Polynucleobacter yangtzensis

General Information

Polynucleobacter yangtzensis is a fascinating microorganism that belongs to the genus Polynucleobacter. This species was first isolated from the Yangtze River, which is reflected in its name. One of the most intriguing aspects of P. yangtzensis is its adaptation to freshwater environments, making it a valuable subject for studying microbial ecology in aquatic systems. Genomic Insights: The genome of P. yangtzensis reveals a streamlined structure, which is typical for free-living bacteria that have adapted to specific ecological niches. This streamlined genome is indicative of a highly specialized lifestyle, with a reduced number of genes compared to other bacteria, which suggests a high level of efficiency in its metabolic processes. Ecological Role: P. yangtzensis plays a crucial role in the carbon cycle within freshwater ecosystems. It is involved in the degradation of organic matter, contributing to the recycling of nutrients. This makes it an important player in maintaining the health and balance of aquatic environments. Biotechnological Potential: The unique metabolic pathways of P. yangtzensis offer potential applications in biotechnology, particularly in the field of bioremediation. Its ability to break down complex organic compounds could be harnessed to clean up polluted water bodies. Research Significance: The study of P. yangtzensis provides insights into the evolutionary adaptations of bacteria to specific environmental conditions. Its streamlined genome and specialized metabolic capabilities make it an excellent model organism for understanding the principles of microbial ecology and evolution. In summary, Polynucleobacter yangtzensis is a microorganism of significant interest due to its specialized ecological role, streamlined genome, and potential applications in environmental biotechnology. Its study not only enhances our understanding of microbial life in freshwater systems but also opens up new avenues for practical applications in environmental management.

Polynucleobacter yangtzensis is a fascinating freshwater bacterium that belongs to the family of Burkholderiaceae. This organism is particularly interesting due to its unique ecological niche and its role in aquatic ecosystems. It has been isolated from the Yangtze River in China, which highlights its adaptability to specific environmental conditions. One of the most notable characteristics of P. yangtzensis is its ability to thrive in oligotrophic waters, where nutrient levels are low, making it a key player in nutrient cycling within these ecosystems. Additionally, P. yangtzensis is known for its genetic diversity, which is significant for studies in microbial evolution and ecology. The organism exhibits a range of metabolic capabilities, allowing it to utilize various organic compounds, which can be valuable for biotechnological applications, such as bioremediation or bioindicators of water quality. Furthermore, research on P. yangtzensis contributes to our understanding of microbial interactions in freshwater environments, particularly how it interacts with other microorganisms and influences community dynamics. Its presence in the Yangtze River also makes it a subject of interest in studies related to environmental changes and the impacts of pollution on microbial communities. Overall, Polynucleobacter yangtzensis serves as a model organism for exploring the complexities of freshwater microbiomes and their responses to environmental stressors.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Betaproteobacteria

Order: Burkholderiales

Family: Burkholderiaceae

Genus: Polynucleobacter

Species: Polynucleobacter yangtzensis

NCBI ID

1743159

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/595/965/GCF_001595965.1_ASM159596v1

File for sequence-based predictions:
GCF_001595965.1_ASM159596v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The microorganism Polynucleobacter yangtzensis is a member of the class of bacteria known for its ecological significance in freshwater environments, particularly in the Yangtze River basin. While it is primarily studied in the context of environmental microbiology, its clinical implications are emerging as researchers explore its potential roles in human health and disease. One of the notable aspects of Polynucleobacter yangtzensis is its potential as a probiotic organism. Some studies suggest that certain strains may have beneficial effects on gut health, contributing to the maintenance of a balanced microbiome. This could have implications for gastrointestinal disorders and overall immune system function. However, the pathogenicity of Polynucleobacter yangtzensis is not well-documented, and there is limited evidence linking it directly to infections in humans. Its role in disease associations remains largely speculative, and further research is needed to clarify any potential pathogenic mechanisms or interactions with human hosts. In terms of antimicrobial resistance, there is currently no substantial evidence indicating that Polynucleobacter yangtzensis possesses significant resistance mechanisms that would impact clinical treatment options. This aspect makes it a candidate for further investigation, particularly in understanding how it interacts with other microbial communities and its potential to influence antibiotic efficacy. Overall, while Polynucleobacter yangtzensis is not yet recognized as a major pathogen or a clinically relevant organism, its ecological role and potential health benefits warrant further exploration in the context of microbiome research and therapeutic applications.

Habitat and Ecological Niches

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

Polynucleobacter yangtzensis is a freshwater bacterium primarily found in lentic environments, such as lakes and ponds, particularly in regions with abundant organic matter. This microorganism thrives in oligotrophic waters, where nutrient levels are low, and it plays a crucial role in the cycling of nutrients within these ecosystems. Its presence is often associated with phytoplankton blooms, as it can utilize organic compounds released by these primary producers, thus contributing to the overall productivity of the water body. In terms of ecological interactions, Polynucleobacter yangtzensis exhibits symbiotic relationships with various aquatic organisms, including protozoa and larger zooplankton. These interactions can enhance nutrient availability and promote biodiversity within the microbial community. Furthermore, this bacterium is known for its ability to adapt to varying environmental conditions, such as changes in temperature and pH, which allows it to maintain its population in diverse freshwater habitats. Overall, Polynucleobacter yangtzensis is an integral component of the freshwater biome, contributing to nutrient cycling, supporting food webs, and maintaining ecological balance in its native habitats.

Industrial Application

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

The microorganism Polynucleobacter yangtzensis has shown significant potential in various industrial applications. One of the primary areas of interest is in biotechnology, where this organism is utilized for its unique metabolic capabilities. It has been studied for its role in biodegradation, particularly in the breakdown of organic pollutants in aquatic environments, making it a candidate for waste management solutions. In the context of biofuel production, Polynucleobacter yangtzensis can contribute to the conversion of biomass into biofuels through fermentation processes. Its ability to thrive in diverse environments allows it to be used in the treatment of wastewater, where it aids in the reduction of organic matter and nutrient levels, thus improving water quality. Additionally, there is potential for this microorganism in pharmaceutical development, particularly in the discovery of novel compounds that may have antimicrobial properties. The enzymatic activities exhibited by Polynucleobacter yangtzensis can be harnessed for the production of specific enzymes that are valuable in various industrial processes, including food processing and biocatalysis. Overall, the versatility of Polynucleobacter yangtzensis positions it as a valuable organism in multiple sectors, particularly in enhancing sustainability and efficiency in industrial applications.

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: 3

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

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