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Root nodules of red alder (Alnus rubra) and sitka alder (Alnus viridis ssp. sinuata) are inhabited by taxonomically diverse cultivable microbial endophytes 红桤木(Alnus rubra)和西特卡桤木(Alnus viridis ssp. sinuata)的根瘤中栖息着分类学上多种多样的可培养微生物内生菌。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-07 DOI: 10.1002/mbo3.1422
Robyn Dove, Emily R. Wolfe, Nathan U. Stewart, Abigail Coleman, Sara Herrejon Chavez, Daniel J. Ballhorn

The root nodules of actinorhizal plants are home to nitrogen-fixing bacterial symbionts, known as Frankia, along with a small percentage of other microorganisms. These include fungal endophytes and non-Frankia bacteria. The taxonomic and functional diversity of the microbial consortia within these root nodules is not well understood. In this study, we surveyed and analyzed the cultivable, non-Frankia fungal and bacterial endophytes of root nodules from red and Sitka alder trees that grow together. We examined their taxonomic diversity, co-occurrence, differences between hosts, and potential functional roles. For the first time, we are reporting numerous fungal endophytes of alder root nodules. These include Sporothrix guttuliformis, Fontanospora sp., Cadophora melinii, an unclassified Cadophora, Ilyonectria destructans, an unclassified Gibberella, Nectria ramulariae, an unclassified Trichoderma, Mycosphaerella tassiana, an unclassified Talaromyces, Coniochaeta sp., and Sistotrema brinkmanii. We are also reporting several bacterial genera for the first time: Collimonas, Psychrobacillus, and Phyllobacterium. Additionally, we are reporting the genus Serratia for the second time, with the first report having been recently published in 2023. Pseudomonas was the most frequently isolated bacterial genus and was found to co-inhabit individual nodules with both fungi and bacteria. We found that the communities of fungal endophytes differed by host species, while the communities of bacterial endophytes did not.

放线菌植物的根瘤是固氮菌共生体(即弗兰科菌)和少量其他微生物的家园。这些微生物包括真菌内生菌和非弗兰克菌。人们对这些根瘤内微生物群落的分类和功能多样性了解不多。在这项研究中,我们调查并分析了一起生长的红桤木和西特卡桤木根瘤中可培养的非弗兰基菌真菌和细菌内生菌。我们研究了它们的分类多样性、共生情况、宿主之间的差异以及潜在的功能作用。我们首次报告了赤杨根瘤中的大量真菌内生菌。其中包括 Sporothrix guttuliformis、Fontanospora sp.、Cadophora melinii、未分类的 Cadophora、Ilyonectria destructans、未分类的 Gibberella、Nectria ramulariae、未分类的 Trichoderma、Mycosphaerella tassiana、未分类的 Talaromyces、Coniochaeta sp.和 Sistotrema brinkmanii。我们还首次报告了几个细菌属:Collimonas、Psychrobacillus 和 Phyllobacterium。此外,我们还是第二次报告沙雷氏菌属,第一次报告最近发表于 2023 年。假单胞菌是最常分离出的细菌属,并发现它与真菌和细菌共同栖息于单个结核中。我们发现真菌内生菌群落因宿主物种而异,而细菌内生菌群落则不然。
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引用次数: 0
Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water 与沉积物和水相比,蜗牛胃肠道细菌群落具有不同的生物地理模式。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-02 DOI: 10.1002/mbo3.1413
Daniel P. R. Herlemann, Helen Tammert, Carmen Kivistik, Kairi Käiro, Veljo Kisand

