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Molecular characterization, carbohydrate metabolism and tolerance to abiotic stress of Eremothecium coryli endophytic isolates from fruits of Momordica indica. 从 Momordica indica 果实中分离出的 Eremothecium coryli 内生菌的分子特征、碳水化合物代谢和对非生物胁迫的耐受性。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1007/s12223-024-01211-x
Jefferson Brendon Almeida Dos Reis, Mayara Oliveira Sousa Rodrigues, Leila Lourenço Furtado, Clemildo de Sousa Queiroz Júnior, Helson Mario Martins do Vale

Yeasts are unicellular fungi that occur in a wide range of ecological niches, where they perform numerous functions. Furthermore, these microorganisms are used in industrial processes, food production, and bioremediation. Understanding the physiological and adaptive characteristics of yeasts is of great importance from ecological, biotechnological, and industrial perspectives. In this context, we evaluated the abilities to assimilate and ferment different carbon sources, to produce extracellular hydrolytic enzymes, and to tolerate salt stress, heavy metal stress, and UV-C radiation of two isolates of Eremothecium coryli, isolated from Momordica indica fruits. The two isolates were molecularly identified based on sequencing of the 18S-ITS1-5.8S-ITS2 region. Our isolates were able to assimilate nine carbon sources (dextrose, galactose, mannose, cellobiose, lactose, maltose, sucrose, melezitose, and pectin) and ferment three (glucose, maltose, and sucrose). The highest values of cellular dry weight were observed in the sugars maltose, sucrose, and melezitose. We observed the presence of hyphae and pseudohyphae in all assimilated carbon sources. The two isolates were also capable of producing amylase, catalase, pectinase, and proteases, with the highest values of enzymatic activity found in amylase. Furthermore, the two isolates were able to grow in media supplemented with copper, iron, manganese, nickel, and zinc and to tolerate saline stress in media supplemented with 5% NaCl. However, we observed a decrease in CFU at higher concentrations of these metals and NaCl. We also observed morphological changes in the presence of metals, which include changes in cell shape and cellular dimorphisms. The isolates were sensitive to UV-C radiation in the shortest exposure time (1 min). Our findings reinforce the importance of endophytic yeasts for biotechnological and industrial applications and also help to understand how these microorganisms respond to environmental variations caused by human activities.

酵母菌是一种单细胞真菌,广泛存在于各种生态位中,具有多种功能。此外,这些微生物还被用于工业加工、食品生产和生物修复。从生态学、生物技术和工业的角度来看,了解酵母菌的生理和适应特性非常重要。在此背景下,我们评估了从 Momordica indica 果实中分离出的两个 Eremothecium coryli 分离物吸收和发酵不同碳源、产生胞外水解酶以及耐受盐胁迫、重金属胁迫和紫外线辐射的能力。根据 18S-ITS1-5.8S-ITS2 区域的测序,对这两个分离株进行了分子鉴定。我们的分离物能够同化九种碳源(葡萄糖、半乳糖、甘露糖、纤维生物糖、乳糖、麦芽糖、蔗糖、麦芽糖和果胶)并发酵三种碳源(葡萄糖、麦芽糖和蔗糖)。麦芽糖、蔗糖和麦芽糖的细胞干重值最高。我们在所有同化碳源中都观察到菌丝和假菌丝的存在。这两种分离物还能产生淀粉酶、过氧化氢酶、果胶酶和蛋白酶,其中淀粉酶的酶活性最高。此外,这两种分离物还能在添加了铜、铁、锰、镍和锌的培养基中生长,并能在添加了 5%氯化钠的培养基中耐受盐胁迫。不过,我们观察到,在这些金属和氯化钠浓度较高时,CFU 会下降。我们还观察到金属存在时的形态变化,包括细胞形状和细胞二形性的变化。在最短的暴露时间(1 分钟)内,分离物对紫外线辐射很敏感。我们的研究结果加强了内生酵母菌在生物技术和工业应用中的重要性,也有助于了解这些微生物如何应对人类活动造成的环境变化。
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引用次数: 0
Prevalence and virulence profiles of ESBL-producing Escherichia coli in urinary and blood infections in South Korea. 韩国泌尿系统和血液感染中产ESBL大肠埃希菌的流行率和毒力特征。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-22 DOI: 10.1007/s12223-024-01205-9
Jong-Hun Ha, Jeong-Ih Shin, Kyu-Min Kim, Jeong-Gyu Choi, Minh Phuong Trinh, Won Jun Anh, Kyung-Min Kang, Hyung-Lyun Kang, Jung-Hyun Byun, Wongwarut Boonyanugomol, Kee Woong Kwon, Myung Hwan Jung, Seung Chul Baik, Woo-Kon Lee, Min-Kyoung Shin

