Empedobacter brevis

General Information

Empedobacter brevis is a fascinating microorganism that belongs to the family Flavobacteriaceae. One of the most intriguing aspects of E. brevis is its ability to produce a variety of bioactive compounds. These compounds have shown potential in antimicrobial and antifungal applications, making E. brevis a subject of interest in pharmaceutical research. Another unique feature of E. brevis is its production of proteolytic enzymes. These enzymes are capable of breaking down proteins, which has significant implications for industrial processes, including the production of detergents and the processing of food products. The organism's enzymatic activity is also being explored for its potential in bioremediation, where it could help in the degradation of environmental pollutants. From a genetic perspective, E. brevis has a relatively small genome, which makes it an attractive model for studying gene function and regulation. Its genetic makeup provides insights into the evolutionary pathways of the Flavobacteriaceae family and offers opportunities for genetic manipulation to enhance its beneficial properties. In summary, Empedobacter brevis stands out due to its bioactive compound production, proteolytic enzyme activity, and genetic tractability, making it a valuable organism for both applied and fundamental research.

Empedobacter brevis is a fascinating bacterium that belongs to the family of Comamonadaceae. This organism is particularly interesting due to its ability to thrive in diverse environments, including soil and aquatic ecosystems. One of the most notable characteristics of E. brevis is its capacity to degrade various organic compounds, which positions it as a potential candidate for bioremediation applications. This ability to metabolize complex organic substances makes it valuable in environmental microbiology, especially in the context of pollution management. Another unique aspect of Empedobacter brevis is its role in the nitrogen cycle. It has been observed to participate in nitrogen fixation, which is crucial for maintaining soil fertility and supporting plant growth. This characteristic not only highlights its ecological importance but also suggests potential agricultural applications, particularly in sustainable farming practices. Furthermore, E. brevis has been studied for its interactions with other microorganisms, contributing to our understanding of microbial communities and their dynamics. Research into these interactions can provide insights into ecosystem functioning and the development of microbial consortia for various biotechnological applications. Overall, Empedobacter brevis stands out as a microbe of significant interest for both environmental and agricultural research, showcasing the intricate relationships within microbial ecosystems.

Taxonomy

Superkingdom: Bacteria

Phylum: Bacteroidota

Class: Flavobacteriia

Order: Flavobacteriales

Family: Weeksellaceae

Genus: Empedobacter

Species: Empedobacter brevis

NCBI ID

247

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/834/475/GCF_009834475.1_ASM983447v1

File for sequence-based predictions:
GCF_009834475.1_ASM983447v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Empedobacter brevis is a Gram-negative organism that has been isolated from various environmental sources, including soil and water. While it is not commonly associated with human disease, its clinical relevance has been noted in specific contexts. Infections caused by Empedobacter brevis are rare but can occur, particularly in immunocompromised patients or those with underlying health conditions. The organism has been implicated in nosocomial infections, where it may act as an opportunistic pathogen. One of the significant concerns regarding Empedobacter brevis is its potential for antimicrobial resistance. Reports indicate that this organism can exhibit resistance to multiple classes of antibiotics, which complicates treatment options for infections. This resistance is often attributed to the presence of beta-lactamase enzymes, which can hydrolyze beta-lactam antibiotics, rendering them ineffective. In terms of its interaction with the human body, Empedobacter brevis may evade the immune response through various mechanisms, including biofilm formation, which protects it from phagocytosis and antibiotic action. This ability to form biofilms is particularly concerning in clinical settings, as it can lead to persistent infections, especially in indwelling medical devices. While Empedobacter brevis is not a primary pathogen, its role as an opportunistic pathogen in specific populations highlights the importance of monitoring its presence in clinical microbiology. Further research is needed to fully understand its pathogenic potential and the mechanisms behind its antimicrobial resistance.

Habitat and Ecological Niches

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

Empedobacter brevis is a bacterium commonly found in various aquatic environments, particularly in freshwater ecosystems such as rivers, lakes, and ponds. This microorganism thrives in nutrient-rich waters, where it plays a crucial role in the decomposition of organic matter, contributing to nutrient cycling within these ecosystems. Its ability to degrade complex organic compounds makes it an important player in maintaining the health of these habitats by facilitating the breakdown of pollutants and organic waste. In addition to its role in decomposition, Empedobacter brevis often exists in symbiotic relationships with other microorganisms, including algae and protozoa. These interactions can enhance nutrient availability and promote biodiversity within the microbial community. The presence of Empedobacter brevis can also indicate the overall quality of the water, as it is sensitive to changes in environmental conditions such as temperature and pollution levels. Furthermore, this bacterium exhibits remarkable environmental adaptability, allowing it to survive in varying conditions, including fluctuations in pH and salinity. Its resilience contributes to its widespread distribution in brackish waters and wetland areas, where it continues to play a vital role in the ecosystem by supporting the food web and influencing biogeochemical cycles.

Industrial Application

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

The microorganism Empedobacter brevis has shown significant potential in various industrial applications. One of the primary areas of interest is in biotechnology, where Empedobacter brevis is utilized for its ability to produce specific enzymes that can be harnessed in biocatalysis processes. These enzymes can facilitate chemical reactions under mild conditions, making them valuable in the production of pharmaceuticals and other fine chemicals. In the realm of waste management, Empedobacter brevis has demonstrated capabilities in biodegradation, particularly in the breakdown of complex organic compounds. This property is crucial for the treatment of wastewater and the remediation of contaminated environments, as the organism can help in the detoxification of pollutants, thereby contributing to more sustainable waste management practices. Furthermore, there is growing interest in the use of Empedobacter brevis in biofuel production. The organism's metabolic pathways can be exploited to convert biomass into biofuels through fermentation processes, potentially leading to more efficient and environmentally friendly energy sources. In summary, Empedobacter brevis is a versatile microorganism with applications spanning biotechnology, waste management, and biofuel production, showcasing its importance in modern industrial processes.

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

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