Relationship between hyperlipidemia and the gut microbiome of rats, characterized using high-throughput sequencing

Objective:To determine the effects of a high-fat diet(HFD)on the gut microbiome in rats,to explore the relationship between the intestinal flora and blood lipid profile.Methods:SpragueeDawley rats were fed an HFD for four weeks to induce hyperlipidemia,then 16S rRNA sequencing was used to compare the intestinal flora between hyperlipidemic and control diet-fed rats.Results:The microbiome of rats fed an HFD for four weeks differed from that of control diet-fed rats.Bacterial species that were less abundant were most affected by HFD feeding,among which were many pathogenic species,which became significantly more abundant.Eighteen genera were present in significantly different numbers in hyperlipidemic and control rats,more than half of which have been linked to infection and inflammation,or energy intake and obesity.The results indicated a type of stress response of the flora to a high-fat environment.In addition,the age of the rats tended to influence the gut microbial composition.Conclusion:These findings suggest that HFD may induce hyperlipidemia by affecting the gut microbial composition.Changes in the abundance of pro-inflammatory and pathogenic bacteria,and those that influence energy intake and obesity,may be important mediators of this.

Next-generation sequencing revealed specific microbial symbionts in Porites lutea with pigment abnormalities in North Sulawesi, Indonesia

Bacterial diseases affecting corals pose an enormous threat to the health of coral reefs. The relationship between certain bacterial species and coral diseases remain largely unknown. Pigment abnormalities are common in Porites lutea. Here we used Illumina 16S rRNA gene sequencing to analyze the bacterial communities associated with healthy P. lutea and P. lutea with pigment abnormalities. We observed an increase of alpha diversity of the bacterial community of P. lutea with pigment abnormalities, relative to healthy corals. We then identified changes in the abundance of individual operational taxonomic units(OTUs) between pigmented and healthy corals. We were able to identify eight OTUs associated with pigment abnormalities, which are possibly the causative agents of pigment abnormalities.

Comparative analysis of the gut microbiota of wild adult rats from nine district areas in Hainan,China

BACKGROUND Wild rats have the potential to hold zoonotic infectious agents that can spread to humans and cause disease.AIM To better understand the composition of gut bacterial communities in rats is essential for preventing and treating such diseases.As a tropical island located in the south of China,Hainan province has abundant rat species.Here,we examined the gut bacterial composition in wild adult rats from Hainan province.METHODS Fresh fecal samples were collected from 162 wild adult rats,including three species(Rattus norvegicus,Leopoldamys edwardsi,and Rattus losea),from nine regions of Hainan province between 2017-2018.RESULTS We analyzed the composition of gut microbiota using the 16S rRNA gene amplicon sequencing.We identified 4903 bacterial operational taxonomic units(30 phyla,175 families,and 498 genera),which vary between samples of different rat species in various habitats at various times of the year.In general,Firmicutes were the most abundant phyla,followed by Bacteroidetes(15.55%),Proteobacteria(6.13%),and Actinobacteria(4.02%).The genus Lactobacillus(20.08%),unidentified_Clostridiales(5.16%),Romboutsia(4.33%),unidentified_Ruminococcaceae(3.83%),Bacteroides(3.66%),Helicobacter(2.40%)and Streptococcus(2.37%)were dominant.CONCLUSION The composition and abundance of the gut microbial communities varied between rat species and locations.This work provides fundamental information to identify microbial communities useful for disease control in Hainan province.

