Nocardia coffeae

General Information

Nocardia coffeae is a fascinating microorganism belonging to the genus Nocardia, which is known for its complex life cycle and ability to degrade a wide range of organic compounds. One of the most intriguing aspects of Nocardia coffeae is its role in biodegradation and bioremediation. This species has been studied for its potential to break down pollutants, making it valuable for environmental cleanup efforts. Nocardia coffeae is also notable for its production of secondary metabolites, which have been found to possess antimicrobial properties. These compounds are of significant interest in the field of natural product research, as they may lead to the development of new antibiotics or other therapeutic agents. Additionally, Nocardia coffeae exhibits a unique filamentous structure, which is characteristic of the Nocardia genus. This structure allows it to form complex networks, which can be advantageous in various ecological niches. From a research perspective, Nocardia coffeae is valuable not only for its environmental applications but also for its potential contributions to medicine and biotechnology. Its ability to produce bioactive compounds and degrade environmental pollutants makes it a subject of ongoing scientific interest. Overall, Nocardia coffeae stands out due to its multifaceted applications and the potential benefits it offers in both environmental and medical fields.

Nocardia coffeae is a fascinating actinobacterium that has garnered attention due to its unique ecological niche and potential applications in biotechnology. This microorganism is primarily known for its role in the degradation of complex organic compounds, particularly in soil environments, where it contributes to nutrient cycling and organic matter decomposition. Its ability to degrade various aromatic compounds makes it a valuable organism for bioremediation efforts, especially in contaminated environments where pollutants such as pesticides and industrial waste are present. One of the most interesting aspects of Nocardia coffeae is its association with coffee plants, which has implications for agriculture and plant health. This organism has been isolated from coffee rhizospheres, suggesting a potential role in promoting plant growth or protecting against pathogens. This symbiotic relationship highlights the importance of microbial communities in agricultural ecosystems, particularly in enhancing crop resilience and productivity. From a research perspective, Nocardia coffeae serves as a model organism for studying the metabolic pathways involved in the degradation of complex organic molecules. Its genetic and enzymatic capabilities can provide insights into the mechanisms of biodegradation, which are crucial for developing sustainable waste management strategies. Furthermore, the study of Nocardia coffeae can lead to the discovery of novel enzymes that may have industrial applications in biocatalysis and environmental cleanup. In summary, Nocardia coffeae stands out not only for its ecological significance but also for its potential contributions to biotechnology and sustainable agriculture. Its unique characteristics make it a subject of interest for researchers aiming to harness microbial processes for environmental and agricultural benefits.

Taxonomy

Superkingdom: Bacteria

Phylum: Actinomycetota

Class: Actinomycetes

Order: Mycobacteriales

Family: Nocardiaceae

Genus: Nocardia

Species: Nocardia coffeae

NCBI ID

2873381

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/019/890/715/GCA_019890715.1_ASM1989071v1

File for sequence-based predictions:
GCA_019890715.1_ASM1989071v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The organism Nocardia coffeae is a member of the genus Nocardia, which is known for its role in human health and disease. It is primarily associated with opportunistic infections, particularly in immunocompromised individuals. Nocardia coffeae can cause pulmonary infections, cutaneous infections, and central nervous system infections, often leading to significant morbidity in affected patients. The organism is notable for its ability to evade the immune response through various mechanisms, including the production of mycolic acids that enhance its survival within macrophages. In terms of pathogenicity, Nocardia coffeae is less commonly reported than other Nocardia species, but it has been implicated in rare cases of nocardiosis, particularly in patients with underlying conditions such as HIV/AIDS, cancer, or those on immunosuppressive therapy. The clinical presentation can vary widely, making diagnosis challenging and often requiring advanced imaging and microbiological techniques. Furthermore, there are concerns regarding antimicrobial resistance in Nocardia species, including Nocardia coffeae. Resistance to common antibiotics can complicate treatment options, necessitating the use of more potent agents such as sulfonamides or imipenem. The emergence of resistant strains highlights the need for ongoing surveillance and research into effective therapeutic strategies. While Nocardia coffeae does not have established medical applications like probiotics or vaccines, understanding its role in human disease is crucial for improving clinical outcomes in affected patients. Awareness of this organism is essential for healthcare providers, especially in regions where it may be endemic or in populations at higher risk for nocardiosis.

Habitat and Ecological Niches

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

Nocardia coffeae is a soil-dwelling bacterium primarily associated with tropical and subtropical ecosystems. This microorganism thrives in well-drained soils that are rich in organic matter, often found in areas with high levels of rainfall and humidity. Its ecological niche is closely linked to the decomposition of organic materials, where it plays a crucial role in nutrient cycling and soil health. Tropical rainforests and coffee plantations are notable habitats where Nocardia coffeae is commonly found. In these environments, it contributes to the breakdown of complex organic compounds, facilitating the release of nutrients that are essential for plant growth. This bacterium is particularly significant in coffee-growing regions, where it can influence the health of coffee plants by enhancing soil fertility. In terms of interactions, Nocardia coffeae exhibits symbiotic relationships with various plant species, aiding in the establishment of healthy root systems. Its ability to form associations with plant roots can enhance nutrient uptake, particularly in nutrient-poor soils. Additionally, it has been observed to produce secondary metabolites that may provide protection against certain pathogens, thus playing a role in plant defense mechanisms. Overall, Nocardia coffeae is an important player in its biome, contributing to soil structure, nutrient availability, and plant health, making it a vital component of the ecosystems it inhabits.

Industrial Application

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

The microorganism Nocardia coffeae has shown potential in various industrial applications, particularly in the fields of biotechnology, waste management, and pharmaceutical development. This actinobacterium is known for its ability to degrade complex organic compounds, making it valuable in biodegradation processes. For instance, it can break down pollutants in contaminated soils and water, contributing to effective waste treatment strategies. In the realm of biofuel production, Nocardia coffeae has been studied for its capacity to metabolize certain substrates, which can be harnessed in fermentation processes to produce biofuels. Its enzymatic activity is particularly noteworthy, as it can produce enzymes that facilitate the breakdown of lignocellulosic biomass, a critical step in biofuel generation. Moreover, in pharmaceutical development, Nocardia coffeae has been explored for its potential to produce bioactive compounds, including antibiotics and other therapeutic agents. The organism's unique metabolic pathways may lead to the discovery of novel drugs, enhancing its significance in the pharmaceutical industry. Overall, Nocardia coffeae exemplifies a versatile microorganism with promising applications across multiple industrial sectors.

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: 8

LLM predicted phenotypes: 5

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

Back to Search