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What is the role of microbial biotechnology and genetic engineering in medicine? 微生物生物技术和基因工程在医学中的作用是什么?
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-31 DOI: 10.1002/mbo3.1406
Fernando Santos-Beneit

Microbial products are essential for developing various therapeutic agents, including antibiotics, anticancer drugs, vaccines, and therapeutic enzymes. Genetic engineering techniques, functional genomics, and synthetic biology unlock previously uncharacterized natural products. This review highlights major advances in microbial biotechnology, focusing on gene-based technologies for medical applications.

微生物产品对于开发各种治疗药物(包括抗生素、抗癌药物、疫苗和治疗酶)至关重要。基因工程技术、功能基因组学和合成生物学解锁了以前未表征的天然产品。本综述重点介绍了微生物生物技术的主要进展,重点是基于基因的医疗应用技术。
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引用次数: 0
Using meta-analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study 利用荟萃分析了解膳食蛋白质和脂肪含量对家犬粪便微生物群组成的影响:一项试点研究。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-21 DOI: 10.1002/mbo3.1404
Francis D. Phimister, Rachel C. Anderson, David G. Thomas, Michelle J. Farquhar, Paul Maclean, Ruy Jauregui, Wayne Young, Christina F. Butowski, Emma N. Bermingham

The interplay between diet and fecal microbiota composition is garnering increased interest across various host species, including domestic dogs. While the influence of dietary macronutrients and their associated microbial communities have been extensively reviewed, these reviews are descriptive and do not account for differences in microbial community analysis, nor do they standardize macronutrient content across studies. To address this, a meta-analysis was performed to assess the impact of dietary crude protein (“protein”) and dietary crude fat (“fat”) on the fecal microbiota composition in healthy dogs. Sixteen publications met the eligibility criteria for the meta-analysis, yielding a final data set of 314 dogs. Diets were classed as low, moderate, high, or supra in terms of protein or fat content. Sequence data from each publication were retrieved from public databases and reanalyzed using consistent bioinformatic pipelines. Analysis of community diversity indices and unsupervised clustering of the data with principal coordinate analysis revealed a small effect size and complete overlap between protein and fat levels at the overall community level. Supervised clustering through random forest analysis and partial least squares-discriminant analysis indicated alterations in the fecal microbiota composition at a more individual taxonomic level, corresponding to the levels of protein or fat. The Prevotellaceae Ga6A1 group and Enterococcus were associated with increasing levels of protein, while Allobaculum and Clostridium sensu stricto 13 were associated with increasing levels of fat. Interestingly, the random forest analyses revealed that Sharpea, despite its low relative abundance in the dog's fecal microbiome, was primarily responsible for the separation of the microbiome for both protein and fat. Future research should focus on validating and understanding the functional roles of these relatively low-abundant genera.

在包括家犬在内的各种宿主物种中,饮食与粪便微生物群组成之间的相互作用正引起越来越多的关注。虽然膳食宏量营养素及其相关微生物群落的影响已被广泛综述,但这些综述都是描述性的,没有考虑到微生物群落分析的差异,也没有对不同研究中的宏量营养素含量进行标准化。为此,我们进行了一项荟萃分析,以评估膳食粗蛋白("蛋白质")和膳食粗脂肪("脂肪")对健康狗粪便微生物群组成的影响。有 16 篇文献符合荟萃分析的资格标准,最终获得了 314 只狗的数据集。日粮的蛋白质或脂肪含量被分为低、中、高或超高。从公共数据库中检索了每篇论文的序列数据,并使用一致的生物信息学管道进行了重新分析。群落多样性指数分析和主坐标分析法对数据进行的无监督聚类显示,在整个群落水平上,蛋白质和脂肪含量之间的影响很小,而且完全重叠。通过随机森林分析和偏最小二乘判别分析进行的有监督聚类表明,粪便微生物群组成在更个体化的分类水平上发生了变化,与蛋白质或脂肪水平相对应。前孢子菌科 Ga6A1 组和肠球菌与蛋白质含量的增加有关,而 Allobaculum 和严格意义上的梭状芽孢杆菌 13 则与脂肪含量的增加有关。有趣的是,随机森林分析表明,尽管沙佩氏菌在狗粪便微生物组中的相对丰度较低,但它却是蛋白质和脂肪微生物组分离的主要原因。未来的研究应侧重于验证和了解这些相对低丰度菌属的功能作用。
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引用次数: 0
Genomic characterization of extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli from urban wastewater in Australia 澳大利亚城市污水中产广谱β-内酰胺酶和耐碳青霉烯类大肠埃希菌的基因组特征。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-15 DOI: 10.1002/mbo3.1403
Zillur Rahman, Mary-Louise McLaws, Torsten Thomas

