Strain identifier
BacDive ID: 140664
Type strain: 
Species: Ruminococcus flavefaciens
Strain Designation: FD-1
NCBI tax ID(s): 1265 (species)
version 8.1 (current version)
General
@ref: 43397
BacDive-ID: 140664
keywords: genome sequence, Bacteria
description: Ruminococcus flavefaciens FD-1 is a bacterium of the family Oscillospiraceae.
NCBI tax id
- NCBI tax id: 1265
- Matching level: species
doi: 10.13145/bacdive140664.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Ruminococcus
- species: Ruminococcus flavefaciens
- full scientific name: Ruminococcus flavefaciens Sijpesteijn 1948 (Approved Lists 1980)
@ref: 43397
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Eubacteriales
family: Ruminococcaceae
genus: Ruminococcus
species: Ruminococcus flavefaciens
strain designation: FD-1
type strain: no
Physiology and metabolism
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43397 | 17057 | cellobiose | + | degradation |
| 43397 | 62968 | cellulose | + | degradation |
enzymes
- @ref: 43397
- value: endo-1,3(4)-beta-glucanase
- activity: +
- ec: 3.2.1.6
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruminococcus flavefaciens FD-1 | GCA_000174895 | scaffold | ncbi | 641112 |
| 66792 | Ruminococcus flavefaciens FD-1 | 641112.4 | wgs | patric | 641112 |
| 66792 | Ruminococcus flavefaciens FD-1 | 645951829 | draft | img | 641112 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 92.822 | no |
| flagellated | no | 96.327 | no |
| gram-positive | yes | 90.532 | no |
| anaerobic | yes | 99.646 | no |
| aerobic | no | 98.14 | no |
| halophile | no | 89.85 | no |
| spore-forming | no | 65.138 | no |
| glucose-util | yes | 78.487 | no |
| thermophile | no | 91.426 | no |
| glucose-ferment | yes | 71.241 | no |
External links
@ref: 43397
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Enzymology | 1335719 | Purification and properties of NADP-dependent glutamate dehydrogenase from Ruminococcus flavefaciens FD-1. | Duncan PA, White BA, Mackie RI | Appl Environ Microbiol | 10.1128/aem.58.12.4032-4037.1992 | 1992 | Animals, Glutamate Dehydrogenase/chemistry/*isolation & purification/metabolism, Glutamate Dehydrogenase (NADP+), Gram-Positive Cocci/*enzymology/growth & development, Hydrogen-Ion Concentration, In Vitro Techniques, Kinetics, Molecular Weight, Rumen/microbiology | Phylogeny |
| Metabolism | 1514805 | Response surface analysis of the effects of pH and dilution rate on Ruminococcus flavefaciens FD-1 in cellulose-fed continuous culture. | Shi Y, Weimer PJ | Appl Environ Microbiol | 10.1128/aem.58.8.2583-2591.1992 | 1992 | Bacteriological Techniques, Cellulose/*metabolism, Culture Media, Evaluation Studies as Topic, Fermentation, Gram-Positive Cocci/*growth & development/*metabolism, Hydrogen-Ion Concentration, Kinetics | Cultivation |
| Metabolism | 1539994 | Partial characterization of a DNA restriction endonuclease from Ruminococcus flavefaciens FD-1 and its inhibition by site-specific adenine methylation. | Morrison M, Mackie RI, White BA | Appl Environ Microbiol | 10.1128/aem.58.1.66-69.1992 | 1992 | Adenine/*metabolism, Base Sequence, DNA, Bacterial/metabolism, Deoxyribonucleases, Type II Site-Specific/*metabolism, Gram-Positive Cocci/*enzymology, Methylation, Molecular Sequence Data, Restriction Mapping, Substrate Specificity | Genetics |
| Metabolism | 2016208 | Degradation of wheat straw and alkaline hydrogen peroxide-treated wheat straw by Ruminococcus albus 8 and Ruminococcus flavefaciens FD-1. | Odenyo AA, Mackie RI, Fahey GC Jr, White BA | J Anim Sci | 10.2527/1991.692819x | 1991 | Animals, Biodegradation, Environmental, Culture Media, Hydrogen Peroxide/*pharmacology, Peptococcaceae/growth & development/*metabolism, Phenylacetates/pharmacology, Phenylpropionates/pharmacology, Rumen/*microbiology, *Triticum | Cultivation |
