Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems

Sekhavati, Mohammad Hadi; Mesgaran, M. Danesh; Nassiri, Mohammadreza; Mohammadabadi, Tahereh; Rezaii, Farkhondeh; Maleki, Adham Fani

doi:10.1016/j.mycres.2009.07.017

Cited by 17 publications

(13 citation statements)

References 31 publications

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“…These techniques may employ DNA profi ling techniques (PCR based), quantitative PCR, sequencing, fl uorescent in situ hybridization (FISH), DNA microarrays and fl ow cytometry (Gong and Yang 2012 ). PCR-based DNA profi ling techniques using PCR primers which target the specifi c genes to amplify the 16S/ITS rDNA sequence template targeted DNA sample (Snel et al 2002 ;Li et al 2003 ), while, on the other hand, bacterial population size of gut microbiota could be measured using qPCR method (Sekhavati et al 2009 ). The quantifi cation is achieved by measuring fl uorescence emitted by the fl uorophore.…”

Section: Rumen Manipulation Using Genomic Approachesmentioning

confidence: 99%

‘Omics’ Approaches to Understand and Manipulate Rumen Microbial Function

Shrivastava

Jain

Kumar

et al. 2015

Rumen Microbiology: From Evolution to Revolution

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Diverse populations of rumen microorganisms in gut contribute to develop ability of breaking down fi brous foods, which are mostly unusable by humans (Owens FN, Goetsch AL (1988) Ruminal fermentation. In: Church DC (ed) The ruminant animal, digestive physiology and nutrition. Prentice-Hall, Englewood Cliffs, p 160). Rumen is having a larger population of microorganisms, more than a trillion organisms and wide diversity (hundreds of species and thousands of subspecies), per ounce of rumen contents (Xu et al., J Anim Sci 85:1024-1029, 2007. There are various traditional approaches through which overall performance of the rumen has been attempted to improve, e.g. plant secondary metabolites, microbial feed additives, chemical feed additives, selective stimulation of benefi cial rumen microbes and selective inhibition of harmful rumen microbes. In spite of these, nowadays various new approaches are being used to improve our understanding of the relationships among the various rumen microorganisms and towards how they interact with their hosts (Chaucheyras-Durand and Ossa, Prof Anim Sci 30:1-12, 2014). To better characterize species in the rumen, new advanced technological aids such as gene sequencing and study of gene (genomics), protein (proteomics) and metabolite (metabolomics) expression are being frequently used. This chapter will majorly emphasize on recent tools used in exploring the diversity of rumen.

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Section: Rumen Manipulation Using Genomic Approachesmentioning

confidence: 99%

‘Omics’ Approaches to Understand and Manipulate Rumen Microbial Function

Shrivastava

Jain

Kumar

et al. 2015

Rumen Microbiology: From Evolution to Revolution

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“…Real-time PCR assay allowed quantitative analysis of many bacteria as well as fungi and ciliates domain as well as bacteria species connected with many of experimental factors (Table 2). There are limited data showing the fungal quantification in rumen with the PCR techniques (Denman and McSweeney, 2006;Sekhavati et al, 2009;Lwin et al, 2011). Recently Lwin et al (2011) showed using real-time PCR that the fungal population tended to decrease after feeding in the rumen of sheep.…”

Section: E T T E T T E E Rementioning

confidence: 99%

“…Quantification of the rumen microorganism can be done also with the competitive PCR method (Sekhavati et al, 2009; Table 3). In this technique a known amount of a DNA fragment (a competitor) is added to the sample.…”

Section: E T T E T T E E Rementioning

confidence: 99%

Development of nucleic acid based techniques and possibilities of their application to rumen microbial ecology research

Pers‐Kamczyc¹,

Zmora²,

Cieślak³

et al. 2011

J. Anim. Feed Sci.

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Despite many years of research elucidating processes occurring in the rumen, still only around 10% of the rumen microbe is known. Molecular biology techniques seem to be a good complement of an information obtained by using the classical microbiology and therefore can enhance our knowledge about processes occurring in the rumen. The aim of this paper is to describe and to summarize a widely used techniques of the molecular biology during analysis of microbes in rumen. The main attention have been focused on the three of them which can be employed for quantitative and qualitative analysis of rumen microorganisms: PCR-DGGE, Real-time PCR and Fluorescence in situ hybridization.

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“…PCR-based DNA profi ling techniques using PCR primers which target the specifi c genes to amplify the 16S/ITS rDNA sequence template targeted DNA sample (Snel et al 2002 ;Li et al 2003 ), while, on the other hand, bacterial population size of gut microbiota could be measured using qPCR method (Sekhavati et al 2009 ). These techniques may employ DNA profi ling techniques (PCR based), quantitative PCR, sequencing, fl uorescent in situ hybridization (FISH), DNA microarrays and fl ow cytometry (Gong and Yang 2012 ).…”

Section: Introductionmentioning

confidence: 99%