Article Figures & Data
Additional Files
Data Supplement
- Supplemental Tables -
Supplementary Table S1. Information on manually curated azoreductase gene families. This table features information about the 40 azoreductase sequences collected for the homology search across the Unified Human Gastrointestinal Genome (UHGG) collection. Columns A-H display the: gene name, organism, functional annotation, amino acid length, reference for azoreductase activity, reference for quinone oxidoreductase activity, link to entry
on the UniProt website www.uniprot.org, and finally, any additional notes written about the sequence. These sequences were clustered using EFI-EST (Gerlt et al. 2015) to generate a sequence similarity network (SSN) at 35% sequence identity between amino acid sequences (Figure 1).Supplementary Table S2. Additional azo-reducing species without gene level information. This table contains additional azo-reducing species found through the literature search that did not have specific gene level information regarding the active azoreductase
Supplementary Table S3. Complete results from homolog search. This table contains the complete list of significant hits to azoreductase HMMs from the homolog search step. Columns of this table include: genome_ID, sequence_ID, pos_start (position start), pos_end (position end), gene_name, hmm_name, hmm_len (HMM length), ali_len (alignment
length, in amino acids), hmm_start and hmm_end (start and end of alignment on the HMM), ali_start and ali_end (start and end of alignment on the bacterial genome, length in amino acid residues), evalue (E-value returned from the HMMER method hmmscan), score (bit score returned from hmmscan), bias (bias score reported by hmmscan), pct_hmm_aligned (the percentage of positions in the HMM which aligned to codons on the specified bacterial genome),
m_log10_evalue (the -log10 transform of the E-value).Supplementary Table S4. UHGG genome ID to taxonomic name. This table contains a mapping of each UHGG genome ID to its closest taxonomic assignment in the Genome Taxonomy Database (GTDB). This table can be used to identify genome IDs of interest for lookup in Table S3
Supplementary Table S5. Raw absorbance (550nm) values from Acid Orange 7 decolorization assay. This table shows the raw absorbance values obtained from the Acid Orange 7 decolorization assay for strains of F. nucleatum, B. fragilis, and C. clostridioforme. The bio_rep column indicates the biological replicate number, the collection column indicates the number of hours post inoculation that the absorbance measurement was taken and the columns t1, t2, and t3 indicate the first, second, and third technical replicate measurements performed for each biological replicate. The
values from the 72-hour collection time point were used in the visualization and statistical calculations shown in Figure 6.
- Supplemental Tables -