| Metabolism | 2036021 | Cellobiose uptake and metabolism by Ruminococcus flavefaciens. | Helaszek CT, White BA | Appl Environ Microbiol | 10.1128/aem.57.1.64-68.1991 | 1991 | Antimetabolites/pharmacology, Biological Transport, Active, Cellobiose/metabolism/*pharmacokinetics, Peptococcaceae/drug effects/growth & development/*metabolism | Enzymology |
| Enzymology | 2129544 | Nucleotide sequence of the celA gene encoding a cellodextrinase of Ruminococcus flavefaciens FD-1. | Wang WY, Thomson JA | Mol Gen Genet | 10.1007/BF00633827 | 1990 | Amino Acid Sequence, Base Sequence, Carboxymethylcellulose Sodium/metabolism, Cellulase/*metabolism, Cloning, Molecular, *DNA, Bacterial, Electrophoresis, Polyacrylamide Gel, *Genes, Bacterial, Molecular Sequence Data, Peptococcaceae/enzymology/*genetics, Promoter Regions, Genetic, Ribosomes/metabolism, Sequence Homology, Nucleic Acid | Metabolism |
| Enzymology | 2383014 | Assessment of the endo-1,4-beta-glucanase components of Ruminococcus flavefaciens FD-1. | Doerner KC, White BA | Appl Environ Microbiol | 10.1128/aem.56.6.1844-1850.1990 | 1990 | Cellulase/*analysis, Chromatography, High Pressure Liquid, Chromatography, Ion Exchange, Electrophoresis, Polyacrylamide Gel, Glycoside Hydrolases/metabolism, Gram-Positive Bacteria/*enzymology, Hydrolysis | Metabolism |
| Enzymology | 3115960 | Purification and characterization of an exo-beta-1,4-glucanase from Ruminococcus flavefaciens FD-1. | Gardner RM, Doerner KC, White BA | J Bacteriol | 10.1128/jb.169.10.4581-4588.1987 | 1987 | Amino Acid Sequence, Cellulose/metabolism, Chromatography, Gel, Chromatography, High Pressure Liquid, Chromatography, Ion Exchange, Chromatography, Thin Layer, Electrophoresis, Polyacrylamide Gel, Glucan 1,4-beta-Glucosidase, Glucosidases/*isolation & purification, Glucosides/metabolism, Hydrogen-Ion Concentration, Kinetics, Molecular Weight, Peptococcaceae/*enzymology, Substrate Specificity, beta-Glucosidase/*isolation & purification/metabolism | Metabolism |
| Enzymology | 3137869 | Methylcellulose inhibition of exo-beta-1,4-glucanase A from Ruminococcus flavefaciens FD-1. | White BA, Rasmussen MA, Gardner RM | Appl Environ Microbiol | 10.1128/aem.54.6.1634-1636.1988 | 1988 | Animals, Glucan 1,4-beta-Glucosidase, Glucosidases/*antagonists & inhibitors, Hydrolysis, Kinetics, Methylcellulose/metabolism/*pharmacology, Peptococcaceae/*enzymology, Surface-Active Agents/pharmacology, beta-Glucosidase/*antagonists & inhibitors | Metabolism |
| Pathogenicity | 3196962 | Analysis of antibiotic susceptibility and extrachromosomal DNA content of Ruminococcus albus and Ruminococcus flavefaciens. | Champion KM, Helaszek CT, White BA | Can J Microbiol | 10.1139/m88-196 | 1988 | DNA, Bacterial/*isolation & purification, *Drug Resistance, Microbial, Extrachromosomal Inheritance/*drug effects, Microbial Sensitivity Tests, Peptococcaceae/*drug effects/genetics | Enzymology |
| Metabolism | 3789721 | Effect of phenolic monomers on ruminal bacteria. | Borneman WS, Akin DE, VanEseltine WP | Appl Environ Microbiol | 10.1128/aem.52.6.1331-1339.1986 | 1986 | Animals, Bacteria/cytology/*growth & development/metabolism, Bacteroidaceae/cytology/*growth & development/metabolism, Benzaldehydes/metabolism/*pharmacology, Carboxylic Acids/metabolism/*pharmacology, Cattle, Cellulose/metabolism, Culture Media, Rumen/*microbiology | Cultivation |
| Phylogeny | 7527201 | The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production. | Odenyo AA, Mackie RI, Stahl DA, White BA | Appl Environ Microbiol | 10.1128/aem.60.10.3688-3696.1994 | 1994 | Animals, Bacteriocins/biosynthesis, Base Sequence, Cellobiose/metabolism, Colony Count, Microbial, Culture Media, DNA, Bacterial/genetics, Gram-Positive Cocci/*genetics/growth & development/metabolism, Molecular Probe Techniques, Molecular Sequence Data, Oligonucleotide Probes/*genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Species Specificity | Metabolism |