Alterations in gut microbiota are related to metabolite profiles in spinal cord injury

Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To investigate the correlation between gut microbiota and metabolites and the possible mechanism underlying the effects of gut microbiota on secondary injury after spinal cord injury, in this study, we established mouse models of T8–T10 traumatic spinal cord injury. We used 16 S rRNA gene amplicon sequencing and metabolomics to reveal the changes in gut microbiota and metabolites in fecal samples from the mouse model. Results showed a severe gut microbiota disturbance after spinal cord injury, which included marked increases in pro-inflammatory bacteria, such as Shigella, Bacteroides, Rikenella, Staphylococcus, and Mucispirillum and decreases in anti-inflammatory bacteria, such as Lactobacillus, Allobaculum, and Sutterella. Meanwhile, we identified 27 metabolites that decreased and 320 metabolites that increased in the injured spinal cord. Combined with pathway enrichment analysis, five markedly differential amino acids(L-leucine, L-methionine, L-phenylalanine, L-isoleucine and L-valine) were screened out, which play a pivotal role in activating oxidative stress and inflammatory responses following spinal cord injury. Integrated correlation analysis indicated that the alteration of gut microbiota was related to the differences in amino acids, which suggests that disturbances in gut microbiota might participate in the secondary injury through the accumulation of partial metabolites that activate oxidative stress and inflammatory responses. Findings from this study provide a new theoretical basis for improving the secondary injury after spinal cord injury through fecal microbial transplantation.

Alterations in the human oral microbiome in cholangiocarcinoma

Dear Editor,Alterations in the human microbiome are closely related to various hepatobiliary diseases.Gut microbial dysbiosis has been found in patients with cholangiocarcinoma(CCA)[1].However,the characteristics of oral microbiome in patients with CCA have not been studied.

Sarcopenia and gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation

Objective: The aim of this study was to investigate the prevalence of sarcopenia(SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation(HSCT).Methods: A total of 108 patients with various hematological disorders were selected from Peking University People’s Hospital. SP was screened and diagnosed based on the 2019 Asian Sarcopenia Diagnosis Strategy. Physical measurements and fecal samples were collected, and 16S rRNA gene sequencing was conducted. Alpha and beta diversity analyses were performed to evaluate gut microbiota composition and diversity.Results: After HSCT, significant decreases in calf circumference and body mass index(BMI) were observed,accompanied by a decline in physical function. Gut microbiota analyses revealed significant differences in the relative abundance of Enterococcus, Bacteroides, Blautia and Dorea species before and after HSCT(P<0.05). Before HSCT, sarcopenic patients had lower Dorea levels and higher Phascolarctobacterium levels than non-sarcopenia patients(P<0.01). After HSCT, no significant differences in species abundance were observed. Alpha diversity analysis showed significant differences in species diversity among the groups, with the highest diversity in the postHSCT 90-day group and the lowest in the post-HSCT 30-day group. Beta diversity analysis revealed significant differences in species composition between pre-and post-HSCT time points but not between SP groups. Linear discriminant analysis effect size(LEfSe) identified Alistipes, Rikenellaceae, Alistipes putredinis, Prevotellaceae defectiva and Blautia coccoides as biomarkers for the pre-HSCT sarcopenia group. Functional predictions showed significant differences in anaerobic, biofilm-forming and oxidative stress-tolerant functions among the groups(P<0.05).Conclusions: This study demonstrated a significant decline in physical function after HSCT and identified potential gut microbiota biomarkers and functional alterations associated with SP in patients with hematological disorders. Further research is needed to explore the underlying mechanisms and potential therapeutic targets.

