Pantoea coffeiphila

General Information

Pantoea coffeiphila is a fascinating microorganism that has garnered attention due to its association with coffee plants. This bacterium was first isolated from the phyllosphere of coffee plants, which refers to the above-ground parts of the plant, such as leaves and stems. One of the most intriguing aspects of Pantoea coffeiphila is its potential role in the plant microbiome, where it may contribute to plant health and growth. Research has shown that Pantoea coffeiphila can produce a variety of bioactive compounds, including antibiotics and plant growth-promoting substances. These compounds can help protect the coffee plant from pathogens and enhance its growth, making Pantoea coffeiphila a candidate for use in sustainable agriculture practices. Additionally, Pantoea coffeiphila has been studied for its ability to degrade complex carbohydrates. This capability is particularly valuable in the context of biotechnological applications, where the bacterium could be used in the breakdown of agricultural waste products or in the production of biofuels. The genetic makeup of Pantoea coffeiphila also offers a wealth of information for researchers. Its genome contains numerous genes associated with metabolic versatility, allowing it to thrive in various environmental conditions. This adaptability makes it an excellent model organism for studying microbial ecology and evolution. In summary, Pantoea coffeiphila is a microorganism of significant interest due to its potential applications in agriculture, biotechnology, and environmental science. Its ability to produce bioactive compounds, degrade complex carbohydrates, and adapt to different environments underscores its value in both research and practical applications.

Pantoea coffeiphila is a fascinating bacterium primarily associated with coffee plants, particularly in the context of coffee wilt disease. This organism is notable for its role in the plant microbiome, where it can influence plant health and disease resistance. One of the most interesting aspects of P. coffeiphila is its ability to produce plant growth-promoting substances, which can enhance the growth and yield of coffee plants. This characteristic makes it a valuable candidate for research in sustainable agriculture and biocontrol strategies against plant pathogens. Additionally, P. coffeiphila has been studied for its potential in bioremediation, particularly in the degradation of environmental pollutants. Its metabolic versatility allows it to thrive in various environments, making it a subject of interest for researchers looking to harness its capabilities for environmental cleanup. Furthermore, the genomic analysis of P. coffeiphila has revealed insights into its evolutionary adaptations and interactions with host plants. This research can provide a deeper understanding of plant-microbe interactions, which is crucial for developing innovative agricultural practices. Overall, Pantoea coffeiphila stands out not only for its ecological significance but also for its potential applications in agriculture and environmental science.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Erwiniaceae

Genus: Pantoea

Species: Pantoea coffeiphila

NCBI ID

1465635

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/976/475/GCF_002976475.1_ASM297647v1

File for sequence-based predictions:
GCF_002976475.1_ASM297647v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The microorganism Pantoea coffeiphila is primarily known for its association with coffee plants, but it has also been implicated in various clinical contexts. Clinical relevance of Pantoea coffeiphila includes its potential role as an opportunistic pathogen, particularly in immunocompromised individuals. It has been isolated from infections in humans, including cases of bacteremia and wound infections, highlighting its pathogenic potential. The organism is known to exhibit antimicrobial resistance, particularly to common antibiotics, which complicates treatment options for infections caused by this bacterium. Its ability to evade the immune response may be attributed to its biofilm-forming capabilities, which can protect it from phagocytosis and antibiotic action. Furthermore, Pantoea coffeiphila has been studied for its potential applications in biotechnology, including its use in biocontrol and as a plant growth-promoting agent, which may indirectly influence human health through agricultural practices. Overall, while Pantoea coffeiphila is not a common pathogen, its presence in clinical settings warrants attention due to its potential for causing infections and its implications for antimicrobial resistance.

Habitat and Ecological Niches

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

Pantoea coffeiphila is primarily associated with the tropical and subtropical regions, particularly in areas where coffee plants (Coffea spp.) are cultivated. This bacterium is often found in the rhizosphere of coffee plants, where it plays a crucial role in promoting plant health and growth. Its presence in the soil enhances nutrient availability and can improve the overall resilience of coffee crops against various stresses, including drought and disease. In addition to its role in the rhizosphere, Pantoea coffeiphila is also known to inhabit the phyllosphere, the leaf surface of coffee plants. Here, it can engage in beneficial interactions with the plant, such as nitrogen fixation and the production of plant growth-promoting substances. These interactions are vital for maintaining the health of coffee plants, especially in the face of environmental challenges. Furthermore, Pantoea coffeiphila exhibits symbiotic relationships with other microorganisms in the soil, contributing to a diverse microbial community that supports the overall health of the ecosystem. Its ability to adapt to varying soil conditions and its role in nutrient cycling underscore its importance in the agricultural biome where coffee is grown. Overall, Pantoea coffeiphila is a key player in the health and productivity of coffee plantations, making it an essential organism in these specific biomes.

Industrial Application

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

The microorganism Pantoea coffeiphila has shown significant potential in various industrial applications. One of the primary areas of interest is in biotechnology, where Pantoea coffeiphila is utilized for its ability to promote plant growth and enhance crop yields, particularly in coffee plants. This is achieved through its biological nitrogen fixation capabilities, which improve soil fertility and nutrient availability. In the realm of waste management, Pantoea coffeiphila has been studied for its role in biodegradation processes. It can effectively break down organic waste materials, contributing to the reduction of environmental pollutants and the enhancement of composting processes. This makes it a valuable organism in the development of sustainable waste treatment solutions. Furthermore, Pantoea coffeiphila has potential applications in biofuel production. Its metabolic pathways can be harnessed to convert biomass into biofuels through fermentation processes, thereby contributing to renewable energy sources and reducing reliance on fossil fuels. In pharmaceutical development, research has indicated that Pantoea coffeiphila may produce bioactive compounds with antimicrobial properties, which could be explored for the development of new drugs or therapeutic agents. This highlights its importance in the field of natural product chemistry. Overall, Pantoea coffeiphila demonstrates versatility across multiple industries, making it a promising candidate for further research and application in sustainable practices and innovative technologies.

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

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