Diversity analysis of lactic acid bacteria in Korean rice wines by culture-independent method using PCR-denaturing gradient gel electrophoresis

A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) method was used to determine the presence and diversity of lactic acid bacteria (LAB) in takju, a traditional Korean rice wine. Bacterial DNAs were extracted from 15 commercial rice wines and amplicons of partial 16S rRNA genes were separated by DGGE and intense bands were sequenced. Lactobacillus (Lb.) paracasei, Lb. plantarum, and Leuconostoc pseudomesenteroides were detected in all samples and Lb. harbinensis and Lb. parabuchneri were found with above 80% frequency of occurrence. Unknown species of Lactobacillus were also widely detected. This result revealed that, regardless of products and raw materials, the distribution profiles of LAB in takju products have a common pattern comprising of above predominant species and, furthermore, takju can be regarded as a LAB-rich fermented food providing various probiotics.     

Analysis of bacterial diversity during the fermentation of inyu, a high-temperature fermented soy sauce,using nested PCR-denaturing gradient gel electrophoresis and the plate count method

The diversity of bacteria associated with the fermentation of inyu, also known as black soy sauce, was studied through the nested PCR-denaturing gradient gel electrophoresis (DGGE) of samples collected from the fermentation stages of the inyu production process. The DGGE profiles targeted the bacterial 16S rDNA and revealed the presence of Citrobacter farmeri, Enterobacter cloacae, Enterobacter hormaechei, Enterococcus faecium, Klebsiella pneumoniae, Pantoea agglomerans, Salmonella enterica, Serratia marcescens, Staphylococcus sciuri and Weissella confusa. The bacterial compositions of 4 fermented samples were further elucidated using the plate count method. The bacteria isolated from the koji-making stage exhibited the highest diversity; Brachybacterium rhamnosum, E. hormaechei, K. pneumoniae, Kurthia gibsonii, Pantoea dispersa, Staphylococcus gallinarum, Staphylococcus kloosii and S. sciuri were identified. Koji collected during the preincubation stage presented the largest cell counts, and E. hormaechei, K. pneumoniae, E. cloacae and Enterobacter pulveris were identified. In brine samples aged for 7 and 31 days, the majority of the bacteria isolated belonged to 4 Bacillus species, but 4 Staphylococcus species and Delftia tsuruhatensis were also detected. This study demonstrates the benefits of using a combined approach to obtain a more complete picture of microbial populations and provides useful information for the control or development of bacterial flora during inyu fermentation.     

Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis

Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method.     

Diversity of lactic acid bacteria from modified atmosphere packaged sliced cooked meat products at sell-by date assessed by PCR-denaturing gradient gel electrophoresis

The predominant lactic acid bacteria (LAB) microbiota associated with three types of modified atmosphere packaged (MAP) sliced cooked meat products (i.e. ham, turkey and chicken) was analyzed at sell-by date using a combination of culturing and molecular population fingerprinting. Likewise routine analyses during industrial MAP production, meat samples were plated on the general heterotrophic Plate Count Agar (PCA) and on the LAB-specific de Man, Rogosa, Sharpe (MRS) agar under different temperature and atmosphere conditions. Subsequently, community DNA extracts were prepared from culturable bacterial fractions harvested from both media and used for PCR targeting the V3 hyper-variable region of the 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE) of PCR amplicons (PCR-DGGE). Irrespective of aerobic or anaerobic incubation conditions, V3-16S rDNA DGGE fingerprints of culturable fractions from PCA and MRS medium displayed a high level of similarity indicating that LAB constituted the most dominant group in the culturable bacterial community. Comparison of DGGE profiles of fractions grown at 20, 28 or 37 °C indicated that part of the culturable community consisted of psychrotrophs. Four DGGE bands were common among cooked ham, turkey and chicken products, suggesting that these represent the microbiota circulating in the plant where all three MAP product types were sliced and packaged. Based on band sequencing and band position analysis using LAB reference strains, these four bands could be assigned to Lactobacillus sakei and/or the closely related Lactobacillus fuchuensis, Lactobacillus curvatus, Carnobacterium divergens and Leuconostoc carnosum. In conclusion, the PCR-DGGE approach described in this study allows to discriminate, identify and monitor core and occasional LAB microbiota of MAP sliced cooked meat products and provides valuable complementary information to the current plating procedures routinely used in industrial plants.     

