Denaturing gradient gel electrophoresis analyses of microbial community from field-scale composter

The diversity of microbial community during the decomposition of waste in a field-scale composter (Hazaka system) was investigated by denaturing gradient gel electrophoresis (DGGE). The composter operates at a high temperature through a self-heating system, creating a thermophilic (60-76 degrees C) stage during the initial phase and a mesophilic (45 degrees C) stage towards the later phase of the composting period. The pH of the system (pH 7.75-8.10) did not vary significantly during the process while moisture content was reduced from 48.8% to 25.1%. DGGE and 16S rDNA analyses showed that the following genera were found throughout the process: Propionibacterium sp., Methylobacterium sp., Pseudomonas sp., and Bradyrhizobium sp. Different Bacillus spp. thrive at the thermophilic or the mesophilic stage while Clostridium sp. was only found at the initial phase of the process. Staphylococcus sp. and Caulobacter sp. or Brevundimonas sp. existed during the later phase of the composting period.     

Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis

Kimchi is a traditional Korean food that is fermented from vegetables such as Chinese cabbage and radish. Many bacteria are involved in kimchi fermentation and lactic acid bacteria are known to perform significant roles. Although kimchi fermentation presents a range of environmental conditions that could support many different archaea and yeasts, their molecular diversity within this process has not been studied. Here, we use PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S and 26S rRNA genes, to characterize bacterial, archaeal and yeast dynamics during various types of kimchi fermentation. The DGGE analysis of archaea expressed a change of DGGE banding patterns during kimchi fermentation, however, no significant change was observed in the yeast DGGE banding patterns during kimchi fermentation. No significant difference was indicated in the archaeal DGGE profile among different types of kimchi. In the case of yeasts, the clusters linked to the manufacturing corporation. Haloarchaea such as Halococcus spp., Natronococcus spp., Natrialba spp. and Haloterrigena spp., were detected as the predominant archaea and Lodderomyces spp., Trichosporon spp., Candida spp., Saccharomyces spp., Pichia spp., Sporisorium spp. and Kluyveromyces spp. were the most common yeasts.     

冷却牦牛肉贮藏过程中优势菌的 PCR-变性梯度凝胶电泳分析

应用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术,研究托盘保鲜膜包装的冷却牦牛肉在4℃贮藏过程中的微生物多样性及其动态变化.直接从样品中提取细菌总的DNA,采用降落PCR扩增16S rDNA的V3可变区序列,再通过DGGE得到动态变化的指纹图谱,并对主要条带进行测序分析.结果表明:检测到的优势腐败菌为Pseudomonas sp.(假单胞菌)、Lactococcus sp.(乳球菌)、Acinetobacter sp.(不动杆菌)、Brochothrix thermosphacta(热死环丝菌)、Enterobacteriaceae bacterium(肠杆菌科细菌),此外还检测到Uncultured Citrobacter sp.(非培养的柠檬酸杆菌)和Staphylococcus sp.(葡萄球菌)     

Dynamics of the microbial community responsible for traditional sour cassava starch fermentation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization

The microbial community developing during the spontaneous fermentation of sour cassava starch was investigated by cultivation-independent methods. Denaturing gradient gel electrophoresis (DGGE) of partially amplified 16S rDNA followed by sequencing of the most intense bands showed that the dominant organisms were all lactic acid bacteria (LAB), mainly close relatives of Bifidobacterium minimum, Lactococcus lactis, Streptococcus sp., Enterococcus saccharolyticus and Lactobacillus plantarum., Close relatives of Lb. panis, Leuconostoc mesenteroides and Ln. citreum were also found. A complementary analysis using hybridization of 16S rRNA with phylogenetic probes was necessary to detect the presence of the recently discovered species Lb. manihotivorans. Although it represented up to 13% of the total lactic acid bacteria of sour cassava starch, this species could not be detected by DGGE as the PCR product migrated to the same position as Lc. lactis. In addition, it was shown that a strong pH decrease in the time course of fermentation was most probably responsible for the competitive selection of acid-resistant LAB vs. both homo and heterofermentative acid-sensitive LAB.     

