氟化物对家蚕肠道微生物菌群的影响

摘要:【目的】探讨氟化物对家蚕肠道微生物菌群的影响,开发具有潜在应用价值的益生菌以提高家蚕对氟化物的抗性。【方法】PCR扩增家蚕肠道内细菌16S rRNA基因并构建克隆文库;用核糖体DNA限制性分析(Amplified ribosomal DNA restriction analysis,ARDRA)方法对克隆子进行分型。从家蚕T6和734肠道样品中共获得14种分类操作单元(Operational taxonomic unit,OTUs),以16S rRNA基因为基础构建系统发育树进行分析。再经巢式PCR-DGGE技术检测家蚕肠道内优势菌群的变化。【结果】结果表明:家蚕氟中毒后肠道内肠球菌属Enterococcus和芽孢杆菌属Bacillus细菌菌群减少,而葡萄球菌属Staphylococcus的细菌增多。【结论】氟化物能通过改变家蚕肠道内细菌的多样性和比例,从而破坏家蚕肠道微生物菌群平衡,且对家蚕734的影响作用大于T6。     

脊尾白虾肠道微生物菌群结构

【目的】研究海水池塘养殖条件下的脊尾白虾肠道微生物菌群组成及多样性。【方法】采用PCR-RFLP技术,以直接提取的脊尾白虾肠道细菌总DNA为模板进行16S rRNA 基因扩增,产物与T载体连接建立质粒文库,从RFLP建立的文库中筛选出不同细菌来源的克隆子,将测定的差异克隆子16S rRNA片段序列与GenBank数据库进行比对。【结果】从脊尾白虾肠道的菌群文库中共获得114个克隆子,Hae Ⅲ和Msp I双酶切得到11种差异克隆子;对差异克隆子测序后,其中8个差异序列与已知细菌具有较高的同源性,分别是假单胞菌属(Pseudomonas)、肠杆菌属(Enterobater)、冰冻小杆菌属(Frigoribacterium)、褐杆菌属(Phaeobacter)、弧菌属(Vibrio)、赤杆菌属(Erythrobacter)、气单胞菌属(Aeromonas)、葡萄球菌属(Staphylococcus)和其他未培养细菌。【结论】初步揭示了脊尾白虾肠道微生物菌群结构的组成,为开发脊尾白虾专用微生态制剂提供基础资料。     

山东肥城寒武纪竹叶状石灰岩菌群分析

为了探讨微生物活动与地层形成的关系,对山东肥城万灵山寒武纪竹叶状石灰岩中的微生物进行了培养分离,用PCR方法获得了它们的16S DNA序列,通过序列比对确定了这些微生物的种属,并对这些细菌进行了系统发育进化分析.结果 表明这些细菌属于芽胞杆菌属(Bacillus)、节杆菌属(Arthrobacter)及未培养细菌(Uncultured bacterium),万灵山竹叶状石灰岩的微生物菌群分布以革兰阳性芽胞杆菌占优势.     

不同饲料饲养家蚕其肠道微生态优势菌群类型的组成及差异性

为探讨鳞翅目昆虫的生长发育及抗病性与肠道微生态状况的关系,以不同的桑科植物柘叶与桑叶分别饲养家蚕,采用纯培养分离检测技术、16S rDNA序列测定和系统发育分析方法,对4、5龄家蚕肠道优势菌群的类型进行了鉴定和差异性分析。结果表明:柘叶与桑叶饲养家蚕共有的优势菌群有短波单胞杆菌属(Brevundimonas)、寡养单胞菌属(Stenotrophomonas)、肠杆菌属(Enterobacter)和葡萄球菌属(Staphylococcus)4个类群。从桑叶饲养家蚕肠道中检索到的优势菌群还有气单胞菌属(Aeromonas)、短杆菌属(Brevibacterium)、柠檬酸杆菌属(Citrobacter)、埃希氏菌属(Escherichia)和克雷伯氏菌属(Klebsiella)5个类群,而从柘叶饲养家蚕肠道中检索到的优势菌群仅有假单胞菌属(Pseudomonas)和土壤杆菌属(Agrobacterium)2个类群。饲料的改变导致家蚕肠道微生态细菌种群组成的变化,从柘叶饲养家蚕肠道中分离出的优势菌群与桑叶饲养的家蚕相比,出现较大差异且不如桑叶饲养家蚕的菌群丰富。推测这种改变可能与柘叶饲养家蚕生长发育不良、容易患病具有相关性。     

