呼吸道合胞病毒感染患儿下呼吸道菌群特征分析

分析呼吸道合胞病毒（RSV）感染患儿与非感染儿童下呼吸道菌群的物种组成和丰度差异,揭示RSV感染影响下呼吸道菌群而介导疾病发生发展的可能机制。

纳入2021年9月至2021年12月首都医科大学附属北京儿童医院和首都医科大学附属北京儿童医院保定医院收治的69例RSV下呼吸道感染患儿（RSV组）及39例非感染儿童（对照组）为研究对象。留取两组儿童痰液样本,使用Illumina NovaSeq 6000平台对细菌16S rRNA基因V3−V4区进行高通量测序。通过QIIME平台对测序数据进行分析,比较组间儿童呼吸道菌群的多样性差异,以及各组在物种组成和丰度上的差异,分析丰度前10位的优势菌属与临床指标的相关性。

与对照组相比,RSV组患儿下呼吸道菌群物种丰富度显著降低,Shannon指数显著下降（P＜0.001）。两组儿童的下呼吸道菌群整体构成存在显著差异（基于Bray-Curtis距离,P=0.001）。在门水平上,与对照组儿童相比,RSV组患儿变形菌门丰度显著升高,而拟杆菌门的丰度显著降低（均P＜0.001）;在属水平上,RSV组患儿下呼吸道链球菌属、劳尔菌属和莫拉菌属的丰度显著升高,而普雷沃菌属和韦荣球菌属等共生菌的丰度显著下降（均P＜0.05）。Spearman秩相关分析结果表明,下呼吸道菌群构成改变与RSV患儿临床指标存在显著关联（均P＜0.05）。

RSV感染患儿存在下呼吸道菌群紊乱、菌群多样性下降。呼吸道菌群特征的变化与疾病进展具有一定相关性。

     

SPF鸡与普通鸡消化道主要正常菌群数量的比较

采用微生态学方法,对SPF鸡和普通鸡嗉囔、腺胃、回肠、盲肠和直肠5个部位的梭杆菌、真杆菌、消化球菌、双歧杆菌、乳酸杆菌、类杆菌、肠球菌、葡萄球菌和肠杆菌等9种主要正常菌群进行定性、定量分析。结果表明,SPF鸡嗉囔中真杆菌、梭杆菌、双歧杆菌、类杆菌、葡萄球菌和肠杆菌数高于普通鸡,其中真杆菌、梭杆菌、葡萄球菌和肠杆菌数差异极显著(P<0.01);腺胃中梭杆菌、真杆菌、消化球菌、双歧杆菌、乳酸杆菌、类杆菌和肠杆菌数高于普通鸡,其中真杆菌数差异显著(P<0.05);回肠中真杆菌、双歧杆菌、类杆菌、葡萄球菌和肠杆菌数高于普通鸡,其中类杆菌数差异极显著(P<0.01);盲肠中梭杆菌、消化球菌、双歧杆菌、乳酸杆菌和肠球菌数低于普通鸡,其中乳酸杆菌数差异显著(P<0.05);直肠中各菌数量都低于普通鸡,其中双歧杆菌和乳酸杆菌差异显著(P<0.05)。     

呼吸道病毒和呼吸道、肠道菌群的相互作用

随着新技术的应用,人们对人体不同部位的微生态系统有了进一步的认识,其中的微生物部分不仅指细菌还包括病毒。病毒的存在可以影响呼吸道和肠道菌群变化,同样呼吸道和肠道菌群状态也影响着病毒对人体的入侵程度。本研究就呼吸道和肠道菌群与呼吸道病毒相互作用关系的研究进展作一综述。     

常见SPF级小鼠和大鼠肠道菌群多样性研究

目的研究常见SPF级小鼠和大鼠的肠道菌群多样性。方法分别采集广东地区三家实验动物生产单位的C57BL/6、ICR、BALB/c小鼠和Wistar、SD大鼠的盲肠内容物样品,用细菌16S rDNA通用引物扩增V4-V5区域,采用Illumina Miseq 2×300 bp测序平台进行测序,使用生物信息学方法进行微生物群落分析、Alpha多样性分析与Beta多样性分析。结果对序列去杂优化后OTU聚类分析,稀释性曲线说明本次测序的数据量合理;实验小鼠和大鼠肠道菌群共分成八个门,其中拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)占据主要地位,属水平上主要是拟杆菌属(Bacteroides)、Hungatella、副杆状菌属(Parabacteroides)、乳酸杆菌属(Lactobacillus)等;样品间差异性分析显示相同设施来源动物的菌群组成相似性较高;Alpha分析结果显示来源于同种设施的动物物种丰富度相近;Beta分析显示相同设施动物的肠道菌群差异较小,但品系对肠道菌群差异性有所影响。结论不同来源设施的饲养环境是动物肠道菌群多样性的主要影响因素,不同品系对肠道菌群多样性有一定影响。     