This study investigates extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli isolates from Sydney's wastewater. These isolates exhibit resistance to critical antibiotics and harbor novel resistance mechanisms. The findings highlight the importance of wastewater-based surveillance in monitoring resistance beyond the clinical setting.

本研究调查了悉尼废水中分离出的产生广谱β-内酰胺酶和耐碳青霉烯类的大肠埃希菌。这些分离菌株表现出对关键抗生素的耐药性,并隐藏着新型耐药机制。研究结果凸显了基于废水的监测对临床环境以外的耐药性监测的重要性。
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引用次数: 0
Effects of color variation and physiological state on ascidian microbiomes 颜色变化和生理状态对腹足类微生物群的影响
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-13 DOI: 10.1002/mbo3.1405
Samantha K. Morrison, Patrick M. Erwin, Susanna López-Legentil

Ascidians, known for their color variation, host species-specific microbial symbiont communities. Some ascidians can also transition into a nonfiltering (resting) physiological state. Recent studies suggest that the microbial symbiont communities may vary across different physiological states and color morphs of the host. The colonial ascidian, Polyclinum constellatum, which exhibits several color morphs in the Caribbean Sea, periodically ceases its filtering activity. To investigate if color variation in P. constellatum is indicative of sibling speciation, we sequenced fragments of the ribosomal 18S rRNA and the mitochondrial cytochrome oxidase subunit I genes. Additionally, we sequenced a fragment of the 16S rRNA gene to characterize the microbial communities of two common color morphs (red and green) in colonies that were either actively filtering (active) or nonfiltering (resting). Phylogenetic analyses of both ascidian genes resulted in well-supported monophyletic clades encompassing all color variants of P. constellatum. Interestingly, no significant differences were observed among the microbial communities of the green and red morphs, suggesting that color variation in this species is a result of intraspecific variation. However, the host's physiological state significantly influenced the microbial community structure. Nonfiltering (resting) colonies hosted higher relative abundances of Kiloniella (Alphaproteobacteria) and Fangia (Gammaproteobacteria), while filtering colonies hosted more Reugeria (Alphaproteobacteria) and Endozoicomonas (Gammaproteobacteria). This study demonstrates that microbial symbiont communities serve as reliable indicators of the taxonomic state of their host and are strongly influenced by the host's feeding condition.

Ascidians 以其颜色变化而闻名,它们寄生于特定物种的微生物共生群落。有些腹足类还能过渡到非过滤(静止)生理状态。最近的研究表明,微生物共生群落可能因宿主的不同生理状态和颜色形态而异。在加勒比海有几种颜色形态的聚合腹足类(Polyclinum constellatum)会周期性地停止过滤活动。为了研究星座聚伞花序的颜色变异是否表明同胞物种的分化,我们对核糖体 18S rRNA 和线粒体细胞色素氧化酶亚单位 I 基因片段进行了测序。此外,我们还对 16S rRNA 基因片段进行了测序,以确定两种常见颜色形态(红色和绿色)的微生物群落的特征。对这两种腹足类基因的系统发育分析结果表明,单系支系得到了很好的支持,涵盖了所有颜色变体的P. constellatum。有趣的是,在绿色和红色形态的微生物群落中没有观察到明显的差异,这表明该物种的颜色变异是种内变异的结果。不过,宿主的生理状态对微生物群落结构有很大影响。非过滤(静止)菌落寄生了相对丰度较高的Kiloniella(低等蛋白菌)和Fangia(高等蛋白菌),而过滤菌落则寄生了较多的Reugeria(低等蛋白菌)和Endozoicomonas(高等蛋白菌)。这项研究表明,微生物共生群落是宿主分类状态的可靠指标,并受到宿主摄食状况的强烈影响。
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引用次数: 0
Complete nucleotide sequence and comparative genomic analysis of microcin B17 plasmid pMccB17 微量元素 B17 质粒 pMccB17 的完整核苷酸序列和比较基因组分析。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-05 DOI: 10.1002/mbo3.1402
Mayokun Ajeigbe, Stephen Childs, Timothy A. Paget, Lewis E. H. Bingle

