https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&feed=atom&action=historyOxalobacter formigenes - Revision history2024-03-29T09:25:26ZRevision history for this page on the wikiMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=55138&oldid=prevBarichD at 19:01, 25 August 20102010-08-25T19:01:30Z<p></p>
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</table>BarichDhttps://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=42569&oldid=prevCharbo25: /* Genome Structure */2009-04-16T22:05:03Z<p><span dir="auto"><span class="autocomment">Genome Structure</span></span></p>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Two separate shotgun sequencing projects are currently under way to sequence the genome of O. formigenes, Neither of these projects are complete (and they each have many unresolved contigs). The length of genetic material currently sequenced is approximately 2.4 MB for both projects, and the GC content of this sequence approximately 50%. The currently available sequence likely does not encompass the entire genome due to toxic or unstable (unable to be cloned) portions of the genome. The genome has not yet been annotated, and the number of chromosomes and characteristics of the genome (such as circularity or linearity) are unknown<del style="font-weight: bold; text-decoration: none;">.</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Two separate shotgun sequencing projects are currently under way to sequence the genome of O. formigenes, Neither of these projects are complete (and they each have many unresolved contigs). The length of genetic material currently sequenced is approximately 2.4 MB for both projects, and the GC content of this sequence approximately 50%. The currently available sequence likely does not encompass the entire genome due to toxic or unstable (unable to be cloned) portions of the genome. The genome has not yet been annotated, and the number of chromosomes and characteristics of the genome (such as circularity or linearity) are unknown [<ins style="font-weight: bold; text-decoration: none;">7</ins>]<ins style="font-weight: bold; text-decoration: none;">.</ins></div></td></tr>
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</table>Charbo25https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=42568&oldid=prevCharbo25: /* References */2009-04-16T22:04:45Z<p><span dir="auto"><span class="autocomment">References</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>6. Siva, S., Barrack, E.R., Reddy, G.P.V., Thamilselvan, V., Thamilselvan, S., Menon, M., Bhandari, M. 2009. "A Critical analysis of the role of gut Oxalobacter formigenes in oxalate stone disease." BJU International. 103 (1): 18-21.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>6. Siva, S., Barrack, E.R., Reddy, G.P.V., Thamilselvan, V., Thamilselvan, S., Menon, M., Bhandari, M. 2009. "A Critical analysis of the role of gut Oxalobacter formigenes in oxalate stone disease." BJU International. 103 (1): 18-21.</div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">7. National center for biotechnology information genome database. Accession numbers NZ_ACDP00000000 and NZ_ACDQ00000000. ncbi.nlm.nih.gov</ins></div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Author==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Author==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Page authored by Mark Charbonneau and Ashley Behan, students of [http://www.kbs.msu.edu/faculty/lennon/ Prof. Jay Lennon] at Michigan State University.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Page authored by Mark Charbonneau and Ashley Behan, students of [http://www.kbs.msu.edu/faculty/lennon/ Prof. Jay Lennon] at Michigan State University.</div></td></tr>
</table>Charbo25https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=42567&oldid=prevCharbo25: /* Cell Structure, Metabolism and Life Cycle */2009-04-16T22:01:18Z<p><span dir="auto"><span class="autocomment">Cell Structure, Metabolism and Life Cycle</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of carbon and energy in order to survive [4,5]. Most anaerobes that metabolize oxalate produce carbon dioxide and formate, and the formate is then further oxidized by dehydrogenases. O. formigenes is unique in that it produces formate as an end product. The oxalate taken in by the cell can be decarboxylated to regenerate formate for export, or further metabolized for the production of glycerate (See Figure 1) [1]. Additionally, O. formigenes has not been documented to utilize glycolytic pathways, and is thus unable to grow on sugars [5] O. formigenes utilizes an oxalate/formate antiporter system to generates a proton motive force for the production of ATP (energy) [5]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. <del style="font-weight: bold; text-decoration: none;">The net inflow </del>of <del style="font-weight: bold; text-decoration: none;">this negative charge generates </del>a <del style="font-weight: bold; text-decoration: none;">pH </del>gradient<del style="font-weight: bold; text-decoration: none;">. The system derives </del>the <del style="font-weight: bold; text-decoration: none;">negative charge by oxalate decarboxylation. </del>[3] Due to the