基于16S rRNA基因测序技术分析急性肝内胆汁淤积大鼠的肠道菌群

目的 探讨ANIT诱导的大鼠急性肝内胆汁淤积(acute intrahepatic cholestasis,AIC)与肠道菌群的关系。方法 以SPF级的SD大鼠为实验对象,随机分为正常对照组、模型组,每组24只,依据取材时间不同又将各组随机分为24 h、48 h、72 h 3个亚组,每组8只。模型组通过一次性予2%ANIT按100 mg·kg^(-1)·d^(-1)灌胃造模诱发AIC模型,正常对照组予等容积色拉油灌胃。通过高通量测序法对肠道粪便细菌16S rRNA的V_(3)~V_(4)区进行基因测序及生物信息学分析。结果 AIC造模后,随着时间增加,α多样性指数逐步升高,造模72 h组相比造模24 h组,Shannon指数有显著性差异;β多样性发现,利用基于加权Unifrac距离PcoA分析或NMDS分析均显示:正常对照组、造模24 h组和造模48 h组的肠道菌群显示比较明显的聚集效应;在门水平上,厚壁菌门(Firmicutes)丰度在造模48 h后显著下降,变形菌门(Proteobacteria)的丰度显著上升,拟杆菌门(Bacteroidetes)的丰度显著上升;LEfSe对组间差异显著的物种分析结果显示,LDA值大于4的微生物类群有35个。结论 模型组干预后大鼠肠道菌群结构和多样性均发生显著变化。

Genetic variation of Leptospira isolated from rats catched in Yogyakarta Indonesia

Objective: To detect genetic variations among pathogenic Leptospira isolated from rats using 16 S r RNA gen as chronometer. Methods: This is an observational study with cross sectional design. Rats saples were taken in Yogyakarta Special Region of Indonesia. Leptospira in the rats was detected by two methods ie. real time PCR(q PCR) by using primers correspond to16 S r RNA gene of Leptospira, and standard PCR by using dif erent set of primer correspond to the 16 S r RNA gene of Leptospira. The standard PCR amplicon then subjected for DNA sequencing. Analysis genetic variation was performed using MEGA 6.2. Software. Results:There were 99 DNA samples from rats included in this study. Detection of Leptospira by using q PCR revealed 25 samples positive for pathogenic Leptospira, while only 6 samples were able to be detected using standard PCR. The new primer set correspond to 16 S r RNA gene was able to detect specii cally pathogenic Leptospira in the rats. Sequencing analysis of 6 PCR amplicons showed that the Leptospira which infect the rats catched in Yogyakarta genetically close related with pathogenic Leptospira which were isolated from human, animal, rodents, and environment. Conclusions: It can be considered that rats are the most important vector and reservoir of Leptospira.

Effect of gastrointestinal heat retention syndrome on gut microbiota in children with upper respiratory tract infection and lung-heat syndrome

Objective:Gastrointestinal heat retention syndrome(GHRS)is associated with lung-heat syndrome and is related to recurrent respiratory infection.Upper respiratory tract infection(URTI)lung heat syndrome is common in children.The study will explore the effect of GHRS on the structure and function of gut microbiota in children with URTI lung-heat syndrome.Methods:Participants were divided into both groups using the self-developed URTI scale and the“GHRS Diagnostic Scale$Pediatric Part”:GHRS-positive children(LS group)and GHRS-negative children(L group).General information,clinical symptoms,and stool were collected.We used 16S rRNA amplicon sequencing technology to determine the gene sequence of the V3eV4 region in feces and measure the gut microbiota of the both groups at the genus level.Results:A total of 23 children were included in the both groups.There were 12 cases in the LS group and 11 cases in the L group.There was no statistical difference between the both groups in age,gender,height,weight,and body mass index.The effective sequences shared by the both groups accounted for 85.66%of the total.In the gut microbiota,there was no difference in the a diversity and the b diversity between the both groups.Compared with the L group,the LS group had a significant increase in the relative abundance of the Ruminococcus gnavus group,Prevotella-9,Staphylococcus,and Actinomyces(P<.05).The functions of the both groups of microbiota primarily concentrate on metabolism,genetic information processing,and environmental information processing.The relative abundance of signaling molecules and interactions in the LS group were higher than that in the L group(P<.05).The redundancy analysis(RDA)showed that the URTI score had the greatest impact on the distribution of microbiota.Conclusion:GHRS may affect the development of URTI lung-heat syndrome by changing the relative abundances of gut microbiota.

