人体鼻咽部微生物群落多样性研究进展

定殖于鼻咽部的微生物与人体始终处于动态生态平衡,对于维持人体健康发挥着重要作用,也与多种上呼吸道疾病的发生发展有密切关系。鼻咽部微生物之间及其与宿主之间的相互作用是引发人体上呼吸道疾病的重要因素。微生物的培养方法与分子生物学技术的结合使人们越来越深入地了解人体鼻咽部微生物群落的组成和结构。定殖于人体鼻咽部的微生物以肺炎链球菌(Streptococcus pneumoniae)和流感嗜血杆菌(Haemophilus influenzae)等潜在致病菌为主。本文将分别从鼻咽部微生物与机体的平衡关系、鼻咽部微生物群落的研究方法以及鼻咽部微生物群落的组成及其相互关系三个方面,综述近年来鼻咽部微生物群落结构的相关研究进展,从而为指导实践提供可靠的理论依据。     

Analysis of subgingival microbiome of periodontal disease and rheumatoid arthritis in Chinese: A case-control study

ObjectivePeriodontitis (PD) and rheumatoid arthritis (RA) share similar pathogenesis. Evidences indicated that oral bacteria play an important role in the etiology of both diseases. For example, Porphyromonas gingvialis connect the two diseases through immune responses. We designed this study to compare bacterial diversity in RA, PD and healthy subjects and to investigate whether there are other oral bacteria play an potential role in linking the two diseases.MethodsThis study included 3 groups of Chinese participants who visited Sichuan Provincial People’s Hospital during August 2018 and March 2019. Subgingival plaques were collected from RA group (n = 54), PD group (n = 45) and normal group (n = 44). Illumina MiSeq was used to compare the composition of subgingival microbiota and analyze correlations between oral bacteria and both diseases.ResultsAlpha diversity Analysis reflected similar microbiome profile in RA, PD and healthy groups. But we found Treponema was significantly more abundant in the PD and RA groups than healthy group at each taxonomic level from the phylum down to the genus level. Porphyromonas, Prevotella, and Veilonella were significantly more abundant in RA while Streptococcus, Gemella, Planobacterium were verified the opposite results.ConclusionsWe found no significant group differences referent to either microbial diversity or richness. But we picked out Spirochaetes which may link the two diseases. Upper/lower regulation of some microbia in RA may remind us a direction to explore the role they play in pathogenesis.     

Rubipodanin B,a New Cytotoxic Cyclopeptide from Rubia podantha

Using the TLC cyclopeptide protosite detection method, a new cyclohexapeptide named rubipodanin B ( 1 ), together with 11 known Rubiaceae‐type cyclopeptides (RAs), RA‐X‐OMe ( 2 ), RA‐IV ( 3 ), RA‐XI ( 4 ), RA‐XIII‐OMe ( 5 ), rubiyunnanin C ( 6 ), RA‐I ( 7 ), RA‐III ( 8 ), RA‐V ( 9 ), RA‐VII ( 10 ), RA‐XII ( 11 ) and rubipodanin A ( 12 ), were obtained from the roots and rhizomes of Rubia podantha Diels . The structures were determined using various spectroscopic methods. Among them, 2 was firstly identified as a natural product, and 3–6 were firstly isolated from this species. Cytotoxicity and NF‐κB signaling pathway activity of 1 , 2 , 4 , 6 , 7 and 9 were evaluated. All these compounds showed cytotoxic activities against three human tumor cell lines, MDA‐MB‐231, SW620 and HepG2, with the IC₅₀ values between 0.015 and 10.27 μm , and only 7 and 9 possessed NF‐κB inhibitory activities with the IC₅₀ values of 2.42 and 0.046 μm , respectively, which demonstrated that 2‐alanine amino acid plays a key role to maintain the RAs bioactivity.     

Microbial pathogenesis and type III interferons

The innate immune system possesses a multitude of pathways to sense and respond to microbial pathogens. One such family are the interferons (IFNs), a family of cytokines that are involved in several cellular functions. Type I IFNs are appreciated to be important in several viral and bacterial diseases, while the recently identified type III IFNs (IFNL1, IFNL2, IFNL3, IFNL4) have been studied primarily in the context of viral infection. Viral and bacterial infections however are not mutually exclusive, and often the presence of a viral pathogen increases the pathogenesis of bacterial infection. The role of type III IFN in bacterial and viral-bacterial co-infections has just begun to be explored. In this mini review we discuss type III IFN signaling and its role in microbial pathogenesis with an emphasis on the work that has been conducted with bacterial pathogens.     