unique oxalate pathways that produce formate and carbon dioxide, the growth yield for O. formigenes is low (only producing 1.0-1.1 grams of cells per mole of oxalate degraded). [2]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of carbon and energy in order to survive [4,5]. Most anaerobes that metabolize oxalate produce carbon dioxide and formate, and the formate is then further oxidized by dehydrogenases. O. formigenes is unique in that it produces formate as an end product. The oxalate taken in by the cell can be decarboxylated to regenerate formate for export, or further metabolized for the production of glycerate (See Figure 1) [1]. Additionally, O. formigenes has not been documented to utilize glycolytic pathways, and is thus unable to grow on sugars [5] O. formigenes utilizes an oxalate/formate antiporter system to generates a proton motive force for the production of ATP (energy) [5]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. <ins style="font-weight: bold; text-decoration: none;">Decarboxylation </ins>of <ins style="font-weight: bold; text-decoration: none;">oxalate consumes </ins>a <ins style="font-weight: bold; text-decoration: none;">proton that 'virtual' proton </ins>gradient<ins style="font-weight: bold; text-decoration: none;">, which is used for </ins>the <ins style="font-weight: bold; text-decoration: none;">synthesis of ATP </ins>[3]<ins style="font-weight: bold; text-decoration: none;">. </ins>Due to the unique oxalate pathways that produce formate and carbon dioxide, the growth yield for O. formigenes is low (only producing 1.0-1.1 grams of cells per mole of oxalate degraded). [2]</div></td></tr>
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</table>Charbo25https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41953&oldid=prevCharbo25: /* Cell Structure, Metabolism and Life Cycle */2009-04-16T01:31:17Z<p><span dir="auto"><span class="autocomment">Cell Structure, Metabolism and Life Cycle</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of energy in order to survive [4<del style="font-weight: bold; text-decoration: none;">]. O. formigenes requires oxalate as both a source of carbon and energy [</del>5]. Most anaerobes that metabolize oxalate produce carbon dioxide and formate<del style="font-weight: bold; text-decoration: none;">. The </del>formate is then further oxidized by dehydrogenases. O. formigenes is <del style="font-weight: bold; text-decoration: none;">different </del>in that it produces formate as an end product. <del style="font-weight: bold; text-decoration: none;">Therefore either </del>the <del style="font-weight: bold; text-decoration: none;">glycerate pathway </del>or the <del style="font-weight: bold; text-decoration: none;">serine pathway is used to convert oxalate into 3-phosphoglycerate. </del>(See Figure 1) [1] <del style="font-weight: bold; text-decoration: none;"> </del>Additionally, <del style="font-weight: bold; text-decoration: none;">it requires acetate as a carbon source, but </del>has <del style="font-weight: bold; text-decoration: none;">no </del>glycolytic pathways, and is thus unable to grow on sugars [5] O. formigenes utilizes an oxalate/formate antiporter system to <del style="font-weight: bold; text-decoration: none;">generate </del>a proton motive force for the production of ATP (energy) [5]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. The net inflow of this negative charge generates a pH gradient. The system derives the negative charge by oxalate decarboxylation. [3] Due to the <del style="font-weight: bold; text-decoration: none;">specific </del>oxalate <del style="font-weight: bold; text-decoration: none;">metabolism of producing </del>formate and carbon dioxide the growth yield for O. formigenes is low only producing 1.0-1.1 grams of cells per <del style="font-weight: bold; text-decoration: none;">mol </del>of oxalate degraded. [2]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of <ins style="font-weight: bold; text-decoration: none;">carbon and </ins>energy in order to survive [4<ins style="font-weight: bold; text-decoration: none;">,</ins>5]. Most anaerobes that metabolize oxalate produce carbon dioxide and formate<ins style="font-weight: bold; text-decoration: none;">, and the </ins>formate is then further oxidized by dehydrogenases. O. formigenes is <ins style="font-weight: bold; text-decoration: none;">unique </ins>in that it produces formate as an end product. <ins style="font-weight: bold; text-decoration: none;">The oxalate taken in by </ins>the <ins style="font-weight: bold; text-decoration: none;">cell can be decarboxylated to regenerate formate for export, </ins>or <ins style="font-weight: bold; text-decoration: none;">further metabolized for </ins>the <ins style="font-weight: bold; text-decoration: none;">production of glycerate </ins>(See Figure 1) [1]<ins style="font-weight: bold; text-decoration: none;">. </ins>Additionally, <ins style="font-weight: bold; text-decoration: none;">O. formigenes </ins>has <ins style="font-weight: bold; text-decoration: none;">not been documented to utilize </ins>glycolytic pathways, and is thus unable to grow on sugars [5] O. formigenes utilizes an oxalate/formate antiporter system to <ins