Characterization of the Dynamic Changes of Microorganisms in Cutlassfish (Trichiurus haumela) under the Cold Storage with Composite Natural Preservatives Based on Culture-Dependent and 16S rRNA-DGGE Technology

2012 ◽  
Vol 554-556 ◽  
pp. 1498-1506
Author(s):  
Wei Qing Lan ◽  
Jing Xie
Keyword(s):  
16S Rrna ◽  
Pseudomonas Fluorescens ◽  
Cold Storage ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sequencing Analysis ◽  
Pseudomonas Sp ◽  
Dynamic Changes ◽  
Dominant Bacteria ◽  
Natural Preservatives ◽  
Culture Dependent

In this study, the main microbe dynamic changes of cutlassfish (Trichiurus haumela) treated with composite natural preservatives under the cold storage (4±1) °C were studied by the methods of culture-dependent and denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis based on the sequence of 16S rRNA V3 region gene, which provided the theory basis and reference to the composite natural preservatives’ mechanism and extended the shelf-life of aquatic products. The results showed that 13 kinds of bacteria were identified by the culture-dependent methods, the dominant bacteria belonged to Shewanella putrefaciens and Pseudomonas fluorescens. By sequencing analysis, 12 kinds of bacteria in main DGGE spectra stripe of cutlassfish. In the later periods, the specific spoilage organism (SSO) for the treatment group with composite natural preservatives and the controlled of cutlassfish were highly similar. Psychrobacter sp. was the main bacterium in the initial stage of the storage. With the extension of storage time, the proportion of Shewanella sp. and Pseudomonas sp. increased gradually and they took the place of Psychrobacter sp. to be the dominant bacteria in the process of storage. Thereinto, Pseudomonas fluorescens and Vibrio sp. both took high proportions in the process of storage. At the same time, composite natural preservatives had an obvious growth inhibition effects on the bacteria of cutlassfish such as Shewanella sp. and Pseudomonas sp..

Comparative Analysis of Bacterial Diversity for Cutlassfish (Trichiurus haumela) during Cold Storage by the Culture-Dependent and Culture-Independent Methods

2012 ◽  
Vol 535-537 ◽  
pp. 1046-1053 ◽  
Author(s):  
Wei Qing Lan ◽  
Jing Xie
Keyword(s):  
16S Rrna ◽  
Pseudomonas Fluorescens ◽  
Cold Storage ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Region Gene ◽  
Gradient Gel Electrophoresis ◽  
Dominant Bacteria ◽  
V3 Region ◽  
Culture Dependent

The methods of culture-dependent and denaturing gradient gel electrophoresis (DGGE) based on the sequence of 16S rRNA V3 region gene were described to comparatively characterize the microbial population and community structure of cutlassfish (Trichiurus haumela) under the cold storage. The results showed that 13 kinds of bacteria were identified by the traditional culture-dependent methods, the dominant bacteria belonged to Shewanella putrefaciens and Pseudomonas fluorescens. To determine the community profiles of the samples on variable V3 region, the bacteria of 16S rRNA gene were amplified by PCR and 11 distinct PCR products were separated by DGGE fingerprinting technology. From the sequence analysis, Psychrobacter sp. was found to be the predominant bacteria in the initial stage of the storage. The proportion of Shewanella sp., Pseudomonas sp. increased gradually with the extension of storage time, and they took the place of Psychrobacter sp. to be the dominant bacteria. Thereinto, both Pseudomonas fluorescens and Vibrio sp. took high proportions in the process of storage due to the deterioration of cutlassfish (Trichiurus haumela).

scholarly journals Bacterial 16S rRNA/rDNA Profiling in the Liquid Phase of Human Saliva

2009 ◽  
Vol 3 (1) ◽  
pp. 80-84 ◽  
Author(s):  
F Gu ◽  
Y Li ◽  
C Zhou ◽  
D.T.W Wong ◽  
C.M Ho ◽  
...  
Keyword(s):  
Liquid Phase ◽  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pearson Correlation ◽  
Operational Taxonomic Unit ◽  
Human Saliva ◽  
Oral Bacteria ◽  
Oral Microbiota ◽  
Sequencing Analysis ◽  
Gradient Gel Electrophoresis