Escherichia coli is a significant pathogen in extraintestinal infections, and ESBL-producing E. coli poses a major clinical challenge due to its antibiotic resistance. This study comprehensively analyzed E. coli isolates from urine and blood samples of patients with urinary tract and bloodstream infections at three major tertiary hospitals in South Korea. The goal was to provide insights into the distribution, antibiotic resistance, and virulence factors of these strains. Our analysis identified CTX-M and TEM as the dominant ESBL types, found in 71.7% and 61.7% of isolates, respectively, with 46.7% showing co-occurrence. Multilocus sequence typing (MLST) revealed the predominance of high-risk clones such as ST131, ST69, ST73, and ST95, with rare sequence types like ST410 and ST405 also identified. The high prevalence of virulence factors, including iutA (80.8%) and kpsMII (74.2%), further highlights the complexity of these strains. In addition, 38.3% of clinical isolates contained a combination of siderophore, adhesin, protectin, and toxin-related genes. There was no significant difference between urinary tract and bloodstream infections or regional differentiation in Korea. This study highlights the importance of controlling ESBL-producing E. coli infections, especially given the increasing incidence among patients with underlying medical conditions and older adults who are more susceptible to urinary tract infections. These findings serve as valuable indicators for pathogen analysis, especially those harboring antibiotic resistance and toxin genes. The insights gained are expected to contribute significantly to the development of infectious disease prevention and control strategies.

大肠埃希菌是肠道外感染的重要病原体,而产ESBL的大肠埃希菌因其抗生素耐药性而成为临床上的一大挑战。本研究全面分析了韩国三家大型三甲医院尿道和血液感染患者尿液和血液样本中分离出的大肠杆菌。目的是深入了解这些菌株的分布、抗生素耐药性和毒力因素。我们的分析结果表明,CTX-M 和 TEM 是主要的 ESBL 类型,分别在 71.7% 和 61.7% 的分离株中发现,其中 46.7% 的分离株出现了共存现象。多焦点序列分型(MLST)显示,ST131、ST69、ST73 和 ST95 等高风险克隆占主导地位,同时还发现了 ST410 和 ST405 等罕见序列类型。包括 iutA(80.8%)和 kpsMII(74.2%)在内的毒力因子的高流行率进一步凸显了这些菌株的复杂性。此外,38.3%的临床分离株含有嗜肽酶、粘附素、保护素和毒素相关基因的组合。在韩国,尿路感染和血液感染之间没有明显差异,也没有地区差异。这项研究强调了控制产ESBL大肠杆菌感染的重要性,尤其是考虑到有基础疾病的患者和老年人的发病率越来越高,他们更容易发生尿路感染。这些发现是病原体分析的重要指标,尤其是那些携带抗生素耐药性和毒素基因的病原体。这些发现有望为制定传染病预防和控制策略做出重要贡献。
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引用次数: 0
Atrazine dependence in cultivated fungal communities. 栽培真菌群落对阿特拉津的依赖性。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-16 DOI: 10.1007/s12223-024-01204-w
Gessyca Fernanda da Silva, Jose Alejandro Morales Gomez, João Victor Fonseca Moreira, Giulio Mendes Braatz, Rafaella Costa Bonugli-Santos

