ABSTRACT
Abstract Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.
Subject(s)
Soil Microbiology , Polymorphism, Restriction Fragment Length , Forests , Polymerase Chain Reaction , Microbiota , Fungi/classification , Fungi/genetics , Soil/chemistry , Calcium Chloride , DNA, Bacterial , DNA, Fungal , Fungi/isolation & purificationABSTRACT
Objective To explore the objectivity and scientificity of fecal sampling , and to provide reference for investigating the relationship between intestinal microbes and diseases . Methods Terminal restriction fragment length polymorphism, degeneration gradient gel electrophoresis and real time fluorescent quantitative PCR techniques were applied to differentially analyze the bacterial community composition and abundance of intestinal contents and feces taken from dif -ferent sites of BALB/c mouse intestine .Results The predominant T-RFLP fragments ( T-RFs) in feces in the rectum and colon were 244 bp, 255 bp and 449 bp, however , those in feces of the small intestine including duodenum , jejunum and il-eum were 60 bp, 73 bp, 261 bp, 268 bp and 272 bp, and with a larger variation of the bacterial community composition in various parts of the small intestine .The bacterial abundance in the contents of duodenum and jejunum were 6.9 log ( cop-ies)/g and 8.3 log (copies)/g, fewer than in the other parts of the intestine , while the bacterial abundance in the feces was as high as 11.8 log (copies)/g, being about 2 times higher than that in the duodenum and jejunum (P0.05).Conclusions The inter-mouse variations of bacterial communi-ty composition in the large intestine contents are small .The bacterial composition and abundance are similar suggest that studies on the relationship between large intestine especially colorectal microbiota and diseases may be conducted via fecal sampling.
ABSTRACT
Objective: To investigate the impact of essential oil (cinnamon oil) from Cinnamomum cassia (EOCC) on Clostridia flora IV and Bacteroides in gut of normal rats. Methods: SD rats were administered with EOCC (0.384 3 g/kg) for 30 d and the colon and rectal contents were sampled. The population, diversity, and distribution of Clostridium flora IV and Bacteroides in the samples were analyzed by the terminal restriction fragment length polymorphism (TRFLP) method based on the intestinal flora 16S ribosomal RNA gene. Results: Both the intestinal flora population, diversity, and distribution of Clostridia flora IV and Bacteroides changed significantly due to the injection, especially for Clostridia flora IV. Additionally, EOCC exerted the different effects on colon and rectal microflora. Conclusion: The effects of EOCC on Clostridia flora IV and Bacteroides in gut might be the functional mechanism of cinnamon oil in curing obesity and diabetes.
ABSTRACT
Terminal Restriction Fragment Length Polymorphism (T-RFLP) is a culture-independent fingerprinting method for microbial community analysis. Profiles generated by an automated electrophoresis system can be analysed quantitatively using either peak height or peak area data. Statistical testing demontrated that peak height data showed to be more reproducible than peak area data.
Terminal Restriction Fragment Length Polymorphism (T-RFLP) é um método molecular, independente de cultivo, para análise de comunidades microbianas. Perfis gerados por um sistema automatizado de eletroforese podem ser analisados quantitativamente usando dados de altura ou área dos picos. Os dados de altura mostraram-se mais reprodutíveis do que os de área.