Human saliva can be separated by centrifugation into cell pellet and cell-free supernatant, which are called cellular phase and liquid phase in this study. While it is well documented that the cellular phase of saliva contains hundreds of oral bacteria species, little is known whether the liquid phase of saliva contains any information related to oral microbiota. In this study, we analyzed the bacterial nucleic acid contents of the liquid phase of saliva. Using primers universal to most eubacterial 16S rDNA, we detected large amounts of bacterial 16S rRNA and rDNA in the cell-free phase of saliva. Random sequencing analysis of forty PCR amplicons from the cell-free phase of saliva led to 15 operational taxonomic unit (OTU) groups. Furthermore, using denaturing gradient gel electrophoresis (DGGE), we compared 16S rRNA/rDNA profiles derived from liquid phases and cellular phases of saliva samples, and found positive correlations (Pearson Correlation=0.822,P<0.001) between these sample groups. These findings indicate that the liquid phase of saliva contains numerous bacterial 16S rRNA/rDNA molecules that have correlations with bacteria existing in the cellular phase.

Bacterial Diversity and Spoilage-Related Microbiota Associated with Freshly Prepared Chicken Products under Aerobic Conditions at 4°C

2012 ◽  
Vol 75 (6) ◽  
pp. 1057-1062 ◽  
Author(s):  
RONGRONG LIANG ◽  
XIAOQIAO YU ◽  
RENHUAN WANG ◽  
XIN LUO ◽  
YANWEI MAO ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Pseudomonas Sp ◽  
Republic Of China ◽  
Spoilage Bacteria ◽  
Gradient Gel Electrophoresis ◽  
Cling Film ◽  
Dominant Bacteria ◽  
First Time

This study analyzed the bacterial diversity and spoilage-related microbiota associated with freshly prepared chicken products stored aerobically at 4°C, using “bone and chicken string,” a product popular in the People's Republic of China, as the study subject. Samples collected from three different factories were tray packaged with cling film and stored at 4°C. Bacterial diversity and dominant bacteria were analyzed using PCR amplification and denaturing gradient gel electrophoresis. Combined with selective cultivation of the dominant bacteria and correlation analysis, the dominant spoilage microbiota was determined. The results showed that bacterial diversity varied with different manufacturers. Such bacteria as Acinetobacter sp., Carnobacterium sp., Rahnella sp., Pseudomonas sp., Brochothrix sp., and Weissella sp. were detected in freshly prepared chicken products during storage. And Carnobacterium sp., Pseudomonas sp., and Brochothrix sp. bacteria were the common dominant spoilage bacteria groups in most freshly prepared chicken products from different factories. Carnobacterium was, for the first time, shown to be an important contributor to the spoilage-related microflora of freshly prepared chicken products stored aerobically under refrigeration. Our work shows the bacterial diversity and dominant spoilage microbiota of freshly prepared chicken products stored aerobically under refrigeration.

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

2005 ◽  
Vol 51 (11) ◽  
pp. 897-909 ◽  
Author(s):  
Marc Viñas ◽  
Jordi Sabaté ◽  
Caterina Guasp ◽  
Jorge Lalucat ◽  
Anna M Solanas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Consortium ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Sole Source ◽  
Rrna Gene ◽  
Dominant Group ◽  
Clone Libraries ◽  
Variable Regions ◽  
Culture Dependent

A microbial consortium (AM) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (PAH) mixture of three- and four-ringed PAHs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (DGGE), and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and seven by both DGGE and clone libraries were obtained. The comparison of three variable regions (V3–V5) of the 16S rRNA gene between the sequences obtained yielded 19 different microbial components. Proteobacteria were the dominant group, representing 83% of the total, while the Cytophaga–Flexibacter–Bacteroides group (CFB) was 11% and the Ascomycota fungi 6%. β-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences were achieved by the cultivation method that showed members of the α-, β-, and γ-Proteobacteria; CFB bacterial group; and Asco mycota fungi. Only six of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1), which were similar to Sphingomonas sp. and Fusarium sp., respectively, achieved the greatest PAH depletion. The results indicate that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium.Key words: microbial consortium, microbial diversity, PAHs, DGGE, 16S rRNA gene.

scholarly journals Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis

2018 ◽  
Vol 83 (5) ◽  
pp. 1333-1341 ◽  
Author(s):  
Maria Teresa P. Gonçalves ◽  
María José Benito ◽  
María de Guía Córdoba ◽  
Conceição Egas ◽  
Almudena V. Merchán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Rrna Gene Sequencing ◽  
Culture Dependent

scholarly journals Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting

2008 ◽  
Vol 74 (8) ◽  
pp. 2414-2423 ◽  
Author(s):  
Ilse Scheirlinck ◽  
Roel Van der Meulen ◽  
Ann Van Schoor ◽  
Marc Vancanneyt ◽  
Luc De Vuyst ◽  
...  
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Type I ◽  
Technological Parameters ◽  
Structure And Stability ◽  
Two Samples ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment rather than the type or batch of flour largely determines the development of a stable LAB population in sourdoughs.