幽门螺杆菌感染对正常胃部菌群多样性和组成的影响

目的 通过高通量测序分析,探讨幽门螺杆菌(Helicobacter pylori)感染在正常胃部菌群多样性和组成中的差异。 方法 选择2017年10月-2018年1月在本院就诊的胃镜体检受试者40例,其中H. pylori阳性20例,阴性20例,均无阳性体征,收集胃液样本行胃部菌群MiSeq高通量测序分析。 结果 H. pylori感染组α 多样性指数Shannon(t=-6.690,P2,P结论 H.pylori感染是影响正常胃部菌群多样性和组成的重要因素,这些改变可能与胃癌发生发展及预后密切相关。     

儿童呼吸道菌群的调查

目的了解儿童呼吸道菌群的分布特征。方法对重庆医科大学附属儿童医院的呼吸内科住院部500例小儿下呼吸道负压吸引法痰标本做分离培养;105例门诊未使用抗生素有咽部体征的上呼吸道患儿咽拭子标本做分离培养;同时对150例健康儿童上呼吸道咽拭子标本做分离培养,对他们的生长菌群进行分类鉴定和药敏试验,并对结果作对比分析讨论。结果草绿色链球菌、表皮葡萄球菌、金黄色葡萄球菌、溶血葡萄球菌、流感嗜血杆菌检出率差异无显著性（P〉0.05）;而儿童下呼吸道痰标本结果和105例门诊上呼吸道患儿咽拭子标本结果比较大肠埃希菌、肺炎克雷伯菌、阴沟肠杆菌、肺炎链球菌、副流感嗜血杆菌、卡他莫拉菌、真菌差异无显著性（P〉0.05）,与150例健康儿童上呼吸道咽拭子标本结果比较差异有显著性（P〈0.05）。革兰阴性杆菌对亚胺硫霉素（IMP）耐药率最低,对哌拉西林/他唑巴坦（TZP）、阿米卡星（AK）、环丙沙星（CIP）耐药率〈30%;革兰阳性球菌未发现耐万古霉素（VA）菌株,对利福平（RD）、哌拉西林/他唑巴坦（TZP）耐药率相对较低;流感嗜血杆菌、副流感嗜血杆菌、卡他莫拉菌对CIP、IMP耐药率〈10%;肺炎链球菌无VA耐药菌株,对氧氟沙星（OFX）、RD耐药率〈10%;草绿色链球菌也无耐VA菌株;对RD、复方磺胺（SXT）、四环素（TE）耐药率〈30%。结论儿童正常菌群的分布特征以草绿色链球菌为主。从病原菌来看,下呼吸道住院患儿痰标本分离的致病菌大于门诊上呼吸道感染患儿咽拭子分离的致病菌大于健康儿童咽拭子标本携带的致病菌。     

引发下呼吸道感染的非发酵菌的菌群分布及耐药性分析

目的了解引发下呼吸道感染的非发酵菌的菌群分布及耐药性分析,为临床合理使用抗生素提供依据。方法对2011年1月至2013年9月深圳罗岗医院门诊及住院患者痰标本分离的非发酵菌的菌群分布及优势菌的耐药性进行回顾性分析。结果702株非发酵菌中铜绿假单胞菌（PA）362株,占51．6％,鲍氏不动杆菌（AB）158株,占22．5％;PA对NIT、CXM、SAM、AMP、CZO、CTF、CRO、SXT耐药率均在99．0％以上,对IPM、LVF和TZP耐药率均在15．0％以下;AB对NIT、CXM、AMP、CZO、CTT耐药率均为100％,对SAM、FEP、TOB、GEN、IPM、LVF和TZP耐药率均在15．0％以下;耐IPM的PA和AB的检出率分别为20．4％和11．4％;耐IPM的PA对NIT、CXM、SAM、AMP、CZO、CTT、CRO、SXT、1PM耐药率均为100％,对其余10种抗生素的耐药率在25．0％～84．0％;耐IPM的AB对NIT、CXM、AMP、CZO、CTT、CRO、SXT、ATM、PIP、IPM耐药率均为100％,对其余9种抗生素的耐药率在21．0％～90．0％。结论引发下呼吸道感染的非发酵菌以PA和AB为主且耐药现象严重,临床医师在选择抗菌药物前应重视病原学培养,根据药敏试验选择用药。     

呼吸道菌群种类和数量与小儿毛细支气管炎的关系

目的 分析呼吸道菌群定植种类和数量与小儿毛细支气管炎之间的关联性.方法 选择2017年5月至2018年5月我院收治的296例毛细支气管炎患儿,将患儿按照疾病严重程度分为重症毛细支气管炎组(n=92)和轻症毛细支气管炎组(n=204),另纳入同期在我院体检的62例健康儿童为对照组,分析各组对象呼吸道菌群的种类及数量.结果...     