| Metabolism | 7527202 | The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: pure-culture studies with cellulose and alkaline peroxide-treated wheat straw. | Odenyo AA, Mackie RI, Stahl DA, White BA | Appl Environ Microbiol | 10.1128/aem.60.10.3697-3703.1994 | 1994 | Animals, Base Sequence, Cellulose/metabolism, Colony Count, Microbial, Culture Media, Dietary Fiber, Fermentation, Gram-Negative Anaerobic Bacteria/*genetics/growth & development/metabolism, Gram-Positive Cocci/*genetics/growth & development/metabolism, Hydrogen Peroxide, Molecular Probe Techniques, Molecular Sequence Data, Oligonucleotide Probes/*genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Triticum | Phylogeny |
| Enzymology | 7728654 | Nucleotide sequence and transcriptional analysis of the celD beta-glucanase gene from Ruminococcus flavefaciens FD-1. | Vercoe PE, Spight DH, White BA | Can J Microbiol | 10.1139/m95-004 | 1995 | Amino Acid Sequence, Bacterial Proteins/*genetics, Base Sequence, Cellulase/*genetics, Cloning, Molecular, Escherichia coli, *Genes, Bacterial, Molecular Sequence Data, Peptococcaceae/enzymology/*genetics, Recombinant Fusion Proteins/biosynthesis, Regulatory Sequences, Nucleic Acid, Sequence Alignment, Sequence Homology, Amino Acid, Transcription, Genetic | Genetics |
| Metabolism | 7958770 | The restriction endonuclease RflFII, isolated from Ruminococcus flavefaciens FD-1, recognizes the sequence 5'-AGTACT-3', and is inhibited by site-specific adenine methylation. | Morrison M, Mackie RI, White BA | FEMS Microbiol Lett | 10.1111/j.1574-6968.1994.tb07162.x | 1994 | Adenine/metabolism, Animals, Base Sequence, DNA Restriction Enzymes/antagonists & inhibitors/*genetics/*metabolism, DNA, Bacterial/genetics, Gram-Positive Cocci/*enzymology, Methylation, Rumen/*microbiology | Enzymology |
| Genetics | 8360615 | Transcriptional regulation of an endoglucanase and a cellodextrinase gene in Ruminococcus flavefaciens FD-1. | Wang W, Reid SJ, Thomson JA | J Gen Microbiol | 10.1099/00221287-139-6-1219 | 1993 | Amino Acid Sequence, *Bacterial Proteins, Base Sequence, Cellulase/*genetics/metabolism, DNA, Bacterial/genetics, Gene Expression Regulation, Bacterial, Genes, Bacterial, Gram-Positive Cocci/*enzymology/*genetics/growth & development, Molecular Sequence Data, Restriction Mapping, Substrate Specificity, Transcription, Genetic | Metabolism |
| Metabolism | 8434909 | Inhibition of ruminal cellulose fermentation by extracts of the perennial legume cicer milkvetch (Astragalus cicer). | Weimer PJ, Hatfield RD, Buxton DR | Appl Environ Microbiol | 10.1128/aem.59.2.405-409.1993 | 1993 | Animals, Cattle, Cellulose/*metabolism, Fabaceae/*chemistry, Fermentation/*drug effects, Gram-Negative Anaerobic Bacteria/*drug effects/metabolism, Gram-Positive Cocci/*drug effects/metabolism, Microscopy, Electron, Scanning, Plant Extracts/chemistry/pharmacology, *Plants, Medicinal, Rumen/*microbiology | Pathogenicity |
| Genetics | 8590402 | DNA sequence and transcriptional characterization of a beta-glucanase gene (celB) from Ruminococcus flavefaciens FD-1. | Vercoe PE, Finks JL, White BA | Can J Microbiol | 10.1139/m95-120 | 1995 | Amino Acid Sequence, Base Sequence, Cellulase/*genetics, Codon/genetics, Genes, Bacterial/*genetics, Gram-Positive Cocci/enzymology/*genetics, Molecular Sequence Data, RNA, Bacterial/biosynthesis, RNA, Messenger/biosynthesis, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Transcription, Genetic/*genetics | Transcriptome |
