Total DNA extractions from faeces were performed using the QIAamp PowerFecal Pro DNA kit (Qiagen, Antwerp, Belgium) according to the type of sample and the manufacturer’s recommendations.
With total bacterial DNA extracted from 83 samples, 16S rDNA profiling targeting the V1-V3 hypervariable region was performed as described previously [25 (link),26 (link)]. All libraries were run with Illumina MiSeq Technology (Illumina, SY—410-1003). The protocol used was the same as that described in the work of Ngo et al. (2018) [26 (link)]. Sequence reads were processed using the MOTHUR software package V1.41.1 and Vsearch for chimera detection [27 (link),28 (link)]. After cleaning and searching chimeras, 13,314,296 sequence reads were obtained, subsampled at 10,000 reads per sample and clustered into 129,317 OTUs (clustering threshold of 0.03). Reference alignment and taxonomic assignments were based on the SILVA database (v1.38.1) [29 (link)] of the full-length 16S rDNA sequences. The file was processed to classify the data into 536 phylotypes at the genus level. Sequencing libraries are available in the GenBank repository under the PRJNA924547 bioproject.
With total bacterial DNA extracted from 83 samples, 16S rDNA profiling targeting the V1-V3 hypervariable region was performed as described previously [25 (link),26 (link)]. All libraries were run with Illumina MiSeq Technology (Illumina, SY—410-1003). The protocol used was the same as that described in the work of Ngo et al. (2018) [26 (link)]. Sequence reads were processed using the MOTHUR software package V1.41.1 and Vsearch for chimera detection [27 (link),28 (link)]. After cleaning and searching chimeras, 13,314,296 sequence reads were obtained, subsampled at 10,000 reads per sample and clustered into 129,317 OTUs (clustering threshold of 0.03). Reference alignment and taxonomic assignments were based on the SILVA database (v1.38.1) [29 (link)] of the full-length 16S rDNA sequences. The file was processed to classify the data into 536 phylotypes at the genus level. Sequencing libraries are available in the GenBank repository under the PRJNA924547 bioproject.
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