Global Methane Hub Wikipedia - User contributions [en]

Selenomonas ruminantium GA192

2026-10-01T01:10:36Z

Wangm3:

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| G(6mA)TC || Example || Example || Example
|-
| G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example
|-
| GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example || Example || Example
|-
| CC(6mA)GNNNNNTCG/ CG(6mA)NNNNNCTGG || Example || Example || Example
|-
| GA(6mA)GNNNNNCTC/ G(6mA)GNNNNNCTTC || Example || Example || Example
|-
| GA(6mA)CNNNNNACT/ (6mA)GTNNNNNGTTC || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG22058

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| Tetracycline || 0.094ug/ml
|-
| Trimethoprim || 8 ug/ml
|-
| Streptomycin || 2 ug/ml
|-
| Spectinomycin || 16ug/ml
|-
| Kanamycin || 3 ug/ml
|-
| Chloramphenicol || 0.5 ug/ml
|-
| Gentamicin || 2 ug/ml
|-
| Erythromycin || 0.2ug/ml
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| PD-Lambda-1 (PD-Lambda-1) || ||
|-
| PrrC (PrrC) || ||
|-
| RM (RM_Type_IV) || ||
|-
| Abi2 (Abi2) || ||
|-
| VP1839 (VP1839) || ||
|-
| Wadjet (Wadjet_I) || || Lacks JetD (endonuclease)
|-
| Eleos (Eleos) || ||
|-
| Cas (CAS_Class1-Subtype-I-F) || ||
|-
| SspBCDE (SspBCDE) || || Lacks SspA & SspE (endonuclease)
|-
| Cas (CAS_Class1-Subtype-III-D) || ||
|-
| AbiD (AbiD) || ||
|-
| Mokosh (Mokosh_Type_I_B) || ||
|-
| VP1851 (VP1851) || ||
|-
| Cas (CAS_Cluster) || ||
|}

Selenomonas ruminantium GA192

2026-10-01T01:10:22Z

Wangm3: Created page with "Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae Bacillota (firmicutes)- Clostridia- Lachnospirales- Lachnospiraceae- Butyrivibrio == Genome == == Methylome == {| class="wikitable" |+ Methylome Motifs |- ! motif !! # site methylated !! total sites !! % methylated |- | G(6mA)TC || Example || Example || Example |- | G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example |- | GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example |..."

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

Bacillota (firmicutes)- Clostridia- Lachnospirales- Lachnospiraceae- Butyrivibrio

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| G(6mA)TC || Example || Example || Example
|-
| G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example
|-
| GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example || Example || Example
|-
| CC(6mA)GNNNNNTCG/ CG(6mA)NNNNNCTGG || Example || Example || Example
|-
| GA(6mA)GNNNNNCTC/ G(6mA)GNNNNNCTTC || Example || Example || Example
|-
| GA(6mA)CNNNNNACT/ (6mA)GTNNNNNGTTC || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG22058

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| Tetracycline || 0.094ug/ml
|-
| Trimethoprim || 8 ug/ml
|-
| Streptomycin || 2 ug/ml
|-
| Spectinomycin || 16ug/ml
|-
| Kanamycin || 3 ug/ml
|-
| Chloramphenicol || 0.5 ug/ml
|-
| Gentamicin || 2 ug/ml
|-
| Erythromycin || 0.2ug/ml
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| PD-Lambda-1 (PD-Lambda-1) || ||
|-
| PrrC (PrrC) || ||
|-
| RM (RM_Type_IV) || ||
|-
| Abi2 (Abi2) || ||
|-
| VP1839 (VP1839) || ||
|-
| Wadjet (Wadjet_I) || || Lacks JetD (endonuclease)
|-
| Eleos (Eleos) || ||
|-
| Cas (CAS_Class1-Subtype-I-F) || ||
|-
| SspBCDE (SspBCDE) || || Lacks SspA & SspE (endonuclease)
|-
| Cas (CAS_Class1-Subtype-III-D) || ||
|-
| AbiD (AbiD) || ||
|-
| Mokosh (Mokosh_Type_I_B) || ||
|-
| VP1851 (VP1851) || ||
|-
| Cas (CAS_Cluster) || ||
|}