Isolation and identification of multidrug-resistant Staphylococcus haemolyticus from a laboratory-breeding mouse

Objective:To analysis and identify a bacterium strain isolated from laboratory breeding mouse far away from a hospital.Methods:Phenotype of the isolate was investigated by conventional microbiological methods,including Gram-staining,colony morphology,tests for haemolysis, catalase,coagulase,and antimicrobial susceptibility test.The meek and 16S rRNA genes were amplified by the polymerase chain reaction(PCR) and sequenced.The base sequence of the PCR product was compared with known 16S rRNA gene sequences in the CenBank database by phylogenetic analysis and multiple sequence alignment.Results:The isolate in this study was a gram positive,coagulase negative,and catalase positive coccus.The isolate was resistant to oxacillin,methicillin,penicillin,ampicillin,cefazolin,cipr of loxacin erythromycin,et al.PCR results indicated that the isolate was meek gene positive and its 16S rRNA was 1465 bp.Phylogenetic analysis of the resultant 16S rRNA indicated the isolate belonged to genus Saphylococcus,and multiple sequence alignment showed that the isolate was Saphylococcus haemolyticus with only one base difference from the corresponding 16S rRNA deposited in the CenBank.Conclusions: 16S rRNA gene sequencing is a suitable technique for non-specialist researchers.Laboratory animals are possible sources of lethal pathogens,and researchers must adapt protective measures when they manipulate animals.

Ganjiang granule regulates cecal microflora and serum biochemical components in a rat model of constipation-predominant irritable bowel syndrome

Objective:To investigate the effects of Ganjiang granule(GG)on cecal microflora and serum biochemical components in rats with constipation-predominant irritable bowel syndrome(IBSeC).Methods:Twenty-four SpragueeDawley rats were randomly divided into four groups:control,model,GG,and probiotics.Rats in the model,GG,and probiotics groups received 3℃ tap water intragastrically;rats in the GG group were treated with GG;rats in the probiotics group were treated with probiotics.For all rats,enzyme-linked immunosorbent assay and colorimetry were used to assess serum biochemical components related to gastrointestinal function;16S rRNA high-throughput sequencing was used to analyze the cecal microflora.Results:The serum level of 5-hydroxytryptamine(HT)was higher in the model group than in the control group(Z=-2.082,P=.037).The model group exhibited changes in cecal microflora:the relative abundances of Lactobacillus decreased(Z=-2.882,P=.004)and Dorea increased(t=-3.030,P=.023),compared with the control group.The GG and probiotics groups exhibited normal serum levels of 5-HT.The GG and probiotics groups exhibited improved serum levels of gastrin;the probiotics group exhibited an improved serum level of vasoactive intestinal peptide.Compared with the model group,The GG group exhibited greater relative abundance of Ruminococcus(Z=-2.402,P=.016);the probiotics group exhibited greater relative abundance of SMB53(Z=-2.823,P=.005)and lower relative abundances of Desulfovibrio(Z=-2.823,P=.005)and Facklamia(Z=-2.608,P=.009).Conclusion:The effects of GG on IBS-C may be related to regulation of the serum level of 5-HT,as well as elevated relative abundance of beneficial bacteria in cecal microflora.