Resveratrol inhibits urban particulate matter-induced COX-2/PGE2 release in human fibroblast-like synoviocytes via the inhibition of activation of NADPH oxidase/ROS/NF-κB

Human fibroblast-like synoviocytes (FLSs) play a role in joint synovial inflammation in rheumatoid arthritis (RA). Some evidence indicates that particulate matter (PM) in air pollution could contribute to the progression of RA. However, more research is needed to clarify this relationship. Up-regulation of cyclooxygenase (COX)-2 and its metabolite prostaglandin E₂ (PGE₂) are implicated in various inflammatory diseases. Resveratrol, a polyphenol found mainly in grapes and red wine, has antioxidant and anti-inflammatory activities. In the present study, we demonstrated that resveratrol reduced PM-induced COX-2/PGE₂ expression in human FLSs, and attenuated PM-enhanced NADPH oxidase activity and ROS generation. In addition, PM induced Akt, ERK1/2, or p38 MAPK activation, which was inhibited by resveratrol. Finally, we demonstrated that PM enhanced NF-κB p65 phosphorylation and the NF-κB promoter activity, which were reduced by pretreatment with a ROS inhibitor or resveratrol. Thus, we concluded that resveratrol functions as a suppressor of PM-induced inflammatory signaling pathways by inhibiting COX-2/PGE₂ expression.     

低龄婴幼儿龋微生物群落的研究进展

低龄婴幼儿龋(early childhood caries,ECC)是影响全世界儿童最常见的疾病之一,然而龋病并不是由单一致龋细菌引起,而是由微生物、宿主、饮食和时间,即"龋病病因四因素"之间复杂的相互作用所引起,其中微生物因素起着主要作用。口腔微生物之间存在着一种稳定关系,与宿主保持着和谐的生态平衡,一旦受到某种特殊环境改变的影响,这种平衡则可能被打破。到目前为止,国内外关于ECC的微生物群落研究方法很多,结果不尽相同,因此了解ECC的组成及动态变化对于儿童龋病的预防和防治极其重要。本文就ECC微生物群落的研究进展作一详细综述。     

Is the microwave irradiation a suitable method for measuring soil microbial biomass?

Soil microbial biomass (SMB), the living part of soil organic matter, is used to quantify the total biomass of microorganisms present in the soil. The importance of studies about SMB has emphasized the need to identify methods which can measure the size of SMB. Among the methods currently available, chloroform-fumigation extraction and incubation are the most commonly used for estimation of SMB. However, several studies have proposed the microwave (MW) irradiation as a quick, simple and safe alternate method. There are different opinions about suitability of this method for measuring SMB. There is a question to do “Is the microwave irradiation a suitable method for measuring soil microbial biomass?” Most of the published papers comparing MW and chloroform-fumigation showed strong relationship between both methods. Therefore, we consider MW a suitable method for measuring SMB; however, it is necessary to calibrate the MW methods in different soils with a range of properties, such as clay content, to find an appropriate conversion factor in order to generate correct values for SMB with MW method.     

Investigation of the microbial community structure and activity as indicators of compost stability and composting process evolution

In a bid to identify suitable microbial indicators of compost stability, the process evolution during windrow composting of poultry manure (PM), green waste (GW) and biowaste was studied. Treatments were monitored with regard to abiotic factors, respiration activity (determined using the SOUR test) and functional microflora. The composting process went through typical changes in temperature, moisture content and microbial properties, despite the inherent feedstock differences. Nitrobacter and pathogen indicators varied as a monotonous function of processing time. Some microbial groups have shown a potential to serve as fingerprints of the different process stages, but still they should be examined in context with respirometric tests and abiotic parameters. Respiration activity reflected well the process stage, verifying the value of respirometric tests to access compost stability. SOUR values below 1 mg O₂/g VS/h were achieved for the PM and the GW compost.     

Infectomics: genomics and proteomics of microbial infections

The completion of genomic sequences is the greatest triumph of molecular reductionism since the discovery of the DNA double helix in 1953. However, the utility of reductionism is becoming limited and holistic approaches, including theories and techniques, are desperately needed in the postgenomic era. In the field of infectious diseases there is an urgent need for global approaches that can efficiently, precisely and integratively study structural and functional genomics and proteomics of microbial infections (infectomics). The combination of new (e.g. DNA and protein microarrays) and traditional approaches (e.g. cloning, PCR, gene knockout and knockin, and antisense) will help overcome the challenges we are facing today. We assume that the global phenotypic changes (infectomes) in microbes and their host during infections are encoded by the genomes of microbial pathogens and their hosts, expressed in certain environmental conditions devoted to specific microbe-host interactions. Global drug responses (pharmacomes) in microbes and their host can be detected by genomic and proteomic approaches. Genome-wide approaches to genotyping and phenotyping or expression profiling will eventually lead to global dissection of microbial pathogenesis, efficient and rapid diagnosis of infectious diseases, and the development of novel strategies to control infections. The key fundamental issue of infectious diseases is how to globally and integratively understand the interactions between microbial pathogens and their hosts by using infectomics. In this review, we focus on the events that are considered important in infectomics. Electronic Publication     

Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest

To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbondioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO₂ production and soil NH₄⁺ concentration, while microbial community characteristics correlated with N₂O production, nitrification potential, gross N-mineralization, and soil NO₃^– concentration, independent of environmentalcontrollers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes,particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2 years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.     

