Yersinia proxima

General Information

Yersinia proxima is a bacterium that belongs to the genus Yersinia, which is well-known for including pathogens such as Yersinia pestis, the causative agent of the plague. However, Yersinia proxima is particularly interesting due to its close genetic relationship to other Yersinia species while being less virulent. This makes it a valuable subject for comparative genomic studies aimed at understanding the evolution of virulence factors within the genus. One of the unique aspects of Yersinia proxima is its environmental adaptability. Unlike some of its more notorious relatives, Yersinia proxima is often found in a variety of environmental samples, including soil and water, which suggests it has a broader ecological niche. This adaptability can provide insights into the mechanisms that allow bacteria to survive in diverse environments. From a research perspective, Yersinia proxima serves as a model organism for studying the genetic and molecular basis of pathogenicity and environmental survival. Its genome has been sequenced, revealing a wealth of information about the genes involved in these processes. Researchers can use this data to identify potential targets for antimicrobial development or to engineer bacteria with beneficial traits. In summary, Yersinia proxima is a fascinating organism due to its genetic proximity to more virulent Yersinia species, its environmental versatility, and its utility in scientific research aimed at understanding bacterial survival and pathogenicity mechanisms.

Yersinia proxima is a fascinating bacterium that belongs to the genus Yersinia, which is known for its pathogenic members, such as Yersinia pestis, the causative agent of plague. However, Y. proxima is notable for its unique ecological niche and its role in the microbiota of various animals, particularly in the gastrointestinal tracts of mammals. This organism has been isolated from a variety of sources, including animal feces and environmental samples, indicating its adaptability and potential role in nutrient cycling. One of the most interesting aspects of Y. proxima is its ability to survive in diverse environments, which makes it a valuable subject for studies on microbial ecology and evolution. Research has shown that it can thrive in both aerobic and anaerobic conditions, showcasing its metabolic versatility. This adaptability not only contributes to its survival but also provides insights into the evolutionary mechanisms that allow bacteria to colonize different habitats. Furthermore, Y. proxima has been studied for its potential interactions with other gut microbiota, which can have implications for understanding gut health and disease. Its presence in the gut may influence the overall microbial community structure, which is crucial for maintaining a balanced ecosystem within the host. In summary, Yersinia proxima stands out due to its ecological significance, metabolic flexibility, and potential implications for gut microbiome research, making it a valuable organism for further scientific exploration.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Yersiniaceae

Genus: Yersinia

Species: Yersinia proxima

NCBI ID

2890316

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/170/665/GCA_902170665.1_IP37838

File for sequence-based predictions:
GCA_902170665.1_IP37838_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The organism Yersinia proxima is a member of the Yersinia genus, which includes several species known for their clinical significance. While Y. proxima is less studied compared to its more notorious relatives like Yersinia pestis (the causative agent of plague), it has been associated with infections in humans, particularly in immunocompromised individuals. Clinical implications of Y. proxima include its potential role in gastrointestinal infections, where it may cause symptoms such as diarrhea and abdominal pain. The organism is often isolated from fecal samples, indicating its presence in the gut microbiota and its possible involvement in enteric diseases. In terms of pathogenicity, Y. proxima is believed to possess virulence factors similar to other Yersinia species, which may contribute to its ability to evade the immune response of the host. This includes mechanisms such as the secretion of virulence proteins that interfere with host cell signaling and promote bacterial survival within the host. Antimicrobial resistance is a growing concern with many bacterial pathogens, and while specific resistance patterns for Y. proxima are not extensively documented, its close relatives have shown varying degrees of antibiotic resistance. This raises the possibility that Y. proxima may also exhibit similar resistance mechanisms, complicating treatment options for infections it may cause. Currently, there are no known medical applications such as probiotics or vaccines specifically targeting Y. proxima. However, understanding its role in the human microbiome and its interactions with other gut flora could provide insights into its potential benefits or risks in human health. Further research is needed to fully elucidate the clinical relevance of Y. proxima and its implications in human disease.

Habitat and Ecological Niches

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

Yersinia proxima is a bacterium that is primarily associated with the gastrointestinal tract of various mammals, particularly in the context of its role as a commensal organism. This microorganism thrives in the intestinal environment, where it contributes to the complex microbial community that aids in digestion and nutrient absorption. Its presence is often linked to the microbiome of the host, playing a significant role in maintaining gut health and homeostasis. In terms of ecological niches, Yersinia proxima is commonly found in environments that are rich in organic matter, such as decaying plant material and animal waste. These habitats provide the necessary nutrients for its growth and reproduction. The bacterium is known to engage in nutrient cycling, breaking down complex organic compounds and contributing to soil fertility. Moreover, Yersinia proxima can exhibit symbiotic relationships with other microorganisms in the gut, enhancing the overall functionality of the microbiome. It may also interact with the host's immune system, potentially influencing immune responses and contributing to the host's health. Overall, Yersinia proxima is an important player in the microbial ecosystems of the gastrointestinal tract, showcasing its adaptability to various environments and its role in ecological balance.

Industrial Application

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

The microorganism Yersinia proxima has shown potential in various industrial applications, particularly in the fields of biotechnology and waste management. While traditionally known for its pathogenicity, recent studies have explored its capabilities in biodegradation processes, where it can break down complex organic compounds, making it useful in the treatment of contaminated environments. This ability to degrade pollutants can be harnessed in waste treatment facilities to improve the efficiency of waste management systems. In the realm of biotechnology, Yersinia proxima has been investigated for its potential in enzyme production, particularly enzymes that can catalyze reactions in industrial processes. These enzymes can be utilized in various applications, including the food industry for fermentation processes, where they may enhance the production of certain food products. Furthermore, the organism's metabolic pathways are of interest for biofuel production, as it may contribute to the conversion of biomass into biofuels through fermentation processes. This could provide a sustainable alternative to fossil fuels, aligning with global efforts to reduce carbon emissions. Overall, while Yersinia proxima is primarily recognized for its pathogenic traits, its emerging roles in biotechnology, waste management, and biofuel production highlight its potential as a valuable microorganism in various industrial sectors.

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: 8

LLM predicted phenotypes: 5

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

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