Microflora assessments using PCR-denaturing gradient gel electrophoresis of ozone-treated and modified-atmosphere-packaged farmed cod fillets

Denaturing gradient gel electrophoresis (DGGE) of a PCR-amplified 16S rDNA sequence was used to characterize changes in the microbial flora caused by ozone (O3) treatment of farmed cod (Gadus morhua). Portions of cod were produced under controlled conditions, bathed in fresh water supplemented with 2 ppm of O3 for 30 min, and packaged in modified atmosphere (MA: 60% CO2 and 40% N2) before 4 degrees C storage. Control samples were packaged in MA or air, without prior O3 treatment. Samples were analyzed by PCR-DGGE to determine the predominant bacterial flora and to examine possible differences in the microbial community due to O3 treatment. The DGGE analysis during the storage period showed that the O3 treatment produced no significant difference in the microbial flora compared with the controls. Sequencing of 16S rDNA detected the specific spoilage bacteria Photobacterium phosphoreum, Pseudomonas spp., Shewanella baltica, and Shewanella putrefaciens as the predominant bacteria in all samples. PCR-DGGE results were supported by culture and sensory analyses used in predicting product shelf life. Aerobic plate count, H2S-producing bacteria, and psychrotrophic bacterial counts demonstrated no significant extension of the shelf life of MA-packaged, O3-treated cod fillets.     

Succession of bacterial and fungal communities during a traditional pot fermentation of rice vinegar assessed by PCR-mediated denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) based on small subunit rRNA gene was applied to a traditional rice vinegar fermentation process in which the conversion of rice starch into acetic acid proceeded in a pot. The fungal DGGE profile indicated that the transition from Aspergillus oryzae to Saccharomyces sp. took place at the initial stage at which alcohol production was observed. The early stage was characterized by the coexistence of Saccharomyces sp. and lactic acid bacteria. Almost all of the bacterial DGGE bands related to lactic acid bacteria were replaced by bands derived from Lactobacillus acetotolerance and Acetobacter pasteurianus at the stage at which acetic acid started to accumulate. The microbial succession, tested in three different pots, was found to be essentially identical. Among the bacteria isolated at the early stage, some species differed from those detected by DGGE. This is the first report to reveal the microbial community succession that occurs during a unique vinegar fermentation process, as determined by a culture-independent method.     

传统分离培养结合PCR-DGGE技术分析传统乳制品中的乳酸菌

采用传统培养分离方法结合聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术对传统乳制品中乳酸菌种群结构进行研究。结果表明:用传统分离与分子鉴定方法得到5种乳酸菌,其中,乳酸片球菌(Pediococcus acidilactici)为优势菌群,对通过PCR-DGGE方法得到的9条16S rDNA条带序列进行了比对,结果表明瑞士乳杆菌(Lactobacillus helveticus)的丰度最高,是酸奶样品中主要的优势菌群,乳酸片球菌(Pediococcus acidilactici)为次优势菌群。传统分离法与PCR-DGGE技术结合能够更有效、更全面地分析传统乳制品中微生物的群落结构及优势菌群。     

Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra

Raw cocoa has an astringent, unpleasant taste and flavour, and has to be fermented, dried and roasted in order to obtain the characteristic cocoa flavour and taste. During the fermentation microbial activity outside the cocoa beans induces biochemical and physical changes inside the beans. The process is complex involving activity of several different groups of microorganisms which bring about numerous biochemical and physical changes inside the beans. Due to the complexity of these processes no thorough investigations of the interactions between the microbial activities on the outside of the beans and the chemical processes inside the beans have been carried out previously. Recently it has been shown that Denaturing Gradient Gel Electrophoresis (DGGE) offers an efficient tool for monitoring the microbiological changes taking place during the fermentation of cocoa. Near Infrared (NIR) spectroscopy has previously been used to determine various components in cocoa beans, offering a rapid alternative compared to traditional analytical methods for obtaining knowledge about changes in the chemical composition of the cocoa beans during fermentation. During a number of cocoa fermentations bean samples were taken with 24 h intervals to be dried and analysed by NIR. Cocoa pulp samples taken simultaneously during the same fermentations have previously been characterised using DGGE [Nielsen, D.S., Teniola, O.D., Ban-Koffi, L., Owusu, M., Andersson, T., Holzapfel, W.H. (2007). The microbiology of Ghanaian cocoa fermentations analysed using culture dependent and culture-independent methods. International Journal of Food Microbiology 114, 168-186.]. Here we report the first study where microbiological changes during the fermentation determined using DGGE are correlated to changes inside the beans determined by NIR using multivariate data analysis. Following data pre-processing (baseline correction followed by Co-shift correction or Correlation Optimised Warping) the DGGE spectra were analysed using Principal Component Analysis (PCA). A clear grouping according to fermentation time was seen demonstrating the microbial succession taking place during the fermentation. Subsequently the DGGE spectra were correlated to the NIR spectra using Partial Least Squares regression models (PLS2). Correlations of 0.87 (bacterial derived DGGE spectra) and 0.81 (yeast derived DGGE spectra) were obtained indicating the relationship between the microbial activities in the pulp and the (bio)chemical changes inside the beans. By comparing the X-block loadings of the PLS2 models and the DGGE spectra it was possible to directly link several microbial species with changes in the NIR spectra and consequently also with changes inside the beans.     

