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.     

Analysis of the Bacterial Community in Zaopei During Production of Chinese Luzhou‐flavor Liquor

Denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene analysis were carried out to analyze the bacterial community in Zaopei during production of Chinese Luzhou‐flavor liquor. Primers PRBA338F and PRUN518R were used for DGGE. Polymerase chain reaction (PCR) for clone analysis was preformed with primers EU27F and 1490R. The results by DGGE showed that with increasing fermentation time the diversity of bacteria in Zaopei decreased and after one week, only one bacterium phylotype was dominant. Gene clone libraries (16S rRNA) containing 55 clonal sequences were constructed. The bacterial diversity shift observed by DGGE was also shown by the clone library analysis. Bacteria closely related to Lactobacillus acetotolerans appeared to play a key role during Chinese liquor fermentation.     

Evaluation of Bacterial Diversity in Palm Wine by 16S rDNA Analysis of Community DNA

Bacterial diversity and fermentation dynamics in palm wine, a traditional alcoholic fermented beverage, collected from upright palm trees from Idiaba community, Abeokuta, Ogun State, Nigeria were evaluated by DNA based method using the 16S rDNA of the microbial community to verify and complement previous reports, improve our understanding and document yet unreported, uncultured microbial diversity associated with palm wine. The 16S rRNA gene fragments were amplified from microbial community and genomic DNA of isolates, by Polymerase Chain Reaction (PCR) using universal primers; and sequenced. The partial sequences were identified by comparison with sequences deposited in the non-redundant nucleotide database of National Center for Biotechnology Information (NCBI). This analysis revealed that 32 community clones were identified as Lactobacillus sp, Lactobacillus casei strain zhang, Lactobacillusplantarum, Leuconostoc mesenteriodes ssp dextranicum, Leuconcostoc lactis, Pediococcusparvulus strain Bpe-299, Acetobacter pomorum, Acetobacter pasteurianus, Gluconobacter oxydans, Acinetobacter calcoaceticus, Enterobacterium bacterium, Acidovorax sp, Comamonas sp, Bacillus subtilis, Staphylococcuspiscifermentans and uncultured bacteria clone D1-78. The results showed that bacterial diversity in the palm wine sample is dominated by Lactobacillus and Leuconostoc species as reported by previous workers and uncultured bacteria clone D1-78 (1 clone) was detected for the first time in palm wine.     

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)     

Analysis of the microflora in Tibetan kefir grains using denaturing gradient gel electrophoresis

The microflora of Tibetan kefir grains was investigated by culture- independent methods. Denaturing gradient gel electrophoresis (DGGE) of partially amplified 16S rRNA for bacteria and 26S rRNA for yeasts, followed by sequencing of the most intense bands, showed that the dominant microorganisms were Pseudomonas sp., Leuconostoc mesenteroides, Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactobacillus kefiri, Lactobacillus casei, Kazachstania unispora, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Kazachstania exigua. The bacterial communities between three kinds of Tibetan kefir grains showed 78–84% similarity, and yeasts 80–92%. The microflora is held together in the matrix of fibrillar material composed largely of a water-insoluble polysaccharide.     

PCR-DGGE技术分析腌制麻竹笋中微生物多样性

采用聚合酶链式反应-变性梯度凝胶电泳（polymerase chain reaction-denaturing gradient gel electrophoresis,PCR-DGGE）技术对盐质量浓度5 g/100 mL和19 g/100 mL腌制麻竹笋的微生物区系进行研究。结果表明,经DNA提取、巢式PCR、DGGE电泳和克隆测序后,从低盐质量浓度（5 g/100 mL）腌制笋中分离出4 条明显的亮带,经鉴定分别为食窦魏斯氏菌（Weissella cibaria）、乳球菌属（Lactococcus sp.）、魏斯氏菌属（Weissella sp.）和乳酸乳球菌（Lactococcus lactis）;从高盐质量浓度（19 g/100 mL）腌制笋中分离出5 条明显的亮带,经鉴定分别为绿色气球菌（Aerococcus viridans）、赖氨酸芽孢杆菌属（Lysinibacillus sp.）、未得到培养的细菌（unculturedbacterium）、厌氧芽孢杆菌属（Anoxybacillus sp.）和芽孢杆菌属（Bacillus sp.）;低盐腌制笋的优势菌多为益生菌,而高盐腌制笋的优势菌则多为抗性较强的菌。基于16S rDNA的PCR-DGGE技术为分析腌制麻竹笋中微生物多样性提供了一条可靠、快速的有效途径。     

