We offer specialized Phage Discovery services to isolate novel phages from complex gut samples. Our protocols are designed to recover diverse phage families, including those that are difficult to culture.
The human gastrointestinal tract is a complex ecosystem inhabited by trillions of microorganisms. While bacteria have traditionally been the primary focus of microbiome research, the gut phageome—the viral component consisting primarily of bacteriophages—has emerged as a critical regulator of this environment. These phages in the gut are not passive bystanders; they are active architects of bacterial community structure, drivers of horizontal gene transfer, and potential modulators of the human immune system.
Understanding the intricate dynamics of the gut bacteriophage population is essential for deciphering the mechanisms of homeostasis and dysbiosis. As a leading service provider in the field of virology, Creative Biolabs offers comprehensive Phage Services designed to help researchers unlock the secrets of the viral dark matter. Our advanced platforms facilitate the discovery, characterization, and production of phages, providing high-quality data for basic research development.
The human gut contains an estimated 109 virus-like particles (VLPs) per gram of feces, the vast majority of which are bacteriophages. This "phageome" is highly diverse and individualized, exhibiting significant temporal stability in healthy adults. Unlike the bacterial microbiome, which shares a core set of species among individuals, the viral component is remarkably unique to each host.
Fig.1 Phage-mediated modulation of the human gut microbiome.1,3
Research into phages in the gut has revealed two primary lifestyles that influence the ecosystem:
Dysbiosis, or the imbalance of the gut microbiota, is often characterized by a shift in the gut bacteriophage community. Alterations in the phageome have been linked to various conditions, including Inflammatory Bowel Disease (IBD), obesity, and malnutrition, highlighting their potential as diagnostic biomarkers.
The functional repertoire of the gut phage extends beyond simple bacterial predation. Emerging evidence suggests they play a multifaceted role in maintaining host health.
Through selective predation, bacteriophages prevent the overgrowth of specific bacterial taxa. This "top-down" control is essential for maintaining the high diversity characteristic of a healthy microbiome. In disease states, the collapse of this diversity is often accompanied by an expansion of pathobionts, which may be targeted by specific lytic phages.
Phages are primary vectors for horizontal gene transfer (HGT) via transduction. In the dense environment of the gut, they facilitate the exchange of genetic material between bacteria, driving evolution and adaptation. This can include the transfer of metabolic genes that aid in nutrient processing or, conversely, antibiotic resistance genes.
Bacteriophages in gut environments can interact directly with the host immune system. Phages can translocate across the epithelial barrier and stimulate innate immune responses. Some studies suggest that phages adhering to the mucosal layer provide a non-host-derived immunity, acting as a first line of defense against invading bacterial pathogens.
Despite the recognized importance of the gut phageome, studying it presents significant technical hurdles. The vast majority of gut viral sequences, often termed "viral dark matter," do not align with any known reference genomes, complicating taxonomic classification. Furthermore, unlike bacteria, there is no universal marker gene (like 16S rRNA) for viruses, which necessitates deep metagenomic sequencing and sophisticated bioinformatics pipelines for identification.
Another major challenge lies in host assignment. Identifying which specific bacterial host a novel phage infects is notoriously difficult using sequence data alone. Without this link, it is challenging to infer the ecological impact of a phage on the microbiome. Additionally, standard protocols for extracting viral DNA often struggle with low yield or contamination from bacterial genomic DNA, requiring optimized enrichment strategies to ensure high-quality data.
We provide a suite of specialized services to support your research into the gut phageome. From initial discovery to functional characterization, our platforms are optimized for the complexity of fecal and environmental samples.
We offer specialized Phage Discovery services to isolate novel phages from complex gut samples. Our protocols are designed to recover diverse phage families, including those that are difficult to culture.
Our Phage Metagenomic Sequencing service allows for the culture-independent analysis of the entire gut virome. We use advanced bioinformatics to assemble viral contigs and identify known and novel viral populations.
Understanding the biological properties of isolated phages is crucial. We provide comprehensive Phage Characterization, including morphology analysis via TEM, host range determination, and stability testing.
We investigate the dynamic relationship between phages and their bacterial hosts. Our Phage-Host Interaction Analysis services can map infection pathways and resistance mechanisms.
Recent research highlights the profound impact of the gut phageome on human health. A comprehensive review published in 2024 synthesizes our current understanding of these interactions. The study details the complex ecology of the gut virome, emphasizing that bacteriophages are not merely transient visitors but integral components of the gut ecosystem. It categorizes the diverse viral families present, noting the predominance of Caudoviricetes and Microviridae. Key findings illustrate how phages maintain bacterial diversity through predator-prey dynamics and facilitate horizontal gene transfer, which can disseminate antibiotic resistance genes. Furthermore, the data underscores the therapeutic potential of manipulating the phageome to treat dysbiosis-related diseases, reinforcing the need for precise phage analysis in clinical research.
Fig.2 Overview of bacteriophage dynamics and their role in modulating the human gut microbiome and host health.2,3
Q: What is the gut phageome?
Q: How do you isolate phages from gut samples?
A: We use a combination of filtration, centrifugation, and enrichment techniques. Fecal samples are homogenized and filtered to remove bacteria and debris. The filtrate can then be used for direct plaque assays or enriched with specific host bacteria to amplify low-abundance phages.
Q: Can gut phages be used for therapy?
A: Yes, there is significant interest in using gut-derived phages for phage therapy to treat antibiotic-resistant infections or to modulate the microbiome (e.g., targeting specific pathobionts in IBD), though this is primarily in the research and clinical trial phase.
Q: Can you analyze RNA phages in the gut?
A: Yes, our advanced pipeline includes specific protocols for viral RNA extraction and cDNA synthesis. This allows us to capture the RNA viral community, which is often overlooked in standard DNA-based metagenomic studies.
Q: Do you require control samples for phageome analysis?
A: While not strictly mandatory, we strongly recommend including appropriate control samples (e.g., from healthy donors) to establish a baseline. This is crucial for accurately identifying dysbiosis-related shifts in the viral community.
Q: What databases do you use for viral identification?
A: We utilize a combination of curated public databases, such as the Gut Virome Database (GVD) and MGV, alongside our proprietary internal databases and custom bioinformatics pipelines to identify both known and novel viral sequences.
Q: Is the gut phageome stable over time?
A: Research indicates that in healthy adults, the gut phageome exhibits a relatively stable "core" over time. However, significant disruptions can occur due to factors such as diet changes, antibiotic usage, or disease onset.
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Please kindly note that our services can only be used to support research purposes (Not for clinical use).
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