.1016/j.crmicr.2025.100525

Liangzhou Zhao , Jinzhao Song , Haiyan Hu , James F. White Jr , Xiuling Ji , Surendra Kumar Gond , Baolin Wang , Haiyan Li

Rice, a staple food for over half of the global population, is an important dietary source of methylmercury (MeHg) due to its high accumulation capacity. Endophytes are known to impact host plants heavy metals (HMs) accumulation, conversely, HMs can alter host plants endophytics communities. However, the specifically addressing mercury-rice endophytic fungal system remains limited. In the present study, the fungal endophytic community of rice from Hg-contaminated and uncontaminated sites were investigated by Illumina sequencing, and its role on rice grains MeHg accumulation was evaluated through pot experiments. Results showed that soil Hg concentration significantly restructured rice fungal endophytic communities, and higher Hg concentration decreased the richness and diversity of fungal endophytes, and the effect differed with tissues and development stages. The endophytic community in grains was distinct from roots, stalks and leaves, enriching specific rare species while reducing others ubiquitous in the vegetative tissues. Pot experiments identified some specific endophytes that significantly modulated grain Hg accumulation. Two Epicoccum nigrum strains (DHJ7, FZT214) reduced grain MeHg by 44.67 % and 48.79 %, respectively (p < 0.05), whereas Phoma herbarum (CSJ51, CHJ4) increased grain MeHg or total mercury (THg) by 50.1 %-51.35 % and 77.39 %-81.81 %, respectively (p < 0.05). Furthermore, 62.5 % of the tested isolates (16) enhanced rice yield, while Mucor sp. DHJ19 and Ceratorhiza sp. CHJ27 improved production by 72.6 %–80.5 % compared to controls. These findings highlight promising fungal endophytes for mitigating grain Hg contamination and improving yield. Future work should elucidate the mechanisms governing the selective enrichment of grain endophytes to deepen understanding of plant-endophyte interactions.

大米是全球一半以上人口的主食，由于其高蓄积能力，是甲基汞（MeHg）的重要膳食来源。已知内生菌影响寄主植物重金属的积累，反过来，重金属可以改变寄主植物的内生菌群落。然而，专门针对汞-水稻内生真菌系统的研究仍然有限。本研究利用Illumina测序技术对hg污染和未污染水稻的内生真菌群落进行了研究，并通过盆栽试验评价了其在水稻MeHg积累中的作用。结果表明：土壤汞浓度显著重构了水稻真菌内生菌群落，高汞浓度降低了真菌内生菌的丰富度和多样性，且影响随组织和发育阶段的不同而不同。籽粒内的内生菌群落与根、茎、叶不同，丰富了特定的稀有物种，减少了营养组织中普遍存在的其他物种。盆栽试验发现一些特定的内生菌能显著调节籽粒汞的积累。2株表occum nigrum （DHJ7、FZT214）分别降低了籽粒MeHg的44.67%和48.79% (p < 0.05)，而Phoma herbarum （CSJ51、CHJ4）分别提高了籽粒MeHg或总汞（THg）的50.1% ~ 51.35%和77.39% ~ 81.81% （p < 0.05）。此外，与对照相比，62.5%的被试菌株（16株）提高了水稻产量，而毛霉sp. DHJ19和Ceratorhiza sp. CHJ27的产量提高了72.6% - 80.5%。这些发现突出了真菌内生菌在减轻粮食汞污染和提高产量方面的前景。未来的工作应阐明谷物内生菌选择性富集的机制，以加深对植物与内生菌相互作用的理解。

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引用次数: 0

Methods to characterize the vaginal microbiome in a rhesus macaque model of simian human immunodeficiency virus (SHIV) transmission uncover epithelium-associated enrichment of Prevotella 在猴人免疫缺陷病毒（SHIV）传播的恒河猴模型中，对阴道微生物组进行表征的方法揭示了普雷沃氏菌的上皮相关富集

