Rhodococcus ruber

General Information

Rhodococcus ruber is a fascinating microorganism known for its remarkable metabolic versatility and biodegradation capabilities. This bacterium is part of the genus Rhodococcus, which is renowned for its ability to degrade a wide range of organic compounds, including pollutants and xenobiotics. One of the most intriguing aspects of R. ruber is its potential in bioremediation. It has been shown to degrade various hydrocarbons, making it a valuable candidate for cleaning up oil spills and other environmental contaminants. Additionally, R. ruber can metabolize complex polymers, such as polyethylene, which is a common plastic. This ability positions R. ruber as a potential player in addressing plastic pollution, a significant environmental challenge. From a research perspective, R. ruber is also interesting due to its genetic and enzymatic diversity. The bacterium possesses a wide array of enzymes that enable it to break down complex molecules. These enzymes are of great interest for industrial applications, including the synthesis of fine chemicals and pharmaceuticals. Moreover, R. ruber has been studied for its role in the production of bioactive compounds. It can produce various secondary metabolites with potential antimicrobial and anticancer properties, making it a subject of interest in drug discovery and development. In summary, Rhodococcus ruber stands out due to its environmental and industrial significance, biodegradation capabilities, and potential in biotechnological applications. Its ability to tackle environmental pollutants and contribute to sustainable practices makes it a valuable organism for ongoing and future research.

Rhodococcus ruber is a fascinating bacterium known for its remarkable metabolic versatility and ability to degrade a wide range of organic compounds, including pollutants. This organism is particularly interesting due to its capacity to break down complex hydrocarbons, making it a valuable candidate for bioremediation applications. Its enzymatic pathways allow it to utilize various carbon sources, which can include aromatic compounds, aliphatic hydrocarbons, and even some xenobiotics. This adaptability not only highlights its ecological significance but also positions it as a potential tool in environmental cleanup efforts. Another unique aspect of Rhodococcus ruber is its ability to produce a variety of secondary metabolites, some of which have been shown to possess antimicrobial properties. This characteristic opens avenues for research into natural product chemistry and the development of new antibiotics. The potential for discovering novel compounds from this organism underscores its importance in pharmaceutical research. Additionally, Rhodococcus ruber has been studied for its role in the degradation of plastics, particularly polycyclic aromatic hydrocarbons (PAHs), which are notorious environmental pollutants. Its enzymatic systems are of great interest for biotechnological applications aimed at developing sustainable methods for waste management and pollution reduction. The ongoing research into its metabolic pathways could lead to innovative strategies for tackling environmental challenges. Overall, Rhodococcus ruber stands out not only for its ecological roles but also for its potential contributions to biotechnology and environmental science, making it a subject of significant interest in microbial research.

Taxonomy

Superkingdom: Bacteria

Phylum: Actinomycetota

Class: Actinomycetes

Order: Mycobacteriales

Family: Nocardiaceae

Genus: Rhodococcus

Species: Rhodococcus ruber

NCBI ID

1830

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/016/804/345/GCA_016804345.1_ASM1680434v1

File for sequence-based predictions:
GCA_016804345.1_ASM1680434v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

Source: gpt-4o-mini-2024-07-18

The microorganism Rhodococcus ruber is a gram-positive bacterium known for its environmental versatility and potential clinical implications. It is primarily recognized for its role in biodegradation processes, but it has also been associated with infections in humans, particularly in immunocompromised individuals. Clinical cases have reported Rhodococcus ruber as a pathogen in patients with underlying conditions, leading to pneumonia, skin infections, and sepsis. The organism's ability to survive in harsh environments contributes to its pathogenicity, as it can evade the immune response through various mechanisms, including biofilm formation and the production of virulence factors. In terms of antimicrobial resistance, Rhodococcus ruber has shown resistance to multiple antibiotics, complicating treatment options for infections. This resistance is often attributed to its intrinsic mechanisms and the acquisition of resistance genes, making it a concern in clinical settings. Interestingly, Rhodococcus ruber has also been explored for its potential medical applications, particularly in the field of biotechnology and environmental health. Its metabolic capabilities may be harnessed for the development of probiotics or as a biocontrol agent in agricultural settings. However, its dual role as both a beneficial and pathogenic organism underscores the need for further research to fully understand its implications in human health and disease.

Habitat and Ecological Niches

Source: gpt-4o-mini-2024-07-18

Rhodococcus ruber is a versatile bacterium commonly found in a variety of terrestrial and aquatic environments. This microorganism thrives in soil ecosystems, particularly in areas rich in organic matter, where it plays a crucial role in the degradation of complex organic compounds. Its ability to metabolize a wide range of substrates, including hydrocarbons, makes it an important player in bioremediation processes, where it helps to detoxify polluted environments, such as oil spills and contaminated soils. In addition to its presence in soil, Rhodococcus ruber can also be found in freshwater habitats, where it contributes to nutrient cycling and organic matter decomposition. This bacterium exhibits a remarkable ability to adapt to varying environmental conditions, including changes in pH, temperature, and the presence of toxic compounds, which allows it to thrive in extreme environments. Furthermore, Rhodococcus ruber engages in symbiotic relationships with plants, enhancing their growth by promoting nutrient availability in the soil. Its interactions with other microorganisms in the soil microbiome are also significant, as it can influence microbial community dynamics and contribute to overall soil health. Overall, Rhodococcus ruber is a key organism in maintaining the ecological balance within its habitats, showcasing its importance in both natural and anthropogenically affected environments.