南美白对虾肠道微生物群落的分子分析

采用分子生物学手段16S rDNA克隆文库方法对实验室养殖条件下的南美白对虾肠道细菌进行了多样性研究。用限制性片段长度多态性(RFLP)方法从文库中筛选出可能不同细菌来源的克隆子12个,测定其16S rDNA片段核甘酸序列,将所获得的序列与GenBank数据库进行BLAST比对,结果表明:南美白对虾肠道的16S rDNA克隆文库中126个克隆子分属2个不同的细菌类群:变形细菌(Proteobacteria)和厚壁细菌(Firmicutes),其中厚壁细菌为优势菌群占到75.4%,且与最相似序列同源性均低于94%;变形细菌占到24.6%,与最相似序列同源性均高于98%,分别为希瓦氏菌属(Shewanella),泛菌属(Pantoea),Aranicola属,假单胞菌属(Pseudomonas)和弧菌属(Vibrio)。     

塔河天然胡杨林地可培养细菌的生态分布研究

目的：研究塔里木河天然胡杨林部分地区可培养细菌的生态分布。方法：通过塔里木河胡杨林采样,可培养菌分离及16S rDNA序列鉴定。结果：从3种不同样品（水样、土样和胡杨树杆分泌物）中分离筛选了22株细菌,其中17株菌为革兰氏阳性菌,5株为革兰氏阴性菌。根据生理生化特征与16S rDNA序列分析结果表明,其中15株菌属于芽孢杆菌属,4株属于不动杆菌属、假单胞菌属、动性球菌属和Agrococcus属各含有1个分离株。结论：塔里木河胡杨林可培养微生物中芽孢杆菌比较丰富,其中有3个可能的新种。     

中国北部湾光裸方格星虫可培养微生物的分离鉴定及其活性代谢物产生菌筛选

【目的】本研究从北部湾海域光裸方格星虫(Sipunculus nudus)肠道中分离鉴定可培养微生物,并对筛选菌株的代谢物活性进行研究,为后续开发和利用光裸方格星虫肠道微生物代谢产物提供理论支持。【方法】通过微生物培养、菌株分离纯化和16S rRNA基因序列分析,分析鉴定湛江、北海、防城港三地光裸方格星虫肠道可培养微生物;采用透明圈法、可见分光光度法、平板打孔法等对产胞外活性代谢物的菌株进行筛选和活性分析。【结果】中国北部湾不同海域光裸方格星虫肠道可培养微生物包括弧菌属(Vibrio)、希瓦氏菌属(Shewanella)、假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)等12个细菌属。弧菌属(Vibrio)是3个地区样本共有的优势菌群。具有产胞外水解蛋白酶、壳聚糖酶、多糖以及抑菌活性等能力的菌株主要来自假交替单胞菌属(Pseudoalteromonas)、发光杆菌属(Photobacterium)和芽孢杆菌属(Bacillus)。【结论】中国北部湾不同海域光裸方格星虫肠道可培养微生物在属的种类上存在显著性差异,且光裸方格星虫肠道菌株具有产生多种胞外活性代谢物的能力,是一种良好的海洋活性代谢物来源。     

豆豉纤溶酶产生菌分离和鉴定

从全国各地收集豆豉样品,采用不同的培养基进行富集培养,并利用纤维蛋白平板法高效获得了13株形态差异较大的产纤溶酶菌株。通过传统方法、化学方法以及16S rRNA序列分析对这13株菌进行分类鉴定,它们分属于芽孢杆菌属、链霉菌属、假单胞菌属以及节杆菌属,包括9种细菌,丰富了豆豉纤溶酶产生菌菌种资源。     

