Arif YAVUZ, Dilek Özgün EKİZ, İlhami KENGER, Uğur ÇÖMLEKCİOĞLU

Metagenomic DNA isolation from sheep feces and PCR detection of several rumen bacteria

Yavuz A, Ekiz Özgün D, Kenger İ, Çömlekcioğlu U. Koyun dışkısından metagenomik DNA izolasyonu ve bazı rumen bakterilerinin varlığının PZR ile tespit edilmesi. Amaç: Bu çalışmanın amacı taze ve kuru koyun dışkısından metagenomik DNA'nın izolasyonunu yapmak ve spesifik primerler kullanarak çeşitli rumen bakterilerini tespit etmektir.Gereç ve Yöntem: Metagenomik DNA izolasyonu ticari I-Genomic Dışkı DNA izolasyon kiti kullanılarak gerçekleştirildi. Anaerovibrio lipolytica, Fibrobacter succinogenes, Prevotella bryantii, Prevotella ruminicola, Ruminobacter amylophilus, Ruminococcus albus, Ruminococcus flavefaciens, Streptococcus bovis, Selenomonas ruminantium ve Succinovibrio dextrinosolvens spesifik primerler ile metagenomik DNA kullanılarak polimeraz zincir reaksiyonu yardımıyla tarandı. R. amylophilus, R. albus ve S. dextrinosolvens yokluğunu doğrulamak için 16S rRNA bölgesinin SphI ile reaksiyonu gerçekleştirildi. Bulgular: Dışkı örnekleri hızlıca kurutuldu ve yaş ağırlığının %53.72'si kaybettirildi. Taze ve kuru örneklerdeki DNA izolasyonlarından sonra DNA konsantrasyonları ve saflığı sırasıyla 25.60-59.50 ng/µL ve 1.72-1.90 arasında değiştiği belirlendi. Dışkıdaki inhibitörlerin PZR üzerinde etkisinin olmadığı görüldü. A. lipolytica, F. succinogenes, P. bryantii, P. ruminicola, R. flavefaciens, S. bovis ve S. ruminantium spesifik primerler ile tespit edildi, fakat PCR ile R. amylophilus, R. albus ve S. dextrinosolvens varlığına rastlanılmadı. 16S rRNA bölgesinin SphI ile kesimi bu sonucu doğruladı. Öneriler: Bu çalışma, doğal şartlarda kurumanın dışkı örneklerinden metagenomik DNA izolasyonu üzerine etkilerini tanımlamıştır. Ayrıca, izole edilen DNA kullanılarak çeşitli rumen bakterilerinin tespiti gerçekleştirilmiştir. Sonuç olarak kurumuş dışkıdan izole edilen metagenomik DNA'nın bakteri populasyonlarının belirlenmesinde kullanılabileceği ifade edilebilir.

Koyun dışkısından metagenomik DNA izolasyonu ve bazı rumen bakterilerinin varlığının PZR ile tespit edilmesi.

. Aim: The aim of this study was to isolate metagenomic DNA from fresh and dry sheep feces and to detect several rumen bacteria using the specific primers. Materials and Methods: The metagenomic DNA isolation was performed by using commercial I-Genomic Stool DNA Isolation Kit. Anaerovibrio lipolytica, Fibrobacter succinogenes, Prevotella bryantii, Prevotella ruminicola, Ruminobacter amylophilus, Ruminococcus albus, Ruminococcus flavefaciens, Streptococcus bovis, Selenomonas ruminantium and Succinovibrio dextrinosolvens were screened using metagenomic DNA with polymerase chain reaction and spesific primers. Reaction of 16S rRNA region with SphI was carried out to confirm the absence of R. amylophilus, R. albus and S. dextrinosolvens.Results: Fecal samples dried rapidly and lost its 53.72% of fresh mass. After the DNA isolations from fresh and dried samples, DNA concentrations and purity were varied between 25.60-59.50 ng/µL and 1.72-1.90, respectively. It was observed that fecal inhibitors had no effect on PCR. A. lipolytica, F. succinogenes, P. bryantii, P. ruminicola, R. flavefaciens, S. bovis and S. ruminantium were detected with specific primers however PCR did not reveal the presence of R. amylophilus, R. albus and S. dextrinosolvens. SphI digestion of 16S rDNA regions has confirmed this result.Conclusions: In this study, effect of drying in natural conditions on metagenomic DNA isolation from fecal samples was determined. Furthermore, PCR detection of several rumen bacteria was performed by using isolated DNA. In conclusion, it may be stated that the metagenomic DNA isolated from dried fecal samples could be an effective tool for the detection of bacterial populations.

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