Bacterial Community of Koumiss from Mongolia Investigated by Culture and Culture-Independent Methods

The bacterial community of fermented horse milk (koumiss) from Mongolia was studied using three methods: cultivation, direct identification by 16S rRNA clone library and denaturing gradient gel electrophoresis (DGGE). Ninety-eight strains were isolated by traditional cultivation and 61 of those were randomly selected for further identification by 16S rRNA gene sequencing. The strains were dominated by lactic acid bacteria (LAB; six different lactobacilli), Acinetobacter, Bacillus and Psychrobacter. Construction of the clone library analysis revealed that 16S sequences of 220 clones, genus Lactobacillus was dominant, but Streptococcus thermophilus, Acetobacter pasteurianus and uncultured clones were also detected. Ten unique bands were sequenced from the DGGE and revealed: Lactococcus lactis, Lactococcus lactis subsp. lactis, Clostridium acidurici, Acinetobacter johnsonii, Dickeya sp., Enterobacter sp., Pseudomonas sp., Raoultella sp., and Ruminococcus sp.. In vitro growth inhibition of three human pathogens, Escherichia coli, Enterobacter sakazakii and Staphylococcus aureus by 14 culturable bacteria displayed that only three of the isolates tested inhibit growth of E. sakazakii while most of the other bacteria delayed growth of the target bacteria.     

一例茶饮料污染源的分析

某企业生产的一批茶饮料中发现某些产品变质,3份样品出现pH值下降,或产气胀罐现象,或有肉眼可观察到浑浊、变色等感官指标的变化。检测发现引起腐败变质的主要是细菌,其数量≥104 CFU/mL,4株主要污染菌菌株经16S rDNA序列比对,鉴定为假单胞菌属(Pseudomonas sp.)、肠杆菌属(Enterobacter sp.)、芽胞杆菌属(Bacillus sp.)和短芽孢杆菌(Brevibacillus sp.)。样品中还有数量很低(101～102 CFU/mL左右)的霉菌检出,经形态观察初步鉴定为交链孢霉(Alternaria spp.)、枝孢霉(Cladosporium spp.)、曲霉(Aspergillus spp.)和青霉(Penicillium spp.)。该案例中霉菌虽然不是主要的腐败变质菌,但是其菌相组成与空气中主要的霉菌菌相一致,显示该污染的源头可能是空气,细菌的组成也能支持这个推论。实践中,通过更换无菌空气过滤器,确实解决了污染问题,证实了该推论。     

The microbial community in a 2,4-dinitrophenol-digesting reactor as revealed by 16S rDNA gene analysis

The microbial community of a 2,4-dinitrophenol-digesting reactor was investigated using different molecular biological techniques based on 16S rDNA gene sequences. A PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the bacterial community in the reactor showed that one strong and five minor bands were observed in the DGGE profile. The results of excising and sequencing DGGE bands suggested that members of Rhodococcus, Nocardioides, and Nitrospira species were present in the reactor. Partial sequencing of cloned 16S rDNAs revealed diversity among the six main divisions--the alpha, delta subclasses of Proteobacteria, Nitrospira, Cytophagal Flexibacter/Bacteroides, Verrucomicrobia, and Actinobacteria--in the reactor. Two cloned sequence types were not closely affiliated with any described bacterial divisions. The isolation and phylogenetic analysis of 2,4-DNP-degrading bacteria from the reactor revealed that isolated strains were classified into two types of bacteria having different 16S rDNA sequences. One of these strain types was identified as a relative of Rhodococcus koreensis, and the other was identified as a relative of Nocardioides simplex FJ21-A.     

Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors

Two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate TCE to ethene. Each electron donor enrichment subculture demonstrated the ability to dechlorinate TCE to ethene through several serial transfers. Microbial community analyses based upon 16S rDNA, including terminal restriction fragment length polymorphism (T-RFLP) and clone library/sequencing, were performed to assess major changes in microbial community structure associated with electron donors capable of stimulating reductive dechlorination. Results demonstrated that five phylogenic subgroups or genera of bacteria were present in all consortia, including Dehalococcoides sp., low G+C Gram-positives (mostly Clostridium and Eubacterium sp.), Bacteroides sp., Citrobacter sp., and delta Proteobacteria (mostly Desulfovibrio sp.). Phylogenetic association indicates that only minor shifts in the microbial community structure occurred between the four alternate electron donor enrichments and the parent consortium. Inconsistent detection of Dehalococcoides spp. in clone libraries and T-RFLP of enrichment subcultures was resolved using quantitative polymerase chain reaction (Q-PCR). Q-PCR with primers specific to Dehalococcoides 16S rDNA resulted in positive detection of this species in all enrichments. Our results suggest that TCE-dechlorinating consortia can be stably maintained on a variety of electron donors and that quantities of Dehalococcoides cells detected with Dehalococcoides specific 16S rDNA primer/probe sets do not necessarily correlate well with solvent degradation rates.     

Effects of long-term ingestion of difructose anhydride III (DFA III) on intestinal bacteria and bile acid metabolism in humans

Changes in the intestinal microbiota of 10 human subjects with long-term ingestion of 3 g/d difructose anhydride III (DFA III; 4 persons, 2 months; 3 persons, 6 months; and 3 persons, 12 months) were examined by denaturing gradient gel electrophoresis (DGGE). According to the answers to questionnaires, the subjects were divided into two groups (constipated and normal). The DGGE profile was different for every individual and each subject had unique profiles of intestinal microbiota. In the DGGE profiles of constipated subjects, the intensities of bands related to Bacteroides spp. increased. Moreover, the DFA III-assimilating bacteria, Ruminococcus sp. were isolated from subjects who ingested DFA III for 12 months. These strains showed 95% similarity of their 16S rDNA sequences with that of Ruminococcus obeum ATCC 29174(T) (X85101) and produced large amounts of acetic acid. DFA III ingestion for 2 months tended to increase total organic acids in feces, and tended to decrease fecal pH and the secondary bile acid (SBA) ratio in total bile acids. The SBA ratio in total bile acids corresponded to fecal pH. The production of SBA was decreased by low pH in vitro. These results indicated that DFA III ingestion in humans tended to lower intestinal pH, inhibited bile acid 7alpha-dehydroxylation activities and also tended to decrease the SBA ratios in total bile acids. Moreover, as another cause for the decrease in the SBA ratio in total bile acids, it was suggested that the number of bile acid 7alpha-dehydroxylating bacteria were decreased by DFA III ingestion.     

酱油发酵过程中细菌群落结构的动态变化

本文采用16S r DNA PCR-DGGE(变性梯度凝胶电泳)指纹图谱和系统发育分析方法,以高盐稀醪发酵工艺生产的广东酱油为研究对象,揭示了酱油生产发酵过程中细菌群落结构的多样性及动态变化。从样品中提取总细菌DNA,用降落PCR扩增16S r DNA V3片段序列,再通过分析DGGE图谱选择特异性条带,进行割胶回收、测序及Blast分析。DGGE图谱表明,发酵初期样品具有丰富的微生物群落,但之后只有少数种类细菌存活,整个酱油发酵过程微生物群落结构的演变规律是由复杂到简单,这也说明酱油发酵环境具有抑制微生物生长的作用。测序结果表明,代表最相似菌为魏斯菌属(Weissella cibaria)和非培养的肠杆菌属(Uncultured Enterobacter sp.),其次是嗜盐四联球菌(Tetragenococcus halophilus)、类肠膜魏斯氏菌(Weissella paramesenteroides)、弗氏柠檬酸杆菌(Citrobacter freundii)、产气肠杆菌(Enterobacter aerogenes)和肠杆菌属(Enterobacter sp.BF1-8)。     

Identifying the bacterial community on the surface of Intralox belting in a meat boning room by culture-dependent and culture-independent 16S rDNA sequence analysis

