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Only five scaffolds containing bacterial sequences were detected and these were removed from the assembly.
Bacterial sequences were detected in most cases, even after treatment of the synovial fluid with DNase, implying the presence of bacterial RNA and therefore of transcriptionally active bacteria.
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Whereas, only one sequence (KJ432887) affiliated with Syntrophaceae, accounts for 1.3% of the total bacterial sequences, was detected in our consortium.
Specific 16S bacterial DNA sequences were detected as contaminants in our process.
Bacterial 16S rDNA sequences were detected in specimens from 8 of the 46 patients.
No chimeric sequences were detected.
No picobiliphyte sequences were detected.
No recombinant sequences were detected.
The most abundantly detected bacterial sequences were Streptococcus pneumoniae, Moraxella bovis, Moraxella bovoculi, Haemophilus influenzae, and Escherichia coli (data not shown), which were present as major bacteria in the respiratory tract of children.
The remaining identified bacterial classes were detected in percentages of <6.0%% of total bacterial sequences (Fig. 3).
The remaining identified bacterial families were detected in percentages of <4.0%% of total bacterial sequences over the sampling period except Aeromonadaceae which was detected at averages of 6%% during day 156 (Fig. 4).
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