Amycolatopsis rifamycinica

General Information

Amycolatopsis rifamycinica is a fascinating microorganism primarily known for its production of rifamycin, a group of antibiotics that are crucial in the treatment of tuberculosis and other bacterial infections. This species belongs to the genus Amycolatopsis, which is renowned for its ability to produce a variety of bioactive compounds. One of the most noteworthy characteristics of A. rifamycinica is its complex secondary metabolism, which enables it to synthesize rifamycin B, the precursor to several clinically important antibiotics. The biosynthetic pathway of rifamycin in A. rifamycinica has been extensively studied, providing valuable insights into the genetic and enzymatic processes involved in antibiotic production. This makes A. rifamycinica a model organism for research in natural product biosynthesis and genetic engineering. Additionally, A. rifamycinica has a unique ability to thrive in diverse environmental conditions, which underscores its ecological versatility and potential for biotechnological applications. Its robust nature allows it to be cultivated in various industrial settings, making it a valuable asset in pharmaceutical manufacturing. The genome of A. rifamycinica has been sequenced, revealing a wealth of genetic information that can be harnessed for the discovery and development of new antibiotics. This genomic data is a treasure trove for researchers aiming to understand the molecular mechanisms of antibiotic resistance and to develop novel strategies to combat resistant bacterial strains. In summary, Amycolatopsis rifamycinica is not only important for its role in antibiotic production but also serves as a critical organism for scientific research, offering insights into microbial metabolism, genetic engineering, and the ongoing battle against antibiotic-resistant pathogens.

Amycolatopsis rifamycinica is a notable actinobacterium primarily recognized for its ability to produce rifamycin, a potent antibiotic that is particularly effective against Mycobacterium tuberculosis, the causative agent of tuberculosis. This organism is of significant interest in the field of microbiology and pharmaceutical research due to its unique biosynthetic pathways that allow it to synthesize complex polyketides, which are crucial for the development of various antimicrobial agents. One of the most fascinating aspects of A. rifamycinica is its genetic and metabolic versatility, which enables it to thrive in diverse environments. This adaptability not only contributes to its survival but also enhances its potential for biotechnological applications, such as the production of novel antibiotics and other bioactive compounds. Furthermore, the genome of A. rifamycinica has been sequenced, providing valuable insights into the genetic basis of its antibiotic production. This genomic information is instrumental for researchers aiming to engineer strains with improved yields of rifamycin or to explore the biosynthesis of other pharmacologically relevant compounds. The organism's ability to produce rifamycin derivatives also opens avenues for the development of new drugs that can combat antibiotic resistance, a growing concern in modern medicine. In summary, Amycolatopsis rifamycinica stands out not only for its role in antibiotic production but also for its potential contributions to drug discovery and development, making it a valuable subject of study in microbiological and pharmaceutical research.

Taxonomy

Superkingdom: Bacteria

Phylum: Actinomycetota

Class: Actinomycetes

Order: Pseudonocardiales

Family: Pseudonocardiaceae

Genus: Amycolatopsis

Species: Amycolatopsis rifamycinica

NCBI ID

287986

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/695/625/GCA_000695625.1_ASM69562v1

File for sequence-based predictions:
GCA_000695625.1_ASM69562v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Amycolatopsis rifamycinica is primarily known for its role in the production of the antibiotic rifamycin, which is crucial in the treatment of tuberculosis and other bacterial infections. This organism has significant clinical implications due to its ability to produce various rifamycin derivatives that exhibit potent activity against a range of Gram-positive and Gram-negative bacteria. In terms of pathogenicity, A. rifamycinica itself is not typically associated with human disease; however, its metabolites are vital in combating serious infections. The use of rifamycins has been linked to the emergence of antimicrobial resistance, particularly in the context of Mycobacterium tuberculosis, where resistance to rifampicin can lead to treatment failure and the development of multidrug-resistant tuberculosis (MDR-TB). Moreover, the organism's ability to produce rifamycins has made it a subject of interest in biotechnology and pharmaceutical applications, where it is utilized in the development of new antibiotics. The study of A. rifamycinica also provides insights into immune evasion strategies employed by bacteria, as rifamycins can modulate the immune response, enhancing their therapeutic efficacy. In summary, while Amycolatopsis rifamycinica is not a pathogen itself, its clinical relevance is underscored by its role in antibiotic production, its implications in antimicrobial resistance, and its contributions to the treatment of serious bacterial infections.

Habitat and Ecological Niches

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

Amycolatopsis rifamycinica is a notable actinobacterium primarily found in soil environments, particularly in areas rich in organic matter. This microorganism thrives in terrestrial biomes where it plays a crucial role in the decomposition of organic materials, contributing to nutrient cycling and soil health. Its ability to produce the antibiotic rifamycin makes it significant in both ecological and medical contexts, as it helps control bacterial populations in its habitat, thus maintaining a balance within the microbial community. In addition to its role in soil ecosystems, A. rifamycinica is often associated with plant rhizospheres, where it can engage in beneficial interactions with plant roots. This symbiotic relationship can enhance plant growth and health by promoting nutrient availability and providing protection against pathogenic microorganisms. Furthermore, A. rifamycinica has demonstrated adaptability to various environmental conditions, allowing it to thrive in nutrient-poor soils as well as in more enriched environments. Its metabolic versatility enables it to utilize a range of organic compounds, which is essential for its survival in diverse habitats. Overall, Amycolatopsis rifamycinica exemplifies the intricate relationships within soil biomes and highlights the importance of microbial diversity in ecosystem functioning.

Industrial Application

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

The microorganism Amycolatopsis rifamycinica is primarily known for its significant role in pharmaceutical development, particularly in the production of the antibiotic rifampicin. This compound is crucial in the treatment of tuberculosis and other bacterial infections. The organism is utilized in fermentation processes to produce rifamycin derivatives, which are essential for combating resistant strains of bacteria. In addition to its pharmaceutical applications, Amycolatopsis rifamycinica has potential in biotechnology for the development of novel antibiotics and other bioactive compounds. Its ability to produce various secondary metabolites can be harnessed for the discovery of new drugs. Furthermore, this microorganism can be explored in waste management due to its capacity to degrade complex organic compounds, making it a candidate for biodegradation processes. This could be particularly useful in the treatment of wastewater containing pharmaceutical residues. Overall, Amycolatopsis rifamycinica demonstrates a multifaceted potential in biofuel production as well, where its metabolic pathways can be studied for the conversion of biomass into biofuels, although this application is less documented compared to its pharmaceutical uses.

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

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