新疆乌尔禾地区盐渍土壤耐盐细菌多样性与群落结构研究

研究新疆北部乌尔禾地区盐渍土壤中微生物群落结构及多样性,以期发现新的高盐环境耐盐性微生物资源菌株。采用传统分离培养法获得可培养耐盐菌株并对菌株形态学、16S rRNA基因测序、耐盐特性进行研究,同时结合高通量测序技术分析新疆乌尔禾地区盐渍土壤耐盐细菌的多样性与群落结构。共分离得到耐盐细菌11株,分属6个属,均为中度耐盐菌,以芽胞杆菌属(Bacillus)为优势菌。对盐渍土壤微生物16S rRNA(V3～V4)基因测序,共获得细菌序列290 952条,分属24个门410个属,变形菌门(Proteobacteria, 60.31%)、厚壁菌门(Firmicutes, 21.52%)、拟杆菌门(Bacteroidetes, 6.9%)和放线菌门(Actinobacteria, 6%)相对丰度较高。优势属为克吕沃尔菌属(Kluyvera,21%)、Hafnia-Obesumbacterium(19.6%)和假单胞菌属(Pseudomonas,7.5%)。结果表明,新疆乌尔禾地区盐渍土壤耐盐细菌优势菌群以芽胞杆菌属(Bacillus)居多,细菌群落结构较复杂,潜在可利用微生物资源较为丰富,对高盐极端环境耐盐微生物新资源有进一步研究的意义。     

不同饲料饲育的家蚕幼虫肠道细菌的多样性分析

【目的】为研究饲料对不同家蚕Bombyx mori品种肠道微生物菌群的影响。【方法】以筛选到的家蚕广食性品种GS和普通品种1015为研究对象,收集从收蚁开始分别饲育桑叶(GS. m和C1015. m组)和人工饲料(GS. b组)至4龄盛时期的家蚕肠道样本,采用高通量测序的方法对其肠道微生物16S r DNA的V3-V4区进行测序分析,比较它们之间肠道微生物的差异。【结果】在门水平上,所测家蚕肠道样本的优势菌为厚壁菌门(Firmicutes)和变形杆菌门(Proteobacteria);在科水平上,所测样本主要优势菌为明串珠菌科(Leuconostocaceae)、乳酸杆菌科(Lactobacillaceae)、肠杆菌科(Enterobacteriaceae)等;在属水平上,所测样本主要的优势菌为魏斯氏属Weissella、乳酸菌属Lactobacillus、布赫纳氏菌属Buchnera、甲基杆菌属Methylobacterium、叶瘤菌属Phyllobacterium、肠球菌属Enterococcus和脆弱拟杆菌属Bacteroides等。家蚕品种GS经桑叶和人工饲料饲育后,甲基杆菌属Methylobacterium、布赫纳氏菌属Buchnera等菌属仅在桑叶饲育的GS肠道内出现,而魏斯氏菌Weissella、短芽孢杆菌属Brevibacillus等菌属只在人工饲料饲育的GS肠道内出现。同是桑叶饲育的家蚕品种GS和1015,其肠道内相同的优势菌有叶瘤菌属Phyllobacterium、脆弱拟杆菌属Bacteroides、不动细菌属Acinetobacter等。相较于广食性蚕品种GS的肠道菌群,肠球菌属Enterococcus、草螺菌属Herbaspirillum、丝硫菌属Thiothrix等菌属仅在普通蚕品种1015肠道中被检测到。GS. b组家蚕肠道细菌的物种多样性低于GS. m和C1015. m。GS. m肠道中丰度差异显著性最高的菌群为变形菌门(Proteobacteria),GS. b肠道中丰度差异显著性最高的菌群为杆菌纲(Bacilli)和乳杆菌目(Lactobacillales),而C1015. m肠道中丰度差异显著性最高的菌群为粪肠球菌属Enterococcus和肠球菌科(Enterococcaceae)。【结论】经桑叶饲育的不同蚕品种(GS和1015)的肠道微生物比人工饲料饲育的家蚕肠道微生物更趋于一致;经桑叶饲育的广食性家蚕肠道微生物物种多样性较高于经人工饲料饲育的广食性家蚕。     