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-12-03 DOI: 10.1016/j.crmicr.2025.100526

Rahul Mohan , Samuel D. Johnson , Paden N. Dean, Arpan Acharya, Siddappa N. Byrareddy

The vaginal microbiome plays a crucial role in maintaining mucosal integrity and mitigating pathogen transmission, yet its comprehensive characterization remains challenging due to limited sampling and analysis methods. In this study, we aimed to characterize bacterial and fungal taxa diversities in the vaginal microbiomes of Simian Human Immunodeficiency (SHIV)-infected rhesus macaques, as well as their metabolic activities, using three sampling methods. The cervicovaginal lavage (CVL), vaginal swab, and vaginal mucosal tissue methods offer novel insights into microbial diversity and their potential impacts on HIV transmission. Using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, we assessed bacterial and fungal community composition and abundances, respectively, across all sampling methods. PICRUSt2 was used for functional predictions, and a modified glycosidase assay to further characterize glycan-degrading enzymatic activity in CVL samples. Our findings reveal that tissue samples were uniquely enriched for microbial taxa such as Prevotella spp. and Helicobacter spp., showing notable abundance differences compared to CVL and swab samples. Tissue samples exhibited higher alpha diversity and distinct metabolic prediction profiles, particularly elevated sialidase activity. While fewer differences were found in fungal microbiome composition and diversity, marked correlations were observed between bacterial and fungal taxa, emphasizing complex interkingdom interactions. These results highlight the significance of sampling methods in microbial ecology studies, which should be carefully considered due to their potential influence on pathogen transmission risk.

阴道微生物组在维持粘膜完整性和减轻病原体传播方面起着至关重要的作用，但由于采样和分析方法的限制，其全面表征仍然具有挑战性。在这项研究中，我们旨在通过三种采样方法表征人类免疫缺陷猴（SHIV）感染的恒河猴阴道微生物群中的细菌和真菌分类群多样性，以及它们的代谢活动。宫颈阴道灌洗（CVL）、阴道拭子和阴道粘膜组织方法为微生物多样性及其对HIV传播的潜在影响提供了新的见解。使用16S rRNA和ITS测序，我们分别评估了所有采样方法中细菌和真菌的群落组成和丰度。PICRUSt2用于功能预测，并使用改良的糖苷酶测定法进一步表征CVL样品中的聚糖降解酶活性。我们的研究结果表明，与CVL和拭子样品相比，组织样品对微生物类群（如普雷沃氏菌和幽门螺杆菌）具有独特的富集，表现出显著的丰度差异。组织样品表现出更高的α多样性和独特的代谢预测谱，特别是唾液酸酶活性升高。虽然真菌微生物组的组成和多样性差异较小，但细菌和真菌分类群之间存在显著相关性，强调了复杂的界间相互作用。这些结果突出了采样方法在微生物生态学研究中的重要性，由于它们对病原体传播风险的潜在影响，应仔细考虑采样方法。

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引用次数: 0

Genome-based reassessment of Sphingobacterium reveals the limitation of the fixed dDDH threshold for prokaryotic species delineation 基于基因组的鞘菌重评估揭示了固定dDDH阈值在原核生物物种划分中的局限性

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-12-01 DOI: 10.1016/j.crmicr.2025.100524

