Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model

Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica’s metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications

Additional file 1: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S1. Physical approaches to separate human from microbial cells does not reduce percentage human DNA. Unless otherwise stated, evaluation of size-driven host DNA depletion methods was performed by qPCR analysis of the human-specific PTGER2 gene normalized to raw sample. A) Raw saliva was passed across a 5-μm filter, and the original sample (raw), residue left on top of the filter (res), and filtrate (fil) were compared. B) The pellet of a raw saliva sample after a 30-s centrifugation at 2500g (P), its supernatant (SS), the SS after pelleting all cells at 10,000g for 8 min (FS), and the FS pellet washed with 1× PBS (FSW) were compared. C) Distinct populations of small, medium (med), and large events by flow cytometry of a human fecal sample. D) Percentage of human DNA by shallow shotgun sequencing normalized to raw sample of distinct FACS populations from C. E) The SS of a raw saliva sample after treatment with DNAse. Significance test ordinary one-way ANOVA with Dunnett’s multiple comparisons test p < 0.01. (PNG 521 kb

Additional file 2: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S2. Optimization of lyPMA conditions for human DNA depletion. qPCR analysis of the relative abundance of the human-specific PTGER2 gene normalized to raw saliva across methods of selective mammalian cell lysis (A) and PMA concentration (B). qPCR analysis of the fold change of the bacteria-specific 16S rRNA gene normalized to raw saliva across methods of selective mammalian cell lysis (C) and PMA concentration (D). SS = slow centrifugation (30 s at 2500 g), son = sonication (15 min at 60 Hz), H2O = osmotic lysis with pure water. (PNG 274 kb

Additional file 6: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S6. Host depletion via PMA treatment is possible for cryopreserved samples. Raw saliva samples were aliquoted and either frozen immediately at − 20 °C or mixed with a final concentration of 20% glycerol for cryopreservation. The percentage of human reads was assessed by Bowtie2, and the top 15 most abundant genera were assessed by MetaPhlAn2. (PNG 550 kb

Additional file 3: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S3. Quality control information. A) DNA quantification pre-library-prep, but post-host-DNA-depletion. The red line indicates the concentration necessary to obtain 1 ng DNA input for library preparation given the volume limitations. B) Total number of quality filtered reads by processing method. Libraries were normalized to obtain twice as many reads for the raw samples compared to host depleted samples. C) Total number non-human reads after filtering using Bowtie 2. (PNG 299 kb

Additional file 5: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S5. Relative taxon abundance correlation between raw and host-depleted samples. Each plot represents data from a single participant. The x-axis represents relative abundance in the raw sample and the y-axis represents relative abundance in the corresponding host depleted sample where each dot represents a distinct taxon. Error bars represent SEM across triplicate samples. The correlation values averaged across individuals for each method were not statistically different from each other (average Spearman’s rank correlation coefficient ± standard deviation: Fil = 0.789 ± 0.09, NEB = 0.75 ± 0.13, Mol = 0.82 ± 0.08, QIA = 0.83 ± 0.05, PMA = 0.82 ± 0.08) (PNG 413 kb

Additional file 4: of Improving saliva shotgun metagenomics by chemical host DNA depletion

Figure S4. Relative abundance of the top 15 most abundant genera assigned by MetaPhlAn2 across individual and host depletion method. (PNG 803 kb

Journal officiel du Haut-Sénégal-Niger

15 novembre 19241924/11/15 (A19,N443)

Sulfide-Driven Microbial Electrosynthesis

Microbial electrosynthesis, the conversion of carbon dioxide to organic molecules using electricity, has recently been demonstrated for acetogenic microorganisms, such as <i>Sporomusa ovata</i>. The energy for reduction of carbon dioxide originates from the hydrolysis of water on the anode, requiring a sufficiently low potential. Here we evaluate the use of sulfide as an electron source for microbial electrosynthesis. Abiotically oxidation of sulfide on the anode yields two electrons. The oxidation product, elemental sulfur, can be further oxidized to sulfate by <i>Desulfobulbus propionicus</i>, generating six additional electrons in the process. The eight electrons generated from the combined abiotic and biotic steps were used to reduce carbon dioxide to acetate on a graphite cathode by <i>Sporomusa ovata</i> at a rate of 24.8 mmol/day·m². Using a strain of <i>Desulfuromonas</i> as biocatalyst on the anode resulted in an acetate production rate of 49.9 mmol/day·m², with a Coulombic efficiency of over 90%. These results demonstrate that sulfide can serve effectively as an alternative electron donor for microbial electrosynthesis

Additional file 8: Table S6. of Metabolic capability and in situ activity of microorganisms in an oil reservoir

Annotation and FPKM value of hydrocarbon degradation and methanogenesis related genes in GBs (separate file). Annotation of studied GBs was done by a combined effort of RAST server and KEGG database. (XLSX 429 kb