Clostridium aminophilum FT

2026-10-01T01:07:30Z

Wangm3:

== Global Methane Hub Metadata ==

== Genome ==
The genome of ''C. aminophilum'' FT consists of a single, circular contig 3.2 Mbp in size. Seven rRNA loci (each with three rRNA genes), 60 tRNA loci, and 2 CRISPR loci were annotated by Prokka.
[[File:Cami genome.jpg|alt=A representation of the C. aminophilum FT genome.|center|''C. aminophilum'' FT genome with tRNA, rRNA, and CRISPR loci annotated. Source: Dr. William G. Alexander|frame]]

== Methylome ==
{| class="wikitable"
!motif
!# sites methylated
!total sites
!% methylated
|-
|G(6mA)TCNNNNNGGT
|1057
|1060
|99.72
|-
|(6mA)CCNNNNNGATC
|1018
|1060
|96.04
|-
|GCC(6mA)NNNNNNNNTGT
|191
|197
|96.45
|-
|AC(6mA)NNNNNNNNTGGC
|186
|197
|94.42
|-
|CG(6mA)CNNNNNNTCG
|191
|191
|100
|-
|CG(6mA)NNNNNNGTCG
|190
|191
|99.48
|-
|ATTA(6mA)T
|440
|466
|94.42
|-
|C(5mC)GCGG
|3276
|3450
|94.96
|}

== Methylating ''E. coli'' strains ==
Completed, AG22091

== Culturing Conditions ==
{| class="wikitable"
|+
|Media
|[[Reinforced Clostridial Medium|RCM]] (+cysteine) + [[Wolin's Vitamin Solution|Wolin's]]
|RCM (+cysteine) +[[Wolin's Vitamin Solution|Wolin's]] +[[Volatile Fatty Acid Solution|VFA]]
|RCM +cysteine +[[Wolin's Vitamin Solution|Wolin's]] +[[Volatile Fatty Acid Solution|VFA]] +TM
|M2GSC
|MDM
|-
|Time to Saturation
|one overnight period
|one overnight period
|one overnight period
|one overnight period
|Not tested
|}

== Antibiotic MIC Tests ==
[[File:Cami MIC.jpg|left|thumb|Raw photographic data of MIC tests on ''C. aminophilum'' FT. Source: Dr. Jill Walton]]
{| class="wikitable sortable mw-collapsible mw-collapsed"
!Antibiotic
!Concentration Range
|-
|Tetracycline
|12-16 ug/mL
|-
|Trimethoprim
|Resistant
|-
|Ampicillin
|0.25-0.38 ug/mL
|-
|Streptomycin
|Resistant
|-
|Chloramphenicol
|8-12 ug/mL
|-
|Gentamycin
|32-48 ug/mL
|-
|Kanamycin
|128-192 ug/mL
|-
|Erythromycin
|0.094-0.19 ug/mL
|-
|Spectinomycin
|Resistant
|}

== Protocols ==

== External Links ==

Butyrivibrio proteoclasticus B316ᵀ

2026-10-01T01:06:32Z

Wangm3: Created page with "Bacillota (firmicutes)- Clostridia- Lachnospirales- Lachnospiraceae- Butyrivibrio == Genome == == Methylome == {| class="wikitable" |+ Methylome Motifs |- ! motif !! # site methylated !! total sites !! % methylated |- | ATTA(6mA)T || Example || Example || Example |- | T(5mC)TGG/C(5mC)AGA || Example || Example || Example |} == ''E.coli'' methylation strain == Completed, AG20914 == Antibiotic MIC tests == ==== MIC test strip result ==== {| class="wikitable" |+ MIC te..."