Shuai Li , Xin-Ran Wang , Wei Zhang , Wen-Jun Li

Accurate species delimitation in prokaryotes increasingly relies on genome-scale comparisons, yet fixed genomic thresholds can be unreliable in lineages shaped by extensive gene flux. In this study, we revisited the taxonomy of genus Sphingobacterium using phylogenomic reconstruction and comprehensive whole-genome comparisons. The genus displays a highly open pan-genome, with only 22 universally conserved genes and nearly 20,000 cloud genes, indicating pronounced genomic plasticity. Within this complex evolutionary context, we detected a rare non-transitive paradox in digital DNA-DNA hybridization (dDDH) within the Sphingobacterium siyangense group. All strains share average nucleotide identity (ANI) values above the accepted species boundary (95%), yet some strain pairs exhibit dDDH values below the species threshold (70%), resulting in a conflict restricted to this metric. Phylogenomic analyses, core genome variation, average amino acid identity (AAI) patterns, and functional gene profiles consistently support the monophyly and genomic cohesion of these strains, showing that dependence on dDDH alone may lead to ambiguous species boundaries. Based on the combined evidence, we treat all members of the S. siyangense cluster as a single species and propose additional taxonomic revisions. Sphingobacterium ginsenosidimutans is recognized as a heterotypic synonym of Sphingobacterium detergens. The species Rhinopithecimicrobium faecis is proposed for reclassification as Sphingobacterium faecis comb. nov. These findings demonstrate that rigid dDDH cutoffs cannot fully capture evolutionary relationships and highlight the value of integrating phylogenomic and pan-genomic evidence for resolving complex species level classifications in prokaryotes.

原核生物中准确的物种划分越来越依赖于基因组规模的比较，然而固定的基因组阈值在由广泛的基因通量形成的谱系中可能不可靠。在这项研究中，我们使用系统基因组重建和全面的全基因组比较重新审视了鞘菌属的分类。泛基因组高度开放，普遍保守基因仅有22个，云基因近2万个，具有明显的基因组可塑性。在这种复杂的进化背景下，我们在siyangense Sphingobacterium类群的数字DNA-DNA杂交（dDDH）中发现了罕见的非传递性悖论。所有菌株的平均核苷酸同一性（ANI）值均高于可接受的物种边界（95%），但一些菌株对的dDDH值低于物种阈值（70%），导致冲突仅限于这一指标。系统基因组学分析、核心基因组变异、平均氨基酸同一性（AAI）模式和功能基因谱一致支持这些菌株的单系性和基因组内聚性，表明仅依赖dDDH可能导致物种边界模糊。在综合证据的基础上，我们将siyangense聚类的所有成员视为一个单一的物种，并提出了进一步的分类修正。人参皂苷异变鞘杆菌被认为是去污剂鞘杆菌的异型同义物。提出将粪鼻微菌重新分类为粪鞘菌梳状。11 .这些发现表明，严格的dDDH截断值不能完全捕获进化关系，并突出了整合系统基因组学和泛基因组学证据对解决原核生物复杂物种水平分类的价值。

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引用次数: 0

A naturally isolated symbiotic Lactobacillus murinus suppresses multidrug-resistant Campylobacter jejuni via microbial metabolites 天然分离的共生鼠乳杆菌通过微生物代谢物抑制多重耐药空肠弯曲杆菌

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-11-25 DOI: 10.1016/j.crmicr.2025.100520

Junhao Wang , Ali Asif , Fangtong Gu , Shuaifeng Gu , Yakun Ding , Yufeng Gu , Muhammad Shahzad Rafiq , Haihong Hao

Multidrug-resistant Campylobacter jejuni (MDR C. jejuni), the leading cause of food-borne gastroenteritis worldwide, poses a significant threat to public health and food safety. The intestinal microbiota prevents MDR C. jejuni colonization, but the specific mechanisms remain poorly understood. In this study, we performed a multi-omics analysis of the gut microbiota in C57BL/6 mice, combined with in vitro experiments, to investigate the role of gut microbiota in C. jejuni colonization. Treatment with tylvalosin, a new macrolide, altered the gut microbiota composition, reducing Bifidobacterium longum communities and decreasing levels of short-chain fatty acids (acetic acid, propionic acid, n-butyric acid, i-butyric acid, and i-valeric acid). This disruption of intestinal homeostasis facilitated C. jejuni colonization. Through metagenomic sequencing, we identified and isolated Lactobacillus murinus (L. murinus) from the mice’s intestinal flora, which exhibited inhibitory activity against C. jejuni in vitro. Metabolomic analysis and in vitro validation further revealed the significance of L. murinus-derived metabolites. Our results indicate that L. murinus inhibits and kills C. jejuni in a co-culture system by secreting acids that synergistically induce apoptosis, leading to cell membrane disruption and the release of cellular contents.