style="font-weight: bold; text-decoration: none;">generates </ins>a proton motive force for the production of ATP (energy) [5]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. The net inflow of this negative charge generates a pH gradient. The system derives the negative charge by oxalate decarboxylation. [3] Due to the <ins style="font-weight: bold; text-decoration: none;">unique </ins>oxalate <ins style="font-weight: bold; text-decoration: none;">pathways that produce </ins>formate and carbon dioxide<ins style="font-weight: bold; text-decoration: none;">, </ins>the growth yield for O. formigenes is low <ins style="font-weight: bold; text-decoration: none;">(</ins>only producing 1.0-1.1 grams of cells per <ins style="font-weight: bold; text-decoration: none;">mole </ins>of oxalate degraded<ins style="font-weight: bold; text-decoration: none;">)</ins>. [2]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The exchanged oxalate (taken in by the cell) can then be decarboxylated to regenerate formate for export, or further metabolized for the production of glycerate (See Figure 1) [Stewart]. </del></div></td><td colspan="2" class="diff-side-added"></td></tr>
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</table>Charbo25https://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41648&oldid=prevBehanash: /* Ecology and Pathogenesis */2009-04-15T19:52:26Z<p><span dir="auto"><span class="autocomment">Ecology and Pathogenesis</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology and Pathogenesis==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology and Pathogenesis==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The habitat of this organism is the large intestine of the human gut, and although it is not initially found in the gut at birth, O. formigenes quickly is established in the gut microflora [<del style="font-weight: bold; text-decoration: none;">Mittal</del>]. O. formigenes plays a unique role in the gut microflora in that it is capable of metabolizing 70 to 100 mg per day of oxalate. [<del style="font-weight: bold; text-decoration: none;">Mittal</del>]. Although soluble dietary oxalate is absorbed in the human small intestine, O. formigenes fulfills the role of metabolizing the remaining dietary oxalate and oxalate produced by the host's metabolism, which can otherwise accumulate, leading to hyperoxaluria and the formation of calcium oxalate stones, which are harmful to the human host [<del style="font-weight: bold; text-decoration: none;">Siva</del>]. This can be considered a symbiosis, in that the organism, a strict anaerobe, is given a safe environment to live and reproduce, along with a steady supply of oxalate to consume. In addition, O. formigenes confers a benefit to its human host in the sense that it degrades the otherwise toxic excess oxalate in the large intestine. O. formigenes is not explicitly pathogenic.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The habitat of this organism is the large intestine of the human gut, and although it is not initially found in the gut at birth, O. formigenes quickly is established in the gut microflora [<ins style="font-weight: bold; text-decoration: none;">4</ins>]. O. formigenes plays a unique role in the gut microflora in that it is capable of metabolizing 70 to 100 mg per day of oxalate. [<ins style="font-weight: bold; text-decoration: none;">4</ins>]. Although soluble dietary oxalate is absorbed in the human small intestine, O. formigenes fulfills the role of metabolizing the remaining dietary oxalate and oxalate produced by the host's metabolism, which can otherwise accumulate, leading to hyperoxaluria and the formation of calcium oxalate stones, which are harmful to the human host [<ins style="font-weight: bold; text-decoration: none;">6</ins>]. This can be considered a symbiosis, in that the organism, a strict anaerobe, is given a safe environment to live and reproduce, along with a steady supply of oxalate to consume. In addition, O. formigenes confers a benefit to its human host in the sense that it degrades the otherwise toxic excess oxalate in the large intestine. O. formigenes is not explicitly pathogenic.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==References==</div></td></tr>
</table>Behanashhttps://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41647&oldid=prevBehanash: /* Cell Structure, Metabolism and Life Cycle */2009-04-15T19:51:33Z<p><span dir="auto"><span class="autocomment">Cell Structure, Metabolism and Life Cycle</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell Structure, Metabolism and Life Cycle==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Cell Structure, Metabolism and Life Cycle==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of energy in order to survive [<del style="font-weight: bold; text-decoration: none;">Mittal</del>]. O. formigenes requires oxalate as both a source of carbon and energy [<del style="font-weight: bold; text-decoration: none;">Stewart</del>]. <del style="font-weight: bold; text-decoration: none;">[Insert Paragraph A]</del>Most anaerobes that metabolize oxalate produce carbon dioxide and formate. The formate is then further oxidized by dehydrogenases. O. formigenes is different in