| Metabolism | 8597554 | Production of caproic acid by cocultures of ruminal cellulolytic bacteria and Clostridium kluyveri grown on cellulose and ethanol. | Kenealy WR, Cao Y, Weimer PJ | Appl Microbiol Biotechnol | 10.1007/s002530050590 | 1995 | Animals, Bacteroides/*metabolism, Butyrates/metabolism, Caproates/*metabolism, Cellulose/*metabolism, Clostridium/*metabolism, Culture Media, Ethanol/*metabolism, Hydrogen-Ion Concentration, Peptococcaceae/*metabolism, Rumen/*microbiology | Cultivation |
| Metabolism | 8975600 | Utilization of individual cellodextrins by three predominant ruminal cellulolytic bacteria. | Shi Y, Weimer PJ | Appl Environ Microbiol | 10.1128/aem.62.3.1084-1088.1996 | 1996 | Animals, Bacteroides/growth & development/*metabolism, Cellulose/*metabolism, Gram-Positive Cocci/growth & development/*metabolism, Kinetics, Rumen/metabolism/*microbiology | Enzymology |
| Phylogeny | 9023950 | Competition for cellulose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. | Shi Y, Odt CL, Weimer PJ | Appl Environ Microbiol | 10.1128/aem.63.2.734-742.1997 | 1997 | Animals, Bacterial Adhesion, Bacteroides/classification/genetics/*metabolism, Cellulose/*metabolism, Culture Media, Fatty Acids/analysis, Fermentation, Gram-Positive Cocci/classification/genetics/*metabolism, Microbiological Techniques, RNA, Ribosomal, 16S/genetics/isolation & purification, Rumen/*microbiology | Metabolism |
| Metabolism | 9023951 | Competition for cellobiose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. | Shi Y, Weimer PJ | Appl Environ Microbiol | 10.1128/aem.63.2.743-748.1997 | 1997 | Animals, Bacteroides/*metabolism, Cellobiose/*metabolism, Cellulose/metabolism, Culture Media, Gram-Positive Bacteria/*metabolism, Microbiological Techniques/instrumentation, Rumen/*microbiology | Cultivation |
| Metabolism | 9298188 | Formation of formate and hydrogen, and flux of reducing equivalents and carbon in Ruminococcus flavefaciens FD-1. | Shi Y, Weimer PJ, Ralph J | Antonie Van Leeuwenhoek | 10.1023/a:1000256221938 | 1997 | Acetates/*metabolism, Anaerobiosis, Bacterial Proteins/analysis/metabolism, Carbon Dioxide/metabolism, Cellobiose/metabolism, Cellulose/metabolism, Fermentation, Formates/*metabolism, Gram-Positive Cocci/enzymology/growth & development/*metabolism, Hydrogen/*metabolism, Hydrogen-Ion Concentration, Hydrogenase/metabolism, Lactic Acid/metabolism, Phosphoenolpyruvate/metabolism, Pyruvic Acid/metabolism, Succinic Acid/*metabolism | Enzymology |
| Metabolism | 9373931 | Production of succinate from glucose, cellobiose, and various cellulosic materials by the ruminal anaerobic bacteria Fibrobacter succinogenes and Ruminococcus flavefaciens. | Gokarn RR, Eiteman MA, Martin SA, Eriksson KE | Appl Biochem Biotechnol | 10.1007/BF02785981 | 1997 | Acetic Acid/metabolism, Animals, Bacteria, Anaerobic/*metabolism, Cellobiose/*metabolism, Cellulose/*metabolism, Fermentation, Formates/metabolism, Glucose/*metabolism, Rumen/*microbiology, Succinic Acid/*metabolism | Biotechnology |
| Metabolism | 11160797 | Competition among three predominant ruminal cellulolytic bacteria in the absence or presence of non-cellulolytic bacteria. | Chen J, Weimer P | Microbiology (Reading) | 10.1099/00221287-147-1-21 | 2001 | Animals, Bacteria/classification/genetics/*growth & development, Cellobiose/metabolism, Cellulose/*metabolism, Coculture Techniques, Culture Media, Rumen/*microbiology, Selenomonas/growth & development, Streptococcus bovis/growth & development | Cultivation |
| Enzymology | 12610723 | Characterization of the gene encoding glutamate dehydrogenase ( gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1. | Antonopoulos DA, Aminov RI, Duncan PA, White BA, Mackie RI | Arch Microbiol | 10.1007/s00203-002-0513-4 | 2003 | Amino Acid Sequence, Ammonia/metabolism, Animals, Base Sequence, Cloning, Molecular, DNA Primers/genetics, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic, *Genes, Bacterial, Glutamate Dehydrogenase/*genetics/metabolism, Gram-Positive Bacteria/*enzymology/*genetics, Molecular Sequence Data, Phylogeny, Rumen/microbiology, Ruminants | Metabolism |