耐多药空肠弯曲杆菌（MDR C. jejuni）是全球食源性胃肠炎的主要病因，对公共卫生和食品安全构成重大威胁。肠道菌群可阻止耐多药空肠梭菌定植，但具体机制尚不清楚。本研究通过对C57BL/6小鼠肠道菌群进行多组学分析，并结合体外实验，探讨肠道菌群在空肠梭菌定植中的作用。用一种新的大环内酯类药物tylvalosin治疗，改变了肠道菌群组成，减少了长双歧杆菌群落，降低了短链脂肪酸（乙酸、丙酸、正丁酸、i-丁酸和i-戊酸）的水平。这种肠道稳态的破坏促进了空肠梭菌的定植。通过元基因组测序，我们从小鼠肠道菌群中鉴定并分离出对空肠杆菌具有体外抑制活性的鼠乳杆菌（Lactobacillus murinus）。代谢组学分析和体外验证进一步揭示了鼠乳杆菌衍生代谢物的意义。我们的研究结果表明，在共培养系统中，L. murinus通过分泌酸抑制和杀死空肠梭菌，这些酸协同诱导细胞凋亡，导致细胞膜破坏和细胞内容物的释放。

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引用次数: 0

The microbial strategies for the management of chemical pesticides: A comprehensive review 化学农药管理中的微生物策略综述

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-11-23 DOI: 10.1016/j.crmicr.2025.100519

Ajay Kumar , Manoj Kumar Solanki , Manish Kumar , Amit Kaushik , Aditi Arya , Mahaswetta Saikia , Vivek Kumar Gaur , Rahul Prashad Singh , Sandeep Kumar Singh , Vipin Kumar Singh , Laurent Dufossé

Chemical pesticides considered as one of the emerging environmental contaminants that severally affect the human health and soil and water ecosystem. Despite their well-documented adverse effects on fruit quality, soil structure, the emergence of pesticide-resistant pests, and human well-being, chemical pesticides are still widely used for crop protection, particularly in developing countries. Although to manage the chemical pesticides, various traditional approaches have been employed, however the higher cost, and the generation of toxic residues have shifted research attention toward eco-friendly and sustainable bioremediation strategies. Microorganisms including the bacteria, fungi, and algae play a crucial role in pesticide degradation by transforming toxic compounds into less toxic forms. However, to optimize microbial bioremediation, a comprehensive understanding of microbial metabolism and physiology is essential. In this context, omics technologies such as genomics, metagenomics, transcriptomics, proteomics, and metabolomics, offer powerful tools for elucidating the molecular mechanisms involved in pesticide degradation. These approaches facilitate the identification of microorganism, key genes, enzymes, and metabolic pathways responsible for the breakdown of pesticide compounds and their by-products. Furthermore, advanced technology like the gene editing can enhance the efficacy of pesticides biodegradation by knocking out undesirable genes or introducing beneficial ones in the microorganisms. The Artificial intelligence also plays a significant role in analysing big data, understanding microbial communities’ structure, identifying nature of pesticides and selecting or predicting the microbial species with enhanced pesticides degrading efficacy.