The isolation and study of fungi within specific contexts yield valuable insights into the intricate relationships between fungi and ecosystems. Unlike culture-independent approaches, cultivation methods are advantageous in this context because they provide standardized replicates, specific species isolation, and easy sampling. This study aimed to understand the ecological process using a microcosm system with pesticide concentrations similar to those found in the soil, in contrast to high doses, from the isolation of the enriched community. The atrazine concentrations used were 0.02 mg/kg (control treatment), 300 ng/kg (treatment 1), and 3000 ng/kg (treatment 2), using a 28-day microcosm system. Ultimately, the isolation resulted in 561 fungi classified into 76 morphospecies. The Ascomycota phylum was prevalent, with Purpureocillium, Aspergillus, and Trichoderma being consistently isolated, denoting robust and persistent genera. Diversity analyses showed that the control microcosms displayed more distinct fungal morphospecies, suggesting the influence of atrazine on fungal communities. Treatment 2 (higher atrazine concentration) showed a structure comparable to that of the control, whereas treatment 1 (lower atrazine concentration) differed significantly, indicating that atrazine concentration impacted community variance. Higher atrazine addition subtly altered ligninolytic fungal community dynamics, implying its potential for pesticide degradation. Finally, variations in atrazine concentrations triggered diverse community responses over time, shedding light on fungal resilience and adaptive strategies against pesticides.

在特定环境中分离真菌并对其进行研究,可为了解真菌与生态系统之间错综复杂的关系提供宝贵的信息。与不依赖培养的方法不同,培养方法在这方面具有优势,因为它们提供了标准化的重复、特定物种的分离和简便的取样。本研究旨在利用微宇宙系统了解生态过程,该系统中的农药浓度与土壤中的浓度相似,而不是高剂量,从富集群落中分离出来。使用的阿特拉津浓度分别为 0.02 毫克/千克(对照处理)、300 纳克/千克(处理 1)和 3000 纳克/千克(处理 2),微生态系统使用期为 28 天。最终分离出 561 种真菌,分为 76 个形态种。子囊菌门是主要菌门,其中紫云英属、曲霉属和毛霉属一直被分离出来,表明这些菌属很强健且具有持久性。多样性分析表明,对照微生态系统显示出更多不同的真菌形态物种,这表明阿特拉津对真菌群落有影响。处理 2(阿特拉津浓度较高)显示出与对照组相当的结构,而处理 1(阿特拉津浓度较低)则差异显著,表明阿特拉津浓度对群落差异有影响。较高的阿特拉津添加量微妙地改变了木质素分解真菌群落的动态,这意味着阿特拉津具有降解农药的潜力。最后,随着时间的推移,阿特拉津浓度的变化引发了不同的群落反应,揭示了真菌的恢复能力和对农药的适应策略。
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引用次数: 0
Bio sulfur granules developed with Methylobacterium thiocyanatum promoted black gram growth and yield in sulfur-deficient calcareous vertisol. 利用硫氰酸甲基杆菌开发的生物硫颗粒促进了缺硫钙质蛭石中黑禾的生长和产量。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-05 DOI: 10.1007/s12223-024-01199-4
G Akila, S Thiyageshwari, R Krishnamoorthy, D Selvi, A Manikandan, R Anandham, M Djanaguirman

