Phocaeicola barnesiae

General Information

Phocaeicola barnesiae is a fascinating microorganism that has garnered attention due to its unique ecological niche and potential applications in biotechnology. This bacterium is part of the human gut microbiota, which plays a crucial role in maintaining gut health and overall well-being. One of the most interesting aspects of Phocaeicola barnesiae is its ability to break down complex carbohydrates, which are otherwise indigestible by the human host. This capability is essential for the production of short-chain fatty acids (SCFAs), which are beneficial for colon health and have anti-inflammatory properties. Another noteworthy characteristic of Phocaeicola barnesiae is its potential role in modulating the immune system. Studies have suggested that this bacterium can influence the balance of pro-inflammatory and anti-inflammatory cytokines, thereby contributing to immune homeostasis. This makes it a subject of interest for research into treatments for inflammatory bowel diseases (IBD) and other gut-related disorders. From a biotechnological perspective, Phocaeicola barnesiae is valuable due to its enzymatic repertoire. The enzymes produced by this bacterium can be harnessed for various industrial applications, including the production of biofuels and bioplastics. The ability to degrade complex polysaccharides also opens up possibilities for its use in waste management and the production of renewable energy. In summary, Phocaeicola barnesiae is a microorganism of significant interest due to its role in gut health, immune modulation, and potential biotechnological applications. Its unique capabilities make it a valuable subject for ongoing and future research.

Phocaeicola barnesiae is a fascinating member of the microbial community, primarily known for its role in the marine environment. This bacterium is part of the diverse group of bacteria that inhabit the gastrointestinal tract of marine mammals, particularly seals. One of the most interesting aspects of P. barnesiae is its ability to thrive in the unique and often extreme conditions of marine ecosystems, showcasing its adaptability and resilience. Ecological Significance: P. barnesiae plays a crucial role in the digestion of complex carbohydrates found in the diets of marine mammals. By breaking down these compounds, it contributes to the nutrient cycling within these ecosystems, making it an essential player in the marine food web. Biotechnological Potential: The enzymes produced by P. barnesiae for carbohydrate degradation are of significant interest for biotechnological applications. These enzymes can be harnessed for industrial processes, such as biofuel production and waste management, where the breakdown of organic materials is necessary. The study of these enzymes could lead to advancements in sustainable practices and the development of new bioproducts. Research Implications: As a relatively newly identified species, P. barnesiae offers a unique opportunity for researchers to explore the evolutionary adaptations of gut microbiota in marine mammals. Understanding its interactions with host organisms and other microbial communities can provide insights into the health and ecology of marine environments, particularly in the face of climate change and habitat degradation. In summary, Phocaeicola barnesiae stands out not only for its ecological role but also for its potential applications in biotechnology and its importance in understanding marine mammal health and microbiome dynamics.

Taxonomy

Superkingdom: Bacteria

Phylum: Bacteroidota

Class: Bacteroidia

Order: Bacteroidales

Family: Bacteroidaceae

Genus: Phocaeicola

Species: Phocaeicola barnesiae

NCBI ID

376804

Genome Info

FTP Path:
ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/359/135/GCF_002359135.1_ASM235913v1

File for sequence-based predictions:
GCF_002359135.1_ASM235913v1_genomic.fasta

Descriptions

Clinical Implications and Relevance

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

The bacterium Phocaeicola barnesiae is a member of the gut microbiota and has been associated with various clinical implications. It is primarily known for its role in infections related to the gastrointestinal tract. While it is generally considered a commensal organism, it can become pathogenic under certain conditions, particularly in immunocompromised individuals. Infections caused by P. barnesiae may include bacteremia and abscess formation, especially in patients with underlying health issues or those undergoing invasive procedures. One of the notable aspects of P. barnesiae is its potential for antimicrobial resistance. Studies have indicated that this organism may exhibit resistance to multiple classes of antibiotics, which complicates treatment options for infections it may cause. This resistance is particularly concerning in the context of increasing rates of antibiotic use and misuse, leading to a greater burden of resistant infections. In terms of immune evasion, P. barnesiae may employ various strategies to survive within the host, including the production of biofilms and the ability to modulate the host's immune response. These mechanisms can contribute to its persistence in the gut and its potential to cause disease when the host's defenses are compromised. While P. barnesiae is not commonly associated with outbreaks, its presence in clinical specimens highlights the importance of understanding the role of gut microbiota in health and disease. Further research is needed to fully elucidate its pathogenic potential and the mechanisms underlying its interactions with the human immune system. Overall, Phocaeicola barnesiae serves as a reminder of the complex relationship between commensal organisms and human health.

Habitat and Ecological Niches

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

Phocaeicola barnesiae is a species of bacteria commonly associated with the gastrointestinal tracts of marine mammals, particularly seals. This organism thrives in marine environments, where it plays a significant role in the digestion of complex carbohydrates and the overall health of its host. The ecological niche of Phocaeicola barnesiae is primarily within the gut microbiome of these marine mammals, where it contributes to nutrient absorption and fermentation processes. Habitat Characteristics: - The bacterium is typically found in the warm, nutrient-rich waters of coastal regions, where its host species reside. - It is adapted to the anaerobic conditions of the gut, allowing it to efficiently break down organic matter in an environment with limited oxygen. Ecological Role: - Phocaeicola barnesiae is involved in symbiotic relationships with its host, aiding in digestion and providing essential nutrients that enhance the health and fitness of marine mammals. - The presence of this bacterium can influence the overall microbial community structure within the gut, impacting the host's immune response and metabolic processes. In summary, Phocaeicola barnesiae is a vital component of the marine mammal gut microbiome, contributing to the ecological balance and health of its host in the dynamic marine ecosystem.

Industrial Application

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

The microorganism Phocaeicola barnesiae has shown potential in various industrial applications, particularly in the fields of biotechnology, waste management, and pharmaceutical development. This organism is notable for its role in fermentation, where it can contribute to the production of short-chain fatty acids (SCFAs) that are beneficial for gut health and can be utilized in the food industry as functional ingredients. In the realm of waste management, Phocaeicola barnesiae has been studied for its ability to degrade complex organic materials, making it a candidate for biodegradation processes that help in the treatment of wastewater and organic waste. Its enzymatic activity can facilitate the breakdown of pollutants, thus contributing to environmental sustainability. Furthermore, in pharmaceutical development, the metabolites produced by Phocaeicola barnesiae during fermentation processes may have therapeutic properties, potentially leading to the discovery of new drugs or health supplements. The organism's ability to produce specific enzymes can also be harnessed for the synthesis of bioactive compounds, which are valuable in the pharmaceutical industry. Overall, Phocaeicola barnesiae represents a promising microorganism with diverse applications across multiple industries, particularly in enhancing processes related to fermentation, biodegradation, and enzyme production.

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

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