基于高通量测序的三峡库区重庆段黄胸鼠肠道菌群分析

研究三峡库区重庆段黄胸鼠肠道细菌的群落结构和多样性,初步了解库区黄胸鼠携带病原体的本底资料。

对三峡库区重庆段32例黄胸鼠的粪便样品进行16S rDNA高通量测序,分析黄胸鼠肠道菌群多样性、丰度和群落结构。

三峡库区重庆段黄胸鼠肠道菌群主要以厚壁菌门、拟杆菌门和变形菌门为主。在属水平上,优势菌属包括乳杆菌属、Cellulosilyticum 、八叠球菌属等。不同县（区）黄胸鼠肠道菌群结构不同,丰都县（FD）和涪陵区（FL）的菌群结构相似度较高,巫山县（WS）、开州区（KZ）、忠县（ZX）、奉节县（FJ）和云阳县（YY）5个区县群落结构相似度较高;三峡库区重庆段黄胸鼠肠道菌群结构相似度秋季明显高于春季。32份鼠粪样本测序结果提示含有葡萄球菌属、双歧杆菌属、沙门氏菌属、螺杆菌属等致病菌和条件致病菌。

初步了解了三峡库区重庆段黄胸鼠的肠道菌群特征以及库区内地域性、季节性差异,黄胸鼠肠道中携带大量的致病菌和条件致病菌,应引起高度重视。

     

大气细颗粒物影响小鼠上、下呼吸道菌群结构

探讨影响人类健康的大气细颗粒物干扰小鼠上呼吸道和下呼吸道菌群定植及可能机制。

建立大气细颗粒物暴露的小鼠模型。BALB/c小鼠随机分为PM2.5暴露组和对照组, 每组10只。收集上呼吸道和下呼吸道灌洗液进行菌群测序分析, 并进行肺组织HE染色, 观察肺组织形态改变情况。

大气细颗粒物暴露小鼠, 破坏肺组织气血屏障结构。16S rRNA测序证实了上、下呼吸道微生态的组成因大气细颗粒物暴露而发生改变。明确了与细颗粒物暴露组相比较, 对照组的噬几丁质菌定植的丰度较高。

大气细颗粒物影响小鼠上、下呼吸道的微生态结构。研究发现的差异菌群改变将会成为新的肺损伤治疗的潜在菌群。

     

Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients

Bacterial pneumonia is a major cause of morbidity and mortality in elderly. We hypothesize that dysbiosis between regular residents of the upper respiratory tract (URT) microbiome, that is balance between commensals and potential pathogens, is involved in pathogen overgrowth and consequently disease. We compared oropharyngeal microbiota of elderly pneumonia patients (n=100) with healthy elderly (n=91) by 16S-rRNA-based sequencing and verified our findings in young adult pneumonia patients (n=27) and young healthy adults (n=187). Microbiota profiles differed significantly between elderly pneumonia patients and healthy elderly (PERMANOVA, P<0.0005). Highly similar differences were observed between microbiota profiles of young adult pneumonia patients and their healthy controls. Clustering resulted in 11 (sub)clusters including 95% (386/405) of samples. We observed three microbiota profiles strongly associated with pneumonia (P<0.05) and either dominated by lactobacilli (n=11), Rothia (n=51) or Streptococcus (pseudo)pneumoniae (n=42). In contrast, three other microbiota clusters (in total n=183) were correlated with health (P<0.05) and were all characterized by more diverse profiles containing higher abundances of especially Prevotella melaninogenica, Veillonella and Leptotrichia. For the remaining clusters (n=99), the association with health or disease was less clear. A decision tree model based on the relative abundance of five bacterial community members in URT microbiota showed high specificity of 95% and sensitivity of 84% (89% and 73%, respectively, after cross-validation) for differentiating pneumonia patients from healthy individuals. These results suggest that pneumonia in elderly and young adults is associated with dysbiosis of the URT microbiome with bacterial overgrowth of single species and absence of distinct anaerobic bacteria. Whether the observed microbiome changes are a cause or a consequence of the development of pneumonia or merely coincide with disease status remains a question for future research.     

Upper respiratory tract infection in mouse and rats

Summary Spontaneous aspergilloma in the para-nasal cavities of 2 rats, and a chronic granuloma with grains, caused by Gram-positive cocci in the maxillary sinus of a mouse, are reported.     

