DOI: 10.17026/dans-xwd-fbj5
title: Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

description: This dataset was created to identify the genes involved in paracetamol biodegradation. To do that, we inoculated a bioreactor with sludge of a hospital wastewater treatment plant (WWTP) (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. (pfast) that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growing Pseudomonas sp. (pslow) that degraded paracetamol without obvious intermediates in more than 90 days. We also sequenced the genome and transcriptome of the two Pseudomonas isolates growing on paracetamol as sole carbon source. All raw data and metadata (isolation site, DNA/RNA extraction method, sequencing platform, etc.) can be found in the read sequence archive (SRA) database of the NCBI under the BioProject ID PRJNA831879. The amino acid sequences and annotation of all genes in the (meta)genomes and the transcripts per million (TPMs) of the transcriptomes are deposited in Dans Easy. More specifically, the Dans Easy dataset contains the following files:- "amidase sequences figure 3.faa": amino acid sequences of the amidases from the amidase signature (AS) protein family that were used to create the phylogenetic tree in Figure 3 of the manuscript. - "amidase sequences figure s2 top 150.faa": amino acid sequences of the top 150 highly expressed amidases in the metagenome, the amidases from the AS family in the two Pseudomonas isolates, and the amidases known to degrade paracetamol. These sequences were used to generate the phylogenetic tree in the supplementary Figure S2 of the manuscript - 14 files containing the aminoacid sequences and the annotation of all the genes present in the 14 metagenome-assembled genomes (MAG) retrieved from the bioreactor DNA ("bjlacckg_microbacterium.all.faa","eaedefln_betaproteobacteria.all.faa","gfmlmoed_myxococcales_1.all.faa","gmpbgjca_chitinophagaceae_3.all.faa","hcldgnca_patescibacteria.all.faa", "hfdflmdg_rubrivivax.all.faa","jmgbclmb_comamonadaceae.all.faa","jpnlmfaj_chitinophagaceae_2.all.faa","kgebagmn_bacteroidetes.all.faa", "mdklgidk_alicycliphilus.all.faa","mmlkoakc_acidobacteria.all.faa","nclidpkb_actinomycetales.all.faa","nlckofof_chitinophagaceae_1.all.faa","opijccok_myxococcales_2.all.faa"). - "kgeggeom_unbinned.all.faa": aminoacid sequences and annotation of all the genes present in the unbinned contigs of the bioreactor metagenome. - 2 files corresponding to the aminoacid sequences and the annotation of all genes present in the genomes of the two Pseudomonas isolates growing on paracetamol as sole carbon source ("bkdbljdl_pslow.all.faa" and "oacklnda_pfast.all.faa"). - Calculated TPMs for all the genes present in the bioreactor metagenomes and the Pseudomonas genomes ("rna-seq_tpm_bioreactor.xlsx", "rna-seq_tpm_pfast.xlsx", and "rna-seq_tpm_pslow.xlsx").