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

影响细菌群落组成分布的因素尚不十分清楚。地理模式的作用表明细菌的扩散受到限制,但这仍然是一个争论不休的话题。与宿主相关的细菌面临着独特的扩散挑战,因为它们通常依赖于宿主,而宿主为其共生体提供了特定的环境。在这项研究中,我们考察了生物地理距离对巴氏栉水母(Ampullaceana balthica)胃肠道细菌多样性和细菌群落组成的影响。我们比较了宿主相关细菌群落与水和沉积物中细菌群落的影响。这种比较是通过 16S 核糖体 RNA 基因测序进行的。我们发现,我们在爱沙尼亚、丹麦和德国北部采样的细菌群落在水、沉积物和胃肠道中各不相同。在每种基质中,不同国家的细菌群落也各不相同。这表明,基质类型是决定细菌群落组成的主要因素。我们分别分析了水体、沉积物和胃肠道细菌群落在地理距离增加时的更替率。我们发现,与水体细菌群落相比,胃肠道细菌群落的更替率较低。这意味着胃肠道细菌群落的组成在不同距离上保持相对稳定,而水体细菌群落则表现出更大的变异性。不过,胃肠道的国家特异性扩增子序列变异比例最低,这表明细菌定植于当地细菌群落。由于水和胃肠道之间的重叠率最高,因此胃肠道细菌群落似乎是由水细菌群落定殖的。我们的研究证实,宿主相关群落的生物地理模式与水和沉积物细菌群落不同。这些宿主相关群落由来自水体细菌群落的大量兼性共生体组成。
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引用次数: 0
Exploring solute binding proteins in Pseudomonas aeruginosa that bind to γ-aminobutyrate and 5-aminovalerate and their role in activating sensor kinases 探索铜绿假单胞菌中与γ-氨基丁酸和 5-氨基戊酸结合的溶质结合蛋白及其在激活感应激酶中的作用。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-05-23 DOI: 10.1002/mbo3.1415
Jean Paul Cerna-Vargas, Tino Krell

The standard method of receptor activation involves the binding of signals or signal-loaded solute binding proteins (SBPs) to sensor domains. Many sensor histidine kinases (SHKs), which are activated by SBP binding, are encoded adjacent to their corresponding sbp gene. We examined three SBPs of Pseudomonas aeruginosa PAO1, encoded near the genes for the AgtS (PA0600) and AruS (PA4982) SHKs, to determine how common this arrangement is. Ligand screening and microcalorimetric studies revealed that the SBPs PA0602 and PA4985 preferentially bind to GABA (KD = 2.3 and 0.58 μM, respectively), followed by 5-aminovalerate (KD = 30 and 1.6 μM, respectively) and ethanoldiamine (KD = 2.3 and 0.58 μM, respectively). In contrast, AgtB (PA0604) exclusively recognizes 5-aminovaleric acid (KD = 2.9 μM). However, microcalorimetric titrations did not show any binding between the AgtS sensor domain and AgtB or PA0602, regardless of the presence of ligands. Similarly, bacterial two-hybrid assays did not demonstrate an interaction between PA4985 and the AruS sensor domain. Therefore, sbp and shk genes located nearby are not always functionally linked. We previously identified PA0222 as a GABA-specific SBP. The presence of three SBPs for GABA may be linked to GABA's role as a trigger for P. aeruginosa virulence.

受体激活的标准方法是将信号或信号负载的溶质结合蛋白(SBP)与传感器结构域结合。许多由 SBP 结合激活的传感器组氨酸激酶(SHKs)的编码与相应的 sbp 基因相邻。我们研究了铜绿假单胞菌 PAO1 的三个 SBPs(在 AgtS(PA0600)和 AruS(PA4982)SHKs 基因附近编码),以确定这种排列的常见程度。配体筛选和微量热研究显示,SBPs PA0602 和 PA4985 优先与 GABA 结合(KD 分别为 2.3 和 0.58 μM),其次是 5-氨基戊酸(KD 分别为 30 和 1.6 μM)和乙醇胺(KD 分别为 2.3 和 0.58 μM)。相比之下,AgtB(PA0604)只能识别 5-氨基戊酸(KD = 2.9 μM)。然而,微量热滴定法并未显示 AgtS 传感器结构域与 AgtB 或 PA0602 有任何结合,无论是否存在配体。同样,细菌双杂交试验也没有证明 PA4985 与 AruS 传感器结构域之间存在相互作用。因此,位于附近的 sbp 和 shk 基因在功能上并不总是相关联的。我们之前发现 PA0222 是一种 GABA 特异性 SBP。GABA 的三个 SBP 的存在可能与 GABA 作为铜绿假单胞菌毒力触发器的作用有关。
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引用次数: 0
Correction to “Staphylococcus argenteus from rabbits in Thailand” 更正 "泰国兔子身上的金黄色葡萄球菌"。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-05-15 DOI: 10.1002/mbo3.1414

Indrawattana N., Pumipuntu N., Suriyakhun N., Jangsangthong A., Kulpeanprasit S., Chantratita N., Sookrung N., Chaicumpa W., & Buranasinsup S. Staphylococcus argenteus from rabbits in Thailand. MicrobiologyOpen. 2018;e665.