High soil pH and excess CaCO3 are major contributors to calcareous soil limitations on crops' access to essential nutrients, especially phosphorus (P) and micronutrients, which in turn impact pulses yields and growth. The purpose of this study was to determine the effect of bio sulfur granules (BSG) on the growth of black gram and the availability of nutrients in calcareous vertisols deficient in sulfur. BSG was developed by using sulfur-oxidizing bacteria (SOB) and elemental sulfur (ES) through an incubation study. Developed BSG was tested in a pot and field conditions to evaluate their effectiveness on black gram growth and yield. In the incubation study, soil treated with Methylobacterium thiocyanatum VRI7-A4 and ES (40 kg S/ha) significantly decreased pH and increased available S (SO42-) in calcareous soils. After 40 days of incubation, the solubility of P, Fe, and Zn was greatly increased by the addition of ES @ 40 kg S/ ha in combination with M. thiocyanatum VRI7-A4 or Pandoraea thiooxydans ATSB16. Black gram in S-deficient calcareous soil was improved by the application of BSG (ES @ 40 kg S/ ha with M. thiocyanatum VRI7-A7) in terms of root and shoot lengths, nodule number, plant biomass, pod yield, and biological yield as compared to control. The same treatment greatly increased plant nutrient intake as well as the concentrations of P, Fe, and Zn in the soil. The results showed that the addition of BSG granules (ES @ 40 kg S/ha + M. thiocyanatum VRI7-A4) to calcareous vertisol deficient in S enhanced the nutrient solubility through S oxidation. The developed bio sulfur granules may be added to the fertilizer schedule of the pulses growers to get improved crop growth and yield of black gram in calcareous soil.

土壤 pH 值过高和 CaCO3 过多是造成石灰性土壤限制作物获得必需养分(尤其是磷(P)和微量营养元素)的主要原因,进而影响豆类的产量和生长。本研究的目的是确定生物硫颗粒(BSG)对黑穗禾的生长和缺硫钙质蛭石土壤中养分供应的影响。通过培养研究,利用硫氧化细菌(SOB)和元素硫(ES)开发了生物硫颗粒。开发的 BSG 在盆栽和田间条件下进行了测试,以评估其对黑禾苗生长和产量的影响。在培养研究中,用硫氰酸甲基杆菌 VRI7-A4 和 ES(40 千克 S/公顷)处理过的土壤显著降低了石灰性土壤的 pH 值,增加了可用硫(SO42-)。培养 40 天后,在硫氰化杆菌 VRI7-A4 或硫氧水蚤 Pandoraea ATSB16 的作用下,添加每公顷 40 千克 S 的 ES 可大大提高磷、铁和锌的溶解度。与对照相比,在缺 S 的石灰性土壤中施用 BSG(ES @ 40 kg S/ ha 与硫氰菌 VRI7-A7)后,黑糯米的根长和芽长、结节数、植株生物量、豆荚产量和生物产量均有所提高。同样的处理大大增加了植物的养分摄入量以及土壤中磷、铁和锌的浓度。结果表明,在缺S的钙质vertisol土壤中添加生物硫颗粒(ES @ 40 kg S/ha + M. thiocyanatum VRI7-A4)可通过S氧化作用提高养分溶解度。开发的生物硫颗粒可添加到豆类种植者的施肥计划中,以改善石灰性土壤中黑禾的作物生长和产量。
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引用次数: 0
Enhancement of carotenogenesis by Blakeslea trispora in a mixed culture with bacteria. 在与细菌混合培养的过程中,三孢叶枯藻可增强胡萝卜素的生成。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-03 DOI: 10.1007/s12223-024-01202-y
Maryam Azizi, Davood Zare, Abbas Akhavan Sepahi, Mehrdad Azin

Among carotenoids, ꞵ-carotene has the highest biological activity and is found as an all-trans isomer in many biological systems. Blakeslea trispora is a microorganism that is of interest to industries for the commercial production of ꞵ-carotene. This study investigated the effect of different bacteria on carotenogenesis in B. trispora. The B. trispora bisexual mold was cultured in a production medium, and different bacterial cells were added to it after 24 h. Then, the culture conditions and the culture medium were optimized in the presence of the selected bacteria using the experimental design. The percentage of carotenoids obtained from the mixed culture was determined using high-performance liquid chromatography (HPLC). Results showed that Kocuria rhizophila had the greatest effect on increasing the production of carotenoids in B. trispora. The highest content of carotenoids obtained during optimization was 770 ± 7.5 mg/L, a 6.8-fold increase compared to the control. HPLC analysis of carotenoids indicated the presence of two main peaks, ꞵ-carotene and γ-carotene, in which the primary carotenoid was ꞵ-carotene followed by γ-carotene with a lower content. Therefore, due to the importance of ꞵ-carotene in industry, the use of biostimulants is one of the appropriate strategies to increase the production of this pigment in industry.