| Metabolism | 12752804 | Differential protein phosphorylation-dephosphorylation in response to carbon source in Ruminococcus flavefaciens FD-1. | Vercoe PE, Kocherginskaya SA, White BA | J Appl Microbiol | 10.1046/j.1365-2672.2003.01929.x | 2003 | Autoradiography, Bacterial Proteins/*metabolism, Carbon/*metabolism, Cellobiose/metabolism, Cellulose/metabolism, Electrophoresis, Polyacrylamide Gel, Peptococcaceae/*metabolism, Phosphoamino Acids/analysis, Phosphorylation | Enzymology |
| Metabolism | 12819957 | Solid residues from Ruminococcus cellulose fermentations as components of wood adhesive formulations. | Weimer PJ, Conner AH, Lorenz LF | Appl Microbiol Biotechnol | 10.1007/s00253-003-1334-3 | 2003 | Adhesives/*metabolism, Cellulose/*metabolism, Fermentation, Ruminococcus/*metabolism, Wood | |
| Phylogeny | 14568141 | Phylogenetic reconstruction of Gram-positive organisms based on comparative sequence analysis of molecular chaperones from the ruminal microorganism Ruminococcus flavefaciens FD-1. | Antonopoulos DA, Russell WM, White BA | FEMS Microbiol Lett | 10.1016/S0378-1097(03)00597-4 | 2003 | Animals, Chaperonin 10/biosynthesis/*genetics, Chaperonin 60/biosynthesis/*genetics, DNA, Bacterial/analysis, *Gene Expression Regulation, Bacterial, Molecular Sequence Data, *Phylogeny, Rumen/microbiology, Ruminococcus/*classification/enzymology/genetics, Sequence Analysis, DNA | Transcriptome |
| Genetics | 15008812 | Strain-specific genomic regions of Ruminococcus flavefaciens FD-1 as revealed by combinatorial random-phase genome sequencing and suppressive subtractive hybridization. | Antonopoulos DA, Nelson KE, Morrison M, White BA | Environ Microbiol | 10.1111/j.1462-2920.2004.00576.x | 2004 | Base Sequence, Cellulase/genetics, DNA Transposable Elements, Databases, Nucleic Acid, Gene Library, *Genome, Bacterial, Molecular Sequence Data, *Nucleic Acid Hybridization, RNA, Ribosomal, 16S/analysis, Ruminococcus/classification/*genetics, *Sequence Analysis, DNA | Phylogeny |
| Metabolism | 15128585 | Albusin B, a bacteriocin from the ruminal bacterium Ruminococcus albus 7 that inhibits growth of Ruminococcus flavefaciens. | Chen J, Stevenson DM, Weimer PJ | Appl Environ Microbiol | 10.1128/AEM.70.5.3167-3170.2004 | 2004 | Amino Acid Sequence, Animals, Bacteriocins/chemistry/genetics/*metabolism/*pharmacology, Culture Media, Conditioned, Molecular Sequence Data, Rumen/*microbiology, Ruminococcus/*drug effects/genetics/growth & development/metabolism, Sequence Alignment, Sequence Analysis, DNA | Cultivation |
| 16347528 | Effects of Cellulolytic Ruminal Bacteria and of Cell Extracts on Germination of Euonymus americanus L. Seeds. | Howard GT, Elliott LP | Appl Environ Microbiol | 10.1128/aem.54.1.218-224.1988 | 1988 | |||
| 16348578 | Differential fermentation of cellulose allomorphs by ruminal cellulolytic bacteria. | Weimer PJ, French AD, Calamari TA | Appl Environ Microbiol | 10.1128/aem.57.11.3101-3106.1991 | 1991 | |||
| 16563536 | Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses. | Frey JC, Angert ER, Pell AN | J Microbiol Methods | 10.1016/j.mimet.2006.02.011 | 2006 | Bacteria/*genetics, *Bias, Butyrivibrio/genetics, DNA Fingerprinting/*methods, DNA, Bacterial/genetics, Fibrobacter/genetics, Polymerase Chain Reaction/methods, *Polymorphism, Restriction Fragment Length, RNA, Ribosomal/genetics, Ruminococcus/genetics, Streptococcus bovis/genetics | ||