In “abstract” section, line 4, the text “the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014–2016.” should read as “the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014–2015.”

In “material and method section, 2.1 | Specimen collection and bacterial isolation, line 3, the text “Sixty-seven pus samples were collected from rabbits with clinical abscesses by a veterinarian at Prasu-Arthorn Animal Hospital, Thailand during 2014–2016.” should read as “Sixty-seven pus samples were collected from rabbits with clinical abscesses by a veterinarian at Prasu-Arthorn Animal Hospital, Thailand, during 2014–2015.”

We apologize for this error.

Indrawattana N., Pumipuntu N., Suriyakhun N., Jangsangthong A., Kulpeanprasit S., Chantratita N., Sookrung N., Chaicumpa W., & Buranasinsup S. 来自泰国兔子的金黄色葡萄球菌。MicrobiologyOpen.2018;e665.In "abstract" section, line 4, the text "the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014-2016." should read as "the presence of S. argenteus in isolated S. aureus was investigated in 67 rabbits with abscess lesions during 2014-2015. "In "material and method section, 2.1 | 标本采集和细菌分离 "中,第 3 行,"2014-2016 年期间,泰国 Prasu-Arthorn 动物医院的一名兽医从患有临床脓肿的兔子身上采集了 67 份脓液样本 "应为 "2014-2015 年期间,泰国 Prasu-Arthorn 动物医院的一名兽医从患有临床脓肿的兔子身上采集了 67 份脓液样本"。
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引用次数: 0
Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment 实现电缆细菌的生物工艺工程:建立合成沉积物
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-05-06 DOI: 10.1002/mbo3.1412
Judith Stiefelmaier, Joshua Keller, Wiebke Neupert, Roland Ulber

Cable bacteria, characterized by their multicellular filamentous growth, are prevalent in both freshwater and marine sediments. They possess the unique ability to transport electrons over distances of centimeters. Coupled with their capacity to fix CO2 and their record-breaking conductivity for biological materials, these bacteria present promising prospects for bioprocess engineering, including potential electrochemical applications. However, the cultivation of cable bacteria has been limited to their natural sediment, constraining their utility in production processes. To address this, our study designs synthetic sediment, drawing on ion exchange chromatography data from natural sediments and existing literature on the requirements of cable bacteria. We examined the effects of varying bentonite concentrations on water retention and the impacts of different sands. For the first time, we cultivated cable bacteria on synthetic sediment, specifically the freshwater strain Electronema aureum GS. This cultivation was conducted over 10 weeks in a specially developed sediment bioreactor, resulting in an increased density of cable bacteria in the sediment and growth up to a depth of 5 cm. The creation of this synthetic sediment paves the way for the reproducible cultivation of cable bacteria. It also opens up possibilities for future process scale-up using readily available components. This advancement holds significant implications for the broader field of bioprocess engineering.

电缆细菌以多细胞丝状生长为特征,普遍存在于淡水和海洋沉积物中。它们具有独特的电子传输能力,传输距离可达数厘米。再加上它们固定二氧化碳的能力和破纪录的生物材料导电性,这些细菌为生物工艺工程(包括潜在的电化学应用)带来了广阔的前景。然而,缆索细菌的培养仅限于其自然沉积物,限制了它们在生产过程中的应用。为了解决这个问题,我们的研究借鉴了天然沉积物的离子交换色谱数据和有关电缆细菌需求的现有文献,设计了合成沉积物。我们研究了不同浓度的膨润土对保水的影响以及不同泥沙的影响。我们首次在合成沉积物上培养缆索细菌,特别是淡水菌株 Electronema aureum GS。这种培养在专门开发的沉积物生物反应器中进行了 10 周,结果沉积物中的缆索细菌密度增加,生长深度达 5 厘米。这种合成沉积物的产生为电缆细菌的可重复培养铺平了道路。它还为未来使用现成成分扩大工艺规模提供了可能性。这一进展对更广泛的生物工艺工程领域具有重要意义。
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引用次数: 0
Turbidimetric bioassays: A solution to antimicrobial activity detection in asymptomatic bacteriuria isolates against uropathogenic Escherichia coli 比浊生物测定法:无症状菌尿分离物对尿路致病性大肠杆菌抗菌活性检测的解决方案
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-05-06 DOI: 10.1002/mbo3.1411
Ciara Kenneally, Craig P. Murphy, Roy D. Sleator, Eamonn P. Culligan

