I am trying to extract the microbiome from the intestine of a few small arachnids and how it influences their behavior.
You need to read about metagenomics sequencing approaches (amplicon or whole genome based).
Hi Ramy Jhasser Martínez ,
To identify the microbiome present in the insect intestine, you can use 16s rDNA amplicon sequencing (if you are interested in bacteria).
16s rDNA amplicon sequencing will give you an overview of types of bacteria present in the intestine.
16s rDNA amplicon sequencing is a 'culture-independent' method.
Another method is the culture-dependent method.
If you are planning to isolate and make pure cultures of bacteria present in the intestine, you have to follow traditional bacterial culture techniques. After obtaining pure cultures, you can identify the bacterial strains by molecular taxonomy.
one drawback of the culture-dependent method is,- you may lose a majority of the bacterial diversity during the establishment of pure cultures, due to the difficulty in mimicking the growth requirements for different bacterial species.
So in my opinion, the first method will be more accurate and convenient.
Find a way to get clean samples of the fecal excreta, then you can do the suggestions above.
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