在类胡萝卜素中,ꞵ-胡萝卜素具有最高的生物活性,在许多生物系统中都能发现其全反式异构体。Blakeslea trispora 是一种微生物,工业界对其商业化生产ꞵ-胡萝卜素很感兴趣。本研究调查了不同细菌对三孢蝙蝠蛾胡萝卜素生成的影响。在生产培养基中培养 B. trispora 双性霉,24 小时后加入不同的细菌细胞。使用高效液相色谱法(HPLC)测定了混合培养物中类胡萝卜素的百分比。结果表明,Kocuria rhizophila 对提高三孢蝙蝠藻类胡萝卜素产量的作用最大。在优化过程中,类胡萝卜素的最高含量为 770 ± 7.5 mg/L,比对照组增加了 6.8 倍。类胡萝卜素的 HPLC 分析表明存在两个主峰:ꞵ-胡萝卜素和 γ-胡萝卜素,其中主要的类胡萝卜素是ꞵ-胡萝卜素,其次是含量较低的γ-胡萝卜素。因此,鉴于ꞵ-胡萝卜素在工业中的重要性,使用生物刺激剂是提高工业中该色素产量的适当策略之一。
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引用次数: 0
Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis. 利用脓液元基因组新一代测序技术有效识别败血症患者体内的病原体。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-01 Epub Date: 2024-02-11 DOI: 10.1007/s12223-024-01134-7
Zhendong Chen, Tingting Ye, Yuxi He, Aijun Pan, Qing Mei

The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information.

血液元基因组新一代测序(mNGS)的阳性检出率仍然太低,无法满足临床需要,而来自原发感染部位的脓液可能有利于病原体的鉴定。为了评估使用败血症患者脓液进行 mNGS 的价值,研究人员收集了 35 份样本。比较了使用 mNGS 或培养方法获得的病原体鉴定和混合感染诊断结果。mNGS 将需氧或兼性厌氧菌感染诊断的准确率从 44.4% 提高到 94.4%;mNGS 还将兼性厌氧菌感染诊断的灵敏度从 52.9% 提高到 100.0%;但 mNGS 在真菌感染方面没有显示出任何优势。培养和 mNGS 分别发现了 1 名和 24 名混合感染患者。对于强制性厌氧菌,分析了微生物的来源。牙源性细菌均引起了肺水肿(7 例)或皮肤和软组织感染(5 例),而肠道源微生物均引起了腹腔内感染(7 例)。我们还比较了非厌氧菌感染组和必须厌氧菌感染组的临床特征。SOFA评分[9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005]、降钙素原值[4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035]、脓毒性休克比例(66.7% vs. 35.3%,P = 0.044)和急性肝损伤(66.7% vs. 23.5%,P = 0.018)的比例明显高于非厌氧菌感染组。对于化脓性感染引起的败血症患者,使用原发病灶的脓液进行 mNGS 可能会获得更有价值的微生物信息。
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引用次数: 0
Efficacy of outer membrane permeabilization in promoting aromatic isothiocyanates-mediated eradication of multidrug resistant Gram-negative bacteria and bacterial persisters. 外膜渗透在促进芳香族异硫氰酸盐介导的多药耐药性革兰氏阴性菌和细菌宿主根除方面的功效。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-01 Epub Date: 2024-02-06 DOI: 10.1007/s12223-024-01143-6
Chung-Cheng Lo, Tzu-Hui Yeh, Ya-Hsuan Jao, Tzu-Hui Wang, Horng-Ren Lo