Bacillota (firmicutes)- Clostridia- Lachnospirales- Lachnospiraceae- Butyrivibrio

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| ATTA(6mA)T || Example || Example || Example
|-
| T(5mC)TGG/C(5mC)AGA || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG20914

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.25ug/ml
|-
| Streptomycin || 8 ug/ml
|-
| Spectinomycin || 12ug/ml
|-
| Kanamycin || 16ug/ml
|-
| Chloramphenicol || 3ug/ml
|-
| Gentamicin || 0.5ug/ml
|-
| Erythromycin || 0.02ug/ml
|-
| Tetracycline || Resistant
|-
| Trimethoprim || Resistant
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| Gabija (Gabija) || ||
|-
| AbiD (AbiD) || Against phage infection ||
|-
| RM (RM_Type_IV) || ||
|-
| Wadjet (Wadjet_I) || against closed-circular DNA (regardless of supercoiling state) || Full system present
|}

Butyrivibrio fibrisolvens TB

2026-10-01T01:03:05Z

Wangm3:

Bacillota (firmicutes)- Clostridia- Lachnospirales- Lachnospiraceae- Butyrivibrio

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Caption text
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| ATTA(6mA)T || Example || Example || Example
|-
| C(5mC)TGA || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG20809

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| streptomycin || 6ug/ml
|-
| gentamicin || 0.38ug/ml
|-
| Spectinomycin || 2ug/ml
|-
| Chloramphenicol || 0.5ug/ml
|-
| Erythromycin || Resistant
|-
| Tetracycline || Resistant
|-
| kanamycin || Resistant
|}

== Defensefinder prediction ==
* Predicted RM I, II, III is not listed
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| SspBCDE (SspBCDE) || Cut DNA without phosphorothioate modification || Lacks SspA & SspE (endonuclease)
|-
| HEC-02 (HEC-02) || ||
|-
| Wadjet (Wadjet_I) || against closed-circular DNA (regardless of supercoiling state) || Lacks JetD (endonuclease)
|-
| AbiL (AbiL) || Against phage ||
|-
| MazEF (MazEF) || Against phage ||
|-
| AbiD (AbiD) || Against phage ||
|}

Butyrivibrio fibrisolvens TB

2026-10-01T00:43:58Z

Wangm3:

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Caption text
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| ATTA(6mA)T || Example || Example || Example
|-
| C(5mC)TGA || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG20809

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| streptomycin || 6ug/ml
|-
| gentamicin || 0.38ug/ml
|-
| Spectinomycin || 2ug/ml
|-
| Chloramphenicol || 0.5ug/ml
|-
| Erythromycin || Resistant
|-
| Tetracycline || Resistant
|-
| kanamycin || Resistant
|}

== Defensefinder prediction ==
* Predicted RM I, II, III is not listed
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| SspBCDE (SspBCDE) || Cut DNA without phosphorothioate modification || Lacks SspA & SspE (endonuclease)
|-
| HEC-02 (HEC-02) || ||
|-
| Wadjet (Wadjet_I) || against closed-circular DNA (regardless of supercoiling state) || Lacks JetD (endonuclease)
|-
| AbiL (AbiL) || Against phage ||
|-
| MazEF (MazEF) || Against phage ||
|-
| AbiD (AbiD) || Against phage ||
|}

Butyrivibrio fibrisolvens TB

2026-10-01T00:39:21Z

Wangm3: Created page with "== Genome == == Methylome == {| class="wikitable" |+ Caption text |- ! motif !! # site methylated !! total sites !! % methylated |- | ATTA(6mA)T || Example || Example || Example |- | C(5mC)TGA || Example || Example || Example |} == ''E.coli'' methylation strain == Completed, AG20809 == Antibiotic MIC tests == ==== MIC test strip result ==== {| class="wikitable" |+ MIC test strip result |- ! Antibiotic !! MIC |- | Ampicillin || 0.016ug/ml |- | streptomycin || 6ug/ml..."