化学农药被认为是影响人类健康和水土生态系统的新兴环境污染物之一。尽管化学农药对水果质量、土壤结构、抗农药害虫的出现和人类福祉有充分的不利影响，但化学农药仍被广泛用于作物保护，特别是在发展中国家。虽然化学农药的治理采用了多种传统方法，但由于成本较高，有毒残留物的产生，研究重点转向了生态友好和可持续的生物修复策略。包括细菌、真菌和藻类在内的微生物通过将有毒化合物转化为毒性较小的形式，在农药降解中起着至关重要的作用。然而，为了优化微生物生物修复，对微生物代谢和生理的全面了解是必不可少的。在此背景下，基因组学、宏基因组学、转录组学、蛋白质组学和代谢组学等组学技术为阐明农药降解的分子机制提供了有力的工具。这些方法有助于鉴定微生物、关键基因、酶和农药化合物及其副产物分解的代谢途径。此外，像基因编辑这样的先进技术可以通过敲除不需要的基因或在微生物中引入有益的基因来提高农药生物降解的功效。人工智能在分析大数据、了解微生物群落结构、识别农药性质、选择或预测具有增强农药降解效果的微生物种类等方面也发挥着重要作用。

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引用次数: 0

Characteristics and longitudinal stability of Gut Microbiota in healthy individuals across different age groups 不同年龄组健康个体肠道菌群的特征和纵向稳定性

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-11-20 DOI: 10.1016/j.crmicr.2025.100512

Biao Zou , Qian’er Huo , Xianfeng Zhou , Yongling Lv , Guolong Li , Guang Fu , Hexiao Shen , Sainan Shu

Fecal microbiota transplantation (FMT) efficacy relies on donor microbiome composition and temporal stability, yet the influence of donor age remains inadequately investigated. This longitudinal analysis addressed this gap by examining 81 healthy individuals (3–30 years), stratified into four age groups, who provided monthly fecal samples over 12 months (n = 972 samples). Gut microbiota composition (16S rDNA sequencing) and temporal stability were assessed using Bray–Curtis dissimilarity, intraclass correlation coefficient (ICC), and genus-level co-occurrence network analysis. Results demonstrated a strong age-dependency in microbiota stability. The teenage cohort (13–17 years) exhibited the highest stability, characterized by minimal fluctuations in α- and β-diversity and significantly stronger network centrality. Furthermore, specific genera, notably Faecalibacterium and Bifidobacterium, displayed exceptionally high ICC values (>0.90), identifying them as core taxa associated with temporal consistency. These findings underscore the critical role of donor age in microbial stability and highlight teenagers as possessing optimal microbiota characteristics for FMT. They strongly support the development of an ICC-based screening framework to enhance donor selection protocols.

粪便微生物群移植（FMT）的疗效取决于供体微生物群组成和时间稳定性，但供体年龄的影响仍未得到充分研究。这项纵向分析通过检查81名健康个体（3-30岁），将其分为四个年龄组，在12个月内每月提供粪便样本（n = 972个样本），解决了这一差距。采用bry - curtis不相似性、类内相关系数（ICC）和属级共发生网络分析评估肠道菌群组成（16S rDNA测序）和时间稳定性。结果表明，微生物群的稳定性具有很强的年龄依赖性。青少年群体（13-17岁）表现出最高的稳定性，α-和β-多样性波动最小，网络中心性显著增强。此外，特定属，特别是Faecalibacterium和Bifidobacterium，显示出异常高的ICC值（>0.90），这表明它们是与时间一致性相关的核心分类群。这些发现强调了供体年龄在微生物稳定性中的关键作用，并强调青少年具有FMT的最佳微生物群特征。他们强烈支持制定基于国际刑事法院的筛查框架，以加强供体选择方案。

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引用次数: 0

The role of opsonophagocytosis in killing of Klebsiella pneumoniae in human blood. 调理吞噬作用在人血肺炎克雷伯菌杀灭中的作用。

IF 5.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-07-24 eCollection Date: 2025-01-01 DOI: 10.1016/j.crmicr.2025.100449

Charlotte Mejlstrup Hymøller, Trine S Jensen, Pernille Vigsø Rasmussen, Ditte Bech, Gunna Christiansen, Svend Birkelund

