In your case I'll increase sequencing depth with sequencing more sample and removing host (chicken) genome after sequencing.

to remove host genome you can just map the data to reference genome with BWA and then remove mapped reads with Samtools.

you can download the reference genome with this link:

https://www.ncbi.nlm.nih.gov/genome/111?genome_assembly_id=451987

for more details check this website:

https://www.metagenomics.wiki/

Thank you Musa Mohammadi for your input during the data analysis phase. But sequencing more samples will add significant cost. Any help on wet-lab host DNA depletion?

Amro Hashish if it is possible please explain more about your project.

3. If we are targeting e.g Haemophilus, Is there any way for target enrichment of this specific mo "with the aim to generate WG". :

just try to culture it and sequence bacterial culture.

Musa Mohammadi Thank you. We couldnt culture it. Multiple culture trial ended up as negative. At the same time the qPCR is positive. Also, first metagenomic sequencing run showed positive but with only about 450 reads classified as Haemophilus

I don't know any methods for host dna depletion, but maybe you could perform whole genome amplification (e.g. QIAGEN kit). Then the signal from Haemophilus should be easier to detect, while the proportions between different species genome should remain the same. And then use bioinformatic methods, like Musa Mohammadi suggested.

Thank you Mohamed Tarek Badr