蝎子肠道内微生物多样性研究

蝎子是一种重要的药用动物,还具有很高的营养价值。分别采用非培养和纯培养方法研究蝎子肠道内的微生物群落,结果表明,非培养方法检测到的蝎子肠道内微生物大部分属于α,β,γ-Proteobacteria类群,纯培养法分离到的菌株多属于高G C含量的革兰氏阳性菌,两种方法都检测到肠杆菌属(Enterobacter)、沙雷氏菌属(Serratia)、苍白杆菌属(Ochrobactrum)菌株,综合两种方法检测结果,蝎子肠道微生物共包括23个属,分别是肠杆菌属(Enterobacter)、沙雷氏菌属(Serratia)、假单胞菌属(Pseudomonas)、不动杆菌属(Acinetobacter)、气单胞菌属(Aeromonas)、柠檬酸杆菌属(Citrobacter)、土地杆菌属(Pedobacter)、代尔夫特菌属(Delftia)、罗尔斯通氏菌属(Ralstonia)、苍白杆菌属(Ochrobactrum)、鞘鞍醇单胞菌属(Sphingomonas)、微小杆菌属(Exiguobacterium)、戈登氏菌属(Gordonia)、诺卡氏菌属(Nocardia)、红球菌属(Rhodococcus)、两面神菌属(Janibacter)、考克氏菌属(Kocuria)、微球菌属(Micrococcus)、壤霉菌属(Agromyces)、微杆菌属(Microbacterium)、土壤球菌属(Agrococcus)、异常球菌属(Deinococcus)、鸟氨酸微菌属(Ornithinimicrobium),还有一些属于不能培养的未知菌。     

传统分离培养结合DGGE法检测榨菜腌制过程的细菌多样性

采用传统分离培养和基于16S rRNA 作为分子标记的变性梯度凝胶电泳(Denaturing gradient gel electrophoresis, DGGE)的方法, 分析榨菜腌制过程中不同时期的可培养细菌数量、多样性及其群落结构。结果表明, 用传统分离与分子鉴定方法获得7个属的细菌类群, 其中乳杆菌属(Acidobacterium)是优势菌群, 明串珠菌属(Leuconostoc)是次优势菌群。对通过DGGE方法得到的11条16S rRNA优势条带序列进行了比对, 结果表明明串珠菌属(Leucon     

Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample

Compared with culture-independent approaches, traditionally used culture-dependent methods have a limited capacity to characterize water microbiota. Nevertheless, for almost a century the latter have been optimized to detect and quantify relevant bacteria. A pertinent question is if culture-independent diversity surveys give merely an extended perspective of the bacterial diversity or if, even with a higher coverage, focus on a different set of organisms. We compared the diversity and phylogeny of bacteria in a freshwater sample recovered by currently used culture-dependent and culture-independent methods (DGGE and 454 pyrosequencing). The culture-dependent diversity survey presented lower coverage than the other methods. However, it allowed bacterial identifications to the species level, in contrast with the other procedures that rarely produced identifications below the order. Although the predominant bacterial phyla detected by both approaches were the same (Proteobacteria, Actinobacteria, Bacteroidetes), sequence similarity analysis showed that, in general, different operational taxonomical units were targeted by each method. The observation that culture-dependent and independent approaches target different organisms has implications for the use of the latter for studies in which taxonomic identification has a predictive value. In comparison to DGGE, 454 pyrosequencing method had a higher capacity to explore the bacterial richness and to detect cultured organisms, being also less laborious.     

Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16 S rRNA gene clone library

Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, starting with yeasts, followed by lactic acid bacteria and acetic acid bacteria. So far, all microbiological studies about cocoa bean fermentation were based on culture-dependent (isolation, cultivation, and identification), or, more recently, culture-independent (PCR-DGGE, or polymerase chain reaction denaturing gradient gel electrophoresis) methods. Using a metagenomic approach, total DNA was extracted from heap and box fermentations at different time points and from different locations (Ghana and Brazil, respectively) to generate a 16 S rDNA clone library that was sequenced. The sequencing data revealed a low bacterial diversity in the fermentation samples and were in accordance with the results obtained through culture-dependent and a second, culture-independent analysis (PCR-DGGE), suggesting that almost all bacteria involved in the fermentation process are cultivable. One exception was the identification by 16 S rDNA library sequencing of Gluconacetobacter species of acetic acid bacteria that were not detected by the two other approaches. The presence of Enterobacteriaceae related to Erwinia/Pantoea/Tatumella, as revealed by 16 S rDNA library sequencing, suggests an impact of these bacteria on fermentation.     

水体粪便污染的微生物溯源方法研究进展

畜禽粪便和生活污水是造成水体污染的主要因素之一,明确和区分水体污染的来源对污染控制和治理尤为重要.因此,利用微生物进行水体污染的溯源近年来成为国际上的研究热点.本文对两种类型微生物溯源方法的研究现状、优缺点以及应用中存在的问题进行了综述和展望.认为在培养建库微生物溯源方法中重复序列分型应用性最强,而在非培养建库方法中基于大肠杆菌特异性基因的PCR-DGGE具有广阔的应用前景.非培养建库微生物溯源是今后主要的研究方向,培养建库和非培养建库溯源方法相结合才能使溯源结果更加可信.     

Monitoring the bacterial community during fermentation of sunki, an unsalted, fermented vegetable traditional to the Kiso area of Japan

Aims:  To investigate the microbial community in sunki , an indigenous, unsalted, fermented vegetable, made from the leaves of red beet.
Methods and Results:  Fermenting samples were collected at 1- to 2-day intervals from four houses and investigated by culture-dependent and culture-independent techniques. PCR-Denaturing-Gradient-Gel-Electrophoresis profiles indicated that the bacterial community was stable and Lactobacillus delbrueckii , Lact. fermentum and Lact. plantarum were dominant during the fermentation. This result agreed well with that obtained by the culturing technique. Moulds, yeasts or bacteria other than lactic acid bacteria (LAB) were not detected.
Conclusions:  The bacterial community was stable throughout the fermentation, and Lact. delbrueckii , Lact. fermentum and Lact. plantarum were dominant. The acidic pH and lactic acid produced by LAB probably preserve the sunki from spoilage.
Significance and Impact of the Study:  This is the first report on the use of both culture-dependent and culture-independent techniques to study the bacterial community in sunki . A combination of culture-dependent and culture-independent techniques is necessary for the analysis of complex microbial communities.     

Structure analysis of a soil community of predatory bacteria using culture-dependent and culture-independent methods reveals a hitherto undetected diversity of Bdellovibrio-and-like organisms

Bdellovibrio-and-like organisms (BALOs) are widespread obligatory predators of other Gram-negative bacteria. Their detection by culture-dependent methods is complicated as their replication is totally dependent upon the availability of an appropriate prey. Because BALOs do not form numerically dominant groups within microbial communities, non-specific culture-independent tools also generally fail to detect them. We designed sets of 16S rRNA primers that specifically target BALOs. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined, yielding partial 16S rDNA sequences. This simple method that allows specific in situ culture-independent detection of BALOs was applied to the soil environment. Bdellovibrio-and-like organisms were also isolated from the same soil and the phylogeny and prey range of the isolates analysed. Seventeen isolates retrieved using five different potential preys exhibited eight different spectra of prey utilization and formed nine operational taxonomic units (OTUs). These OTUs were affiliated with the Bdellovibrionaceae, Bacteriovorax, Peredibacter or Micavibrio, i.e. the known BALO groups. In comparison, 15 OTUs including 10 that were not detected by the culture-dependent approach were obtained using the specific primers in a PCR-DGGE approach. The occurrence of a complex BALO community suggests that predation occurs on a much wider range of prey than can be detected by the classical culture-dependent technique.     