Klebsiella pneumoniae is an opportunistic, gram-negative pathogen causing life-threatening sepsis in patients with co-morbidity. In contrast, in healthy persons, K. pneumoniae rarely causes sepsis. To elucidate how K. pneumoniae is eliminated from normal human blood, eleven K. pneumoniae sepsis isolates were analysed. Most of the isolates were serum-resistant. They solely activated the alternative pathway (AP), and only iC3b was present on their surface due to a rapid cleavage of C3b. Despite serum resistance, all isolates were killed in normal blood. To analyse the mechanism of uptake, two isolates (serum-resistant HA391 and partially resistant HA569) were transfected with a plasmid encoding red fluorescent protein, added to whole blood, analysed by flow cytometry and uptake in neutrophil granulocytes. HA391 was not phagocytosed in 50% heat-inactivated serum (HIHS), but in normal human serum (NHS), it was phagocytosed and subsequently killed. The iC3b deposited on the bacterial surface, colocalised with complement receptor 3 (CR3) and myeloperoxidase (MPO), confirming opsonophagocytosis. HA569 was rapidly phagocytosed by granulocytes in NHS but more slowly in HIHS. Thus, the complement system is essential for the elimination of serum-resistant K. pneumoniae isolates, as neutrophil granulocytes phagocytose HA391 through opsonophagocytosis, while HA569 is also phagocytosed independently of complement. AP lacks specific pattern recognition; however, it plays an essential role in the elimination of serum-resistant K. pneumoniae, as AP is activated by these bacteria, which, nonetheless, escape complement lysis by cleaving C3b to iC3b. Hereby, the bacteria are susceptible to opsonophagocytosis, an ancient function of AP that is crucial for eliminating bacteria.

肺炎克雷伯菌是一种机会性的革兰氏阴性病原体，可在合并发病的患者中引起危及生命的败血症。相反，在健康人中，肺炎克雷伯菌很少引起败血症。为了阐明肺炎克雷伯菌是如何从正常人类血液中消除的，对11株肺炎克雷伯菌败血症进行了分析。大多数分离株具有血清耐药。它们单独激活了替代途径（AP），并且由于C3b的快速裂解，只有iC3b存在于它们的表面。尽管血清耐药，但所有分离株在正常血液中均死亡。为了分析摄取机制，用编码红色荧光蛋白的质粒转染2个分离株（血清耐药HA391和部分耐药HA569），加入全血，流式细胞术和中性粒细胞摄取分析。HA391在50%热灭活血清（HIHS）中不被吞噬，但在正常人血清（NHS）中被吞噬并随后被杀死。iC3b沉积在细菌表面，与补体受体3 （CR3）和髓过氧化物酶（MPO）共定位，证实了opsonophagocytosis。在NHS中，HA569被粒细胞迅速吞噬，而在HIHS中则较慢。因此，补体系统对于消除血清耐药肺炎克雷伯菌分离株至关重要，因为中性粒细胞通过调性吞噬作用吞噬HA391，而HA569也独立于补体被吞噬。AP缺乏特定的模式识别；然而，它在消除血清耐药肺炎克雷伯菌中起着至关重要的作用，因为AP被这些细菌激活，尽管如此，这些细菌通过将C3b切割成iC3b来逃避补体裂解。因此，细菌易受调理吞噬作用的影响，这是AP的一种古老功能，对消灭细菌至关重要。

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引用次数: 0

Process optimization and evaluation of quality properties of natto with co-culture of Bacillus subtilis natto and Limosilactobacillus fermentum 纳豆枯草芽孢杆菌与发酵乳酸杆菌共培养工艺优化及品质评价

IF 4.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-01-01 DOI: 10.1016/j.crmicr.2025.100347