that it produces formate as an end product. Therefore either the glycerate pathway or the serine pathway is used to convert oxalate into 3-phosphoglycerate. (See Figure 1) [<del style="font-weight: bold; text-decoration: none;">Cornick</del>] Additionally, it requires acetate as a carbon source, but has no glycolytic pathways, and is thus unable to grow on sugars [<del style="font-weight: bold; text-decoration: none;">Stewart</del>] O. formigenes utilizes an oxalate/formate antiporter system to generate a proton motive force for the production of ATP (energy) [<del style="font-weight: bold; text-decoration: none;">Stewart</del>]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. The net inflow of this negative charge generates a pH gradient. The system derives the negative charge by oxalate decarboxylation. [<del style="font-weight: bold; text-decoration: none;">Liwen</del>] Due to the specific oxalate metabolism of producing formate and carbon dioxide the growth yield for O. formigenes is low only producing 1.0-1.1 grams of cells per mol of oxalate degraded. [<del style="font-weight: bold; text-decoration: none;">Kuhner</del>]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a rod-shaped, gram negative obligate anaerobe. This organism requires oxalate as a source of energy in order to survive [<ins style="font-weight: bold; text-decoration: none;">4</ins>]. O. formigenes requires oxalate as both a source of carbon and energy [<ins style="font-weight: bold; text-decoration: none;">5</ins>]. Most anaerobes that metabolize oxalate produce carbon dioxide and formate. The formate is then further oxidized by dehydrogenases. O. formigenes is different in that it produces formate as an end product. Therefore either the glycerate pathway or the serine pathway is used to convert oxalate into 3-phosphoglycerate. (See Figure 1) [<ins style="font-weight: bold; text-decoration: none;">1</ins>] Additionally, it requires acetate as a carbon source, but has no glycolytic pathways, and is thus unable to grow on sugars [<ins style="font-weight: bold; text-decoration: none;">5</ins>] O. formigenes utilizes an oxalate/formate antiporter system to generate a proton motive force for the production of ATP (energy) [<ins style="font-weight: bold; text-decoration: none;">5</ins>]. The antiporter system creates an electric potential (negative inside) by the inward transportation of oxalate and the outward flow of formate. The net inflow of this negative charge generates a pH gradient. The system derives the negative charge by oxalate decarboxylation. [<ins style="font-weight: bold; text-decoration: none;">3</ins>] Due to the specific oxalate metabolism of producing formate and carbon dioxide the growth yield for O. formigenes is low only producing 1.0-1.1 grams of cells per mol of oxalate degraded. [<ins style="font-weight: bold; text-decoration: none;">2</ins>]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The exchanged oxalate (taken in by the cell) can then be decarboxylated to regenerate formate for export, or further metabolized for the production of glycerate (See Figure 1) [Stewart]. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The exchanged oxalate (taken in by the cell) can then be decarboxylated to regenerate formate for export, or further metabolized for the production of glycerate (See Figure 1) [Stewart]. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Figure 1: Oxalate metabolism by Oxalobacter formigenes [<del style="font-weight: bold; text-decoration: none;">Stewart</del>]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Figure 1: Oxalate metabolism by Oxalobacter formigenes [<ins style="font-weight: bold; text-decoration: none;">5</ins>]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Oxalate degradation.jpg]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Oxalate degradation.jpg]]</div></td></tr>
</table>Behanashhttps://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41642&oldid=prevBehanash: /* Description and Significance */2009-04-15T19:50:08Z<p><span dir="auto"><span class="autocomment">Description and Significance</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Description and Significance==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Description and Significance==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a nonmotile, non-spore-forming, gram negative beta-proteobacterium that colonizes the human large intestine (colon) [<del style="font-weight: bold; text-decoration: none;">stewart</del>] This organism has also been isolated from the gut of ruminant and other non-ruminant herbivores [<del style="font-weight: bold; text-decoration: none;">Kuhner</del>]. O. formigenes is a strict anaerobe and is thought to be largely important in the metabolism of oxalate in the large intestine that may be remaining from the diet or a byproduct of host metabolism [<del style="font-weight: bold; text-decoration: none;">stewart</del>]. The absence of O. formigenes is thought to be a cause of hyperoxaluria and the formation of calcium oxalate stones in the kidney [<del style="font-weight: bold; text-decoration: none;">Siva</del>], and it is thought that O. formigenes may be useful as a probiotic agent for the treatment of these conditions [<del style="font-weight: bold; text-decoration: none;">stewart</del>].