Assessment of Microbial Diversity in Saudi Springs by Culture-Dependent and Culture-Independent Methods

Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in two hot springs of the Aljouf region in Saudi Arabia, including Qasr Kaff and Ain Hawas. Physicochemical characteristics of the springs were examined to establish their effect on the biodiversity of thermophilic bacteria and fungi. We employed culture-dependent techniques to study microbial diversity using four different complex media for bacteria and fungi. In addition, the direct count for algal populations from two springs was investigated. We surveyed the microbial diversity in water and sediment samples from both springs by denaturing gradient gel electrophoresis (DGGE) and clone library construction. Bacillariophycaea (18 species) was the most diverse group, followed by Cyanophyceaea. Bacterial isolates closer to the genera Bacillus spp., Geobacillus, Thermoactinomyces, and unidentified actinobacteria were recovered. Fungal isolates were related to Aspergillus, Pezizaceae, Penicillium, Acremonium, Fusarium, Chrysosporium, and Stachybotrys. Using molecular-based techniques, the results were slightly different from those obtained by culture-dependent methods, and more genera were obtained. However, most genera were uncultured microbes, particularly from bacterial communities.     

Culture-independent analysis of probiotic products by denaturing gradient gel electrophoresis

In order to obtain functional and safe probiotic products for human consumption, fast and reliable quality control of these products is crucial. Currently, analysis of most probiotics is still based on culture-dependent methods involving the use of specific isolation media and identification of a limited number of isolates, which makes this approach relatively insensitive, laborious, and time-consuming. In this study, a collection of 10 probiotic products, including four dairy products, one fruit drink, and five freeze-dried products, were subjected to microbial analysis by using a culture-independent approach, and the results were compared with the results of a conventional culture-dependent analysis. The culture-independent approach involved extraction of total bacterial DNA directly from the product, PCR amplification of the V3 region of the 16S ribosomal DNA, and separation of the amplicons on a denaturing gradient gel. Digital capturing and processing of denaturing gradient gel electrophoresis (DGGE) band patterns allowed direct identification of the amplicons at the species level. This whole culture-independent approach can be performed in less than 30 h. Compared with culture-dependent analysis, the DGGE approach was found to have a much higher sensitivity for detection of microbial strains in probiotic products in a fast, reliable, and reproducible manner. Unfortunately, as reported in previous studies in which the culture-dependent approach was used, a rather high percentage of probiotic products suffered from incorrect labeling and yielded low bacterial counts, which may decrease their probiotic potential.     

Culture-Independent Analysis of Probiotic Products by Denaturing Gradient Gel Electrophoresis

In order to obtain functional and safe probiotic products for human consumption, fast and reliable quality control of these products is crucial. Currently, analysis of most probiotics is still based on culture-dependent methods involving the use of specific isolation media and identification of a limited number of isolates, which makes this approach relatively insensitive, laborious, and time-consuming. In this study, a collection of 10 probiotic products, including four dairy products, one fruit drink, and five freeze-dried products, were subjected to microbial analysis by using a culture-independent approach, and the results were compared with the results of a conventional culture-dependent analysis. The culture-independent approach involved extraction of total bacterial DNA directly from the product, PCR amplification of the V3 region of the 16S ribosomal DNA, and separation of the amplicons on a denaturing gradient gel. Digital capturing and processing of denaturing gradient gel electrophoresis (DGGE) band patterns allowed direct identification of the amplicons at the species level. This whole culture-independent approach can be performed in less than 30 h. Compared with culture-dependent analysis, the DGGE approach was found to have a much higher sensitivity for detection of microbial strains in probiotic products in a fast, reliable, and reproducible manner. Unfortunately, as reported in previous studies in which the culture-dependent approach was used, a rather high percentage of probiotic products suffered from incorrect labeling and yielded low bacterial counts, which may decrease their probiotic potential.