We examined the bacterial community present on an Intralox conveyor belt system in an operating lamb boning room by sequencing the 16S ribosomal DNA (rDNA) of bacteria extracted in the presence or absence of cultivation. RFLP patterns for 16S rDNA clone library and cultures were generated using HaeIII and MspI restriction endonucleases. 16S rDNA amplicons produced 8 distinct RFLP pattern groups. RFLP groups I-IV were represented in the clone library and RFLP groups I and V-VIII were represented amongst the cultured isolates. Partial DNA sequences from each RFLP group revealed that all group I, II and VIII representatives were Pseudomonas spp., group III were Sphingomonas spp., group IV clones were most similar to an uncultured alpha proteobacterium, group V was similar to a Serratia spp., group VI with an Alcaligenes spp., and group VII with Microbacterium spp. Sphingomonads were numerically dominant in the culture-independent clone library and along with the group IV alpha proteobacterium were not represented amongst the cultured isolates. Serratia, Alcaligenes and Microbacterium spp. were only represented with cultured isolates. Pseudomonads were detected by both culture-dependent (84% of isolates) and culture-independent (12.5% of clones) methods and their presence at high frequency does pose the risk of product spoilage if transferred onto meat stored under aerobic conditions. The detection of sphingomonads in large numbers by the culture-independent method demands further analysis because sphingomonads may represent a new source of meat spoilage that has not been previously recognised in the meat processing environment. The 16S rDNA collections generated by both methods were important at representing the diversity of the bacterial population associated with an Intralox conveyor belt system.     

PCR-DGGE技术分析传统臭鳜鱼发酵过程中细菌群落结构

应用聚合酶链式反应-变性梯度凝胶电泳(polymerase chain reaction-denaturing gradient gel electrophoresis,PCR-DGGE)技术对黄山臭鳜鱼发酵过程中的细菌群落结构组成进行研究。以发酵0~8 d的臭鳜鱼为研究对象,每2 d取样,提取样品的总DNA,同时进行16S r DNA V6~V8区的PCR扩增,产物纯化后进行DGGE分析。结果表明:肠球菌(Enterococcus sp.,D带)、腐败西瓦氏菌(Shewanella putrefaciens,C带)、溶酪大球菌(Macrococcus caseolyticus,A带)和乙酰微小杆菌(Exiguobacterium acetylicum,F带)在整个发酵过程,特别是发酵后期占较大比例,是黄山臭鳜鱼发酵过程中的优势菌。臭鳜鱼样品的PCR-DGGE图谱相似度分析显示,臭鳜鱼发酵后期菌群结构比较相似,微生物菌落结构趋于稳定。本研究结果为筛选适合工业化生产的发酵菌株,有效控制臭鳜鱼生产中存在的腐败菌、致病菌,对提高臭鳜鱼安全性和产品品质具有一定应用价值。     

冰鲜鸡肉贮藏过程中微生物菌相变化分析

应用基于16S rDNA的PCR-DGGE(变性梯度凝胶电泳)技术对冰鲜鸡肉微生物多样性进行研究。分别取鸡胸肉和鸡腿肉贮藏0、3、5、7、9d的样品,提取样品总DNA,通过PCR扩增、变性梯度凝胶电泳,将16S rDNA(V6～V8区)的PCR扩增片段割胶测序确定样品中的微生物群落,与传统培养方法进行比较。传统培养方法表明：鸡胸肉和鸡腿肉在低温低氧分压条件下贮藏,导致腐败的优势菌相差不明显,且变化趋势相一致;DGGE图谱表明,初始污染数量较多的微生物不一定是腐败优势菌,能适应低温低氧分压的微生物最终成为腐败优势菌,且鸡胸肉和鸡腿肉的腐败优势菌有一定差异性。传统培养和DGGE割胶测序所得腐败优势菌的菌相不完全相同,综合两种研究方法,确定冰鲜鸡肉腐败优势菌为乳酸菌、大肠菌群、热杀索丝菌、腐败希瓦氏菌链菌和肉杆菌。     

Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste

The methanogenic pathway and microbial community in a thermophilic anaerobic digestion process of organic solid waste were investigated in a continuous-flow stirred-tank reactor using artificial garbage slurry as a feedstock. The decomposition pathway of acetate, a significant precursor of CH₄ and a key intermediate metabolite in the anaerobic digestion process, was analyzed by using stable isotopes. A tracer experiment using ¹³C-labeled acetate revealed that approximately 80% of the acetate was decomposed via a non-aceticlastic oxidative pathway, whereas the remainder was converted to methane via an aceticlastic pathway. Archaeal 16S rRNA analyses demonstrated that the hydrogenotrophic methanogens Methanoculleus spp. accounted for > 90% of detected methanogens, and the aceticlastic methanogens Methanosarcina spp. were the minor constituents. The clone library targeting bacterial 16S rRNA indicated the predominance of the novel Thermotogales bacterium (relative abundance: ~ 53%), which is related to anaerobic acetate oxidizer Thermotoga lettingae TMO, although the sequence similarity was low. Uncultured bacteria that phylogenetically belong to municipal solid waste cluster I were also predominant in the microflora (~ 30%). These results imply that the microbial community in the thermophilic degrading process of organic solid waste consists exclusively of unidentified bacteria, which efficiently remove acetate through a non-aceticlastic oxidative pathway.     

贮藏温度对冷鲜羊肉微生物菌群生长变化的影响

本实验以传统微生物的检测方法结合16S r DNA V6^V8可变区聚合酶链式反应-变性梯度凝胶电泳指纹图谱技术（polymerase chain reaction-denaturing gradient gel electrophoresis,PCR-DGGE）研究在10、4℃及冰温贮藏条件下,冷鲜羊肉菌相的动态变化及其货架期。经微生物计数及DGGE图谱分析,10℃贮藏条件下,6 d已达到腐败临界值,其优势腐败菌为肠杆菌属、乳酸菌属等;4℃条件下,货架期为27 d,优势腐败菌有假单胞菌属、弧菌属、嗜冷菌属、不动杆菌等;冰温贮藏,其货架期为39 d,其中假单胞菌属、嗜冷菌、不动杆菌、清酒乳杆菌等成为优势腐败菌。结果表明:冰温可有效延长冷鲜羊肉的货架期。      

Development and analysis of microbial characteristics of an acidulocomposting system for the treatment of garbage and cattle manure

An acidulocomposting system for the treatment of cattle manure with little emission of ammonia gas was developed, and the structure of its microbial community was investigated by denaturing gradient gel electrophoresis (DGGE) and clone library construction. An acidulocomposting apparatus (BC20, 20 L) was operated for 79 days to treat 2 kg (wet wt) of garbage per 1 or 2 days. On day 80 of operation, the substrate was changed from garbage to cattle manure (1 kg of beef cattle manure was added to the apparatus every 2 or 3 days), and the system continued operating from days 80 to 158. The compost in the vessel was under acidic conditions at pH 5.2–5.8, and ammonia emission was below the detectable level (< 5 ppm) throughout the period of cattle manure feeding. Total nitrogen and total carbon in the compost were 26–29 and 439 – 466 mg/g of dry weight, respectively, which are higher than those in general cattle manure compost. The main acids accumulated during operation were lactic and acetic. Sequencing analysis targeting the 16S rRNA gene revealed the stable dominance of the bacterial phylum Firmicutes, with a high proportion of the isolates belonging to the genus Bacillus. Using a culturing method with MRS agar, we isolated lactic acid bacteria (LAB) related to Pediococcus acidilactici, Weissella paramesenteroides, and Lactobacillus salivarius, indicating the existence of LAB in the system. These results indicate that acidulocomposting treatment of cattle manure is not accompanied by ammonia emission and that Bacillus and LAB may be the key components in the system.     

变性梯度凝胶电泳法初步解析茯砖茶渥堆发酵过程中细菌群落结构

为解析茯砖茶渥堆发酵过程中细菌群落结构和种类,对渥堆过程中不同时间段细菌16S rDNA 的V3可变区进行扩增,对细菌变性梯度凝胶电泳（denaturing gradient gel electrophoresis,DGGE）图谱中条带进行克隆、测序和序列比对。结果表明：黑毛茶在渥堆过程中以渥堆24 h为分界点,前后各自细菌群落结构相似,但前后的差异较大;从16S rDNA 的V3可变区比对结果证明黑毛茶渥堆过程中有诺卡氏菌属、新鞘脂菌属、短波单胞菌属、韦龙氏假单胞菌属、突那梭菌属、克雷伯氏菌属、乳杆菌属及不可培养的ε-变形菌、腐败螺旋菌属、黏球菌属、根瘤菌属和未知分类地位的不可培养细菌6 种。采用DGGE指纹图谱能更全面、更真实地反映黑毛茶渥堆发酵过程中细菌群落的结构和多样性变化。     

