Amycolatopsis japonica

General Information

Amycolatopsis japonica is a fascinating microorganism belonging to the genus Amycolatopsis, which is renowned for its ability to produce a wide array of bioactive compounds. One of the most intriguing aspects of A. japonica is its capacity to synthesize novel antibiotics and other secondary metabolites, making it a valuable subject for pharmaceutical research. The genus Amycolatopsis is closely related to Streptomyces, another prolific producer of antibiotics, and shares many of its biosynthetic capabilities. A. japonica is particularly interesting due to its potential in bioremediation. It has been studied for its ability to degrade complex organic compounds, including pollutants, which highlights its environmental significance. This microorganism's enzymatic machinery allows it to break down substances that are otherwise resistant to degradation, offering a sustainable solution to environmental contamination. Another unique feature of A. japonica is its genomic plasticity. The organism's genome harbors numerous gene clusters responsible for the production of diverse secondary metabolites. This genetic diversity not only underscores its adaptability but also provides a rich resource for the discovery of new drugs and industrial enzymes. In addition to its biotechnological applications, A. japonica has been a subject of interest in evolutionary studies. Its phylogenetic position within the Actinobacteria phylum provides insights into the evolutionary pathways that have led to the development of complex secondary metabolite biosynthesis pathways. Overall, Amycolatopsis japonica stands out as a microorganism of significant scientific interest due to its antibiotic production, bioremediation potential, and genomic diversity. Its study continues to contribute to advancements in medicine, environmental science, and evolutionary biology.

Amycolatopsis japonica is a fascinating actinobacterium that has garnered attention for its unique metabolic capabilities and potential applications in biotechnology. This organism is particularly notable for its ability to produce a variety of bioactive compounds, including antibiotics and other secondary metabolites, which are of great interest in pharmaceutical research. The discovery of novel compounds from A. japonica could lead to the development of new therapeutic agents, especially in the face of rising antibiotic resistance. One of the most intriguing aspects of A. japonica is its ecological role in soil environments, where it contributes to the degradation of complex organic materials. This ability not only highlights its importance in nutrient cycling but also positions it as a potential candidate for bioremediation efforts, particularly in the breakdown of pollutants. Research into the enzymatic pathways utilized by A. japonica could provide insights into sustainable practices for environmental cleanup. Furthermore, A. japonica has been studied for its genetic and metabolic diversity, which can be harnessed for synthetic biology applications. The organism's genome contains genes that are involved in the biosynthesis of various natural products, making it a valuable model for understanding the genetic basis of secondary metabolite production. This genetic richness opens up possibilities for genetic engineering and the development of strains with enhanced production capabilities. In summary, Amycolatopsis japonica stands out not only for its biotechnological potential but also for its ecological significance, making it a subject of ongoing research in microbiology, pharmacology, and environmental science.

Taxonomy

Superkingdom: Bacteria

Phylum: Actinomycetota

Class: Actinomycetes

Order: Pseudonocardiales

Family: Pseudonocardiaceae

Genus: Amycolatopsis

Species: Amycolatopsis japonica

NCBI ID

208439

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/732/925/GCA_000732925.1_ASM73292v1

File for sequence-based predictions:
GCA_000732925.1_ASM73292v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The microorganism Amycolatopsis japonica is a member of the Actinobacteria phylum and has garnered attention for its potential clinical implications. This organism is primarily known for its role in the production of antibiotics, particularly the antibiotic amikacin, which is used to treat various bacterial infections. Its ability to produce bioactive compounds makes it a subject of interest in the field of pharmaceutical microbiology. In terms of pathogenicity, Amycolatopsis japonica is generally considered non-pathogenic; however, its close relatives within the genus may exhibit pathogenic traits. The organism's interaction with the human body is primarily beneficial, as it contributes to the microbial diversity of the human microbiome, which is essential for maintaining immune homeostasis and overall health. Despite its beneficial aspects, there is a growing concern regarding antimicrobial resistance associated with some of its relatives. The mechanisms of resistance observed in related species may pose challenges in clinical settings, particularly in the treatment of infections caused by resistant strains. Understanding these mechanisms is crucial for developing effective treatment strategies. Furthermore, research into the use of Amycolatopsis japonica in probiotics and therapeutics is ongoing, with the potential for applications in enhancing gut health and modulating the immune response. Overall, while Amycolatopsis japonica itself is not directly associated with significant disease, its role in antibiotic production and its relationship with other microorganisms highlight its importance in the context of human health and disease management.