基于16S rRNA基因测序技术分析非酒精性脂肪性肝病大鼠的肠道菌群

目的 基于16S rRNA基因测序技术分析非酒精性脂肪性肝病(non-alcoholic fatty liver disease,NAFLD)大鼠的肠道菌群。方法 以SPF级SD大鼠为实验对象,随机分为普通饮食组(对照组)和高脂饮食组(模型组)。高脂饮食组通过进食高脂饲料8周诱发NAFLD模型。8周后检测大鼠血清丙氨酸氨基转移酶(alanine aminotransferase,ALT)、天门冬氨酸氨基转移酶(aspartate aminotransferase,AST)、高密度脂蛋白胆固醇(high-density lipoprotein cholesterol,HDL-C)、低密度脂蛋白胆固醇(low density lipoprotein cholesterol,LDL-C)、甘油三酯(triglyceride,TG)和总胆固醇(total cholesterol,TC)水平,取肝组织进行HE及油红O染色,采集大鼠新鲜粪便通过高通量测序法对肠道粪便细菌16S rRNA的V3-V4区进行基因测序。利用UPARSE软件进行类单元(operational taxonomic unit,OTU)聚类,采用RDP Classifier算法对OTU代表序列进行比对分析,并在门、纲、目、科、属、种等水平上进行注释其群落的物种信息。基于OTU聚类结果,利用mothur软件和Qimme(V.1.8)进行Alpha多样性分析和Beta多样性分析,并通过LEfSe软件进行组间菌落差异分析。结果 与正常组相比,模型组大鼠AST [(23.63±4.82)U/L vs (10.61±1.17)U/L]、ALT [(9.98±2.27)U/L vs(3.40±0.81)U/L]、LDL-C [(0.69±0.11)mmol/Lvs(0.34±0.10)mmol/L]、TG [(0.90±0.24)mmol/L vs (0.33±0.13)mmol/L]及TC [(5.69±0.72)mmol/L vs(2.10±0.42)mmol/L]水平均显著升高,HDL-C [(0.62±0.14)mmol/L vs (1.07±0.17)mmol/L]水平显著降低,差异均有统计学意义(P均<0.05)。两组共获得2607个OTU,经过抽平处理后获得2547个OTU,其中对照组2367个,模型组2168个,两组共享OTU为1988个。随样本量增加物种累积曲线趋于平缓,表明样本量充分。在Alpha多样性指数中,模型组的香农指数(7.0673±0.4812 vs 6.1695±0.7165)、物种个数[(968.6250±233.0221)个vs (1155.9500±129.0011)个]和PD_Whole_Tree指数(69.3449±14.2872vs82.0219±10.2012)显著低于对照组,差异有统计学意义(P均<0.05),Chao1指数也低于对照组(1418.4503±277.8639 vs 1599.1725±100.1048),但差异无统计学意义(P>0.05)。采用主成分分析、主坐标分析、层次聚类分析、偏最小二乘法判别分析和非度量多维尺度法等Beta多样性分析方法均能将模型组与对照组大鼠完全区分开来,进一步说明二者间的菌群有明显区别。采用RDP Classifier算法对OTU代表序列进行比对分析,结果表明,从门水平分析,NAFLD大鼠厚壁菌门和放线菌门丰度增加,其中放线菌门丰度显著增加,拟杆菌门和变形菌门的丰度降低。从纲水平分析,NAFLD大鼠放线菌纲和丹毒丝菌纲相对丰度显著升高,而杆菌纲相对丰度显著下降。从目水平分析,NAFLD大鼠红椿菌目和丹毒丝菌目相对丰度显著升高,而乳杆菌目和酸微菌目相对丰度显著降低。从科水平分析,NAFLD大鼠毛螺菌科(Lachnospiraceae)、瘤胃菌科(Ruminococcaceae)、消化链球菌科(Peptostreptococcus)、丹毒丝菌科(Erysipelotrichaceae)和双歧杆菌科(Bifidobacteriaceae)等增加,其中双歧杆菌科、肽链球菌科显著增加,乳酸杆菌科(Lactobacillaceae)、普雷沃氏菌科(Prevotellaceae)和拟杆菌目S24-7组比例下降,其中乳酸杆菌科显著性减少。采用LEfSe对组间差异显著的物种分析,结果表明两组间差异起重要作用的肠道微生物类群共126个,LDA值大于3.6的微生物类群共24个。结论与普通饮食组相比,高脂饮食组干预8周后大鼠肠道菌群结构和多样性均发生显著变化。

High-throughput 16S rDNA sequencing of the pulmonary microbiome of rats with allergic asthma