应用PCR-DGGE技术研究宰后羊肉经不同处理后的微生物动态变化

应用16S rDNA变性梯度凝胶电泳(DGGE)指纹图谱和系统发育分析方法,揭示了羊屠宰后经电刺激、吊挂两种方式处理后在4℃贮藏条件下主要微生物的动态变化。DGGE图谱表明,电刺激处理组在贮藏初期具有丰富的微生物群落,但经过一段时间后,只有少数种类细菌存活并最终成为主导菌群。吊挂组较电刺激组相比细菌群落较少。DGGE优势条带经DNA序列分析表明,羊肉中的主要细菌为嗜冷杆菌、葡萄球菌、克雷伯氏菌、假单胞菌、寡养单胞菌、肠杆菌、乳酸杆菌、热死环丝菌。两个处理组在储藏初期微生物菌群差异不大,但吊挂组在第10d后以葡萄球菌为主导菌群。电刺激组在贮藏过程后期才凸显的腐败菌为假单胞菌。      

产细菌素弯曲乳杆菌的分离鉴定及细菌素特性初步研究

从西班牙传统色拉米香肠中分离到一株产细菌素菌株RX-6,其发酵液在排除有机酸、过氧化氢及菌体细胞干扰后,抑菌活性基本无变化;经硫酸铵盐析及透析处理后,抑菌活性明显增强;蛋白酶K处理后,抑菌活性消失,表明起抑菌作用的是蛋白类物质。通过菌体形态观察、生理生化特征实验、16SrRNA序列比对及系统发育分析,鉴定菌株RX-6为弯曲乳杆菌（Lactobacillus curvatus）。抑菌特性研究结果显示该菌株所产细菌素具有很好的热稳定性和酸碱耐受性,在121℃20min的高温处理后仍能保持一定活性,活性pH范围为3¹0;使用安全性高,胃蛋白酶和胰蛋白酶可将其完全分解,而酸性蛋白酶可将其部分分解;抑菌谱较广,对受试的7株李斯特菌（Listeria spp.）、3株金黄色葡萄球菌（Staphylococcus aereu）、1株大肠杆菌（Escherichia coli）及1株假单胞菌（Pseudomonas spp.）等都有明显抑制作用,显示出作为天然食品生物防腐剂的巨大应用潜力。      

Investigation of the microbial changes during koji‐making process of Douchi by culture‐dependent techniques and PCR‐DGGE

Douchi as a traditional fermentation soyfood with an acquired taste had been appreciated by consumers for thousands of years in China and few Asian countries. Unfortunately, few studies had been conducted on the changes of microbial community during the koji‐making process, and whether the pathogenic microorganisms involving the fermentation process is still unclear. Therefore, the PCR‐denaturing gradient gel electrophoresis (DGGE) targeting the 16S and 18S rRNA genes was applied to characterise the dynamic changes of Bacteria, Bacilli and Fungi during koji‐making process. The results of DGGE showed that eleven species of bacteria, nine species of bacilli and seven species of Fungi had been detected during the koji‐making progress, of which the Bacillus subtilis and Aspergillus oryzae belonged to the dominant microorganisms. Also, eleven strains were isolated from Koji‐making samples and were identified as B. subtilis, Bacillus amyloliquefaciens, A. oryzae, Brachybacterium sp., Aspergillus niger, Staphylococcus saprophyticus, Micrococcus sp., Staphylococcus gallinarum, Absidia corymbifera, Saccharomyces cerevisiae, Malassezia sp.; Our results revealed that pathogenic microorganisms were involved in the koji‐making process, but the probiotic microorganisms occupied the dominant position of community in the koji‐making process.