Artisanal and experimental Pecorino Siciliano cheese: microbial dynamics during manufacture assessed by culturing and PCR-DGGE analyses

Traditional artisanal Pecorino Siciliano (PS) cheeses, and two experimental PS cheeses were manufactured using either raw or pasteurised ewes' milk with the addition of starter cultures. The bacterial diversity and dynamics of the different cheese types were evaluated both by culturing and characterisation of isolates, and a culture-independent approach based on the 16S ribosomal RNA (rRNA) gene. Following cultivation, artisanal and experimental cheese types showed similar microbial counts, and isolates belonging to Lactococcus lactis, Streptococcus thermophilus, Enterococcus faecalis and Leuconostoc mesenteroides were identified by phenotypic characterisation and comparison of the restriction fragment length polymorphism (RFLP) of the 16S rRNA gene to that of reference species. The culture-independent fingerprinting technique PCR and denaturing gradient gel electrophoresis (DGGE) of V6 to V8 regions of the 16S rRNA gene of samples taken during artisanal PS cheese manufacture, from raw milk to the ripened cheese, indicated relevant shifts in the microbial community structure. The dominance of Streptococcus bovis and Lactococcus lactis species in the traditional artisanal PS was revealed by 16S rRNA gene sequencing. Comparison of DGGE profiles of samples from milk to ripened cheese, derived from artisanal procedure and the two experimental PS cheeses during production showed similar trends with the presence of intense bands in common. Nevertheless, the profiles of several artisanal cheeses from different farms appeared more diverse, and these additional species are probably responsible for the generally superior flavour and aroma development of traditional PS cheese.     

利用16S rDNA部分序列聚类分析鉴定乳球菌

在表型鉴定的基础上，应用已发表的16SrDNA序列设计引物，扩增L．sp．F001菌株16S rDNA基因，并进行测序，将结果与同属及非同属的乳酸菌进行同源性比较。结果表明，L.sp．F001菌株与同属的乳酸乳球菌同源性为99％上，尤其与乳酸乳球菌叶蝉亚种NC-DO2181T同源性为100％，与不同属的肉明串珠菌、漫游球菌、嗜盐四联球菌同源性分别为77．0％，82．1％，78．2％。结论：菌株L.sp．F001为乳酸乳球菌。     

Metagenomic Microbial Diversity in Aguamiel from Two Agave Species During 4-Year Seasons

Aguamiel is the sap of “maguey pulquero” and can be consumed as a fresh beverage or after a cooking process. Further, it is also fermented for the production of “pulque,” a traditional Mexican alcoholic beverage. Use of aguamiel as a functional beverage has been suggested due to prebiotic activity of its fructooligosaccharides and probiotic activity of lactic acid bacteria that it contains. There are some reports about the culturable microbial diversity in aguamiel; however, the total microbial diversity has not been characterized. The objective of this study was to identify metagenomic populations in aguamiel using denaturing gradient gel electrophoresis and sequencing of the 16S rRNA gene and 26SrRNA gene regions. Microbial diversity in aguamiel from two maguey species was evaluated: Agave salmiana and Agave atrovirens, during the four seasons of the year. The highest diversity was found during summer season in aguamiel samples from both Agave species, detecting presence of Leuconostoc sp., Leuconostoc gelidum, Lactococcus lactis, Enterococcus casseliflavus, Pediococcus sp., uncultured Trichococcus sp., uncultured Leuconostoc, uncultured Lactococcus, Kazachstania zonata (not previously reported in aguamiel), Kluyveromyces marxianus, and Saccharomyces cerevisiae. Knowledge about the microbial populations of this beverage throughout the different seasons will provide advantages through understanding of aguamiel for application areas such as syrup elaboration and pulque making. In addition, this beverage could be industrialized as a functional beverage with a consistent quality.     

