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Ninety-nine percent of the microbial genes were bacterial.
From the resulting scaffolds, microbial genes were predicted using Prokka [ 71], and compared to Pfam [ 35] using HMMER [ 72].
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Still, because current chips offer complete surveys only of relatively small genomes, or samples of larger ones, advances in identifying the microbial genes are expected to come much faster.
(16S rRNA gene-based approaches) What microbial genes are present in the GI tract?
Second, sequence reads are mapped back to the gene scaffold, and abundance levels of microbial genes are estimated.
In one approach, microbial genes are inserted into a DNA plasmid taken up passively by the host cell following injection.
Numerous gut microbial genes are related to xenobiotic degradation, including non-modified and halogenated aromatic compounds [ 44].
Third, microbial genes are further mapped to known microbial organisms or a gene category, and abundance levels of organisms or gene groups are obtained.
Therefore, active expression of microbial genes is not required for detection by DNA-based approaches, and latent microbial genomic fragments can potentially be identified.
Recently, in a large-scale metagenomic analysis of 124 European individuals, a catalogue of over 3.3 million human gut microbial genes was created [ 97].
high-quality paired-end reads from each sample were used for de novo assembly and for predicting genes (Table S8), from which a non-redundant gene catalogue of 2,077,766 microbial genes was constructed.
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