Traditional bacteriocin screening methods often face limitations due to diffusion-related challenges in agar matrices, which can prevent the peptides from reaching their target organism. Turbidimetric techniques offer a solution to these issues, eliminating diffusion-related problems and providing an initial quantification of bacteriocin efficacy in producer organisms. This study involved screening the cell-free supernatant (CFS) from eight uncharacterized asymptomatic bacteriuria (ABU) isolates and Escherichia coli 83972 for antimicrobial activity against clinical uropathogenic E. coli (UPEC) strains using turbidimetric growth methods. ABU isolates exhibiting activity against five or more UPEC strains were further characterized (PUTS 37, PUTS 58, PUTS 59, S-07-4, and SK-106-1). The inhibition of the CFS by proteinase K suggested that the antimicrobial activity was proteinaceous in nature, potentially bacteriocins. The activity of E. coli PUTS 58 and SK-106-1 was enhanced in an artificial urine medium, with both inhibiting all eight UPECs. A putative microcin H47 operon was identified in E. coli SK-106-1, along with a previously identified microcin V and colicin E7 in E. coli PUTS 37 and PUTS 58, respectively. These findings indicate that ABU bacteriocin-producers could serve as viable prophylactics and therapeutics in the face of increasing antibiotic resistance among uropathogens.

传统的细菌素筛选方法往往受到琼脂基质中与扩散有关的难题的限制,这些难题会阻碍肽到达目标生物体。比浊技术为这些问题提供了一种解决方案,它消除了与扩散相关的问题,并能初步量化细菌素在生产者生物体中的效力。本研究采用浊度生长法对来自 8 个未定性无症状菌尿症(ABU)分离物和大肠杆菌 83972 的无细胞上清液(CFS)进行筛选,以确定其对临床尿路致病性大肠杆菌(UPEC)菌株的抗菌活性。对五株或五株以上 UPEC 菌株具有活性的 ABU 分离物(PUTS 37、PUTS 58、PUTS 59、S-07-4 和 SK-106-1)被进一步鉴定。蛋白酶 K 对 CFS 的抑制作用表明,其抗菌活性本质上是蛋白性的,可能是细菌素。在人工尿培养基中,大肠杆菌 PUTS 58 和 SK-106-1 的活性增强,两者都能抑制所有八种 UPECs。在大肠杆菌 SK-106-1 中发现了一个推定的微素 H47 操作子,以及之前在大肠杆菌 PUTS 37 和 PUTS 58 中分别发现的微素 V 和大肠杆菌素 E7。这些研究结果表明,面对泌尿道病原体对抗生素的耐药性不断增加,ABU 细菌素生产者可作为可行的预防和治疗药物。
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引用次数: 0
Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality 利用新型大肠埃希氏菌特异性保守特征蛋白加强对休闲水质的监测
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-04-29 DOI: 10.1002/mbo3.1410
Faizan Saleem, Enze Li, Kevin L. Tran, Bashudev Rudra, Thomas A. Edge, Herb E. Schellhorn, Radhey S. Gupta

Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24 h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developed quantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.

大肠杆菌是水生生态系统中粪便污染的替代指标。应用 DNA 标记,如保守特征蛋白(CSPs)基因(特定类群的所有物种/菌株所独有),可为新型聚合酶链式反应(PCR)测试奠定基础,从而明确识别和检测感兴趣的目标细菌类群。本文报告了三个新的高保守 CSP(基因)的鉴定结果,即 YahL、YdjO 和 YjfZ,它们是大肠杆菌/志贺氏菌独有的。利用基于这些 CSP 高度保守区域的 PCR 引物,我们开发出了定量 PCR(qPCR)检测方法,用于评估水生态系统中的大肠杆菌/志贺菌物种。在对其他细菌进行测试时,我们都通过室内和实验 PCR 测试确认了序列匹配的缺失,从而证实了所测试的 CSP 对大肠杆菌/志贺氏菌具有 100% 的特异性。三种 CSP 中每一种的 qPCR 检测都能对所有检测的肠出血性大肠杆菌和环境大肠杆菌菌株进行可靠的定量,这也是水质检测的一项要求。对于娱乐性水样,基于 CSP 的定量与传统的大肠杆菌计数显示出很高的相关性(r > 7, p < 0.01)。这表明,基于 CSP 的新型大肠杆菌 qPCR 检测方法可作为监测水生态系统和其他关键领域(包括食品监测)的有力工具。
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引用次数: 0
Multidrug-resistant Stenotrophomonas maltophilia in residential aged care facilities: An emerging threat 养老院中的嗜麦芽霉单胞菌对多种药物产生耐药性:新出现的威胁
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-04-29 DOI: 10.1002/mbo3.1409
Sylvia A. Sapula, Bradley J. Hart, Naomi L. Siderius, Anteneh Amsalu, Jack M. Blaikie, Henrietta Venter

