View source for Ruminococcus flavefaciens FD-1

[[File:Image3.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1.
<small>This photo belongs to the GMH Project  and was taken by Kingsley Boateng.</small>]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''FD-1'''

''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellulosomes, which are highly modular enzymatic complexes [1]. The efficient degradation of lignocellulose by strain FD-1 results in the production of volatile fatty acids that are absorbed across the rumen epithelium, directly supporting the metabolic and energetic requirements of the ruminant host. Furthermore, the hydrogen evolved during its fermentation process is utilized by syntrophic methanogens, linking the robust fibrolytic activity of FD-1 to ruminal methanogenesis. The extensive genetic and structural mapping of ''R. flavefaciens'' FD-1 has established it as a critical benchmark strain for understanding the molecular assembly of bacterial cellulosomes and exploring biotechnological applications in lignocellulose bioconversion. 

LPSN: ''Ruminococcus flavefaciens'' Sijpesteijn 1948 

NCBI: ''Ruminococcus flavefaciens'' FD-1

GTDB: ''Ruminococcus flavefaciens''

Risk group: 1 

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|United States of America, Mackie lab
|-
|Sequenced by:
|Makoto Adachi
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Roy Rodriguez Carrero
|-
|MIC and Culturing Conditions by:
|Roy Rodriguez Carrero
|-
|Transformation by:
|
|}

== Genome ==
[[File:MRGXBF 2 FD1 2 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' FD-1. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GA(6mA)GG
| align="right" |99.08
|-
|TGAA(6mA)T
| align="right" |80.83
|-
|GC(6mA)YNNNNNTCG
| align="right" |95.53
|-
|(6mA)CGNNNNNNTCAA
| align="right" |96.06
|-
|CGCC(6mA)G
| align="right" |89.77
|-
|CCN(6mA)CC
| align="right" |93.94
|-
|TTG(6mA)NNNNNNCGT
| align="right" |98.13
|-
|GTA(6mA)NNNNNGRTA
| align="right" |97.72
|-
|CG(6mA)NNNNNRTGC
| align="right" |98.68
|-
|T(6mA)YCNNNNNTTAC
| align="right" |92.71
|-
|CACA(6mA)TW
| align="right" |77.18
|-
|SAG(5mC)TS
| align="right" |81.6
|-
|GGN(5mC)C
| align="right" |47.52
|}

== Methylating ''E. coli'' ==
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== Culturing Conditions ==
''R. flavefaciens'' FD-1 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' FD-1 on M10 agar is close to 72%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.13
|-
|Chlorhamphenicol
|1.8
|-
|Erythromycin
|1.7
|-
|Gentamycin
|0.5
|-
|Kanamycin
|Resistance (>200)
|-
|Streptomycin
|0.1
|-
|Tetracycline
|0.1
|}

== Protocols ==
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== Transformation Results ==
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== External Links ==
[1] Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. 2017. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 7:42355.