Isolation and characterization of lactic acid bacteria from fresh Chinese traditional rice wines using denaturing gradient gel electrophoresis

Food Science and Biotechnology - Lactic acid bacteria (LAB) are a prevalent bacterial group in rice wine maturation that contributes to flavor, texture, and nutritive value. To better understand...     

To improve the gel properties of liquid whole egg by short-term lactic acid bacteria fermentation

Fermentation, as a simple, safe and environmentally friendly technology, is promising in the modification of proteins. In this study, the liquid whole egg (LWE) was fermented at 37 °C by Lactiplantibacillus plantarum 90 (L. plantarum 90) which the dose of inoculation was about 8 Log 10 CFU mL⁻¹. During the process, the total aerobic mesophilic count (TAM) and the number of lactic acid bacteria (LAB) of LWE increased at 3 h and then decreased, consistent with the changes in protein solubility. Besides, the T₂ relaxation time of fermented egg gels moved to low relaxation time (T₂₂ shifted from 2154.44 ms (0 h) to 1232.85 ms (9 h)), indicating that the water retention of fermented egg gels was enhanced. After fermentation, it could be seen intuitively that the porous structure of the gel surface almost disappeared, along with the improved springiness and brightness by texture and color measurement. This study suggested that moderate fermentation (L. plantarum 90, 1% v/v, 9 h) could effectively improve the gel property of LWE, and thus had a potential to expand the application of LWE in the food industry.     

Identification of the bacterial biodiversity in koumiss by denaturing gradient gel electrophoresis and species-specific polymerase chain reaction

Bacterial biodiversity in traditional koumiss fermented milk was studied by denaturing gradient gel electrophoresis (DGGE). Target DNA bands were identified according to the reference species ladder, constructed in this study. Comigrating bands present in the DGGE profiles were resolved by species-specific PCR. The results revealed a novel bacterial profile and extensive bacterial biodiversity in koumiss. The dominant lactic acid bacteria included Lactobacillus acidophilus, Lactobacillus helveticus, Lactobacillus fermentum, and Lactobacillus kefiranofaciens. Frequently encountered bacterial species were Enterococcus faecalis, Lactococcus lactis, Lactobacillus paracasei, Lactobacillus kitasatonis, and Lactobacillus kefiri. Leuconostoc mesenteroides, Streptococcus thermophilus, Lactobacillus buchneri, and Lactobacillus jensenii were occasionally found in this product. In addition, L. buchneri, L. jensenii, and L. kitasatonis, which were never previously isolated by culture-dependent methods, were identified for the first time in the Xinjiang koumiss. Furthermore, conventional cultivation was performed by plating samples on M17, de Man-Rogosa-Sharpe, Halligan-Pearce, and Kenner fecal media. The results revealed that lactobacilli were the dominant species in the koumiss ecosystem, which was consistent with the results obtained by the DGGE analysis. This is the first systematic study of the microbial composition in koumiss, and our findings will be helpful in selecting appropriate strains for the manufacture of this product at the industrial level.     