We present a comprehensive sequence and bioinformatic analysis of the prototypical microcin plasmid, pMccb17, which includes a definitive sequence for the microcin operon, mcb. Microcin B17 (MccB17) is a ribosomally synthesized and posttranslationally modified peptide produced by Escherichia coli. It inhibits bacterial DNA gyrase similarly to quinolone antibiotics. The mcb operon, which consists of seven genes encoding biosynthetic and immunity/export functions, was originally located on the low copy number IncFII plasmid pMccB17 in the Escherichia coli strain LP17. It was later transferred to E. coli K-12 through conjugation. In this study, the plasmid was extracted from the E. coli K-12 strain RYC1000 [pMccB17] and sequenced twice using an Illumina short-read method. The first sequencing was conducted with the host bacterial chromosome, and the plasmid DNA was then purified and sequenced separately. After assembly into a single contig, polymerase chain reaction primers were designed to close the single remaining gap via Sanger sequencing. The resulting complete circular DNA sequence is 69,190 bp long and includes 81 predicted genes. These genes were initially identified by Prokka and subsequently manually reannotated using BLAST. The plasmid was assigned to the F2:A-:B- replicon type with a MOBF12 group conjugation system. A comparison with other IncFII plasmids revealed a large proportion of shared genes, particularly in the conjugative plasmid backbone. However, unlike many contemporary IncFII plasmids, pMccB17 lacks transposable elements and antibiotic resistance genes. In addition to the mcb operon, this plasmid carries 25 genes of unknown function.

我们对原型 microcin 质粒 pMccb17 进行了全面的序列和生物信息学分析,其中包括 microcin 操作子 mcb 的确定序列。microcin B17(MccB17)是由大肠杆菌产生的一种经核糖体合成和翻译后修饰的多肽。它对细菌 DNA 回旋酶的抑制作用与喹诺酮类抗生素类似。mcb 操作子由 7 个编码生物合成和免疫/输出功能的基因组成,最初位于大肠杆菌菌株 LP17 中的低拷贝数 IncFII 质粒 pMccB17 上。它后来通过共轭转入大肠杆菌 K-12。本研究从大肠杆菌 K-12 菌株 RYC1000 [pMccB17] 中提取了该质粒,并使用 Illumina 短读方法进行了两次测序。第一次测序与宿主细菌染色体一起进行,然后对质粒 DNA 进行纯化和单独测序。组装成单个序列后,设计聚合酶链式反应引物,通过桑格测序填补剩余的单个缺口。最后得到的完整环状 DNA 序列长 69,190 bp,包括 81 个预测基因。这些基因最初由 Prokka 鉴定,随后使用 BLAST 进行了人工重新标注。该质粒属于 F2:A-:B- 复制子类型,具有 MOBF12 组连接系统。与其他 IncFII 质粒的比较显示,该质粒有很大一部分共享基因,特别是在共轭质粒骨架中。然而,与许多当代的 IncFII 质粒不同,pMccB17 缺乏转座元件和抗生素抗性基因。除了 mcb 操作子外,该质粒还携带了 25 个功能未知的基因。
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引用次数: 0
Multidrug-resistant Enterococcus faecium strains enter the Norwegian marine environment through treated sewage 耐多药粪肠球菌菌株通过经处理的污水进入挪威海洋环境。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-05 DOI: 10.1002/mbo3.1397
Vera Radisic, Didrik H. Grevskott, Nadja Junghardt, Lise Øvreås, Nachiket P. Marathe

This study aimed to understand the antibiotic resistance prevalence among Enterococcus spp. from raw and treated sewage in Bergen city, Norway. In total, 517 Enterococcus spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with Enterococcus faecium as the most prevalent (n = 492) species. E. faecium strains (n = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. E. faecium strains (n = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) E. faecium strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the Enterococcus spp. strains (n = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR Enterococcus spp. strains are entering the marine environment through treated sewage.

