Kandleria vitulina WCE2011: Difference between revisions
Created page with "== Information ==" |
|||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
== | == Introduction == | ||
'''Kandleria vitulina WCE2011''' | |||
Kandleria vitulina WCE2011 (DSM 118843) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. WCE2011 ferments glucose, fructose, galactose and cellobiose with D-lactate as the main fermentation product together with small amounts of acetate, formate and ethanol [2]. It is a member of the family Coprobacillaceae. | |||
Sharpea and Kandleria were identified as key bacteria associated with the S-type (Sharpea-enriched) bacterial community, one of the two low-CH<sub>4</sub> community types in rumen samples from sheep that differed in the amount of CH<sub>4</sub> formed per unit of feed consumed when these sheep were fed pelletized lucerne [3]. | |||
The draft genome for WCE2011 (2,036,146 bp) was generated through the Hungate1000 project with JGI [4]. Resequencing gave a single chromosome of 2,143,850 bp. | |||
This species was formerly named as Lactobacillus vitulinus [5]. | |||
LPSN: Kandleria vitulina (Sharpe et al. 1973) Salvetti et al. 2011 | |||
NCBI: Kandleria vitulina. Tax ID: 1410659. | |||
GTDB: Kandleria vitulina. WCE2011 groups with the type strain (RL2, DSM 20405) [6] | |||
Risk group: 1 | |||
=== Strain characteristics and function in the rumen === | |||
=== Strain history and information === | |||
== Global Methane Hub Metadata == | |||
{| class="wikitable" | |||
| valign="top" |Strain origin: | |||
| valign="top" |New Zealand<sup>1</sup> | |||
|- | |||
| valign="top" |Isolated from: | |||
| valign="top" |Cow rumen | |||
|- | |||
| valign="top" |Sequenced by: | |||
| valign="top" |Rhiannon Cecil<sup>2</sup> | |||
|- | |||
| valign="top" |Assembled by: | |||
| valign="top" |William G. Alexander<sup>3</sup> | |||
|- | |||
| valign="top" |Genome and methylome analysis by: | |||
| valign="top" |William G. Alexander<sup>3</sup> & Ashley Hall<sup>2</sup> | |||
|- | |||
| valign="top" |MIC and culturing conditions by: | |||
| valign="top" |Rhiannon Cecil | |||
|- | |||
| valign="top" |Transformed by: | |||
| valign="top" |Rhiannon Cecil | |||
|} | |||
<sup>1</sup>Institute for Bioeconomy Science, Palmerston North, New Zealand. <sup>2</sup>BiomEdit, Indianapolis, Indiana, United States. <sup>3</sup>Oak Ridge National Lab, Oak Ridge, Tennessee, United States. | |||
== Genome == | |||
{| class="wikitable" | |||
| colspan="2" valign="top" |''K. vitulina'' WCE2011 Genome Summary | |||
|- | |||
| valign="top" |Sequencing method | |||
| valign="top" |Oxford Nanopore | |||
|- | |||
| valign="top" |Contigs | |||
| valign="top" |1 | |||
|- | |||
| valign="top" |Base pairs | |||
| valign="top" |2.1 Mb | |||
|- | |||
| valign="top" |CDSs | |||
| valign="top" |2,021 | |||
|- | |||
| valign="top" |CRISPR | |||
| valign="top" |2 | |||
|- | |||
| valign="top" |Genes | |||
| valign="top" |2,166 | |||
|- | |||
| valign="top" |rRNA | |||
| valign="top" |24 | |||
|- | |||
| valign="top" |tRNA | |||
| valign="top" |89 | |||
|- | |||
| valign="top" |Miscellaneous RNA | |||
| valign="top" |31 | |||
|- | |||
| valign="top" |Antimicrobial resistance genes | |||
| valign="top" |None | |||
|} | |||
== Methylome == | |||
=== Methylome analysis summary results === | |||
{| class="wikitable" | |||
| colspan="2" |''K. vitulina'' WCE2011 Methylome Summary | |||
|- | |||
| valign="top" |Isolation Motif | |||
| valign="top" |% Motif Methylation | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|} | |||
=== DefenseFinder Results === | |||
{| class="wikitable" | |||
| colspan="2" valign="top" |''K. vitulina'' WCE2011 DefenseFinder Results | |||
|- | |||
| valign="top" |DefenseFinder System | |||
| valign="top" |# Found | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|- | |||
| valign="top" | | |||
| valign="top" | | |||
|} | |||
=== Methylating ''Escherichia coli'' strains === | |||
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''K. vitulina'' WCE2011. | |||
== Culturing Conditions == | |||
== Antimicrobial Susceptibility == | |||
== Transformation Results == | |||
== External Links == | |||
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>. | |||