荆州地区鲊广椒乳酸菌多样性解析及其分离株发酵特性的评价

运用纯培养技术从荆州地区鲊广椒中分离纯化乳酸菌,并采用分子生物学方法并对其进行同源性分析和系统发育树的构建,同时使用电子舌和电子鼻技术对乳酸菌分离株纯种发酵制备鲊广椒的滋味品质进行了评价。结果表明:从10个鲊广椒样品中共分离出22株疑似乳酸菌,分为4个属,8个种,其中优势菌为Lactobacillus plantarum(植物乳杆菌)。通过电子舌分析发现,添加乳酸菌的多数鲊广椒样品其酸味均有较明显的提升。通过电子鼻分析发现,传感器W5S、W1S、W1W、W2S和W2W对添加L. plantarum和肠球菌制备的鲊广椒样品响应值明显较低,而传感器W1C、W3C和W5C呈现出相反的趋势。通过主成分分析发现,L.plantarum HBUAS52151和L. plantarum HBUAS52166发酵制备的鲊广椒样品具有较好的品质。由此可见,荆州地区鲊广椒乳酸菌具有较高的多样性,且添加乳酸菌进行鲊广椒纯种发酵可明显改善产品的滋味和气味品质。     

蜂蜜对酸奶生产中乳酸菌生长和产酸能力的影响

在脱脂乳粉制成的全乳固体含量为12%(w/v) 的复原乳中,分别添加5%(w/v)的蔗糖、果糖或蜂蜜,并以不添加甜味剂的复原乳作为对照,经过70℃、15min灭菌,冷却至室温,分别接种唾液链球菌嗜热亚种、德氏乳杆菌保加利亚亚种和嗜酸乳杆菌,接种量5%(v/v),培养温度37℃,分别在培养初始和经过24h培养时取样,测定其乳酸菌活性、pH值和乳酸含量。结果表明,添加量为5%(w/v)的蜂蜜对于3种乳酸菌均没有抑制作用,是酸奶生产的合适甜味剂。     

Application of denaturing gradient gel electrophoresis to microbial diversity analysis in Chinese Douchi

BACKGROUND: Douchi is a traditional Chinese soybean food which has been consumed for thousands years as an important protein source and flavouring ingredient. Studies have rarely been carried out to investigate its microbial composition and these are urgently required for the commercial labels and safety considerations. RESULTS: Microbial counts were statistically significant different among Douchi samples. Although the maximum diversity indexes of bacterial, bacillus and fungal polymerase chain reaction–denaturing gradient gel electrophoresis (PCR‐DGGE) patterns were only 79%, 70% and 64%, some microorganisms, e.g. Bacillus subtilis, Bacillus amyloliquefaciens, Pseudomonas sp., Saccharomyces cerevisiae and Pichia farinose, were found to share dominant positions in most Douchi samples. In addition, some pathogens, e.g. Staphylococcus saprophyticus, Pantoea sp., Staphylococcus sciuri, Enterobacter sp. and Staphylococcus sp., were also identified. CONCLUSION: The PCR‐DGGE technique was used for the first time as an effective method to assess the microbial communities in different Chinese Douchi samples. This information may be useful in improving the product quality, reformatting production methods, extending shelf life and scaling up the fermentation process. Copyright © 2012 Society of Chemical Industry     

Microbiota during fermentation of chum salmon (Oncorhynchus keta) sauce mash inoculated with halotolerant microbial starters: Analyses using the plate count method and PCR-denaturing gradient gel electrophoresis (DGGE)

Nine different combinations of mugi koji (barley steamed and molded with Aspergillus oryzae) and halotolerant microorganisms (HTMs), Zygosaccharomyces rouxii, Candida versatilis, and Tetragenococcus halophilus, were inoculated into chum salmon sauce mash under a non-aseptic condition used in industrial fish sauce production and fermented at 35 ± 2.5 °C for 84 days to elucidate the microbial dynamics (i.e., microbial count and microbiota) during fermentation. The viable count of halotolerant yeast (HTY) in fermented chum salmon sauce (FCSS) mash showed various time courses dependent on the combination of the starter microorganisms. Halotolerant lactic acid bacteria (HTL) were detected morphologically and physiologically only from FCSS mash inoculated with T. halophilus alone or with T. halophilus and C. versatilis during the first 28 days of fermentation. Only four fungal species, Z. rouxii, C. versatilis, Pichia guilliermondii, and A. oryzae, were detected throughout the fermentation by PCR-denaturing gradient gel electrophoresis (PCR-DGGE). In FCSS mash, dominant HTMs, especially eumycetes, were nonexistent. However, under the non-aseptic conditions, undesirable wild yeast such as P. guilliermondii grew fortuitously. Therefore, HTY inoculation into FCSS mash at the beginning of fermentation is effective in preventing the growth of wild yeast and the resultant unfavorable flavor.     