本研究旨在了解挪威卑尔根市未经处理的污水中肠球菌的抗生素耐药性流行情况。在三次采样中,从五个污水处理厂(STPs)的原污水和处理过的污水中共分离出 517 株肠球菌,其中粪肠球菌(Enterococcus faecium)是最常见的菌种(n = 492)。从进水样本中获得的粪肠球菌菌株(n = 307)对奎奴普汀/达尔福普汀的耐药性最高(67.8%)。我们观察到这些菌株对红霉素(30.6%)和四环素(6.2%)的敏感性降低。从污水样本中获得的粪肠球菌菌株(n = 185)对喹诺酮/达福布星的耐药性最高(68.1%),对红霉素(24.9%)和四环素(8.6%)的敏感性降低。我们没有在任何菌株中发现对利奈唑胺、万古霉素和替加环素等最后抗生素的耐药性。在进水样本(2.3%)和出水样本(2.2%)中都检测到了耐多药(MDR)的粪肠球菌菌株。肠球菌属菌株(n = 25)的全基因组测序显示,其中存在多个抗生素耐药基因,可耐受氨基糖苷类、四环素类和大环内酯类药物,以及多个毒力基因和质粒复制子。从污水中测序出的两株 MDR 菌株属于医院相关克隆复合体 17,并携带多种毒力基因。我们的研究表明,与临床相关的 MDR 肠球菌属菌株正通过经处理的污水进入海洋环境。
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引用次数: 0
The copy number of the eukaryotic rRNA gene can be counted comprehensively 真核生物 rRNA 基因的拷贝数可以全面计数。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-03-04 DOI: 10.1002/mbo3.1399
Akinori Yabuki, Tatsuhiko Hoshino, Tamiko Nakamura, Keiko Mizuno

Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass can also be estimated by applying quantitative sequencing with information on rRNA gene copy numbers in genomes; however, information on rRNA gene copy numbers is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this study, we report an alternative approach that is more appropriate than the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.

基因序列已广泛应用于分子生态学。例如,核糖体 RNA(rRNA)基因已被广泛用作了解微生物群落的生物标记。检测到的 rRNA 基因序列的多样性反映了分析样本中微生物的多样性。利用基因组中 rRNA 基因拷贝数的信息进行定量测序,还可以估算微生物的生物量。特别是对微生物真核生物拷贝数的了解远远少于原核生物,这可能是因为真核生物基因组庞大且结构复杂。在本研究中,我们报告了一种比现有定量测序方法更合适的替代方法,并证明可以高效、全面地测量真核生物 rRNA 的拷贝数。通过广泛应用这种方法,可以确定真核生物 rRNA 的拷贝数信息,并更有效地描述和比较它们的群落结构。
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引用次数: 0
Ultrastructural and glycoproteomic characterization of Prevotella intermedia: Insights into O-glycosylation and outer membrane vesicles 中间普雷沃茨菌的超微结构和糖蛋白组学特征:对 O-糖基化和外膜囊泡的深入了解。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-02-26 DOI: 10.1002/mbo3.1401
Xi Ye, Bindusmita Paul, Joyce Mo, Eric C. Reynolds, Debnath Ghosal, Paul D. Veith

Prevotella intermedia, a Gram-negative bacterium from the Bacteroidota phylum, is associated with periodontitis. Other species within this phylum are known to possess the general O-glycosylation system. The O-glycoproteome has been characterized in several species, including Tannerella forsythia, Porphyromonas gingivalis, and Flavobacterium johnsoniae. In our study, we used electron cryotomography (cryoET) and glycoproteomics to reveal the ultrastructure of P. intermedia and characterize its O-glycoproteome. Our cryoET analysis unveiled the ultrastructural details of the cell envelope and outer membrane vesicles (OMVs) of P. intermedia. We observed an electron-dense surface layer surrounding both cells and OMVs. The OMVs were often large (>200 nm) and presented two types, with lumens being either electron-dense or translucent. LC-MS/MS analyses of P. intermedia fractions led to the identification of 1655 proteins, which included 62 predicted T9SS cargo proteins. Within the glycoproteome, we identified 443 unique O-glycosylation sites within 224 glycoproteins. Interestingly, the O-glycosylation motif exhibited a broader range than reported in other species, with O-glycosylation found at D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P). We identified a single O-glycan with a delta mass of 1531.48 Da. Its sequence was determined by MS2 and MS3 analyses using both collision-induced dissociation and high-energy collisional dissociation fragmentation modes. After partial deglycosylation with trifluoromethanesulfonic acid, the O-glycan sequence was confirmed to be dHex-dHex-HexNAc (HPO3-C6H12O5)-dHex-Hex-HexA-Hex(dHex). Bioinformatic analyses predicted the localization of O-glycoproteins, with 73 periplasmic proteins, 53 inner membrane proteins, 52 lipoproteins, 26 outer membrane proteins, and 14 proteins secreted by the T9SS.