[2] Kumar S, Treloar BP, Teh KH, McKenzie CM, Henderson G, Attwood GT, Waters SM, Patchett ML, Janssen PH. 2018. Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen. Anaerobe 54: 31-38. doi: 10.1016/j.anaerobe.2018.07.008. | |||
[3] Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9: e103171. doi: 10.1371/journal.pone.0103171 | |||
[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110. | |||
[5] Salvetti E, Felis GE, Dellaglio F, Castioni A, Torriani S, Lawson PA. 2011. Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 61: 2520-2524. doi: 10.1099/ijs.0.029231-0. | |||
[6] Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O. 1973. Two new species of Lactobacillus isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus sp.nov. J Gen Microbiol 77: 37-49. doi: 10.1099/00221287-77-1-37. | |||
Latest revision as of 22:25, 20 October 2026
Introduction
Kandleria vitulina WCE2011
Kandleria vitulina WCE2011 (DSM 118843) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. WCE2011 ferments glucose, fructose, galactose and cellobiose with D-lactate as the main fermentation product together with small amounts of acetate, formate and ethanol [2]. It is a member of the family Coprobacillaceae.
Sharpea and Kandleria were identified as key bacteria associated with the S-type (Sharpea-enriched) bacterial community, one of the two low-CH4 community types in rumen samples from sheep that differed in the amount of CH4 formed per unit of feed consumed when these sheep were fed pelletized lucerne [3].
The draft genome for WCE2011 (2,036,146 bp) was generated through the Hungate1000 project with JGI [4]. Resequencing gave a single chromosome of 2,143,850 bp.
This species was formerly named as Lactobacillus vitulinus [5].
LPSN: Kandleria vitulina (Sharpe et al. 1973) Salvetti et al. 2011
NCBI: Kandleria vitulina. Tax ID: 1410659.
GTDB: Kandleria vitulina. WCE2011 groups with the type strain (RL2, DSM 20405) [6]
Risk group: 1
Strain characteristics and function in the rumen
Strain history and information
Global Methane Hub Metadata
| Strain origin: | New Zealand1 |
| Isolated from: | Cow rumen |
| Sequenced by: | Rhiannon Cecil2 |
| Assembled by: | William G. Alexander3 |
| Genome and methylome analysis by: | William G. Alexander3 & Ashley Hall2 |
| MIC and culturing conditions by: | Rhiannon Cecil |
| Transformed by: | Rhiannon Cecil |
1Institute for Bioeconomy Science, Palmerston North, New Zealand. 2BiomEdit, Indianapolis, Indiana, United States. 3Oak Ridge National Lab, Oak Ridge, Tennessee, United States.
Genome
| K. vitulina WCE2011 Genome Summary | |
| Sequencing method | Oxford Nanopore |
| Contigs | 1 |
| Base pairs | 2.1 Mb |
| CDSs | 2,021 |
| CRISPR | 2 |
| Genes | 2,166 |
| rRNA | 24 |
| tRNA | 89 |
| Miscellaneous RNA | 31 |
| Antimicrobial resistance genes | None |
Methylome
Methylome analysis summary results
| K. vitulina WCE2011 Methylome Summary | |
| Isolation Motif | % Motif Methylation |
DefenseFinder Results
| K. vitulina WCE2011 DefenseFinder Results | |
| DefenseFinder System | # Found |
Methylating Escherichia coli strains
E. coli strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for K. vitulina WCE2011.
Culturing Conditions
Antimicrobial Susceptibility
Transformation Results
External Links
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content.
[2] Kumar S, Treloar BP, Teh KH, McKenzie CM, Henderson G, Attwood GT, Waters SM, Patchett ML, Janssen PH. 2018. Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen. Anaerobe 54: 31-38. doi: 10.1016/j.anaerobe.2018.07.008.
[3] Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9: e103171. doi: 10.1371/journal.pone.0103171
[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.
[5] Salvetti E, Felis GE, Dellaglio F, Castioni A, Torriani S, Lawson PA. 2011. Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al. 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 61: 2520-2524. doi: 10.1099/ijs.0.029231-0.
[6] Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O. 1973. Two new species of Lactobacillus isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus sp.nov. J Gen Microbiol 77: 37-49. doi: 10.1099/00221287-77-1-37.
