Figure 4. | The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

Figure 4.

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Cornell University, United States; University of California, Berkeley, United States; King’s College London, United Kingdom
Figure 4.
Download figureOpen in new tabFigure 4. The physiological and metabolic landscape of Melainabacteria.

Metabolic predictions for Melainabacteria based on genes identified in Figure 4—source data 1. Genes in pathways detected in the genomes of the subsurface and at least one gut genome (white box), only in the subsurface genome (grey box), only in at least one gut genome (orange box), and genes missing from pathways in all genomes (red box). Glycolysis proceeds via the canonical Embden-Meyerhof-Parnas (EMP) pathway with the exception of fructose-6-phosphate 1-phosphotransferase (EC:2.7.1.90, gene 3). Names of pathways and fermentation end-products are bolded and ATP generated by substrate-level phosphorylation are noted. All Melainabacteria genomes sampled lack electron transport chain components (including cytochromes (Cyto), succinate dehydrogenase (sdh), flavins, quinones), terminal respiratory oxidases or reductases, and photosystem I or II (PS1, PS2). The genomes also lack a complete TCA cycle (absent enzymes noted by red boxes), with the TCA enzymes instead linked to the fermentation of amino acids and organic acids denoted (pathways, blue arrows). Ferredoxin (Fd, green text) is important for hydrogen (H2) production via hydrogenases (yellow background box). Proton translocation mechanisms (green background box) may be achieved by the activity of trimeric oxaloacetate (OAA) decarboxylase and sodium-hydrogen antiporter, pyrophosphate (PPi) hydrolysis with pyrophosphatases, 11 subunit NADH dehydrogenase, and an annotated NiFe hydrogenase (green enzyme). Annotations for the gene numbers are in Figure 4—source data 2. The complete metabolic comparison of the Melainabacteria can be accessed at http://ggkbase.berkeley.edu/genome_summaries/81-MEL-Metabolic-Overview-June2013.

DOI: http://dx.doi.org/10.7554/eLife.01102.010

Figure 4—source data 1.Examination of enzymes (steps) in near-complete KEGG based modules shared among or unique to subsurface ACD20 and gut Melainabacteria genomes MEL.A1, MEL.B1, and MEL.B2.

Analysis is based on the KEGG Module database (Kanehisa and Goto, 2000).

DOI: http://dx.doi.org/10.7554/eLife.01102.011

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Figure 4—source data 2.Gene annotations corresponding to the numbers in Figure 4.

If the gene occurs in both the ACD20 and gut genomes, the reported annotation is based on ACD20.

DOI: http://dx.doi.org/10.7554/eLife.01102.012

Download source data [figure-4—source-data-2.media-3.docx]