中间普雷沃特氏菌(Prevotella intermedia)是类杆菌科的一种革兰氏阴性细菌,与牙周炎有关。已知该菌门内的其他菌种也拥有一般的 O-糖基化系统。O-糖蛋白组已在多个菌种中得到表征,包括连翘坦奈氏菌(Tannerella forsythia)、牙龈卟啉单胞菌(Porphyromonas gingivalis)和约翰逊黄杆菌(Flavobacterium johnsoniae)。在我们的研究中,我们利用电子低温显像(cryoET)和糖蛋白组学揭示了中间卟啉单胞菌的超微结构,并描述了其 O 型糖蛋白组的特征。我们的低温电子显微镜分析揭示了介壳虫细胞膜和外膜囊泡的超微结构细节。我们观察到围绕细胞和外膜囊泡的电子致密表层。外膜囊泡通常很大(大于 200 nm),有两种类型,内腔要么是电子致密的,要么是半透明的。通过对中间体部分进行 LC-MS/MS 分析,鉴定出 1655 种蛋白质,其中包括 62 种预测的 T9SS 货物蛋白。在糖蛋白组中,我们在 224 个糖蛋白中发现了 443 个独特的 O-糖基化位点。有趣的是,与其他物种相比,O-糖基化位点的范围更广,在D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P)处发现了O-糖基化位点。我们发现了一个δ质量为 1531.48 Da 的单一 O-糖基。利用碰撞诱导解离和高能碰撞解离碎片模式,通过 MS2 和 MS3 分析确定了其序列。经三氟甲磺酸部分脱糖基化后,确认 O-糖序列为 dHex-dHex-HexNAc (HPO3 -C6 H12 O5 )-dHex-Hex-HexA-Hex(dHex) 。生物信息学分析预测了 O-糖蛋白的定位,T9SS 可分泌 73 种周质膜蛋白、53 种内膜蛋白、52 种脂蛋白、26 种外膜蛋白和 14 种蛋白质。
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引用次数: 0
Effect of the polysaccharide capsule and its heptose on the resistance of Campylobacter jejuni to innate immune defenses 多糖胶囊及其庚糖对空肠弯曲杆菌抵抗先天性免疫防御的影响。
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-02-20 DOI: 10.1002/mbo3.1400
Matthew Myles, Heba Barnawi, Mahmoud Mahmoudpour, Sargon Shlimon, Adrienne Chang, Daniel Zimmermann, Chiwon Choi, Najwa Zebian, Carole Creuzenet

Campylobacter jejuni is a commensal in many animals but causes diarrhea in humans. Its polysaccharide capsule contributes to host colonization and virulence in a strain- and model-specific manner. We investigated if the capsule and its heptose are important for interactions of strain NCTC 11168 with various hosts and their innate immune defenses. We determined that they support bacterial survival in Drosophila melanogaster and enhance virulence in Galleria mellonella. We showed that the capsule had limited antiphagocytic activity in human and chicken macrophages, decreased adherence to chicken macrophages, and decreased intracellular survival in both macrophages. In contrast, the heptose increased uptake by chicken macrophages and supported adherence to human macrophages and survival within them. While the capsule triggered nitric oxide production in chicken macrophages, the heptose mitigated this and protected against nitrosative assault. Finally, the C. jejuni strain NCTC 11168 elicited strong cytokine production in both macrophages but quenched ROS production independently from capsule and heptose, and while the capsule and heptose did not protect against oxidative assault, they favored growth in biofilms under oxidative stress. This study shows that the wild-type capsule with its heptose is optimized to resist innate defenses in strain NCTC 11168 often via antagonistic effects of the capsule and its heptose.

