Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples.

نویسندگان

  • Sonia M Tiquia
  • Liyou Wu
  • Song C Chong
  • Sergei Passovets
  • Dong Xu
  • Ying Xu
  • Jizhong Zhou
چکیده

Microarrays fabricated with oligonucleotides longer than 40 bp have been introduced for monitoring whole genome expression but have not been evaluated with environmental samples. To determine the potential of this type of microarray for environmental studies, a 50-mer oligonucleotide microarray was constructed using 763 genes involved in nitrogen cycling: nitrite reductase (nirS and nirK), ammonia monooxygenase (amoA), nitrogenase (nifH), methane monooxygenase (pmoA), and sulfite reductase (dsrAB) from public databases and our own sequence collections. The comparison of the sequences from pure cultures indicated that the developed microarrays could provide species-level resolution for analyzing microorganisms involved in nitrification, denitrification, nitrogen fixation, methane oxidation, and sulfite reduction. Sensitivity tests suggested that the 50-mer oligonucleotide arrays could detect dominant populations in the environments, although sensitivity still needs to be improved. A significant quantitative relationship was also obtained with a mixture of DNAs from eight different bacteria. These results suggest that the 50-mer oligonucleotide array can be used as a specific and quantitative parallel tool for the detection of microbial populations in environmental samples.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems.

To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. The functional genes in the microarray were involved ...

متن کامل

Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays.

To effectively monitor biodegrading populations, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the 2,402 known genes and pathways involved in biodegradation and metal resistance. This array contained 1,662 unique and group-specific probes with <85% similarity to their nontarget sequences. Based on artificial probes, our results showed that under hybridiz...

متن کامل

Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.

High-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. However, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic DNA) for the study of pure cultures are not applicable. In this study,...

متن کامل

Strain/species-specific probe design for microbial identification microarrays.

Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel k-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-speci...

متن کامل

Use of microarrays with different probe sizes for monitoring gene expression.

Microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole-genome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal i...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • BioTechniques

دوره 36 4  شماره 

صفحات  -

تاریخ انتشار 2004