scholarly journals Qualidade microbiológica da água da área de preservação ambiental: Fazenda Guajuviras – Canoas (RS)

2019 ◽  
Vol 11 (2) ◽  
pp. 13-21
Author(s):  
Priscila Ribeiro Jankoski ◽  
Mateus De Oliveira Negreiros ◽  
Anelise Beneduzi da Silveira ◽  
Francisco Fernando de Castilho Koller
Keyword(s):  
Bacillus Subtilis ◽  
16S Rrna ◽  
Pseudomonas Fluorescens ◽  
Pseudomonas Sp ◽  
Lactococcus Garvieae ◽  
Gene 16S Rrna

As áreas úmidas compreendem vários ecossistemas, dentre eles, os banhados, que são locais estratégicos para conservação devido à sua alta diversidade biológica e produtividade resultante das relações estabelecidas entre a água, solo, vegetação e fauna. A Área de Proteção Ambiental (APA) Fazenda Guajuviras está localizada no município de Canoas (RS) e compreende cerca de 560ha. O objetivo desse estudo foi analisar os níveis de contaminação por bactérias heterotróficas e do grupo coliforme, traçar o perfil bioquímico e identificar alguns isolados bacterianos presentes em dois banhados da APA Guajuviras. Para tanto, as coletas foram realizadas em março de 2015, sendo que cada banhado foi dividido em quatro quadrantes, de onde foram coletadas amostras de 250mL de água. O banhado 2 foi o que apresentou os maiores níveis tanto para coliformes totais como para termotolerantes. Na quantificação das bactérias heterotróficas, os maiores níveis encontrados foram no quadrante norte do banhado 1 e 2. Foram isoladas oito linhagens bacterianas destes banhados. Das linhagens bacterianas obtidas destes banhados, foi possível a identificação, a partir do sequenciamento do gene 16S rRNA, de oito isolados de dois gêneros: Pseudomonas sp. e Serratia sp., e de mais três espécies: Bacillus subtilis, Lactococcus garvieae e Pseudomonas fluorescens.

scholarly journals Bacterial communities associated to the urethra of healthy gilts and pregnant sows undergoing different reproductive protocols

2020 ◽  
Vol 98 (9) ◽  
Author(s):  
Andrea Torres Luque ◽  
Cecilia Fontana ◽  
Sergio E Pasteris ◽  
Daniela Bassi ◽  
Pier S Cocconcelli ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Future Research ◽  
Rrna Gene ◽  
Pseudomonas Sp ◽  
Core Microbiome ◽  
Urinary Infections ◽  
Urinary Microbiome ◽  
Culture Dependent

Abstract Nowadays, it is known that the urogenital microbiota plays a key role in the urinary health of mammalians. Despite the urinary infections affect the health and the welfare of breeding sows, the urethral microbiota of healthy sows remains unknown. Therefore, this work evaluates the urethral bacterial communities of healthy gilts and sows to determine the presence of Enterobacteriaceae populations, and the structure of this microbiota in gilts (G) and pregnant (P) sows. Samples were collected by scraping the urethral mucosa of G (n = 9) and P sows, which included natural mating (NM, n = 9) and artificial inseminated (AI, n = 7) sows. Samples were analyzed by culture-dependent techniques and 16S-rRNA gene high-throughput-sequencing. All females were positive for Enterobacteriaceae culture, without significant differences (Kruskal–Wallis) between G and P groups (median values: 2.78 and 3.09 log CFU/mL, respectively; P = 0.497). Also, the rate of Enterobacteriaceae/total mesophilic microorganisms was individually calculated, without significant differences between G and P sows (median values: 0.61 and 0.66, respectively; P = 0.497). When analyzing the bacterial communities, it was found similar richness in G, NM, and AI; however, diversity was lower in P sows than G (Mann Whitney/Kruskal–Wallis test, P &lt; 0.01). The dominating phyla that constituted a “core microbiome” included Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, which were common for all the studied females. The relative abundance for phyla, families, and genera was estimated, and Firmicutes was significantly higher in NM than AI sows (P = 0.02, Mann–Whitney/Kruskal Wallis test for univariate statistical comparisons); Pseudomonadaceae and Enterobacteriaceae were higher in AI than in NM (Mann–Whitney/Kruskal–Wallis, P &lt; 0.05). Lactobacillus and Pseudomonas were among the dominant genera; however, only Pseudomonas sp. was significantly higher in AI than NM (Mann–Whitney/Kruskal–Wallis, P = 0.006). The results represent the first evidence about the existence of a urethral microbiota that includes Enterobacteriaceae, as well as the patterns of this microbiota in G and P sows. The knowledge of this urethral microbiota might allow for future research to develop innovative protocols to restore and/or preserve the healthy ecology of the urinary microbiome to prevent diseases ensuring the welfare of breeding sows.