| Metabolism | 16997963 | Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens. | Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, Berg ME, White BA, Bayer EA, Lamed R | J Bacteriol | 10.1128/JB.00973-06 | 2006 | Bacterial Proteins/*chemistry/*genetics, Cellulose/metabolism, Cellulosomes/*chemistry/*genetics/metabolism, Genes, Bacterial, Multigene Family, Phylogeny, Ruminococcus/*cytology/metabolism, Sequence Homology | Phylogeny |
| Phylogeny | 18564339 | Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens. | Jindou S, Brulc JM, Levy-Assaraf M, Rincon MT, Flint HJ, Berg ME, Wilson MK, White BA, Bayer EA, Lamed R, Borovok I | FEMS Microbiol Lett | 10.1111/j.1574-6968.2008.01234.x | 2008 | Animals, Bacterial Proteins/genetics, Cell Cycle Proteins/genetics, Cellulosomes/*genetics, Chromosomal Proteins, Non-Histone/genetics, DNA Primers/genetics, DNA, Bacterial/chemistry/genetics, DNA, Intergenic, DNA, Ribosomal/chemistry/genetics, Gene Order, *Genes, Bacterial, Molecular Sequence Data, *Multigene Family, Phylogeny, Polymerase Chain Reaction/methods, *Polymorphism, Genetic, Protein Structure, Tertiary, RNA, Ribosomal, 16S/genetics, Ruminococcus/*classification/*genetics, Sequence Analysis, DNA, Synteny | Genetics |
| Genetics | 19680555 | Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1. | Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA | PLoS One | 10.1371/journal.pone.0006650 | 2009 | Amino Acid Sequence, Biocatalysis, Cell Wall/*metabolism, Enzymes/chemistry/*metabolism, Gene Expression Profiling, Genome, Bacterial, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Open Reading Frames, Phylogeny, Reverse Transcriptase Polymerase Chain Reaction, Ruminococcus/*enzymology/genetics, Species Specificity | Phylogeny |
| Metabolism | 20814577 | Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1. | Rincon MT, Dassa B, Flint HJ, Travis AJ, Jindou S, Borovok I, Lamed R, Bayer EA, Henrissat B, Coutinho PM, Antonopoulos DA, Berg Miller ME, White BA | PLoS One | 10.1371/journal.pone.0012476 | 2010 | Amino Acid Sequence, Bacterial Proteins/chemistry/*classification/*metabolism, Carbohydrate Metabolism, Cell Cycle Proteins/chemistry/metabolism, Chromosomal Proteins, Non-Histone/chemistry/metabolism, Conserved Sequence, Gene Expression Regulation, Bacterial, Molecular Sequence Data, Ruminococcus/genetics/*metabolism | Genetics |
| Phylogeny | 21831789 | Development of a signature probe targeting the 16S-23S rRNA internal transcribed spacer of a ruminal Ruminococcus flavefaciens isolate from reindeer. | Praesteng KE, Mackie RI, Cann IK, Mathiesen SD, Sundset MA | Benef Microbes | 10.3920/BM2010.0044 | 2011 | Animals, Genetic Variation, Molecular Sequence Data, Oligonucleotide Probes, Probiotics/isolation & purification, RNA, Ribosomal/genetics, Reindeer/*microbiology, Rumen/*microbiology, Ruminococcus/*genetics/isolation & purification, Sequence Analysis, RNA | Genetics |
| Metabolism | 22112767 | Kinetic characterization of a glycoside hydrolase family 44 xyloglucanase/endoglucanase from Ruminococcus flavefaciens FD-1. | Warner CD, Go RM, Garcia-Salinas C, Ford C, Reilly PJ | Enzyme Microb Technol | 10.1016/j.enzmictec.2010.08.009 | 2010 | Biotechnology/*methods, Carbohydrate Metabolism, Carboxymethylcellulose Sodium/*metabolism, Catalytic Domain, Cellulase/chemistry/genetics/*metabolism, Cellulose/metabolism, Glucans/*metabolism, Glycoside Hydrolases/chemistry/classification/genetics/*metabolism, Kinetics, Ruminococcus/*enzymology/genetics, Substrate Specificity, Xylans/*metabolism | Enzymology |
| Metabolism | 22528314 | Expression patterns of Ruminococcus flavefaciens 007S cellulases as revealed by zymogram approach. | Vodovnik M, Marinsek Logar R | Folia Microbiol (Praha) | 10.1007/s12223-012-0144-3 | 2012 | Bacterial Proteins/chemistry/*genetics/metabolism, Cellobiose/metabolism, Cellulases/chemistry/*genetics/metabolism, Cellulose/metabolism, Enzyme Assays, Gene Expression, Molecular Sequence Data, Molecular Weight, Protein Structure, Tertiary, Ruminococcus/chemistry/*enzymology/genetics/growth & development | Genetics |