空肠弯曲菌是许多动物的共生菌,但会导致人类腹泻。其多糖胶囊以菌株和模型特异性的方式促进宿主定植和毒力。我们研究了多糖胶囊及其庚糖对 NCTC 11168 株与各种宿主及其先天免疫防御系统的相互作用是否重要。我们确定,它们支持细菌在黑腹果蝇中的存活,并增强了其在黑腹果蝇中的毒力。我们发现,在人和鸡的巨噬细胞中,胶囊的抗虹吸活性有限,对鸡巨噬细胞的粘附性降低,两种巨噬细胞的细胞内存活率降低。与此相反,七糖增加了鸡巨噬细胞的吸收,并支持人巨噬细胞的粘附和在其中存活。鸡巨噬细胞中的胶囊会引发一氧化氮的产生,而七聚糖则会减轻这种情况,并保护巨噬细胞免受亚硝酸攻击。最后,空肠大肠杆菌菌株 NCTC 11168 在两种巨噬细胞中都能引起强烈的细胞因子产生,但能独立于胶囊和庚糖淬灭 ROS 的产生,虽然胶囊和庚糖不能抵御氧化攻击,但它们有利于氧化应激下生物膜的生长。这项研究表明,野生型胶囊及其庚糖往往通过胶囊及其庚糖的拮抗作用,优化了菌株 NCTC 11168 抵抗先天防御的能力。
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引用次数: 0
Characterizing living ocular bacterial communities and the effects of antibiotic perturbation in house finches 家雀眼部细菌群落活体特征及抗生素干扰的影响
IF 3.4 3区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-02-04 DOI: 10.1002/mbo3.1398
Chava L. Weitzman, Dana M. Hawley, Bahman Rostama, Meghan May, Lisa K. Belden

DNA-based methods to measure the abundance and relative abundance of bacterial taxa can be skewed by the presence of dead or transient bacteria. Consequently, the active, functional members of the community may be a small subset of the detected bacterial community. This mismatch can make inferences about the roles of communities in host health difficult and can be particularly problematic for low-abundance microbiomes, such as those on conjunctival surfaces. In this study, we manipulated bacterial communities on bird conjunctiva with a bacteriostatic antibiotic, reducing bacterial activity while preserving viability, to identify the living and active conjunctival communities using comparisons of 16S ribosomal DNA and RNA in paired samples. DNA amplicons included many more sequence variants than RNA amplicons from the same communities, with consequent differences in diversity. While we found that changes in communities in DNA samples broadly represent shifts in the living (RNA-amplicon) communities, assessments of community function may be better described by RNA samples, reducing background noise from dead cells. We further used these data to test RNA:DNA ratios, used in other microbiological contexts, to detect shifts in bacterial activity after antibiotic disruption but were unable to detect changes in bacterial activity with this method.

以 DNA 为基础的细菌分类群丰度和相对丰度测量方法可能会因死亡细菌或瞬时细菌的存在而产生偏差。因此,群落中活跃的功能性成员可能只是检测到的细菌群落的一小部分。这种不匹配会使推断群落在宿主健康中的作用变得困难,对于低丰度微生物群落(如结膜表面的微生物群落)尤其如此。在这项研究中,我们用一种抑菌抗生素处理鸟类结膜上的细菌群落,在保持活力的同时降低细菌活性,从而通过比较配对样本中的 16S 核糖体 DNA 和 RNA 来确定活的和活跃的结膜群落。与来自相同群落的 RNA 扩增片段相比,DNA 扩增片段包含更多的序列变异,因此多样性也存在差异。我们发现,DNA 样本中群落的变化大致代表了活体(RNA 扩增子)群落的变化,而 RNA 样本可以更好地描述群落功能,减少死亡细胞带来的背景噪音。我们进一步利用这些数据测试了 RNA 与 DNA 的比率,这种比率在其他微生物学环境中被用来检测抗生素破坏后细菌活性的变化,但这种方法无法检测到细菌活性的变化。
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