Stenotrophomonas maltophilia is a multidrug-resistant (MDR), Gram-negative bacterium intrinsically resistant to beta-lactams, including last-resort carbapenems. As an opportunistic pathogen, it can cause serious healthcare-related infections. This study assesses the prevalence, resistance profiles, and genetic diversity of S. maltophilia isolated from residential aged care facilities (RACFs). RACFs are known for their overuse and often inappropriate use of antibiotics, creating a strong selective environment that favors the development of bacterial resistance. The study was conducted on 73 S. maltophilia isolates recovered from wastewater and facility swab samples obtained from three RACFs and a retirement village. Phenotypic and genotypic assessments of the isolates revealed high carbapenem resistance, exemplifying their intrinsic beta-lactam resistance. Alarmingly, 49.3% (36/73) of the isolates were non-wild type for colistin, with minimum inhibitory concentration values of > 4 mg/L, and 11.0% (8/73) were resistant to trimethoprim-sulfamethoxazole. No resistance mechanisms were detected for either antimicrobial. Genotypic assessment of known lineages revealed isolates clustering with Sm17 and Sm18, lineages not previously reported in Australia, suggesting the potential ongoing spread of MDR S. maltophilia. Lastly, although only a few isolates were biocide tolerant (2.7%, 2/73), their ability to grow in high concentrations (64 mg/L) of triclosan is concerning, as it may be selecting for their survival and continued dissemination.

嗜麦芽血单胞菌是一种耐多药(MDR)革兰氏阴性细菌,对β-内酰胺类药物(包括最后的碳青霉烯类)具有内在耐药性。作为一种机会性病原体,它可引起严重的医疗相关感染。本研究评估了从养老院(RACF)中分离出的嗜麦芽糖酵母菌的流行率、耐药性特征和遗传多样性。众所周知,养老院过度使用抗生素,而且往往使用不当,这就形成了一个有利于细菌耐药性发展的强大选择性环境。这项研究针对从三家 RACF 和一家退休村的废水和设施拭子样本中分离出的 73 个嗜麦芽汁酵母菌进行了研究。对分离菌株的表型和基因型评估显示,这些菌株对碳青霉烯类耐药性较高,体现了其固有的β-内酰胺耐药性。令人担忧的是,49.3%(36/73)的分离株对可乐定具有非野生型耐药性,最低抑菌浓度值为 4 毫克/升,11.0%(8/73)的分离株对三甲双胍-磺胺甲噁唑具有耐药性。对这两种抗菌素均未发现耐药机制。对已知菌系的基因型评估显示,分离物与 Sm17 和 Sm18 菌系聚集在一起,而这两个菌系以前在澳大利亚未曾报道过,这表明嗜麦芽糖酵母菌的 MDR 有可能正在蔓延。最后,虽然只有少数分离物对杀菌剂有耐受性(2.7%,2/73),但它们在高浓度(64 毫克/升)三氯生中的生长能力令人担忧,因为这可能会促进它们的生存和继续传播。
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引用次数: 0
Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications 未开发岩溶生态系统沉积物微生物亚群落的生物合成潜力及其生态影响
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-04-09 DOI: 10.1002/mbo3.1407
Pablo Suárez-Moo, Alejandra Prieto-Davó

Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.