The impact of bacteriophages on probiotic bacteria and gut microbiota diversity

The human body is colonized by a vast array of bacteria whose diversity is largely affected by predation of bacteriophages. Here, we discussed the impact of bacteriophages on the composition of human intestinal microbiota as well as on the survival and thus efficacy of probiotic bacteria in the human gut.     

Using mouse models to understand normal and abnormal urogenital tract development

The central objective of diabetes research and management is to restore the deficient secretion of insulin, thereby restoring a state of euglycemia and minimizing short- and long-term risks associated with poor glucose control. The development of the artificial pancreas seeks to imitate the action of the pancreatic beta cell by employing closed-loop control to respond to glycemic excursions by appropriately infusing appropriate amounts of insulin. This article examines progress towards implementing an artificial pancreas in the context of the pancreatic islet as the ideal model for controlling blood glucose. Physiologic insulin secretion will form our foundation for considering the technical design elements relevant to electromechanically imitating the beta cell. The most recent clinical trials using closed-loop control are reviewed and this modality is compared to other curative approaches including islet cell transplantation and preservation. Finally, the potential of the artificial pancreas as a method to adequately reestablish euglycemia is considered.     

Microflora of the upper respiratory tract of normal young children and in respiratory tract diseases. Normal microflora and dysbiosis at different levels of the upper respiratory tract in healthy children and pneumonia patients

Material obtained from the mucous membranes of the upper respiratory tract (the anterior section of the nasal cavity, the fauces) in young children, both healthy and suffering with different forms of acute pneumonia, has been analyzed with due regard to the structure of the microflora, its specific composition and the size of populations formed by different species constituting the microflora. This analysis has made it possible to determine the species constituting normal microflora, to detect its dysbiotic changes, and to determine their degree (partial or complete dysbacteriosis). The degree of pathologic changes in the microecological balance of the upper respiratory tract has been shown to reflect the severity of acute pneumonia and to be determined by the characteristics of the natural resistance system in young children.     

Microflora of the upper respiratory tract in young children under normal conditions and in respiratory tract diseases. Microbial count of the upper respiratory tract in healthy children and in children with pneumonia

The results of the inoculation of material taken from the anterior section of the nasal cavity and from the pharyngeal mucosa of 50 healthy young children and 298 acute pneumonia patients were analyzed. 23 microbial species were isolated. In the samples taken from the anterior section of the nasal cavity, monocultures were detected in 86 samples and 54 variants of associations including 2-4 species, in 139 samples. In the samples taken from the pharynx, monocultures were detected in 59 samples and 180 variants of associations including 2-6 species, in 282 samples. Differences in the contamination of the nasal cavity and the pharynx in healthy children and in pneumonia patients were revealed. These differences were manifested in the structure of the microflora (monocultures, associations, their composition), the assortment of microbial species and their concentration. In young children with pneumonia the microflora of the upper respiratory tract was found to reflect the severity of acute pneumonia and the intensity of the pathological process in the lungs (uncomplicated, pyodestructive pneumonia, pyodestructive pneumonia with fatal termination, acute purulent pleurisy).     

Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation

Background

Bacterial vaginosis (BV) is an enigmatic disease of unknown origin that affects a large percentage of women. The vaginal microbiota of women with BV is associated with serious sequelae, including abnormal pregnancies. The etiology of BV is not fully understood, however, it has been suggested that it is transmissible, and that G. vaginalis may be an etiological agent. Studies using enzymatic assays to define G. vaginalis biotypes, as well as more recent genomic comparisons of G. vaginalis isolates from symptomatic and asymptomatic women, suggest that particular G. vaginalis strains may play a key role in the pathogenesis of BV.

Methodology/Principal Findings

To explore G. vaginalis diversity, distribution and sexual transmission, we developed a Shannon entropy-based method to analyze low-level sequence variation in 65,710 G. vaginalis 16S rRNA gene segments that were PCR-amplified from vaginal samples of 53 monogamous women and from urethral and penile skin samples of their male partners. We observed a high degree of low-level diversity among G. vaginalis sequences with a total of 46 unique sequence variants (oligotypes), and also found strong correlations of these oligotypes between sexual partners. Even though Gram stain-defined normal and some Gram stain-defined intermediate oligotype profiles clustered together in UniFrac analysis, no single G. vaginalis oligotype was found to be specific to BV or normal vaginal samples.

Conclusions

This study describes a novel method for investigating G. vaginalis diversity at a low level of taxonomic discrimination. The findings support cultivation-based studies that indicate sexual partners harbor the same strains of G. vaginalis. This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.