A decrease in microbial infection in adolescents is implicated with an increase in the incidence of asthma and allergic diseases in adulthood,indicating that the microbiome plays a critical role in asthma.However,the microbial composition of the lower respiratory tract remains unclear,hindering the further exploration of the pathogenesis of asthma.This study aims to explore the microbial distribution and composition in the lungs of normal rats and rats with allergic asthma via 16S rDNA sequencing.The DNA of the pulmonary microbiome was extracted from the left lungs collected from normal control group(NC),saline control group(SC),and allergic asthma group(AA)under aseptic conditions.After the 16s rDNA V4eV5 region was amplified,the products were sequenced using Illumina high-throughput technology and subjected to operational taxonomic unit(OTU)cluster and taxonomy analysis.The OTU values of AA increased significantly compared with those of NC and SC.Microbiome structure analysis showed that the dominant phylum of the pulmonary microbiome changed from Proteobacteria in NC to Firmicutes in AA.Linear discriminant analysis indicated that the key microbiomes involved in the three groups varied.

Identification of Bacterial Fish Pathogens in Brazil by Direct Colony PCR and 16S rRNA Gene Sequencing

Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.

Fecal microbiota of three bactrian camels(Camelus ferus and Camelus bactrianus) in China by high throughput sequencing of the V3-V4 region of the 16S rRNA gene

This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit（OTU） clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel（Camelus ferus）, the domestic camel（C. bactrianus） and Dunhuang wild camel（C. ferus）, respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.

Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots

China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.

16S rRNA Gene-Based Metagenomic Analysis of Soil Bacterial Diversity in Brazzaville, Republic of the Congo

Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.

中国对虾16SrRNA基因序列多态性的研究

利用PCR技术扩增获得中国对虾 (Penaeuschinensis)线粒体DNA的 16SrRNA基因片段 ,通过测定该基因片段的序列 ,分析了取自我国烟台、长岛、青岛近海和宁波养殖的 17只中国对虾遗传多态性。结果发现 ,不同地理种群存在丰富的DNA序列多态性 ,17只个体具有 17种基因型 ,在扩增的长为 5 2 3bp的基因片段中 ,共检测到 3 7个多态性核苷酸位点 ( 7 0 7% )。UPGMA法构建的分子系统树表明不同地理种群中国对虾存在一定程度的遗传分化 ,长岛群体与烟台群体遗传关系较近 ,宁波群体次之 ,青岛群体为相对独立的一支。

福建华溪蟹线粒体DNA COI和16S rRNA基因序列的遗传多样性

目的探讨福建华溪蟹(Sinopotamon fukienense)的遗传多样性。方法采用PCR结合DNA测序技术,测定S.fukienense的线粒体COI和16SrRNA基因序列的组成。经比对获得639bp长度的COI基因序列和526bp的16SrRNA基因序列,以对比分析S.fukienense的遗传多样性。结果 S.fukienense基于COI基因核苷酸多样性(Pi)为0.048 4,高于其基于16SrRNA基因核苷酸多样性(Pi)为0.021 6。同时,S.fukienense基于COI基因单倍型间的平均遗传距离(P)为0.048,大于其基于16SrRNA基因单倍型间的平均遗传距离(P)0.026。结论 COI序列在分析S.fukienense遗传异变时的作用更优于16SrRNA基因序列。

5种经济海胆线粒体16S rRNA基因片段的序列分析

对光棘球海胆、中间球海胆、马粪海胆,海刺猬和紫海胆线粒体DNA 16SrRNA基因片段进行了PCR扩增和测序,得到395 bp的可信片段。通过ClustalX 1.83和Mega 3.0软件对所得线粒体16SrRNA片段序列进行比较,共检测到118个碱基变异,其中简约信息位点为33个。应用Mega 3.0计算各种间的相对遗传距离,以糙海参为外类群,得到NJ系统树和MP系统树,系统树各分支的置信度由“Bootstrap”1000次循环检验。结果表明,马粪海胆与光棘球海胆的亲缘关系较近,其次为中间球海胆,而紫海胆、海刺猬与这3种海胆的关系相对较远。