Inhibition of spoilage lactic acid bacteria by lysozyme during wine alcoholic fermentation

The efficacy of lysozyme against indigenous lactic acid bacteria (LAB) and four inoculated spoilage LAB cultures was investigated in laboratory scale Chardonnay winemaking trials (at pH 3.8). These LAB cultures included Lactobacillus kunkeei, Lactobacillus brevis, Pediococcus parvulus , and Pediococcus damnosus . Three concentrations of lysozyme were used: 0, 125 and 250 mg/L. Alcoholic fermentation of the grape juice was carried out at 20±0.5°C using Saccharomyces cerevisiae . Lysozyme did not have any negative impact on yeast growth and sugar reduction. This enzyme was found to be very effective in inhibiting the growth of all four LAB cultures investigated. Under the given experimental conditions, as high as an 8 log cell reduction was obtained for some of the strains. The acetic acid production by L. brevis and L. kunkeei was significantly reduced in the treatments with 125 and 250 mg/L lysozyme added ( P < 0.01). The effect of lysozyme on the cells of the LAB cultures was examined under a scanning electron microscope. It is evident that lysozyme had a detrimental impact on the cells of these cultures. Based on these observations, it is concluded that lysozyme may be a useful tool for winemakers to control the growth of spoilage LAB and to reduce the production of volatile acids. The addition of lysozyme may also prevent the increase of volatile acidity during stuck/sluggish alcoholic fermentation. This tool is particularly useful in high pH wines where SO₂ is less effective.     

Ultrafiltration flux of acid whey obtained by lactic acid fermentation

Acid whey was prepared from reconstituted ultra-low heat skimmed milk powder fermented with Lactobacillus helveticus, clarified by centrifugation, pH adjusted and ultrafiltered (cut-off limit 10 or 30 kDa) at 50 °C to a volume reduction ratio of 10. Centrifugation primarily removed the serum albumin and, to a lesser extent, immunoglobulins, considered the most critical membrane foulants during ultrafiltration of acid whey. Below pH 3.9 the flux improvement was directly dependent on pH lowering. At pH 3.9 a deviation point in the relationship between pH and flux of acid whey was observed. Above this pH a severe flux decline was detected and at pH 4.6 the fermented acid whey was non-filterable. Largest flux increase was obtained at a transmembrane pressure of 2.0 bar and 50 °C. Under these conditions the permeation flux achieved using a 30 kDa membrane was about 34 ± 5 kg h⁻¹m⁻², comparable with that for sweet whey.     

Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis

Samples of Coffea arabica were collected during the different stages of the fermentation from two production sites in Tanzania. The yeasts community was identified by genotyping using ITS-PCR and sequence analysis of the D1/D2 domain of the 26S rRNA gene. For confirmation, denaturating gradient gel electrophoresis (DGGE) of PCR-amplified 26S rRNA gene was performed to detect yeast directly from coffee samples without cultivation. Yeast counts were in the range 4.0 x 10(4) - 5.0 x 10(7) CFU/g with an increase during fermentation. Three yeasts species were dominant. The predominant yeast found during fermentation and drying was Pichia kluyveri. Pichia anomala was found in high numbers during drying of coffee beans. Hanseniaspora uvarum was the predominant yeast during fermentation but decreased during drying. Kluyveromyces marxianus, Candida pseudointermedia, Issatchenkia orientalis, Pichia ohmeri and Torulaspora delbrueckii occurred in concentrations of 10(3) CFU/g or below in coffee samples. Saccharomyces cerevisiae and Candida xestobii were not isolated by cultivation, but by the DGGE technique. A good agreement was found between the sequence analysis of the D1/D2 domain of the 26S rRNA gene and sequencing of the DGGE bands.     

蔬菜乳酸菌腌渍发酵过程亚硝酸盐变化研究

研究了蔬菜腌渍发酵过程中添加乳酸菌纯培养液对亚硝酸盐含量变化的影响。实验结果表明,接种乳酸菌能降低蔬菜腌渍发酵过程中亚硝酸盐含量。4组乳酸菌腌渍发酵实验中,接种混合菌种(干酪乳杆菌∶鼠李糖乳杆菌∶植物乳杆菌=1∶1∶1)对蔬菜湿腌发酵时菜料和菜汤的亚硝酸盐含量降低效果最佳,接种植物乳杆菌对蔬菜干腌发酵时菜料亚硝酸盐含量降低作用最显著。