</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Oxalobacter formigenes is a nonmotile, non-spore-forming, gram negative beta-proteobacterium that colonizes the human large intestine (colon) [<ins style="font-weight: bold; text-decoration: none;">5</ins>] This organism has also been isolated from the gut of ruminant and other non-ruminant herbivores [<ins style="font-weight: bold; text-decoration: none;">2</ins>]. O. formigenes is a strict anaerobe and is thought to be largely important in the metabolism of oxalate in the large intestine that may be remaining from the diet or a byproduct of host metabolism [<ins style="font-weight: bold; text-decoration: none;">5</ins>]. The absence of O. formigenes is thought to be a cause of hyperoxaluria and the formation of calcium oxalate stones in the kidney [<ins style="font-weight: bold; text-decoration: none;">6</ins>], and it is thought that O. formigenes may be useful as a probiotic agent for the treatment of these conditions [<ins style="font-weight: bold; text-decoration: none;">5</ins>].</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Genome Structure==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Genome Structure==</div></td></tr>
</table>Behanashhttps://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41639&oldid=prevBehanash: /* Ecology and Pathogenesis */2009-04-15T19:49:01Z<p><span dir="auto"><span class="autocomment">Ecology and Pathogenesis</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology and Pathogenesis==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Ecology and Pathogenesis==</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Habitat; symbiosis; biogeochemical significance; contributions to environment.<br></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br><br></del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The habitat of this organism is the large intestine of the human gut, and although it is not initially found in the gut at birth, O. formigenes quickly is established in the gut microflora [Mittal]. O. formigenes plays a unique role in the gut microflora in that it is capable of metabolizing 70 to 100 mg per day of oxalate. [Mittal]. Although soluble dietary oxalate is absorbed in the human small intestine, O. formigenes fulfills the role of metabolizing the remaining dietary oxalate and oxalate produced by the host's metabolism, which can otherwise accumulate, leading to hyperoxaluria and the formation of calcium oxalate stones, which are harmful to the human host [Siva]. This can be considered a symbiosis, in that the organism, a strict anaerobe, is given a safe environment to live and reproduce, along with a steady supply of oxalate to consume. In addition, O. formigenes confers a benefit to its human host in the sense that it degrades the otherwise toxic excess oxalate in the large intestine. O. formigenes is not explicitly pathogenic.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The habitat of this organism is the large intestine of the human gut, and although it is not initially found in the gut at birth, O. formigenes quickly is established in the gut microflora [Mittal]. O. formigenes plays a unique role in the gut microflora in that it is capable of metabolizing 70 to 100 mg per day of oxalate. [Mittal]. Although soluble dietary oxalate is absorbed in the human small intestine, O. formigenes fulfills the role of metabolizing the remaining dietary oxalate and oxalate produced by the host's metabolism, which can otherwise accumulate, leading to hyperoxaluria and the formation of calcium oxalate stones, which are harmful to the human host [Siva]. This can be considered a symbiosis, in that the organism, a strict anaerobe, is given a safe environment to live and reproduce, along with a steady supply of oxalate to consume. In addition, O. formigenes confers a benefit to its human host in the sense that it degrades the otherwise toxic excess oxalate in the large intestine. O. formigenes is not explicitly pathogenic.</div></td></tr>
</table>Behanashhttps://microbewiki.kenyon.edu/index.php?title=Oxalobacter_formigenes&diff=41634&oldid=prevBehanash: /* References */2009-04-15T19:47:29Z<p><span dir="auto"><span class="autocomment">References</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>4. Mittal, R.D, Kumar, R. 2004. "Gut-inhabiting bacterium Oxalobacter formigenes: Role in calcium oxalate urolithiasis." Jorunal of Endourology. 18 (5): 418-424</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>4. Mittal, R.D, Kumar, R. 2004. "Gut-inhabiting bacterium Oxalobacter formigenes: Role in calcium oxalate urolithiasis." Jorunal of Endourology. 18 (5): 418-424</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>5. Stewart, C.S., Duncan, S. H., Cave, D.R. 2004. "Oxalobacter formigenes and its role in oxalate metabolism in the human gut." FEMS Microbiology Letters. 230: 1-7.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>5. Stewart, C.S., Duncan, S. H., Cave, D.R. 2004. "Oxalobacter formigenes and its role in oxalate metabolism in the human gut." FEMS Microbiology Letters. 230: 1-7.</div></td></tr>
</table>Behanash