Nocardia donostiensis

General Information

Nocardia donostiensis 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. This species is particularly interesting due to its clinical significance and its role in bioremediation. Nocardia donostiensis has been isolated from human clinical specimens, indicating its potential as an opportunistic pathogen. It is known to cause nocardiosis, a serious infection that can affect the lungs, brain, and skin, particularly in immunocompromised individuals. This makes it a subject of intense study in medical microbiology, as understanding its pathogenic mechanisms can lead to better diagnostic and therapeutic strategies. From an environmental perspective, Nocardia donostiensis is valuable due to its ability to degrade complex organic pollutants. This characteristic is harnessed in bioremediation efforts to clean up contaminated environments, such as soil and water bodies polluted with hydrocarbons and other persistent organic pollutants. The metabolic versatility of this organism is a key area of research, as it holds promise for developing sustainable methods to manage environmental pollution. In summary, Nocardia donostiensis is a microorganism of significant interest due to its dual role as a pathogen and a bioremediation agent. Its study not only advances our understanding of infectious diseases but also contributes to environmental science and engineering.

Nocardia donostiensis is a notable species within the genus Nocardia, which is known for its unique characteristics and significance in both environmental and clinical contexts. This actinobacterial species was first isolated from soil in the Basque region of Spain, highlighting its ecological niche and adaptability to terrestrial environments. What makes N. donostiensis particularly interesting is its ability to degrade complex organic compounds, which positions it as a potential candidate for bioremediation applications. Its metabolic versatility allows it to thrive in diverse habitats, contributing to nutrient cycling in ecosystems. From a clinical perspective, N. donostiensis has been associated with opportunistic infections, particularly in immunocompromised individuals. This underscores the importance of understanding its pathogenic potential and the mechanisms it employs to evade host defenses. The organism's unique lipid composition, including mycolic acids, contributes to its resilience and virulence, making it a subject of interest in medical microbiology. Furthermore, research into N. donostiensis can provide insights into the broader Nocardia genus, which includes species that are significant in both environmental microbiology and human health. The study of its genomic and metabolic pathways may reveal novel biotechnological applications, particularly in the fields of biodegradation and antibiotic production. Overall, Nocardia donostiensis stands out as a fascinating organism that bridges ecological and medical research, offering valuable opportunities for scientific exploration.

Taxonomy

Superkingdom: Bacteria

Phylum: Actinomycetota

Class: Actinomycetes

Order: Mycobacteriales

Family: Nocardiaceae

Genus: Nocardia

Species: Nocardia donostiensis

NCBI ID

1538463

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/081/795/GCF_002081795.1_ASM208179v1

File for sequence-based predictions:
GCF_002081795.1_ASM208179v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The organism Nocardia donostiensis is a member of the genus Nocardia, which is known for its role in human health and disease. It is primarily associated with pulmonary infections and can lead to opportunistic infections in immunocompromised individuals. The clinical implications of N. donostiensis include its potential to cause nocardiosis, a serious infection that can manifest as pneumonia, skin lesions, or disseminated disease affecting the central nervous system. This organism is particularly relevant in patients with underlying conditions such as HIV/AIDS, diabetes, or those undergoing immunosuppressive therapy. In terms of pathogenicity, N. donostiensis exhibits several strategies to evade the immune response, including the ability to survive and replicate within macrophages. This characteristic allows it to persist in the host and complicate treatment efforts. The organism's cell wall structure contributes to its virulence, making it resistant to phagocytosis. Furthermore, N. donostiensis has shown varying degrees of antimicrobial resistance, which poses challenges in clinical management. Resistance to common antibiotics, such as sulfonamides, has been documented, necessitating the use of alternative therapeutic options. While N. donostiensis is not commonly associated with outbreaks, its role as an opportunistic pathogen highlights the importance of early diagnosis and appropriate treatment in susceptible populations. Understanding the clinical implications of this organism is crucial for effective management of infections it may cause.

Habitat and Ecological Niches

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

Nocardia donostiensis is a species of actinobacteria commonly found in various soil environments and aquatic habitats. This microorganism thrives particularly well in nutrient-rich soils that are often disturbed or have been subjected to organic matter decomposition. Its presence is frequently noted in urban soils and agricultural fields, where it plays a significant role in the breakdown of complex organic materials, contributing to nutrient cycling and soil health. In terms of ecological interactions, Nocardia donostiensis is known for its ability to degrade pollutants, including hydrocarbons, which makes it an important player in bioremediation processes. This capability allows it to thrive in environments contaminated with organic pollutants, where it can help restore ecological balance. Additionally, this microorganism exhibits symbiotic relationships with various plants, aiding in nutrient uptake and enhancing plant growth. Its presence in the rhizosphere can promote a healthier plant microbiome, which is crucial for plant resilience against pathogens. Overall, Nocardia donostiensis is well-adapted to diverse terrestrial ecosystems and plays a vital role in maintaining ecological integrity through its interactions with both abiotic and biotic components of its environment.

Industrial Application

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

The microorganism Nocardia donostiensis has shown significant 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 a wide range of organic compounds, making it a valuable asset in biodegradation processes. Its enzymatic activity allows it to break down complex pollutants, which is particularly useful in the treatment of contaminated environments, such as soil and water. In the realm of waste management, Nocardia donostiensis can be employed in bioremediation strategies to clean up hazardous waste sites, especially those contaminated with hydrocarbons and other toxic substances. This capability not only helps in restoring ecological balance but also in recycling valuable resources from waste materials. Furthermore, the organism has been explored for its potential in biofuel production. Its metabolic pathways can be harnessed to convert organic waste into biofuels through fermentation processes, thus contributing to sustainable energy solutions. In pharmaceutical development, Nocardia donostiensis has been studied for its production of bioactive compounds, which may lead to the discovery of new antibiotics or other therapeutic agents. The unique metabolic capabilities of this microorganism make it a promising candidate for further research in drug development. Overall, Nocardia donostiensis exemplifies the versatility of microorganisms in addressing industrial challenges, particularly through its roles in biodegradation, bioremediation, and fermentation.

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: 9

LLM predicted phenotypes: 4

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

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