Industrial Application

Source: gpt-4o-mini-2024-07-18

The microorganism Rhodococcus ruber has shown significant potential in various industrial applications due to its versatile metabolic capabilities. One of the most notable areas is in biotechnology, where Rhodococcus ruber is utilized for its ability to perform biodegradation of complex organic compounds, including pollutants such as hydrocarbons and pesticides. This makes it a valuable agent in waste management, particularly in the bioremediation of contaminated soils and water, where it can effectively break down toxic substances into less harmful products. In the realm of biofuel production, Rhodococcus ruber has been explored for its capacity to convert lignocellulosic biomass into fermentable sugars, which can subsequently be transformed into bioethanol. The organism's enzymatic activity is crucial in this process, as it produces various enzymes that facilitate the breakdown of plant materials. Furthermore, Rhodococcus ruber has applications in pharmaceutical development. It is known to participate in the biotransformation of certain compounds, which can lead to the synthesis of valuable pharmaceuticals and intermediates. This biocatalytic ability allows for more environmentally friendly and efficient production methods compared to traditional chemical synthesis. Overall, the diverse metabolic pathways and enzymatic capabilities of Rhodococcus ruber position it as a key player in several industries, particularly in processes involving fermentation, biodegradation, and enzyme production, making it a microorganism of great interest for future industrial applications.

Phenotypes and Predictions

The table shows the phenotypes and predictions. Cell colors indicate the class of the value. When literature-based data is available, a checkmark (✓) indicates a correct prediction, while an ✗ indicates an incorrect prediction.

Literature-based phenotypes: 11

LLM predicted phenotypes: 2

Phenotype	High-quality annotation	meta-llama/llama-3-70b-instruct:nitro	google/gemini-flash-1.5	google/gemini-pro-1.5	google/gemini-pro	mistralai/mistral-7b-instruct	mistralai/mixtral-8x7b-instruct:nitro	perplexity/llama-3-sonar-small-32k-chat	openchat/openchat-7b	openai/gpt-3.5-turbo-0125	openai/gpt-3.5-turbo-0125	meta-llama/llama-3-8b-instruct:nitro	meta-llama/llama-3-8b-instruct:nitro	openai/gpt-4	openai/gpt-4	microsoft/wizardlm-2-8x22b	microsoft/wizardlm-2-8x22b	openai/gpt-4o	openai/gpt-4o	anthropic/claude-3.5-sonnet	anthropic/claude-3.5-sonnet	google/gemma-7b-it	google/gemma-7b-it	google/palm-2-chat-bison-32k	google/palm-2-chat-bison-32k	microsoft/phi-3-mini-128k-instruct	microsoft/phi-3-mini-128k-instruct	anthropic/claude-3-haiku:beta	anthropic/claude-3-haiku:beta
Motility	FALSE	true ✗	false ✓	true ✗	true ✗	false ✓	false ✓	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗	false ✓	false ✓
Gram staining	gram stain positive	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain negative ✗	N/A	gram stain positive ✓	N/A	gram stain variable ✗	N/A	gram stain positive ✓
Aerophilicity	aerobic	aerobic ✓	N/A	aerobic ✓	N/A	N/A	N/A	N/A	N/A	aerobic ✓	aerobic ✓	aerotolerant ✗	aerotolerant ✗	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Extreme environment tolerance	TRUE	true ✓	true ✓	true ✓	false ✗	true ✓	true ✓	true ✓	false ✗	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓
Biofilm formation	TRUE	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓
Animal pathogenicity	FALSE	false ✓	true ✗	false ✓	true ✗	false ✓	false ✓	true ✗	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Biosafety level	biosafety level 1	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 2 ✗
Health association	N/A	true	true	true	true	false	true	true	false	false	false	true	true	false	false	true	true	false	false	false	false	true	true	true	true	false	false	true	true
Host association	FALSE	true ✗	true ✗	false ✓	true ✗	true ✗	true ✗	true ✗	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗
Plant pathogenicity	FALSE	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Spore formation	FALSE	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Hemolysis	N/A	N/A	gamma	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Cell shape	bacillus	bacillus ✓	coccus ✗	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	bacillus ✓	coccus ✗	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	coccus ✗	coccus ✗	coccus ✗	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	coccus ✗	bacillus ✓	bacillus ✓

Back to Search