人们研究了各种环境中的微生物群落,以寻找新的天然产品,这些产品在医学和生物技术领域有着广泛的应用。我们采用富集方法和基因组挖掘工具,研究了墨西哥尤卡坦半岛喀斯特生态系统中沿海天坑沉积物中微生物群落的生物合成潜力。通过研究,我们在这些亚群落的 35 个高质量元基因组组装基因组(MAGs)中发现了 203 个生物合成基因簇(BGCs)和 55 个次级代谢产物(SMs)。最丰富的 BGC 类型是萜烯、非核糖体肽合成酶和 III 型多酮合成酶。以前曾有报道称,一些在硅学中鉴定出的 BGCs 和 SMs 具有抗病原菌和真菌的生物活性。其他一些则可能在水坑生态系统中发挥重要作用,如铁增溶和渗透压保护。有趣的是,75%的BGCs与MiBIG数据库中之前报道的细菌BGCs没有序列同源性。这表明,这种环境中的微生物群落可能是编码新型特化化合物基因的一个尚未开发的来源。大多数 BGCs 都是在 Virgibacillus 属的途径中发现的,其次是 Sporosarcina、Siminovitchia、Rhodococcus 和 Halomonas。后者与副梭菌和溶血芽孢杆菌一起,拥有数量最多的已鉴定 BGC 类型。这项研究对未开发环境中沉积物微生物群落中的 SMs 的潜在生态作用提供了新的见解,强调了它们作为新型天然产品来源的价值。
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引用次数: 0
Characterizing arginine, ornithine, and putrescine pathways in enteric pathobionts 鉴定肠道致病菌中的精氨酸、鸟氨酸和腐胺途径
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-04-01 DOI: 10.1002/mbo3.1408
Ian M. Lillie, Charles E. Booth, Adelaide E. Horvath, Matthew Mondragon, Melinda A. Engevik, Thomas D. Horvath

Arginine-ornithine metabolism plays a crucial role in bacterial homeostasis, as evidenced by numerous studies. However, the utilization of arginine and the downstream products of its metabolism remain undefined in various gut bacteria. To bridge this knowledge gap, we employed genomic screening to pinpoint relevant metabolic targets. We also devised a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics method to measure the levels of arginine, its upstream precursors, and downstream products in cell-free conditioned media from enteric pathobionts, including Escherichia coli, Klebsiella aerogenes, K. pneumoniae, Pseudomonas fluorescens, Acinetobacter baumannii, Streptococcus agalactiae, Staphylococcus epidermidis, S. aureus, and Enterococcus faecalis. Our findings revealed that all selected bacterial strains consumed glutamine, glutamate, and arginine, and produced citrulline, ornithine, and GABA in our chemically defined medium. Additionally, E. coli, K. pneumoniae, K. aerogenes, and P. fluorescens were found to convert arginine to agmatine and produce putrescine. Interestingly, arginine supplementation promoted biofilm formation in K. pneumoniae, while ornithine supplementation enhanced biofilm formation in S. epidermidis. These findings offer a comprehensive insight into arginine-ornithine metabolism in enteric pathobionts.

大量研究证明,精氨酸-鸟氨酸代谢在细菌平衡中发挥着至关重要的作用。然而,精氨酸的利用及其代谢的下游产物在各种肠道细菌中仍未确定。为了弥补这一知识空白,我们采用了基因组筛选技术来确定相关的代谢靶标。我们还设计了一种有针对性的液相色谱-串联质谱(LC-MS/MS)代谢组学方法,以测量肠道致病菌(包括大肠埃希菌、产气克雷伯氏菌、肺炎克雷伯氏菌、流感假单胞菌等)无细胞条件培养基中精氨酸、其上游前体和下游产物的水平。肺炎双球菌、荧光假单胞菌、鲍曼不动杆菌、无乳链球菌、表皮葡萄球菌、金黄色葡萄球菌和粪肠球菌。我们的研究结果表明,在化学定义的培养基中,所有选定的细菌菌株都消耗谷氨酰胺、谷氨酸和精氨酸,并产生瓜氨酸、鸟氨酸和 GABA。此外,还发现大肠杆菌、肺炎双球菌、产气荚膜杆菌和荧光团菌能将精氨酸转化为矢车菊碱并产生腐胺。有趣的是,补充精氨酸可促进肺炎双球菌生物膜的形成,而补充鸟氨酸可促进表皮葡萄球菌生物膜的形成。这些发现为精氨酸-鸟氨酸在肠道致病菌中的代谢提供了一个全面的视角。
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引用次数: 0
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