Methanocatella gottschalkii HO: Difference between revisions
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== Introduction == | == Introduction == | ||
[[File:Mgot HO.gif|thumb|Phase-contrast (top) and epifluorescence (bottom) microscopy of ''Methanocatella gottschalkii'' HO. '''Source:''' Christian Heryakusuma.]] | |||
''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens. | ''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens. | ||
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== Genome == | == Genome == | ||
[[File:Circos Methanocatella gottschalkii HO-edt.png|thumb|Circos plot of ''Methanocatella gottschalkii'' HO. '''Source:''' Christian Heryakusuma]] | [[File:Circos Methanocatella gottschalkii HO-edt.png|thumb|left|Circos plot of ''Methanocatella gottschalkii'' HO. '''Source:''' Christian Heryakusuma|550x550px]] | ||
{| class="wikitable" style="float: left; margin-right: 2em;" | {| class="wikitable" style="float: left; margin-right: 2em;" | ||
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{| class="wikitable" style="float: left;" | {| class="wikitable" style="float: left;" | ||
|+ | |+ | ||
! colspan=" | ! colspan="4" |Annotation Summary | ||
|- | |- | ||
|Coding density | |Coding density | ||
|88.1% | |style="border-right: 3px solid gray;"| 88.1% | ||
|CDSs | |CDSs | ||
|1847 | |1847 | ||
|- | |- | ||
|tRNAs | |||
|style="border-right: 3px solid gray;"| 33 | |||
|Pseudogenes | |Pseudogenes | ||
|2 | |2 | ||
|- | |- | ||
|tmRNAs | |||
|style="border-right: 3px solid gray;"| 0 | |||
|Hypotheticals | |Hypotheticals | ||
|1585 | |1585 | ||
|- | |- | ||
|rRNAs | |||
|style="border-right: 3px solid gray;"| 7 | |||
|sORFs | |sORFs | ||
|0 | |0 | ||
|- | |- | ||
|ncRNAs | |||
|style="border-right: 3px solid gray;"| 1 | |||
|Gaps | |Gaps | ||
|0 | |0 | ||
|- | |- | ||
|ncRNAs regions | |||
|style="border-right: 3px solid gray;"| 1 | |||
|oriCs | |oriCs | ||
|0 | |0 | ||
|- | |- | ||
|CRISPR arrays | |||
|style="border-right: 3px solid gray;"| 0 | |||
|oriVs | |oriVs | ||
|0 | |0 | ||
|- | |- | ||
| | |||
|style="border-right: 3px solid gray;"| | |||
|oriTs | |oriTs | ||
|0 | |0 | ||
| Line 102: | Line 97: | ||
<div style="clear: both;"></div> | <div style="clear: both;"></div> | ||
Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage pseudomurein endoisopeptidase of '' | Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following the manufacturer's protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with the phage ΨM2 pseudomurein endoisopeptidase of ''Methanothermobacter marburgensis'' (PeiP)<ref>Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x. </ref>. | ||
The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility. | The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility. | ||
== Methylome == | == Methylome == | ||
| Line 129: | Line 125: | ||
=== DefenseFinder Results === | === DefenseFinder Results === | ||
{| class="wikitable" | |||
|+ | |||
!Type | |||
!Subtype | |||
!Components | |||
|- | |||
|CRISPR-Cas | |||
|CAS Cluster | |||
|cas1_I_II_III_IV_V_VI_10, <br>cas2_I_II_III_IV_V_VI_3 | |||
|- | |||
|RM Type I | |||
|N6-adenine methylating (m6A) Type I RM | |||
|Type I RM methyltransferase (HsdM), <br>Type I RM restriction endonuclease (HsdR), <br>Type I RM specificity subunit (HsdS) | |||
|- | |||
|Prometheus | |||
|Prometheus | |||
|ProA | |||
|- | |||
|RAZR | |||
|RAZR | |||
|PD-T7-4 | |||
|- | |||
|RM Type II | |||