Habitat and Ecological Niches

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

Amycolatopsis japonica is a species of actinobacteria that is primarily found in soil environments and marine ecosystems. This microorganism thrives in nutrient-rich substrates, often associated with decaying organic matter, which provides essential nutrients for its growth and metabolic activities. Its presence is particularly noted in tropical and subtropical regions, where the warm and humid conditions favor its proliferation. In terms of ecological roles, Amycolatopsis japonica is known for its ability to produce a variety of bioactive compounds, including antibiotics and enzymes, which play a significant role in soil health and nutrient cycling. These compounds can inhibit the growth of pathogenic microorganisms, thus contributing to the overall balance of the microbial community in its habitat. Furthermore, Amycolatopsis japonica exhibits notable interactions with its surroundings, often engaging in symbiotic relationships with plants. This can enhance plant growth by promoting nutrient availability and protecting against soil-borne pathogens. Its adaptability to various environmental conditions, including salinity and pH variations, allows it to occupy diverse niches within its habitats, making it a vital component of the ecosystems it inhabits.

Industrial Application

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

The microorganism Amycolatopsis japonica has shown significant potential in various industrial applications. One of the most notable areas is in biotechnology, where Amycolatopsis japonica is utilized for its ability to produce a range of bioactive compounds, including antibiotics and enzymes. This organism is particularly known for its role in fermentation, where it can be employed to synthesize valuable metabolites that have pharmaceutical significance. In the realm of waste management, Amycolatopsis japonica has demonstrated capabilities in biodegradation, particularly in the breakdown of complex organic materials. This property makes it a candidate for use in bioremediation processes, where it can help in the detoxification of contaminated environments, such as soil and water polluted with hazardous substances. Furthermore, the organism has been explored for its potential in biofuel production. Through fermentation processes, Amycolatopsis japonica can convert biomass into biofuels, contributing to sustainable energy solutions. The efficiency of this microorganism in degrading lignocellulosic materials positions it as a valuable asset in the development of second-generation biofuels. In pharmaceutical development, the antibiotic-producing capabilities of Amycolatopsis japonica are particularly noteworthy. The organism is known to produce compounds that can be harnessed for the development of new drugs, especially in the fight against antibiotic-resistant bacteria. This highlights its importance in the ongoing search for novel therapeutic agents. Overall, Amycolatopsis japonica stands out as a versatile microorganism with diverse applications across biotechnology, waste management, biofuel production, and pharmaceutical development, making it a significant player in the industrial microbiology landscape.

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	google/gemini-pro-1.5	anthropic/claude-3.5-sonnet	google/palm-2-chat-bison-32k	google/gemini-flash-1.5	meta-llama/llama-3-70b-instruct:nitro	google/gemini-pro	anthropic/claude-3-haiku:beta	perplexity/llama-3-sonar-small-32k-chat	openchat/openchat-7b	openai/gpt-3.5-turbo-0125	openai/gpt-3.5-turbo-0125	openai/gpt-4o	openai/gpt-4o	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	microsoft/phi-3-mini-128k-instruct	microsoft/phi-3-mini-128k-instruct	mistralai/mixtral-8x7b-instruct:nitro	mistralai/mixtral-8x7b-instruct:nitro	mistralai/mistral-7b-instruct	mistralai/mistral-7b-instruct
Motility	FALSE	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 ✓
Gram staining	gram stain positive	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain positive ✓	N/A	gram stain variable ✗
Aerophilicity	aerobic	aerobic ✓	aerobic ✓	aerobic ✓	N/A	aerobic ✓	aerobic ✓	N/A	N/A	N/A	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	aerotolerant ✗	aerotolerant ✗	aerobic ✓	aerobic ✓	aerobic ✓	aerobic ✓	N/A	N/A	N/A	N/A	N/A	N/A	N/A	N/A
Extreme environment tolerance	FALSE	true ✗	false ✓	false ✓	true ✗	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗	true ✗
Biofilm formation	N/A	false	true	true	true	false	true	true	true	false	true	true	true	true	true	true	false	false	true	true	true	true	false	false	true	true	false	false
Animal pathogenicity	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 ✓
Biosafety level	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 ✓	biosafety level 2 ✗	biosafety level 2 ✗	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓	biosafety level 1 ✓
Health association	N/A	false	false	true	false	false	true	true	true	false	false	false	false	false	false	false	false	false	false	false	true	true	false	false	false	false	false	false
Host association	N/A	false	false	false	true	false	true	false	true	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 ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓	true ✗	true ✗	false ✓	false ✓	false ✓	false ✓	false ✓	false ✓
Spore formation	TRUE	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	true ✓	false ✗	false ✗	false ✗	false ✗	false ✗	false ✗	true ✓	true ✓	true ✓	true ✓
Hemolysis	N/A	N/A	N/A	N/A	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	N/A
Cell shape	N/A	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	bacillus	coccus	coccus	bacillus	bacillus	bacillus	bacillus

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