Yi-Ni Ma , Xun Xu , Lai-Feng Chen , Jin-Ping Zhou , Zhen-Hui Cao , Qiu-Ye Lin

The present study aimed to optimize the processing technology of natto fermented with Bacillus subtilis natto and Limosilactobacillus fermentum 2–2 and its effect on quality characteristics as well as volatile compounds. The results of single-factor tests and response surface methodology (RSM) showed that the optimal fermentation conditions of natto were L. fermentum inoculation amount of 0.3 %, fermentation temperature at 39 °C, fermentation time of 48 h, and after-ripening time of 24 h. Compared with natto control with B. subtilis natto only, natto co-cultured with B. subtilis natto and L. fermentum 2–2 showed higher scavenging ability of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and greater nattokinase activity. Volatomics analysis revealed that 71 differential volatile compounds were identified with 23 up-regulated and 48 down-regulated. Especially, co-fermentation of B. subtilis natto and L. fermentum 2–2 increased generation of alcohols, ketones and esters while reduced pyrazines formation. The above results indicate that co-culture of B. subtilis natto and L. fermentum can enhance the antioxidant and nattokinase activity and modify the volatile profile in natto and have the potential for application as the mixed starter in natto production.

以纳豆枯草芽孢杆菌和发酵芽孢杆菌2-2为原料，优化纳豆的发酵工艺及其对纳豆品质和挥发性成分的影响。单因素试验和响应面法（RSM）结果表明，纳豆的最佳发酵条件为发酵乳杆菌接种量为0.3%，发酵温度为39℃，发酵时间为48 h，后熟时间为24 h。与枯草芽孢杆菌纳豆和发酵乳杆菌2- 2共培养的纳豆对1,1-二苯基-2-苦酰肼（DPPH）和2,2′-氮基-双（3-乙基苯并噻唑啉-6-磺酸）（ABTS）具有较强的清除能力和纳豆激酶活性。挥发原子学分析表明，共鉴定出71种差异挥发性化合物，其中23种上调，48种下调。特别是，枯草芽孢杆菌纳豆和发酵乳杆菌2-2的共发酵增加了醇、酮和酯的生成，减少了吡嗪的生成。综上所述，纳豆中枯草芽孢杆菌与发酵乳杆菌共培养可提高纳豆的抗氧化活性和纳豆激酶活性，改变纳豆的挥发谱，具有作为纳豆生产混合发酵剂的应用潜力。

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引用次数: 0

First whole genome report of Mangrovibacter phragmitis PSU-3885–11 isolated from a patient in Thailand 从泰国患者中分离出的芦苇红树杆菌PSU-3885-11首次全基因组报道

IF 4.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-01-01 DOI: 10.1016/j.crmicr.2025.100350

Nattarika Chaichana , Thunchanok Yaikhan , Mingkwan Yingkajorn , Nonthawat Thepsimanon , Sirikan Suwannasin , Kamonnut Singkhamanan , Sarunyou Chusri , Rattanaruji Pomwised , Monwadee Wonglapsuwan , Komwit Surachat

Mangrovibacter phragmitis is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of M. phragmitis strain PSU-3885–11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the Enterobacter cloacae complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as M. phragmitis. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885–11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including ompA, hcp/tssD, and rpoS, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of M. phragmitis PSU-3885–11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.

芦苇红树杆菌是一种革兰氏阴性细菌，通常存在于植物根部，在红树林生态系统等营养贫乏的环境中支持固氮。虽然主要在环境生态位中发现，但在泰国，从一名29岁脊柱结核女性患者的痰中分离出了一种罕见的phagmitis菌株PSU-3885-11。该分离物最初被MALDI-TOF错误地鉴定为阴沟肠杆菌复合体（ECC）的一部分。然而，WGS随后证实了它的正确身份，即羊膜分枝杆菌。基因组包含4651个编码序列，以及72个tRNA基因和1个tmRNA。此外，比较基因组分析显示，PSU-3885-11基因组中有99.32%的平均核苷酸同源性（ANI）与phragmitis MP23相似，并且在PSU-3885-11基因组中发现了多个抗生素耐药基因（ARGs）和移动遗传元件（MGEs），这可能是其能够在包括人类宿主在内的多种环境中生存的原因之一。PSU-3885-11对氨苄西林和头孢噻肟等β -内酰胺类抗生素有耐药性，同时对其他多种抗生素保持敏感。关键毒力基因包括ompA、hcp/tssD和rpoS，这些基因可能在其作为机会致病菌在人类宿主中持续存在中发挥作用。核糖体合成和翻译后修饰肽（RiPPs）和细菌素的存在表明，该菌株的抗菌特性可能在环境和临床环境中提供竞争优势。因此，本研究为phragmitis PSU-3885-11的基因组特征、抗生素耐药性和潜在致病性提供了有价值的见解。研究结果还强调了持续监测和基因组分析环境细菌的重要性，这些细菌可能作为人类感染的机会致病菌出现。