|DNA methylase and Type II REase of the PD-(D/E)xK superfamily | |||
|Type II DNA methyltransferase, <br>Type II restriction endonuclease (profile 12) | |||
|} | |||
'''''Abbreviation:''''' CRISPR-Cas, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated enzymes; RM, restriction-modification; Prometheus, DNA replication helicase/nuclease 2 (DNA2)-containing anti-phage defense protein<ref>van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe. 2024 Aug 14;32(8):1427-1443.e8. https://doi.org/10.1016/j.chom.2024.07.007.</ref>; RAZR, ring-activated zinc-finger RNase<ref>Zhang, T., Lyu, Y., Beck, C.R. ''et al.'' Bacterial immune activation via supramolecular assembly with phage triggers. ''Nature'' '''651''', 1051–1059 (2026). https://doi.org/10.1038/s41586-025-10060-8. </ref>; PD-T7-4, phage defense selecting against T7 bacteriophage system 4<ref>Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol. 2022 Oct;7(10):1568-1579. doi: 10.1038/s41564-022-01219-4. Epub 2022 Sep 19. Erratum in: Nat Microbiol. 2024 Oct;9(10):2760-2761. https://doi.org/10.1038/s41564-024-01724-8. </ref>; REase, restriction endonuclease. | |||
=== Methylating ''E. coli'' === | === Methylating ''E. coli'' === | ||
''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above. | ''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above. | ||
Latest revision as of 20:35, 3 November 2026
Introduction
Methanocatella gottschalkii HOT (formerly Methanobrevibacter gottschalkii) is a type strain isolated from the enrichment of horse faeces[1]. M. gottschalkii, along with Methanobrevibacter ruminantium, comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets[2]. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.
Global Methane Hub Metadata
| Origin: | Leibniz Institute DSMZ, Germany |
|---|---|
| Sequenced by: | Plasmidsaurus, ONT sequencing |
| Assembled by: | Christian Heryakusuma |
| Methylome called by: | William G. Alexander |
| Methyltransferases cloned by: | Guss Lab, ORNL |
| MIC and Culturing Conditions by: | Christian Heryakusuma |
| Transformation by: |
Abbreviation: ONT, Oxford Nanopore Technologies; ORNL, Oak Ridge National Laboratory.
Genome
| Assembly Summary | |
|---|---|
| Completeness | 99.97% |
| Contamination | 0.16% |
| Total contigs | 1 |
| Max contig length | 1,887,794 bp |
| GC content | 30.07% |
| Annotation Summary | |||
|---|---|---|---|
| Coding density | 88.1% | CDSs | 1847 |
| tRNAs | 33 | Pseudogenes | 2 |
| tmRNAs | 0 | Hypotheticals | 1585 |
| rRNAs | 7 | sORFs | 0 |
| ncRNAs | 1 | Gaps | 0 |
| ncRNAs regions | 1 | oriCs | 0 |
| CRISPR arrays | 0 | oriVs | 0 |
| oriTs | 0 | ||
Genomic DNA (gDNA) of M. gottschalkii HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch® Spin gDNA Extraction Kit following the manufacturer's protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with the phage ΨM2 pseudomurein endoisopeptidase of Methanothermobacter marburgensis (PeiP)[3].
The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye[4] and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST[5] and CheckM2[6]. Bakta v1.12.0[7] with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.
Methylome
Methylation pattern
| #motif | methylCounts | totalCounts | %motifsMethyl |
|---|---|---|---|
| C(6mA)YNNNNNRTTG | 1495 | 1558 | 95.96 |
| CA(6mA)YNNNNNRTG | 1522 | 1558 | 97.69 |
Methylation motifs were analyzed using MIJAMP[8]. 4mC and 5mC motifs were not present in this isolate.
