Microbiota Sequencing
Microbiota Sequencing - Related Videos
01:27
Oral Infection Alters the Gut Microbiota in a Rat Model
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2026
Begin with a rat model with sutures tied around its upper molar teeth to support bacterial colonization.Repeatedly smear the sutures with a gum disease-causing oral pathogenic bacterium using a gel-like solution.The bacteria colonize the gum around the sutures.Colonization triggers inflammation and damages the tissues.The bacteria release toxins that diffuse through damaged tissues and enter the bloodstream.These circulating toxins reach the gut, cause inflammation, disrupt the epithelial...
11:22
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Cited by 65 •
2019
Described here is a simplified standard operating procedure for microbiome profiling using 16S rRNA metagenomic sequencing and analysis using freely available tools. This protocol will help researchers who are new to the microbiome field as well as those requiring updates on methods to achieve bacterial profiling at a higher resolution.
01:15
Assessing the Role of Gut Microbiota in Modulating Hepatitis B Infection in Mice
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2026
Take a control mouse with a normal gut microbiota and an experimental mouse with depleted gut microbiota. The depletion compromises the integrity of the gut barrier.This enables bacteria to translocate through the blood vessel into the liver tissue.Inject both mice with the hepatitis B virus or HBV plasmid to induce an HBV infection in the liver tissue.In the control mouse, the T cell detects an infected liver cell through the interaction of its receptors with viral antigens, and produces...
07:54
A Method to Assess Bacteriocin Effects on the Gut Microbiota of Mice
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Cited by 9 •
2017
Bacteriocins are believed to play a key role in defining microbial diversity in different ecological niches. Here, we describe an efficient procedure to assess how bacteriocins affect gut microbiota composition in an animal model.
01:27
The Oral Microbiota
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2026
The oral microbiome includes a complex ecosystem comprising over 700 microbial species, identified through genomic sequencing and culture-based analyses to date. This community includes a core microbiome, found universally among individuals, and a variable component influenced by environmental factors such as diet, lifestyle, and host genetics. Site-specific conditions, including oxygen gradients, pH levels, and nutrient availability, determine the spatial distribution of these microorganisms...
FAQs
Marker-gene analysis selectively amplifies genes such as 16S rRNA, commonly used for bacteria and archaea, to characterize community membership. Shotgun metagenomics instead sequences all recovered DNA from the community. Consequently, marker-gene analysis focuses on taxonomic composition, whereas shotgun data can support taxonomic analysis alongside assessment of the community’s potential function.
Bioinformatic analysis converts sequence data into biological descriptions by assigning sequences to taxa and estimating their relative abundance. These steps allow researchers to compare which microorganisms occur in different communities and how their proportions vary. The resulting profiles support analysis of community composition, diversity, and changes associated with environmental or biological conditions.
Researchers compare sequence-derived community profiles from different conditions, such as contrasting diets, habitats, or treatments. Differences in detected taxa, diversity, or relative abundance can indicate that community structure varies between those conditions. In biology, these comparisons help identify associations with health or disease, although the sequencing results describe relationships rather than independently establishing causation.
The genetic target determines which information is captured from the microbial community. A commonly used 16S rRNA marker provides a basis for studying bacteria and archaea, while sequencing all recovered DNA broadens the genetic material available for analysis. Selecting between these approaches therefore affects the types of taxonomic and potential functional comparisons researchers can make.
A typical workflow begins with extracting DNA from microorganisms inhabiting a defined environment. Researchers then either amplify a marker gene, commonly a 16S rRNA gene, or sequence all recovered DNA through shotgun metagenomics. Bioinformatic analysis follows, assigning sequences to taxa and estimating relative abundance so community composition can be compared across samples or conditions.
Researchers use microbiota sequencing when they need to compare microbial communities across defined environments or experimental conditions. Applications described for biology include examining gut, soil, and host-surface communities; identifying associations with health or disease; and evaluating how diet, habitat, or treatment alters community structure and potential function. The method therefore supports both ecological and health-related investigations.
The analysis can identify the taxa represented in a microbial community, estimate their relative abundance, and support comparisons of community diversity and structure. When shotgun metagenomics is used, the recovered genetic material can also contribute to evaluating potential function. These outcomes help researchers determine whether communities differ and relate those differences to biological conditions or treatments.