Multidrug resistant (MDR) bacteria are recognized to be one of the most important problems in public health. The outer membrane permeability is a critical intrinsic mechanism of bacterial resistance. In addition, bacteria produce a small number of dormant persister cells causing multidrug tolerance that reduces antimicrobial efficacy. This study aimed to evaluate the inhibitory effects of the combination of aromatic isothiocyanates (ITCs) with membrane-active agents on bacterial persisters and MDR Gram-negative bacteria. Our study demonstrated that membrane-active agents, particularly ethylenediaminetetraacetic acid (EDTA) synergistically enhanced the inhibitory activity of aromatic benzyl ITC and phenethyl ITC against most Gram-negative bacteria strains with fractional inhibitory concentration index values ranging from 0.18 to 0.5 and 0.16 to 0.5, respectively, and contributed to an 8- to 64-fold minimal inhibitory concentration reduction compared with those of aromatic ITCs alone. The EDTA-aromatic ITCs combination effectively reduced the survival rates of tested bacteria and significantly eradicated bacterial persisters (p = 0.033 and 0.037, respectively). The growth kinetics analysis also supported the enhanced inhibitory effect of EDTA-aromatic ITCs combination against tested bacteria. Our results suggested an alternate treatment strategy against Gram-negative bacteria, promoting the entry of aromatic ITCs into bacterial cytoplasm to facilitate bacterial clearance and thus preventing the development of bacterial resistance.

耐多药(MDR)细菌被认为是公共卫生领域最重要的问题之一。外膜渗透性是细菌产生耐药性的一个重要内在机制。此外,细菌会产生少量休眠持久细胞,导致耐多药,从而降低抗菌效果。本研究旨在评估芳香族异硫氰酸酯(ITCs)与膜活性剂联合使用对细菌宿主和多重耐药革兰氏阴性菌的抑制作用。我们的研究表明,膜活性剂,尤其是乙二胺四乙酸(EDTA)可协同增强芳香族异硫氰酸苄酯和苯乙基异硫氰酸苄酯对大多数革兰氏阴性菌株的抑制活性,其抑制浓度指数值分别为 0.18 至 0.5 和 0.16 至 0.5,与单独使用芳香族异硫氰酸苄酯相比,其最小抑制浓度降低了 8 至 64 倍。乙二胺四乙酸-芳香族 ITCs 组合能有效降低受试细菌的存活率,并显著根除细菌宿主(p = 0.033 和 0.037)。生长动力学分析也证实了乙二胺四乙酸-芳香族 ITCs 组合物对受测细菌的抑制作用。我们的研究结果为革兰氏阴性细菌提供了另一种治疗策略,即促进芳香族 ITC 进入细菌细胞质,促进细菌清除,从而防止细菌产生耐药性。
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引用次数: 0
Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8. 抗金属环境分离物铜绿假单胞菌 S-8 分泌组的蛋白质谱分析和免疫形式分析。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-01 Epub Date: 2024-03-08 DOI: 10.1007/s12223-024-01152-5
Kiran Kumari, Jyotirmayee Dey, Soumya Ranjan Mahapatra, Ying Ma, Parva Kumar Sharma, Namrata Misra, Rajnish Prakash Singh

The bacterial secretome represents a comprehensive catalog of proteins released extracellularly that have multiple important roles in virulence and intercellular communication. This study aimed to characterize the secretome of an environmental isolate Pseudomonas aeruginosa S-8 by analyzing trypsin-digested culture supernatant proteins using nano-LC-MS/MS tool. Using a combined approach of bioinformatics and mass spectrometry, 1088 proteins in the secretome were analyzed by PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb tool for their subcellular localization and further categorization of secretome proteins according to signal peptides. Using the gene ontology tool, secretome proteins were categorized into different functional categories. KEGG pathway analysis identified the secreted proteins into different metabolic functional pathways. Moreover, our LC-MS/MS data revealed the secretion of various CAZymes into the extracellular milieu, which suggests its strong biotechnological applications to breakdown complex carbohydrate polymers. The identified immunodominant epitopes from the secretome of P. aeruginosa showed the characteristic of being non-allergenic, highly antigenic, nontoxic, and having a low risk of triggering autoimmune responses, which highlights their potential as successful vaccine targets. Overall, the identification of secreted proteins of P. aeruginosa could be important for both diagnostic purposes and the development of an effective candidate vaccine.