口腔微生物多样性研究进展

口腔微生物多样性的改变是口腔常见感染性疾病的发病机制之一,随着分子生物学技术的普遍应用,研究者能够不通过纯培养技术即可对人类口腔不同生态系的微生物组成及变化进行研究。本文综述了当前口腔微生物多样性研究的常用方法及各自的特点,从而为口腔微生物生态方面的进一步深入研究提供参考。     

Human Hsp40 proteins, DNAJA1 and DNAJA2, as potential targets of the immune response triggered by bacterial DnaJ in rheumatoid arthritis

Hsp40 proteins of bacterial and human origin are suspected to be involved in the pathogenesis of rheumatoid arthritis (RA). It has been shown that sera of RA patients contain increased levels of antibodies directed to bacterial and human Hsp40s. The aim of this work was to explore immunological similarities between the bacterial (DnaJ) and human (DNAJA1 and DNAJA2) Hsp40 proteins in relation to their possible involvement in the RA. Using polyclonal antibodies directed against a full-length DnaJ or its domains, against DNAJA1 and DNAJA2, as well as monoclonal anti-DnaJ antibodies, we found immunological similarities between the bacterial and human Hsp40s. Both ELISA and Western blotting showed that these similarities were not restricted to the conserved J domains but were also present in the C-terminal variable regions. We also found a positive correlation between the levels of the anti-DnaJ and anti-DNAJA1 antibodies in the sera of RA patients. This finding supports the molecular mimicry hypothesis that human Hsp40 could be the targets of antibodies originally directed against bacterial DnaJ in RA.     

Induction of human aquaporin-1 gene by retinoic acid in human erythroleukemia HEL cells

Retinoids have been implicated in the control of cell proliferation, differentiation, and developmental processes. We report here that aquaporin-1 (AQP1) is specifically induced by retinoic acid (RA) in human erythroleukemia HEL cells. Both all-trans-RA (ATRA) and 9-cis-RA (9CRA) strongly induced the AQP1 mRNA and protein in a dose-dependent manner. AQP1 protein was mainly expressed in plasma membrane in cells induced by RAs. To identify the RA response element (RARE) in the human AQP1 promoter, the 5(')-flanking region of AQP1 promoter was isolated and transient transfection experiment in HEL cells was performed. Deletion analysis of the AQP1 promoter revealed that one putative DR5-like RARE with five spaces was located in the region from -2218 to -2202; AGGGCAgggacAGGTGA. Electrophoretic mobility shift assay (EMSA) experiment demonstrated that two slowly migrated complexes (C1 and C2) capable of binding the RARE sequence were present in nuclear extracts prepared from cells and the complex C1 was strongly increased in nuclear extracts by RA stimulation. The complexes C1 and C2 were significantly abolished by an excess unlabeled probe. These results indicate that RAs strongly stimulate the human AQP1 gene expression through the RARE and define a novel role in the regulation of erythropoiesis.     

Linking soil bacterial diversity to satellite-derived vegetation productivity: a case study in arid and semi-arid desert areas

Increasing studies have begun to focus on biodiversity–productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long-term experiments were analysed using high-throughput sequencing, and satellite-derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low- and high-productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed operational taxonomic units and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large-scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi-arid areas and confirm the potential value of satellite-derived datasets in research on soil microbial diversity at large spatial scales.     

现代分子生物学技术在瘤胃微生态系统研究中的应用

瘤胃中栖息着大量的微生物,由于这些微生物组成复杂且有些细菌在体外无法培养,目前对这些微生物的了解仍然很少。现代分子生物学技术的发展为研究瘤胃微生物提供了有效的方法,利用核酸探针、基因序列分析、遗传指纹技术、全细胞杂交和实时定量PCR等技术可以对瘤胃微生物的分类及进化关系、区系结构图、重要酶的表达以及目的微生物的准确定量进行更为深入和透彻的研究。发展和利用这些技术不仅可以研究微生物之间的关系以及微生物与饲料颗粒之间时间与空间的关系,还能直接在细菌自然生长的环境中对其各种特征进行研究。     