| Enzymology | 23653262 | Antimicrobial activity of Brazilian propolis extracts against rumen bacteria in vitro. | de Aguiar SC, Zeoula LM, Franco SL, Peres LP, Arcuri PB, Forano E | World J Microbiol Biotechnol | 10.1007/s11274-013-1361-x | 2013 | Animals, Anti-Bacterial Agents/chemistry/isolation & purification/*pharmacology, Bacteria/*drug effects/*growth & development/isolation & purification, Brazil, Chromatography, High Pressure Liquid, Phenols/chemistry/isolation & purification/*pharmacology, Propolis/*chemistry, Rumen/*microbiology | Phylogeny |
| Metabolism | 24992679 | Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. | Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, Duncan SH, Henrissat B, Coutinho P, Morrison M, Mosoni P, Yeoman CJ, White BA, Bayer EA | PLoS One | 10.1371/journal.pone.0099221 | 2014 | Bacterial Proteins/*genetics/metabolism, Cellulose/metabolism, Genome, Bacterial/*physiology, *Genome-Wide Association Study, Ruminococcus/classification/*genetics/metabolism | Genetics |
| Enzymology | 25084382 | Overexpression, crystallization and preliminary X-ray characterization of Ruminococcus flavefaciens scaffoldin C cohesin in complex with a dockerin from an uncharacterized CBM-containing protein. | Bule P, Ruimy-Israeli V, Cardoso V, Bayer EA, Fontes CM, Najmudin S | Acta Crystallogr F Struct Biol Commun | 10.1107/S2053230X14012667 | 2014 | Bacterial Proteins/*chemistry, Cell Cycle Proteins/*chemistry, Chromosomal Proteins, Non-Histone/*chemistry, Crystallization, Crystallography, X-Ray/*methods, Electrophoresis, Polyacrylamide Gel, Protein Binding, Ruminococcus/*chemistry | Genetics |
| Enzymology | 25484220 | Expression, purification and crystallization of a novel carbohydrate-binding module from the Ruminococcus flavefaciens cellulosome. | Venditto I, Centeno MS, Ferreira LM, Fontes CM, Najmudin S | Acta Crystallogr F Struct Biol Commun | 10.1107/S2053230X14024248 | 2014 | Amino Acid Sequence, Carbohydrates/*chemistry, Crystallization, Electrophoresis, Polyacrylamide Gel, Molecular Sequence Data, Ruminococcus/*chemistry | Genetics |
| Genetics | 25615967 | Crystallization and preliminary crystallographic studies of a novel noncatalytic carbohydrate-binding module from the Ruminococcus flavefaciens cellulosome. | Venditto I, Goyal A, Thompson A, Ferreira LM, Fontes CM, Najmudin S | Acta Crystallogr F Struct Biol Commun | 10.1107/S2053230X14025576 | 2015 | Amino Acid Sequence, Bacterial Proteins/*chemistry, Binding Sites, Cellulosomes/*chemistry, Crystallization, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, *Ruminococcus | |
| Enzymology | 26249681 | Purification and crystallographic studies of a putative carbohydrate-binding module from the Ruminococcus flavefaciens FD-1 endoglucanase Cel5A. | Pires AJ, Ribeiro T, Thompson A, Venditto I, Fernandes VO, Bule P, Santos H, Alves VD, Pires V, Ferreira LM, Fontes CM, Najmudin S | Acta Crystallogr F Struct Biol Commun | 10.1107/S2053230X15009784 | 2015 | Amino Acid Sequence, Bacterial Proteins/*chemistry/genetics, Catalytic Domain, Cellulase/*chemistry/genetics, Cloning, Molecular, Crystallization, Crystallography, X-Ray, Escherichia coli/genetics/metabolism, Gene Expression, Molecular Sequence Data, Protein Binding, Recombinant Proteins/chemistry/genetics, Ruminococcus/*chemistry/enzymology, Sequence Alignment | Genetics |
