Gastrointestinal microbiota play an essential role not only in digestion, but also in colonic diseases. The gut microbiome is one of the densest, most dynamic, and complex microorganism populations located in the body . This unbalanced microbiome allows opportunistic and pathogenic bacteria to proliferate and can cause numerous gastrointestinal diseases, which can result in colic and death.
In literature, the gastrointestinal microbiome, in general, has been the most studied microbiota; however, equine hindgut microorganisms have not been extensively studied . Only superficial knowledge exists on the equine hindgut microbiome due to a majority of bacteria that have not yet been identified because they cannot be cultured. However, with new technological advances and next generation sequencing, scientists can now achieve great strides in identifying bacteria down to the genus and species level.
Next Generation Sequencing
Many veterinarians and horse caretakers can recognize the symptoms of colic. However, little information has been conducted on what is happening internally, specifically to the cecum microbiome. Past studies, have used sacrificed and cannulated horses to collect cecal fluid to analyze the population of the microbiome with DNA sequencing. DNA sequencing is used to determine the exact order of nucleotides within a DNA strand. This allows scientists to study normal genes, but also compares normal genes to disease-causing versions. However, lack of technology and sequencing techniques has hindered scientists to develop a full picture of the changes to the microbiome. Currently, next generation sequencing (NGS) is of the latest technology, which allows the genomic content of intere...
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... have a small similarity at the genomic level . Secondly, is shotgun sequencing, also called metagenome sequencing. In shotgun sequencing, DNA strands have been extracted and shred into tiny fragments before the sequencing process can begin. Shotgun sequencing uses chain termination to obtain “reads”. The “reads” become overlapped and a machine connects the overlapping reads to create a sequence. Shotgun sequencing advantages include, giving complete genomes of all the organisms in a population, accurately identifying phylogenetic information, and providing information about genes present in the population without assembling individual genomes . With these new technological advances, this could revolutionize how veterinarians diagnose and treat colic causes. This is vital information because it could help prevent recurrence cases and decrease mortality rates.
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