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引用次数: 0

Towards a comprehensive view of wetland benthic communities 迈向湿地底栖生物群落的综合视野

IF 4.8 Q1 MICROBIOLOGY

Current Research in Microbial Sciences

Pub Date : 2025-01-01 DOI: 10.1016/j.crmicr.2025.100391

Clélia Duran , Christine Dupuy , Hélène Agogué , Robert Duran , Cristiana Cravo-Laureau

Benthic prokaryotic communities, utmost important for wetlands and marine environments functioning, are influenced by physical-chemical parameters and interactions with other communities, especially micro-eukaryotes and meiofauna. Thus, a holistic view of the benthic community is necessary to fully understand their organization and functioning. This study assesses the implementation of a comprehensive view, using mock communities and environmental samples. A DNA extraction strategy combining two procedures is proposed: one to obtain DNA from micro-organisms, using 0.25 g of sediment, and the other from meiofauna, using 0.25 g of sieving refluxes from 5 g of sediment. Three conditions were considered to create mock communities: (i) varying eukaryotes’ abundance, (ii) adding meiofauna from salted or freshwater wetlands, and (iii) including or not a sediment matrix. Most organisms composing the mock communities were detected, except a filamentous cyanobacteria. All mock communities showed similar composition indicating that sediment did not affect the DNA extraction. This result also demonstrated that sieving, necessary to enrich meiofauna from sediment, does not significantly affect any of the communities. For the environmental samples investigated, most of the taxa usually described in the literature were retrieved in the salted, brackish and freshwater marshes sediment. The proposed approach was successful in analysing organisms from the three domains of life in a unique environmental sample, providing a holistic view of the benthic community. Furthermore, the significant differences observed between samples from the three different marshes, indicated that our approach can be used for conducting successful ecological studies, especially useful for understanding benthic communities’ interactions.

底栖原核生物群落对湿地和海洋环境的功能至关重要，它们受到物理化学参数和与其他群落，特别是微真核生物和小动物的相互作用的影响。因此，全面了解底栖生物群落是充分了解其组织和功能的必要条件。本研究使用模拟社区和环境样本，评估了综合观点的实施情况。提出了一种结合两种程序的DNA提取策略：一种是从微生物中提取DNA，使用0.25 g沉积物；另一种是从小型动物中提取DNA，使用0.25 g从5 g沉积物中筛选回流液。模拟群落的创建考虑了三种条件：(i)真核生物的丰度不同，（ii）添加来自咸水或淡水湿地的小型动物，（iii）包括或不包括沉积物基质。除了丝状蓝藻外，大多数组成模拟群落的生物都被检测到。所有模拟群落的组成相似，表明沉积物不影响DNA的提取。这一结果还表明，筛分对任何群落都没有显著影响，筛分是丰富沉积物中微量动物群所必需的。对于所调查的环境样本，文献中通常描述的分类群大多来自咸水、半咸水和淡水沼泽沉积物。提出的方法成功地分析了独特环境样本中三个生命领域的生物，提供了底栖生物群落的整体视图。此外，从三个不同的沼泽中观察到的样本之间的显著差异表明，我们的方法可以用于成功的生态学研究，特别是对了解底栖生物群落的相互作用有用。

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引用次数: 0