| Metabolism | 27028884 | Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium. | Zhao X, van der Donk WA | Cell Chem Biol | 10.1016/j.chembiol.2015.11.014 | 2016 | Amino Acid Sequence, Animals, Anti-Bacterial Agents/*chemistry/metabolism/*pharmacology, Bacteriocins/*chemistry/metabolism/*pharmacology, Biological Products/*chemistry/metabolism/pharmacology, Microbial Sensitivity Tests, Micrococcus luteus/drug effects, Molecular Structure, Peptides/*chemistry/metabolism/pharmacology, Protein Processing, Post-Translational, Ruminants, Ruminococcus/*metabolism, Sequence Alignment | Pathogenicity |
| Metabolism | 28186207 | Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. | Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Morais S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CM, Bayer EA | Sci Rep | 10.1038/srep42355 | 2017 | Amino Acid Sequence, Bacterial Proteins/chemistry/*metabolism, Cell Cycle Proteins/metabolism, Cellulose/metabolism, Cellulosomes/*metabolism, Chromosomal Proteins, Non-Histone/metabolism, Models, Biological, Phylogeny, Protein Array Analysis, *Protein Interaction Maps, Ruminococcus/*metabolism | Phylogeny |
| Metabolism | 29725056 | Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin-dockerin interaction. | Bule P, Pires VMR, Alves VD, Carvalho AL, Prates JAM, Ferreira LMA, Smith SP, Gilbert HJ, Noach I, Bayer EA, Najmudin S, Fontes CMGA | Sci Rep | 10.1038/s41598-018-25171-8 | 2018 | Bacterial Proteins/chemistry/*metabolism, Calorimetry, Carrier Proteins/chemistry/*metabolism, Cellulosomes/metabolism, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Protein Binding, Protein Conformation, *Protein Multimerization, Ruminococcus/*enzymology/metabolism | Enzymology |
| Enzymology | 31435842 | Molecular Cloning, Expression and Biochemical Characterization of a Family 5 Glycoside Hydrolase First Endo-Mannanase (RfGH5_7) from Ruminococcus flavefaciens FD-1 v3. | Goyal D, Kumar K, Centeno MSJ, Thakur A, Pires VMR, Bule P, Fontes CMGA, Goyal A | Mol Biotechnol | 10.1007/s12033-019-00205-2 | 2019 | Amino Acid Sequence/genetics, Cellulase/biosynthesis/chemistry/genetics/*metabolism, Cellulosomes/enzymology, Chelating Agents, Chromatography, Thin Layer, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics, Galactans/chemistry/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Kinetics, Mannans/chemistry/metabolism, Oligosaccharides/chemistry, Plant Gums/chemistry/metabolism, Ruminococcus/*enzymology/genetics, Substrate Specificity, Temperature, beta-Mannosidase/chemistry/genetics/*metabolism | Metabolism |
| Genetics | 33658330 | In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses. | Yeoman CJ, Fields CJ, Lepercq P, Ruiz P, Forano E, White BA, Mosoni P | mBio | 10.1128/mBio.03533-20 | 2021 | Age Factors, Animals, Female, Fibrobacter/*genetics/physiology, *Gene Expression Profiling, Germ-Free Life, Male, *Metagenome, Metagenomics, Microbial Interactions/*genetics, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Ruminococcus/*genetics/physiology, Sheep/microbiology | Phylogeny |
| Metabolism | 35421411 | Highly efficient, processive and multifunctional recombinant endoglucanase RfGH5_4 from Ruminococcus flavefaciens FD-1 v3 for recycling lignocellulosic plant biomasses. | Gavande PV, Nath P, Kumar K, Ahmed N, Fontes CMGA, Goyal A | Int J Biol Macromol | 10.1016/j.ijbiomac.2022.04.059 | 2022 | Biomass, Carboxymethylcellulose Sodium, *Cellulase/chemistry, Cellulose, Lignin, Ruminococcus, *Saccharum/metabolism, Substrate Specificity, Tegafur/analogs & derivatives |
Reference
| @id | authors | title | doi/url | journal | pubmed |
|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | ||
| 43397 | Kinchel C. Doerner , Gary T. Howard, Roderick I. Mackie and Bryan A. White | beta-Glucanase expression by Ruminococcus flavefaciens FD-1 | 10.1111/j.1574-6968.1992.tb05081.x | ||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | ||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |