Yokenella regensburgei

General Information

Yokenella regensburgei is a fascinating microorganism that belongs to the family Enterobacteriaceae. This bacterium is particularly interesting due to its relatively recent discovery and the ongoing research into its ecological roles and potential clinical significance. One of the most intriguing aspects of Yokenella regensburgei is its ability to inhabit diverse environments, including soil, water, and various clinical settings. This adaptability suggests a versatile metabolic capacity, which could be valuable for biotechnological applications, such as bioremediation or the development of novel antimicrobial agents. Another notable feature of Yokenella regensburgei is its genetic makeup, which includes genes that may confer resistance to certain antibiotics. This characteristic is of significant interest to researchers studying antibiotic resistance mechanisms and the spread of resistant genes among bacterial populations. Understanding these mechanisms can help in developing strategies to combat antibiotic-resistant infections. Furthermore, Yokenella regensburgei has been isolated from various clinical specimens, indicating its potential role as an opportunistic pathogen. This aspect makes it a subject of interest in medical microbiology, particularly in understanding how it interacts with human hosts and other microorganisms in the microbiome. In summary, Yokenella regensburgei is a bacterium with unique ecological versatility, genetic traits related to antibiotic resistance, and potential clinical relevance, making it a valuable subject for ongoing research in multiple scientific fields.

Yokenella regensburgei is a fascinating bacterium that belongs to the family Neisseriaceae. This organism is particularly notable for its role in human health, as it has been isolated from clinical specimens, including cases of bacteremia and endocarditis. Its presence in these conditions highlights its potential as an opportunistic pathogen, making it a subject of interest in medical microbiology. One of the unique aspects of Yokenella regensburgei is its metabolic versatility. It is capable of utilizing a variety of substrates, which allows it to thrive in diverse environments, including the human body. This adaptability raises questions about its ecological niche and the mechanisms it employs to survive in different conditions. Furthermore, Yokenella regensburgei has been studied for its biochemical properties, particularly its ability to ferment certain carbohydrates. This characteristic can provide insights into the metabolic pathways that are active in this organism, contributing to our understanding of bacterial metabolism and its implications for human health. In addition to its clinical significance, Yokenella regensburgei serves as a model organism for studying the interactions between commensal and pathogenic bacteria. Research into this bacterium can shed light on the dynamics of microbial communities and the factors that influence pathogenicity. Overall, the study of Yokenella regensburgei is valuable not only for its implications in infectious diseases but also for its contributions to our understanding of microbial ecology and metabolism.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Enterobacteriaceae

Genus: Yokenella

Species: Yokenella regensburgei

NCBI ID

158877

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/109/195/GCA_012109195.1_ASM1210919v1

File for sequence-based predictions:
GCA_012109195.1_ASM1210919v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Yokenella regensburgei is a gram-negative, facultatively anaerobic rod that is part of the normal flora of the human gastrointestinal tract. However, it has been associated with various infections in immunocompromised patients, particularly in cases of bacteremia and endocarditis. Its clinical relevance is underscored by its ability to cause intra-abdominal infections and soft tissue infections, especially in individuals with underlying health conditions. Pathogenicity of Y. regensburgei is attributed to its capacity to evade the immune response, which may involve the production of biofilms and the ability to survive in hostile environments. This organism has been noted for its antimicrobial resistance, particularly to commonly used antibiotics, which complicates treatment options. Resistance mechanisms include the production of beta-lactamases, which can hydrolyze beta-lactam antibiotics, making infections difficult to manage. While Y. regensburgei is not commonly recognized as a primary pathogen, its role in polymicrobial infections highlights the importance of accurate identification in clinical microbiology. There are limited studies on its potential as a probiotic or therapeutic agent, but its presence in the gut microbiome suggests a complex interaction with human health that warrants further investigation. Overall, the clinical implications of Yokenella regensburgei emphasize the need for vigilance in monitoring its pathogenic potential and resistance patterns in clinical settings.

Habitat and Ecological Niches

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

Yokenella regensburgei is a gram-negative bacterium that is primarily associated with the human gastrointestinal tract and is known for its role in the microbiome. This organism thrives in the anaerobic environments of the intestines, where it contributes to the complex ecosystem of gut microbiota. Its presence is often linked to the breakdown of organic matter and the fermentation of carbohydrates, which are essential processes in maintaining gut health and nutrient absorption. In terms of ecological niches, Yokenella regensburgei plays a critical role in symbiosis with the host, aiding in digestion and the synthesis of certain vitamins. It can also interact with other microorganisms, contributing to the overall balance of the gut microbiome. This bacterium is particularly notable for its ability to adapt to varying conditions within the gut, such as changes in pH and the presence of competing microbial species. Furthermore, Yokenella regensburgei has been identified in clinical settings, where it may be associated with certain infections, indicating its potential role in pathogenic environments. Understanding its interactions within the gut ecosystem is crucial for insights into human health and disease management.

Industrial Application

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

The microorganism Yokenella regensburgei has shown potential in various industrial applications, particularly in the fields of biotechnology, waste management, and pharmaceutical development. This organism is known for its ability to participate in fermentation processes, which can be harnessed for the production of valuable metabolites and bioactive compounds. In the realm of biotechnology, Yokenella regensburgei can be utilized for the production of enzymes that are essential in various industrial processes. These enzymes can facilitate biodegradation of complex organic materials, making the organism valuable in waste management strategies aimed at reducing environmental pollution. Moreover, its metabolic pathways can be exploited for the production of biofuels, as the organism can convert organic substrates into energy-rich compounds through fermentation. This capability positions Yokenella regensburgei as a potential candidate for sustainable energy solutions. In pharmaceutical development, the unique metabolic products of Yokenella regensburgei may lead to the discovery of new drugs or therapeutic agents, particularly those that can combat antibiotic-resistant bacteria. The organism's role in enzyme production also opens avenues for the development of biocatalysts used in drug synthesis. Overall, Yokenella regensburgei presents a multifaceted opportunity for innovation across several industries, leveraging its natural capabilities for enhanced 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	google/gemini-flash-1.5	google/gemini-pro	meta-llama/llama-3-8b-instruct:nitro	mistralai/mixtral-8x7b-instruct:nitro	google/gemini-pro-1.5	anthropic/claude-3.5-sonnet	google/gemma-7b-it	google/palm-2-chat-bison-32k	perplexity/llama-3-sonar-small-32k-chat	openchat/openchat-7b	microsoft/phi-3-mini-128k-instruct	anthropic/claude-3-haiku:beta	mistralai/mistral-7b-instruct	mistralai/mistral-7b-instruct	openai/gpt-3.5-turbo-0125	openai/gpt-3.5-turbo-0125	openai/gpt-4	openai/gpt-4	openai/gpt-4o	openai/gpt-4o	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 ✓	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	true ✓	false ✗	false ✗	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 ✓	gram stain negative ✓	gram stain negative ✓	gram stain variable ✗	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 ✗	N/A	aerotolerant ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	N/A	N/A	N/A	N/A	N/A	N/A	aerotolerant ✗	aerotolerant ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	facultatively anaerobic ✗	N/A	N/A	N/A	N/A
Extreme environment tolerance	FALSE	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Biofilm formation	N/A	true	true	true	true	true	true	true	true	true	false	true	true	false	false	true	true	false	false	true	true	true	true	true	true
Animal pathogenicity	TRUE	true ✓	true ✓	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	true ✓	false ✗	false ✗	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	true ✓	true ✓
Biosafety level	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 2 ✓	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 2 ✓	biosafety level 2 ✓	biosafety level 1 ✗	biosafety level 1 ✗	biosafety level 2 ✓	biosafety level 2 ✓
Health association	N/A	true	true	false	true	true	true	true	true	true	false	false	true	true	true	false	false	true	true	true	true	true	true	true	true
Host association	FALSE	true ✗	true ✗	false ✓	true ✗	true ✗	true ✗	false ✓	true ✗	true ✗	false ✓	false ✓	true ✗	true ✗	true ✗	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗
Plant pathogenicity	N/A	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 ✓
Hemolysis	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	N/A	N/A	N/A	N/A
Cell shape	bacillus	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	coccus ✗	coccus ✗	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓	bacillus ✓

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