Circular representation of the “Candidatus Cloacamonas acidaminovorans” chromosome. The circles, from the inside out, show the following. (Circle 1) GC deviation (GC_window − average GC of the genome, using a 1-kb window); regions with a GC deviation of less than twice the standard deviation are highlighted in red. (Circles 2 and 3) Predicted CDSs transcribed in clockwise/counterclockwise directions. Color coding for genes is as follows: amino acid biosynthesis, salmon; nucleotides/nucleosides, orange; central metabolism, brown; DNA metabolism, yellow; energy, green; fatty acid metabolism, purple; cell envelope, light green; protein synthesis/fate, pink; transcription, gray; transport, peach; regulatory functions, slate blue; extrachromosomal origin, violet-red; hypothetical and conserved hypothetical proteins, black. (Circle 4) CRISPR (violet-brown) and prophagic regions, (dark blue). (Circle 5) tRNAs (green), rRNA (violet-blue), insertion elements and transposases (pink). (Circle 6) Coordinates in Mb beginning at the dnaA gene. Circles 6 and 7 show the gene content comparison between the “Candidatus Cloacamonas acidaminovorans” and P. carbinolicus (light green), Synthrophus aciditrophicus (dark green), K. stuttgartiensis (orange), and T. tengcongensis (red) genomes using a similarity threshold of 30% identity and a ratio of 0.8 of the length of the smallest protein.

Iterative assembly process schema. Each iteration of the assembly process consists of the following steps. (Step 1) Nucleotide similarities between environmental reads and seed sequences are computed, and highly similar reads are selected. (Step 2) Paired reads are recruited, along with the highly similar reads. (Step 3) Both similar and paired reads are subjected to the assembly process. (Step 4) The resulting contigs are screened both for length and coverage, and those selected are used as seed sequences for the next iteration.

Overview of the main metabolic pathways in “Candidatus Cloacamonas acidaminovorans.” Shown are the oxygen defense process, glycolysis and pyruvate degradation, amino acid fermentation, and systems involved in energy production. The question mark means that the presence of the reaction was not clearly identified.