Table 1. Features of the Modulibacteria KSB3 population genomes.
| Genome bin identifier | UASB14 | UASB270 |
|---|---|---|
| Candidatus name | Moduliflexus flocculans | Vecturathrix granuli |
| Closest environmental 16S clone | YM-1 (AB218870) | SmB78fl (AB266927) |
| No. of scaffolds | 8 | 21 |
| Total length (bp) | 7,147,157 | 8,384,694 |
| N50 | 1,183,318 | 597,372 |
| GC (%) | 50.6 | 47.2 |
| Average coverage | 278 | 38 |
| Genome completenessa | 92.8% (103/111) | 93.6% (104/111) |
| Revised genome completenessa | 98.1% (103/105) | 99.0% (104/105) |
| Genome contaminationa | 5.4% (6/111) | 6.3% (7/111) |
| Revised genome contaminationa | 0.0% (0/105) | 1.9% (2/105) |
| Relative abundance in UASB metagenomes (%)b | 9.22 | 0.40 |
| No. tRNA genes | 54 | 43 |
| rRNA genes found in genome | 5S, 16S, 23S | 5S, 16S, 23S |
| Inferred no. of rRNA operonsc | 3 | 2 |
| No. CDS | 5,989 | 7,048 |
| No. CRISPR array | 4 (125 repeats in total) | 5 (550 repeats in total) |
| Coding density | 84.6 % | 84.3 % |
| Putative glycoside hydrolasesd | ||
| Cellulase | 5 (0.1%) | 14 (0.2%) |
| Amylase | 19 (0.3%) | 8 (0.1%) |
| Debranching enzyme | 3 (0.1%) | 2 (0.1%) |
| Amino-sugar-degrading enzyme | 35 (0.6%) | 45 (0.6%) |
| Oligosaccharide-degrading enzyme | 43 (0.7%) | 23 (0.3%) |
| Putative protease/peptidased | ||
| Protease | 27 (0.5% of total ORFs) | 28 (0.4% of total ORFs) |
| Peptidase | 60 (1.0%) | 78 (1.1%) |
| Putative environmental signaling system genes | ||
| Transmembrane sensore | 135 (2.3%) | 114 (1.6%) |
| Response regulator containing CheY-like domainf | 131 (2.2%) | 116 (1.6%) |
| Proposed class | Moduliflexia | Vecturatrichia |
| Proposed order | Moduliflexales | Vecturatrichales |
| Proposed family | Moduliflexaceae | Vecturatrichaceae |
Notes.
Genome completeness and contamination were estimated based on the presence/absence of a 111 single-copy gene set from Dupont et al. (2012). Revised genome completeness and contamination were calculated based on a revised total of 105 single-copy genes estimated to be present in the KSB3 genomes (Table S2). Numbers in parentheses indicats detected number of genes per total number of each gene set.
Relative genome abundance for each KSB3 genome was determined based on 16S rRNA gene profiling using shotgun metagenome data (Table S1).
Number of rRNA operons in the KSB3 genomes were inferred based on relative coverage profiles of KSB3 16S rRNA genes and the genome averages (Fig. S2).
Counts (% of total ORFs).
Predicted number of transmembrane sensors based on the possession of a sensor domain (Galperin, 2004) and >1 transmembrane segments (Table S8).
Number of all two-domain response regulators containing CheY-like domains estimated from PSI-BLAST searches of domain-specific profiles against the protein set described in Galperin (2004) (Table S8).