Xenorhabdus nematophila

General Information

Xenorhabdus nematophila is a fascinating bacterium primarily known for its symbiotic relationship with entomopathogenic nematodes of the genus Steinernema. This relationship is particularly interesting because it involves a mutualistic partnership where the bacterium and the nematode work together to infect and kill insect hosts. This makes X. nematophila a valuable organism in biological control and pest management. One of the most unique aspects of X. nematophila is its ability to produce a wide array of secondary metabolites, including antibiotics, bacteriocins, and insecticidal toxins. These compounds not only help in suppressing the immune response of the insect host but also inhibit the growth of competing microorganisms, ensuring a favorable environment for both the bacterium and the nematode. Additionally, X. nematophila exhibits a complex life cycle that includes both a symbiotic phase within the nematode and a pathogenic phase within the insect host. During the symbiotic phase, the bacterium resides in a specialized vesicle in the nematode's gut, where it is protected and nourished. Upon release into the insect hemocoel, X. nematophila rapidly proliferates, producing toxins and enzymes that contribute to the insect's death. From a research perspective, X. nematophila is also notable for its genetic tractability. The bacterium's genome has been sequenced, and various genetic tools have been developed to manipulate its genes, making it an excellent model organism for studying host-microbe interactions, symbiosis, and pathogenesis. In summary, Xenorhabdus nematophila is a bacterium of significant interest due to its symbiotic relationship with nematodes, its production of bioactive compounds, and its utility in biological control. Its complex life cycle and genetic tractability further enhance its value as a model organism in scientific research.

Xenorhabdus nematophila is a fascinating bacterium that forms a symbiotic relationship with entomopathogenic nematodes, particularly those of the genus Steinernema. This unique association allows X. nematophila to thrive in the insect host environment, where it plays a crucial role in the nematode's lifecycle. The bacterium is known for its ability to produce a variety of bioactive compounds, including antibiotics and insecticidal proteins, which contribute to its effectiveness in killing insect hosts. This characteristic makes X. nematophila a valuable organism in biological pest control, offering an environmentally friendly alternative to chemical pesticides. Moreover, X. nematophila has garnered interest in the field of biotechnology due to its potential applications in agriculture and medicine. The metabolites produced by this bacterium have been studied for their antimicrobial properties, which could lead to the development of new antibiotics. The ability of X. nematophila to degrade chitin, a major component of insect exoskeletons, further highlights its ecological significance and potential utility in bioremediation efforts. In addition to its practical applications, X. nematophila serves as a model organism for studying host-microbe interactions, particularly in the context of symbiosis and pathogenicity. Researchers are particularly interested in the genetic and biochemical pathways that enable this bacterium to adapt to its unique lifestyle, making it a subject of ongoing scientific inquiry. Overall, Xenorhabdus nematophila stands out not only for its ecological role but also for its potential contributions to sustainable agriculture and novel therapeutic strategies.

Taxonomy

Superkingdom: Bacteria

Phylum: Pseudomonadota

Class: Gammaproteobacteria

Order: Enterobacterales

Family: Morganellaceae

Genus: Xenorhabdus

Species: Xenorhabdus nematophila

NCBI ID

628

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/295/015/GCA_014295015.1_ASM1429501v1

File for sequence-based predictions:
GCA_014295015.1_ASM1429501v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Xenorhabdus nematophila is primarily known for its symbiotic relationship with entomopathogenic nematodes, particularly Steinernema species. This organism has significant implications in the field of biocontrol, as it is utilized in the biological control of insect pests. The pathogenicity of X. nematophila is largely attributed to its ability to produce a variety of toxins and antimicrobial compounds, which can effectively kill insects and suppress competing microorganisms. In terms of human health, while X. nematophila is not typically associated with human infections, its metabolites have been studied for potential therapeutic applications, including the development of novel antibiotics. The organism's ability to evade the immune response of its insect hosts through the production of immunosuppressive factors is of particular interest, as it may provide insights into similar mechanisms in human pathogens. Furthermore, the study of X. nematophila contributes to our understanding of antimicrobial resistance, as its interactions with both nematodes and insects can reveal strategies that may be applicable to human medicine. Overall, while X. nematophila is not a direct human pathogen, its ecological role and biochemical properties hold promise for future medical applications and pest management strategies.

Industrial Application

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

The bacterium Xenorhabdus nematophila is a notable organism with significant potential in various industrial applications. Primarily, it is recognized for its role in biotechnology, particularly in the development of biopesticides. This organism is symbiotically associated with nematodes, and together they can effectively target and control pest populations in agriculture, reducing the need for chemical pesticides. The process involves the production of toxins that are lethal to specific insect larvae, making it a valuable tool for sustainable pest management. In the realm of waste management, Xenorhabdus nematophila has demonstrated capabilities in biodegradation, where it can help in the breakdown of organic waste materials. This is particularly useful in composting processes, where the bacterium contributes to the decomposition of complex organic compounds, enhancing nutrient cycling and soil health. Furthermore, there is growing interest in the use of Xenorhabdus nematophila in biofuel production. The bacterium's metabolic pathways can be harnessed to convert biomass into biofuels through fermentation processes. This application is still under research but shows promise for developing sustainable energy sources. In pharmaceutical development, Xenorhabdus nematophila is being studied for its potential to produce bioactive compounds with antimicrobial properties. These compounds could lead to the development of new antibiotics or therapeutic agents, addressing the growing concern of antibiotic resistance. Overall, Xenorhabdus nematophila exemplifies a microorganism with diverse industrial applications, particularly in agriculture, waste management, biofuel production, and pharmaceuticals, showcasing its versatility and importance in modern biotechnology.

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

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