细菌分泌组代表了细胞外释放的蛋白质的综合目录,这些蛋白质在毒力和细胞间通讯中具有多种重要作用。本研究旨在利用纳米液相色谱-质谱/质谱工具分析胰蛋白酶消化的培养上清蛋白,从而描述环境分离物铜绿假单胞菌 S-8 的分泌组特征。采用生物信息学和质谱分析相结合的方法,利用 PREDLIPO、SecretomeP 2.0、SignalP 4.1 和 PSORTb 工具对分泌组中的 1088 个蛋白质进行了亚细胞定位分析,并根据信号肽对分泌组蛋白质进行了进一步分类。利用基因本体工具,分泌组蛋白被分为不同的功能类别。KEGG 通路分析将分泌蛋白确定为不同的代谢功能通路。此外,我们的LC-MS/MS数据揭示了多种CAZymes分泌到细胞外环境中,这表明其在分解复杂碳水化合物聚合物方面具有很强的生物技术应用价值。从铜绿假单胞菌分泌物组中鉴定出的免疫显性表位具有非过敏性、高抗原性、无毒性和引发自身免疫反应风险低的特点,这突显了它们作为成功疫苗靶点的潜力。总之,鉴定铜绿假单胞菌的分泌蛋白对于诊断和开发有效的候选疫苗都非常重要。
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引用次数: 0
Screening and identification of Paenibacillus polymyxa GRY-11 and its biological control potential against apple replant disease. 多粘毛芽孢杆菌 GRY-11 的筛选和鉴定及其对苹果再植病害的生物防治潜力。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-01 DOI: 10.1007/s12223-024-01196-7
Xiaoxuan Li, Jian Wang, Yi Lv, Lei Zhao, Weitao Jiang, Jinhui Lv, Xin Xu, Yajing Yu, Yusong Liu, Xuesen Chen, Chengmiao Yin, Zhiquan Mao

Apple replant disease (ARD) is a significant factor restricting the healthy development of the apple industry. Biological control is an important and sustainable method for mitigating ARD. In this study, a strain of Paenibacillus polymyxa GRY-11 was isolated and screened from the rhizosphere soil of healthy apple trees in old apple orchards in Shandong Province, China, and the effects of strain GRY-11 on soil microbial community and ARD were studied. The result showed that P. polymyxa GRY-11 could effectively inhibit the growth of the main pathogenic fungi that caused ARD, and the inhibition rates of the strain against Fusarium moniliforme, Fusarium proliferatum, Fusarium solani, and Fusarium oxysporum were 80.00%, 71.60%, 75.00%, and 70.00%, respectively. In addition, the fermentation supernatant played an active role in suppressing the growth of pathogenic fungi. The results of the pot experiment showed that the bacterial fertilizer of the GRY-11 promoted the growth of Malus hupehensis seedlings, improved the activity of protective enzymes in plant roots, enhanced the soil enzyme content, and optimized the soil microbial environment. In general, the GRY-11 can be used as an effective microbial preparation to alleviate ARD. Our study offers novel perspectives for the prevention of ARD.

