Shewanella profunda

General Information

Shewanella profunda is a fascinating microorganism primarily due to its ability to thrive in deep-sea environments. This bacterium was originally isolated from deep-sea sediments, which highlights its adaptation to extreme conditions such as high pressure and low temperatures. One of the most intriguing aspects of S. profunda is its versatile metabolic capabilities. It can utilize a wide range of electron acceptors, including nitrate, nitrite, and various metal oxides, making it a key player in biogeochemical cycles, particularly in the reduction of metal ions. Another remarkable feature of Shewanella profunda is its potential for bioremediation. Its ability to reduce toxic metals like uranium and chromium to less harmful forms makes it a valuable candidate for cleaning up contaminated environments. Additionally, the bacterium's genomic and proteomic profiles have been extensively studied, providing insights into the molecular mechanisms underlying its adaptability and metabolic diversity. From a research perspective, S. profunda serves as an excellent model organism for studying microbial life in extreme environments and the mechanisms of metal reduction. Its unique properties not only contribute to our understanding of deep-sea microbial ecology but also offer practical applications in environmental biotechnology.

Shewanella profunda is a fascinating marine bacterium that has garnered attention for its unique metabolic capabilities and ecological significance. This organism is known for its ability to reduce a variety of metal ions, including iron and manganese, which plays a crucial role in biogeochemical cycling in marine environments. Its capacity to utilize a wide range of electron acceptors makes it a model organism for studying anaerobic respiration. One of the most interesting aspects of S. profunda is its ability to thrive in extreme conditions, such as high-pressure environments found in deep-sea ecosystems. This adaptability not only highlights the organism's resilience but also provides insights into the potential for life in extreme habitats, which is valuable for astrobiology research. Additionally, S. profunda has been studied for its potential applications in bioremediation, particularly in the detoxification of heavy metals and organic pollutants. The organism's unique electron transfer mechanisms and metabolic pathways could be harnessed for environmental cleanup efforts, making it a valuable asset in the field of environmental microbiology. Furthermore, the genomic and proteomic studies of S. profunda have revealed a wealth of information about its metabolic versatility and evolutionary adaptations, contributing to our understanding of microbial diversity and evolution in extreme environments. Overall, Shewanella profunda stands out as a remarkable organism with significant implications for both ecological research and practical applications in biotechnology.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Alteromonadales

Family: Shewanellaceae

Genus: Shewanella

Species: Shewanella profunda

NCBI ID

254793

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/283/765/GCA_023283765.1_ASM2328376v1

File for sequence-based predictions:
GCA_023283765.1_ASM2328376v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The organism Shewanella profunda is a gram-negative bacterium that has garnered attention due to its potential clinical implications. It is primarily known for its role in infections associated with marine environments, particularly in individuals with compromised immune systems or those with open wounds exposed to seawater. Clinical cases have reported S. profunda as a pathogen in soft tissue infections, particularly in patients with underlying health conditions such as diabetes or liver disease. One of the notable aspects of S. profunda is its ability to thrive in anaerobic conditions, which can complicate diagnosis and treatment of infections. The organism exhibits pathogenicity through its production of various virulence factors, including enzymes that can degrade host tissues, facilitating its spread. In terms of antimicrobial resistance, S. profunda has shown resistance to multiple classes of antibiotics, which poses a significant challenge in clinical settings. This resistance is often attributed to its genetic adaptability and the presence of efflux pumps that can expel antimicrobial agents, making infections difficult to treat. Despite its pathogenic potential, S. profunda is also studied for its bioremediation capabilities and its role in the marine ecosystem, where it contributes to the cycling of nutrients. However, its clinical relevance cannot be overlooked, especially in the context of outbreaks linked to exposure to contaminated water. Understanding the interactions of S. profunda with the human body, including its immune evasion strategies, is crucial for developing effective therapeutic approaches and preventive measures against infections.

Industrial Application

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

The microorganism Shewanella profunda has shown significant potential in various industrial applications due to its unique metabolic capabilities. One of the most notable areas is in biotechnology, where Shewanella profunda is utilized in bioremediation processes. This organism can reduce metal ions, such as iron and manganese, which is crucial for the detoxification of contaminated environments. Its ability to transfer electrons to metals makes it a valuable agent in the cleanup of heavy metal pollutants in soil and water. In the realm of biofuel production, Shewanella profunda is recognized for its role in fermentation processes that convert organic substrates into biofuels. The organism can utilize a variety of carbon sources, including complex organic materials, to produce hydrogen gas, which is a clean energy carrier. This capability is particularly important in the development of sustainable energy solutions. Furthermore, Shewanella profunda has applications in pharmaceutical development. Its enzymatic activities are being explored for the production of bioactive compounds, which can lead to the discovery of new drugs. The organism's ability to produce specific enzymes can facilitate the synthesis of complex organic molecules, making it a candidate for use in enzyme production. Additionally, Shewanella profunda is involved in waste management through its capacity for biodegradation. It can break down organic waste materials, contributing to waste treatment processes and enhancing the efficiency of composting systems. This not only helps in reducing waste but also in recycling nutrients back into the ecosystem. Overall, Shewanella profunda demonstrates a multifaceted potential across various industries, making it a significant microorganism for future research and application in sustainable practices.

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: 10

LLM predicted phenotypes: 3

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

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