Molecular Identification of Microbial Community in Surface and Undersurface Douchi During Postfermentation

To find the reason for fermentation failure of surface Douchi during postfermentation, the microbial communities in undersurface and surface samples were investigated using cell counting method and denaturing gradient gel electrophoresis (DGGE). The results showed that the microbial biomass in surface Douchi was obviously different from that in undersurface Douchi even sampled from the same fermentation tanks, and a 10‐ to 100‐fold reduction of microbial cell counts in undersurface had been observed. The bacterial DGGE profile and principal component analysis (PCA) results indicated that only Lactococcus lacts subsp. lactis and Bacillus thermoamylovorans were detected from surface Douchi, while Lactococcus lacts subsp. lactis, Staphylococcus lentus and 2 uncultured strains occupied the dominant positions in undersurface Douchi; when amplified using Bacillus‐specific primers, Bacillus thermoamylovorans, Bacillus subtilis, and Enterobacter sp. were found in undersurface Douchi, while only Bacillus thermoamylovorans were detected from surface Douchi; compared to the bacteria and Bacillus, the DGGE profiles and PCA plot of fungi indicated that the fungal community between surface and undersurface Douchi was similar and mainly composed by yeasts. In this study, we detected the microbial biomass and species in postfermentation stage of Douchi, and the various microbial diversity in undersurface and surface samples might be the cause of the fermentation failure in surface fermentation tanks.     

A survey of the bacterial composition of kurut from Tibet using a culture-independent approach

Kurut (fermented yak milk) made by natural fermentation is a very important dairy food for the local people in Tibet (China). It is important to fully understand the bacterial composition of kurut for quality improvement and industrial production. Because more than 99% of prokaryotes cannot be cultured and identified by methods currently used in taxonomy, we applied a culture-independent approach to explore the microbial biodiversity of this traditional food. In this study, a bacterial 16S rRNA gene clone library, including 460 clones, was constructed using total DNA extracted from 30 samples of kurut. After screening by restriction fragment length polymorphism (RFLP) analysis, 56 operational taxonomic units (OTU) with unique RFLP patterns were obtained. Then, 1 representative sequence of every OTU was sequenced and phylogenetically analyzed. The representative phylotypes were affiliated with 5 groups, including Lactococcus lactis ssp. lactis, Lactobacillus helveticus, Streptococcus thermophilus, Lactobacillus delbrueckii ssp. bulgaricus, and Acetobacter. In addition, nearly one-third of the representative clones (132 clones) had low similarity to species in GenBank (<97%), and these phylotypes were regarded as unknown bacteria. The characteristics of kurut are determined not only by lactic acid bacteria well known by the culture-dependent approach but also by bacteria that have not yet been identified.     

Analyses of archaeal communities in Doenjang and Ganjang using a culture-independent manner based on 16S rRNA sequences

The archaeal diversity in the soybean fermented food was analysed by culture-independent methods based on the 16S rRNA sequences. The 21 doenjang archaea — clones from the doenjang library were grouped into 5 groups: uncultured archaeon clone AE34 (42.8%), uncultured archaeon clone AS17 (28.6%), uncultured compost archaeon clone 4A29 (4.8%), uncultured compost archaeon clone 0A10 (19.0%), and uncultured compost archaeon clone 5A16 (4.8%). The 21 ganjang archaea — clones from the ganjang library were grouped into 5 groups: Halophilic archaeon MH1-34-1 (19.0%), H. archaeon MH1-16-3 (61.9%), Halococcus thailandensis (4.8%), Haloplanus sp. RO5-8 (9.5%), and H. archaeon MH1-136-2 (4.8%).     

真空包装冷却猪肉冷藏过程中菌相变化

应用传统微生物培养和PCR-DGGE方法研究真空包装冷却猪肉4℃贮藏过程中的菌相变化。细菌培养计数结果表明,乳酸菌生长迅速,在贮藏后期即超过了细菌总数值。DGGE结合16S rRNA基因序列分析结果表明,贮藏初期肉中初始菌相较复杂,贮藏末期主要是漫游球菌、肉食杆菌、乳杆菌、乳球菌和热死环丝菌成为优势腐败菌。     

Bacterial diversity dynamics of traditional Turkish Ezine Cheese as evaluated by PCR‐DGGE and SSCP analysis

The aim of this study was to evaluate the bacterial ecosystem of milk and Ezine cheese by PCR amplification of the V3 region of the bacterial 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE) and by monitoring the bacterial diversity dynamics using PCR single‐strand conformation polymorphism (SSCP) analysis. PCR‐DGGE analysis revealed that 17 different bands and strains belonging to the Lactococcus lactis group and Streptococcus thermophilus were predominant during manufacturing and ripening. SSCP analysis revealed that the bacterial profiles of the two cheese samples were similar.     

