Ruminococcus flavefaciens AE3010

Scanning electron microscopic image of Ruminococcus flavefaciens AE3010. This photo belongs to the GMH Project and was taken by Kingsley Boateng.

Introduction

Ruminococcus flavefaciens AE3010

Ruminococcus flavefaciens AE3010 is an obligately anaerobic, fibrolytic bacterium isolated from the rumen of a cow in New Zealand and selected as a key reference genome for the global Hungate1000 project [1]. Exhibiting the core phenotypic traits of the species, AE3010 relies on the breakdown of complex structural polysaccharides for growth, utilizing an extensive array of highly conserved cohesin and dockerin modules to assemble its specialized cell-surface cellulosome [2].

Ruminococcus flavefaciens AE3010 (DSM 115568) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [3, cow E]. AE3010 has not been phenotypically characterized but its genome encodes a broad range of carbohydrate active enzymes, many of which contain cohesion and dockerin domains. Like other rumen R. flavefaciens strains AE3010 is predicted to be cellulolytic and to produce a functional cellulosome [4].

The draft genome for AE3010 (3,705,946 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: Ruminococcus flavefaciens.

GTDB: Ruminococcus flavefaciens_D. AE3010 belongs to a different species group than the type strain of R. flavefaciens (C94, ATCC 19208).

Risk group: 1.

Global Methane Hub Metadata

Origin:	United States of America, Macike 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

Circos plot of R. flavefaciens AE3010. Source: Makoto Adachi

Methylome

Motif	Percent methylated
TGAA(6mA)T	99.49
CTTG(6mA)YG	99.76
CG(6mA)CC	97.15
CACA(6mA)T	97.75

Methylating E. coli

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Culturing Conditions

R. flavefaciens AE3010 grown well in M2GSC and M10 medium at 37°C. Plating efficiency of R. falvefaciens AE3010 on M10 agar is close to 66%.

Antimicrobial MIC Tests

Note: Antimicrobial MIC was assessed using M2GSC liquid medium.

Antibiotic	Concentration (µg/ml)
Ampicilin	0.5
Chlorhamphenicol	0.3
Erythromycin	1.6
Gentamycin	0.5
Kanamycin	4.7
Streptomycin	0.5
Tetracycline	0.1

Protocols

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Transformation Results

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External Links

[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D, 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. 2018. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 36:359–367.

[2] Minor CM, Takayesu A, Ha SM, Salwinski L, Sawaya MR, Pellegrini M, Clubb RT. 2024. A genomic analysis reveals the diversity of cellulosome displaying bacteria. Front Microbiol 15:1473396.

[3] 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.

[4] Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. 2024. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 383(6688): eadj9223. doi: 10.1126/science.adj9223.