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In this paper we compare the antimicrobial activities of tree extracts at order level based on the average minimum inhibitory concentration (MIC) of all the species that we have analysed within each order.
In this approach, the average EC number counts of all annotated genomes from a given taxonomic group, e.g. at order level, are used as reference for the linear combination of the community structure at this level.
The taxonomic information of methanogenic archaea at order level was based on the work of Borrel et al. (2013), in which methanogens are classified into seven orders including six traditional orders and a recently proposed order referred to as Mx in this study for current communication (Borrel et al. 2013).
Based on BLASTN+ identity, sequences were affiliated to distinct taxonomic levels as follows: (1) at OTU level if divergence was less than 3%, (2) at genus level if divergence was in the range 3 5%, (3) at family level if divergence was 5 10%, (4) at order level if divergence was 10 15%, (5) at class level if divergence was 15 20%, and (6) at phylum level if divergence was 20 23%.
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Generally, the A+T content, AT-skew, and GC-skew exhibited complex behaviors that do not appear to be tightly linked, at least at the order level.
While nearly all (97.4%) of the sequences analyzed were identified to the phylum level at ≥95% confidence, the proportion of sequences successfully assigned to lower taxonomic levels decreased to 96.44% at the class level, 93.3% at the order level, 90.1% at the family level and 65.9% at the genus level.
Thus, a substantial drop in nucleotide identity shared by AT-rich regions occurs at the order level, even permitting very permissive gap costs.
While nearly all (98.8%) of the sequences analyzed were identified to the phylum level, the proportion of sequences successfully assigned to lower taxonomic groups decreased to 97.5% at the class level, 95.4% at the order level, 93.2% at the family level and then precipitously to 72.6% at the genus level.
More precisely, the average error rate per bin (one minus precision) was 7.4% at the species level and 4.6% at the order level.
At the order level, the overall fungal compositions were similar to those at the phylum level.
Its sensitivity and precision numbers are also worse than ours at the genus and family levels but become slightly higher at the order level.
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