阿尤恩地区自然发酵牛乳中乳酸菌分离鉴定及多样性研究

为了分离、保藏自然发酵乳中乳酸菌菌种,丰富自然发酵乳中乳酸菌多样性信息。本文采用传统的纯培养分离方法和宏基因组16S rRNA基因测序技术对阿尤恩地区自然发酵牛乳的乳酸菌多样性进行研究。纯培养结果表明:5份自然发酵牛乳中共分离出111株乳酸菌,鉴定为5个属10个种,其中Lactococcus lactis,占总分离株的45.95%;宏基因组测序结果发现,5份样品中的细菌归属于8个门、66个属和131个种,其中优势菌门为Firmicutes(69.63%),优势菌属为Lactococcus(31.80%),优势菌种同样为Lactococcus lactis(22.95%),另外还检测到含量较高的Streptococcus thermophilus(17.12%)、Lactobacillus helveticus(14.44%)等菌种。通过分析发现,Lactococcus lactis为阿尤恩地区5份自然发酵牛乳样品的优势菌种,并且自然发酵牛乳样品中细菌种类丰富,样品间细菌组成存在相似性和差异性。     

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.     

气调包装酱卤鸭翅贮藏过程中菌群结构分析

运用传统细菌平板培养和聚合酶链式反应-变性梯度凝胶电脉方法研究气调包装酱卤鸭翅15 ℃贮藏过程中微生物菌群结构变化。细菌总数计数结果表明,产品生产的卫生条件较好,细菌初始污染菌数较低（小于2（lg（CFU/g）））,至贮藏第9天左右产品细菌总数超过4（lg（CFU/g））。变性梯度凝胶电脉指纹图谱结果表明,贮藏初期产品的初始污染菌主要为不动杆菌属,至贮藏末期,产品中的主要菌群有嗜冷杆菌、莫拉氏菌、链球菌等,其中嗜冷杆菌属成为产品贮藏末期的优势菌。     

PCR-DGGE分析东北自然发酵酸菜中乳酸菌多样性

为了探明传统的自然发酵白菜中乳酸菌的多样性及其优势乳酸菌群,试验主要采用变性梯度凝胶电泳法(denaturing gradient gel electrophoresis,DGGE),对5份采自我国东北地区利用传统方法制作的自然发酵酸菜样品中的乳酸菌多样性进行分析。结果表明,5份传统发酵酸菜样品共鉴定出了9个乳酸菌种,呈现出丰富的多样性。其中,植物乳杆菌、短乳杆菌、清酒乳杆菌和弯曲乳杆菌是酸菜样品的优势菌群,此外,还发现了片球菌、乳酸乳球菌、Hammesii乳杆菌和Odoratitofui乳杆菌,而Hammesii乳杆菌和Odoratitofui乳杆菌在此前文献报道中利用传统方法没有分离到。     

Analysis of the Fungal Community in Zaopei During the Production of Chinese Luzhou‐flavour Liquor

Denaturing gradient gel electrophoresis (DGGE) and 18S rRNA gene analysis were carried out to analyze the fungal community in Zaopei during the production of Chinese Luzhou‐flavour liquor. Two pairs of primers (EF4/Fung5 and EF4/NS2‐GC) were used for the DGGE. Polymerase chain reaction (PCR) for clone analysis was preformed with the primers (EF4/EF3). The results of the DGGE analysis showed that the fungal 18S rRNA genes taken from the Zaopei sample of the pit had high diversity. Gene clone libraries containing 120 clonal sequences of 18S rRNA were constructed. The fungal diversity shift showed that the fungal genera changed with increasing fermentation time and four genera of fungi (Issatchenkia, Talaromyces, Aspergillus and Eurotium) were the main dominant communities during the fermentation of Chinese Luzhou‐flavour liquor. The clonal sequences of the genera Rhizopus and Saccharomyces were found with difficulty from the clone libraries of Zaopei, suggesting that the genera Rhizopus and Saccharomyces perhaps are not necessary for saccharifying and fermenting grains during the production of Chinese Luzhou‐flavour liquor.