scholarly journals The Existence of Endophytic Actinobacteria from Rhododendron zoelerri Revealed by Culture-Dependent and Culture-Independent Approaches

2018 ◽  
Vol 25 (2) ◽  
pp. 54
Author(s):  
Yulin Lestari ◽  
Lia Aseptin Murdini ◽  
Dedy Duryadi Solihin
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Morphological Characteristics ◽  
Rrna Gene ◽  
Culture Independent ◽  
Reference Strains ◽  
Culture Dependent ◽  
Endophytic Actinobacteria

Endophytic actinobacteria from medicinal plant may play a significant role in producing bioactive compounds. The information regarding their diversity is an important.  Rhododendron are traditionally used for treating human disorders. One of the selected Rhododendron used in this study was R.  zoelleri from Papua origin, which has been conserved and grown in Cibodas Botanical Garden, West Java, Indonesia. The aim of this study was to assess the existence of endophytic actinobacteria from R. zoelleri based on a culture-dependent and their community structure based on a culture-independent approach. Culturable actinobacteria were isolated and cultured on HV medium. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) targeting the metagenomic 16S rRNA was used to analyse the structure of the actinobacterial community. Six culturable endophytic actinobacteria (200 cfu/g fresh weight) from R. zoelleri were successfully isolated, three isolates from leaf, and the other isolates were obtained from stem. The six culturable isolates were RZP 1.3, RZP 1.1, RZP 2.2, RZPB 1.1, RZPB 7.1, RZPB 4.1. Based on their morphological characteristics, the endophytes have Streptomyces characters. The existence of Streptomyces spp. were also confirmed with molecular analysis based on 16S rRNA gene. The phylogenetic analysis based on 16S rRNA gene to the reference strains available in EzTaxon-e database showed that six isolates were closely related to S. djakartensis strains of NBRC 15409ᵀ(99.19%), S. tritolerans strains of DAS 165T(99.90%), S. coelicoflavus strains of NBRC 15399T(99.59). However, they showed differences in morphological characteristics as compared with the reference strains. The metagenomic analysis of the DGGE profile based on 16S rRNA gene showed the community structure of endophytic actinobacteria from R. zoelleri which was represented by 13 DGGE bands. The bands were closely related to Agromyces, Gordonia, Microbacterium, Micromonospora, Propionibacterium, Saccharomonospora, Streptomyces which have 93.18%-100% similarity. Based on the data, it showed diversity of endophytic actinobacteria from R. zoelleri which may be further assess for their novelty and bioprospecting.

scholarly journals PENDEKATAN CULTURE INDEPENDENT UNTUK ANALISIS KOMUNITAS BAKTERI

OSEANA ◽  
2019 ◽  
Vol 42 (1) ◽  
pp. 9-17
Author(s):  
Nur Fitriah Afianti ◽  
Yeti Darmayati
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Target Genes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Single Strand Conformation Polymorphism ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Culture Independent ◽  
Culture Dependent

CULTURE INDEPENDENT APPROACH FOR BACTERIAL COMMUNITY ANALYSIS. Analysis of bacterial community can be through two approaches, through cultivation (culture dependent) and without cultivation (culture independent). Culture dependent approach is conventional method which only covered few bacteria because not all bacteria could be cultured. Culture independent approach with molecular techniques based on DNA communities can provide more information about the structure and diversity of bacteria in nature, both culturable bacteria and unculturable bacteria. 16S rRNA gene is commonly target gene used in bacterial communities analysis. Other specific target genes also being developed for specific groups of bacteria. Several methods are developed for the analysis of molecular markers 16S rRNA or other specific genes, including Denaturing Gradient Gel Electrophoresis (DGGE), Terminal Restriction Fragment Length Polymorphism (TRFLP), and Single Strand Conformation Polymorphism (SSCP).

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