一种枯草芽孢杆菌B29菌株拌种剂对大豆根腐病的田间防效研究

根腐病是黑龙江省主栽作物大豆的主要病害之一。生防枯草芽孢杆菌B29菌株对引起大豆根腐病的镰刀菌、腐霉菌和立枯丝核菌具有强拮抗作用。以枯草芽孢杆菌为主要成分的微生物拌种剂对大豆根腐病的田间防效结果: 播种后35 d调查, 4种不同处理的平均防效分别为50.2%、60.0%、48.3%、49.4%, 均高于30%多克福种衣剂的防效(44.9%)。第2次(50 d)调查, 处理4的防效(60.7%)明显好于化学种衣剂(48.6%), 处理3的防效与化学种衣剂的防效差异不显著。通过对生长期大豆出苗率、株高、鲜重和根瘤数等各项生理指标的调查, 结果表明枯草芽孢杆菌微生物拌种剂对大豆的生长和发育是安全的。经过黑龙江省6个不同县市的2年田间示范, 微生物拌种剂对大豆根腐病的田间防效达56.3%~89.1%, 增产率为9.4%~24.6%。     

Investigating the biological and clinical significance of human dysbioses

Culture-independent microbiological technologies that interrogate complex microbial populations without prior axenic culture, coupled with high-throughput DNA sequencing, have revolutionized the scale, speed and economics of microbial ecological studies. Their application to the medical realm has led to a highly productive merger of clinical, experimental and environmental microbiology. The functional roles played by members of the human microbiota are being actively explored through experimental manipulation of animal model systems and studies of human populations. In concert, these studies have appreciably expanded our understanding of the composition and dynamics of human-associated microbial communities (microbiota). Of note, several human diseases have been linked to alterations in the composition of resident microbial communities, so-called dysbiosis. However, how changes in microbial communities contribute to disease etiology remains poorly defined. Correlation of microbial composition represents integration of only two datasets (phenotype and microbial composition). This article explores strategies for merging the human microbiome data with multiple additional datasets (e.g. host single nucleotide polymorphisms and host gene expression) and for integrating patient-based data with results from experimental animal models to gain deeper understanding of how host-microbe interactions impact disease.     

Tools for T-RFLP data analysis using Excel

Background

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed.

Results

The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data.

Conclusions

The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0361-7) contains supplementary material, which is available to authorized users.     

MicroRNA and exosome: Key players in rheumatoid arthritis

Rheumatoid arthritis (RA) is known as one of important autoimmune disorders which can lead to joint pain and damage throughout body. Given that internal (ie, genetic and epigenetic alterations) and external factors (ie, lifestyle changes, age, hormones, smoking, stress, and obesity) involved in RA pathogenesis. Increasing evidence indicated that cellular and molecular alterations play critical roles in the initiation and progression of RA. Among various targets and molecular signaling pathways, microRNAs (miRNAs) and their regulatory networks have key roles in the RA pathogenesis. It has been showed that deregulation of many miRNAs involved in different stages of RA. Hence, identification of miRNAs and their signaling pathways in RA, could contribute to new knowledge which help to better treatment of patients with RA. Besides miRNAs, exosomes have been emerged as key messengers in RA pathogenesis. Exsosomes are nanocarriers which could be released from various cells and lead to changing of behaviors recipient cells via targeting their cargos (eg, proteins, messenger RNAs, miRNAs, long noncoding RNAs, DNAs). Here, we summarized several miRNAs involved in RA pathogenesis. Moreover, we highlighted the roles of exosomes in RA pathogenesis.     

Human IL-36RA production in <Emphasis Type="Italic">Escherichia coli</Emphasis> with coexpression of <Emphasis Type="Italic">E. coli</Emphasis> methionine aminopeptidase. II. Comparison of IL-36RA biological activity from different strains

Proinflammatory cytokines of the interleukin-36 (IL-36) family are involved in the pathogenesis of different skin diseases in human and mice. Administration of exogenous IL-36 receptor antagonist (IL-36RA) may be an approach to therapy of different dermatitises. For its full biological activity, IL-36RA requires cleavage of N-terminal methionine residue. We created three E. coli strains producing IL-36RA coexpressed with E. coli methionine aminopeptidase under control of different promoters. To test the biological activity of IL-36RA from different strains we transfected А549 cells with plasmid carrying the IL-36 receptor gene (IL1RL2). These cells respond to IL-36g treatment with production of IL-8, which can be quantified with ELISA. IL-36RA treatment disrupts IL-36 receptor activation by IL-36g and production of IL-8. Using this system, we proved that IL-36RA from all three producer strains is fully biologically active.