苹果移栽病(ARD)是制约苹果产业健康发展的一个重要因素。生物防治是减轻 ARD 的一种重要且可持续的方法。本研究从山东省老苹果园健康苹果树根瘤土壤中分离筛选出一株多粘毛芽孢杆菌(Paenibacillus polymyxa GRY-11),研究了该菌株对土壤微生物群落和ARD的影响。结果表明,P. polymyxa GRY-11能有效抑制引起ARD的主要病原真菌的生长,其对单孢镰刀菌(Fusarium moniliforme)、增殖镰刀菌(Fusarium proliferatum)、茄镰刀菌(Fusarium solani)和氧孢镰刀菌(Fusarium oxysporum)的抑制率分别为80.00%、71.60%、75.00%和70.00%。此外,发酵上清液在抑制病原真菌生长方面也发挥了积极作用。盆栽实验结果表明,GRY-11 菌肥促进了红豆杉幼苗的生长,提高了植物根系保护酶的活性,提高了土壤酶含量,优化了土壤微生物环境。总的来说,GRY-11 可以作为一种有效的微生物制剂来缓解 ARD。我们的研究为预防 ARD 提供了新的视角。
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引用次数: 0
Identification of safe putative probiotics from various food products. 从各种食品中鉴定安全的假定益生菌。
IF 2.4 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-10-01 Epub Date: 2024-02-20 DOI: 10.1007/s12223-024-01142-7
Karina Arellano, Juwhan Lim, Jorge Enrique Vazquez Bucheli, Haryung Park, Svetoslav Dimitrov Todorov, Wilhelm Heinrich Holzapfel

The objective of this study was to isolate, identify, and assess the safety and functionality in vitro of putative probiotic bacterial strains. Isolation procedures were based on standard methods using elective and selective media. The isolates were identified by comparative 16S rRNA sequencing analysis while their safety was determined according to the safety tests recommended by the FAO/WHO such as antibiotic resistance, hemolysin, and biogenic amine production. Most of the isolates did not pass the in vitro safety tests; therefore, only Lactiplantibacillus plantarum (from ant intestine and cheese), Lacticaseibacillus paracasei (from goat milk and kimchi), Enterococcus faecium (from chili doenjang and vegetables with kimchi ingredients), Limosilactobacillus fermentum (from saliva), and Companilactobacillus alimentarius (from kimchi) were identified and selected for further studies. The isolates were further differentiated by rep-PCR and identified to the strain level by genotypic (16S rRNA) and phenotypic (Gen III) approaches. Subsequently, the strain tolerance to acid and bile was evaluated resulting in good viability after simulated gastrointestinal tract passage. Adhesion to mucin in vitro and the presence of mub, mapA, and ef-tu genes confirmed the adhesive potential of the strains and the results of features associated with adhesion such as hydrophobicity and zeta potential extended the insights. This study reflects the importance of fermented and non-fermented food products as a promising source of lactic acid bacteria with potential probiotic properties. Additionally, it aims to highlight the challenges associated with the selection of safe strains, which often fail in the in vitro tests, thus hindering the possibilities of "uncovering" novel and safe probiotic strains.

本研究的目的是分离、鉴定和评估假定益生菌菌株在体外的安全性和功能性。分离程序基于标准方法,使用选择性培养基。分离菌株通过 16S rRNA 序列比较分析进行鉴定,其安全性则根据粮农组织/世卫组织推荐的安全性测试(如抗生素耐药性、溶血素和生物胺的产生)来确定。大多数分离物没有通过体外安全性测试,因此,只有植物乳杆菌(来自蚂蚁肠和奶酪)、副酸乳杆菌(来自羊奶和泡菜)、粪肠球菌(来自辣椒豆瓣酱和含有泡菜成分的蔬菜)、发酵柠檬乳杆菌(来自唾液)和食品伴乳杆菌(来自泡菜)被鉴定并选作进一步研究。通过基因型(16S rRNA)和表型(Gen III)方法,对分离菌株进行基因型(16S rRNA)和表型(Gen III)鉴定。随后,对菌株对酸和胆汁的耐受性进行了评估,结果表明其在模拟胃肠道通过后具有良好的存活能力。体外粘附粘蛋白以及 mub、mapA 和 ef-tu 基因的存在证实了菌株的粘附潜能,而疏水性和 zeta 电位等与粘附相关的特征结果则扩展了研究的深度。这项研究反映了发酵和非发酵食品作为具有潜在益生特性的乳酸菌来源的重要性。此外,它还旨在强调与选择安全菌株相关的挑战,这些菌株往往在体外测试中失败,从而阻碍了 "发现 "新型安全益生菌株的可能性。
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Folia microbiologica
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