DefenseFinder Results
| Type | Subtype | Components |
|---|---|---|
| CRISPR-Cas | CAS Cluster | cas1_I_II_III_IV_V_VI_10, cas2_I_II_III_IV_V_VI_3 |
| RM Type I | N6-adenine methylating (m6A) Type I RM | Type I RM methyltransferase (HsdM), Type I RM restriction endonuclease (HsdR), Type I RM specificity subunit (HsdS) |
| Prometheus | Prometheus | ProA |
| RAZR | RAZR | PD-T7-4 |
| RM Type II | DNA methylase and Type II REase of the PD-(D/E)xK superfamily | Type II DNA methyltransferase, Type II restriction endonuclease (profile 12) |
Abbreviation: CRISPR-Cas, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated enzymes; RM, restriction-modification; Prometheus, DNA replication helicase/nuclease 2 (DNA2)-containing anti-phage defense protein[9]; RAZR, ring-activated zinc-finger RNase[10]; PD-T7-4, phage defense selecting against T7 bacteriophage system 4[11]; REase, restriction endonuclease.
Methylating E. coli
E. coli strain AG21365 developed by ORNL was used as a host to generate plasmids with M. gottschalkii HO methylation motifs shown above.
Culturing Conditions
M. gottschalkii HO is cultivated in GMH-VT2 medium at 37°C and 50 rpm with a 30 psig gas mixture of H2:CO2 (80:20, v/v) as an energy substrate. Growth is typically observed within 24 to 48 h. This methanogen can also be cultivated on GMH-VT2 plates using 1.5% gelrite or 2% agar as a gelling agent with a 12 to 30 psig H2:CO2 (80:20, v/v) gas mixture as an energy substrate. Visible growth on plate is usually observable within 2 to 5 days. The viability of M. gottschalkii HO on agar plates is 10-30 times higher than that of those grown on gelrite plates.
Antimicrobial MIC Tests
| Antibiotics | Concentration | Observation Period | |
|---|---|---|---|
| Liquid | Solid | ||
| Sodium sulfite | 0.5 mM | 0.3 mM | ~240 h |
| Mevinolin | 40 μM | 20 μM | ~240 h |
| 5-fluoroorotic acid (5-FOA) | Insensitive | Insensitive | ~240 h |
| 8-azahypoxanthine (8-AH) | Insensitive | Insensitive | ~240 h |
| 6-mercaptopurine (6-MP) | Insensitive | Insensitive | ~240 h |
| 5-fluorouracil (5-FU) | 0.25 mg/mL | 0.15 mg/mL | ~240 h |
| Sodium 2-bromoethanesulfonate (BES) | 2 mM | 1 mM | ~240 h |
Susceptibility testing was evaluated in GMH-VT2 medium inoculated with a 4% M. gottschalkii HO culture that has a starting OD600 of ~0.4. M. gottschalkii HO was considered sensitive to the selection or counterselection agents if there was no increase in the OD600 during the ~240 h (10 days) observation period.
Protocols
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Transformation Results
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External Links
- ↑ Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.
- ↑ Henderson, G., Cox, F., Ganesh, S. et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5, 14567 (2015). https://doi.org/10.1038/srep14567.
- ↑ Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x.
- ↑ Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.
- ↑ Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.
- ↑ Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.
- ↑ Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.
- ↑ Alyssa K Tidwell, Evelyn Faust, Carrie A Eckert, Adam M Guss, William G Alexander, Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP, Journal of Industrial Microbiology and Biotechnology, Volume 52, 2025, kuaf022, https://doi.org/10.1093/jimb/kuaf022.
- ↑ van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe. 2024 Aug 14;32(8):1427-1443.e8. https://doi.org/10.1016/j.chom.2024.07.007.
- ↑ Zhang, T., Lyu, Y., Beck, C.R. et al. Bacterial immune activation via supramolecular assembly with phage triggers. Nature 651, 1051–1059 (2026). https://doi.org/10.1038/s41586-025-10060-8.
- ↑ Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol. 2022 Oct;7(10):1568-1579. doi: 10.1038/s41564-022-01219-4. Epub 2022 Sep 19. Erratum in: Nat Microbiol. 2024 Oct;9(10):2760-2761. https://doi.org/10.1038/s41564-024-01724-8.
