Bacterial Community Profiling
Bacterial Community Profiling - Related Videos
09:59
Community DNA Extraction from Bacterial Colonies
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2023
Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona Demonstrating Author: Luisa Ikner Traditional methods of analysis for microbial communities within soils have usually involved either cultural assays utilizing dilution and plating methodology on selective and differential media or direct count assays. Direct counts offer information about the total number of bacteria present, but give no information about the number or diversity of populations present...
02:06
Visualizing Intracellular Bacterial Communities in an Infected Mouse Bladder
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2026
Source: Conover, M. S. et. al., Establishment and Characterization of UTI and CAUTI in a Mouse Model. J. Vis. Exp. (2015)This video demonstrates the detection of intracellular bacterial communities (IBCs) in mouse bladder tissue infected with β-galactosidase-expressing Escherichia coli. Following tissue fixation, permeabilization, and staining with X-gal, IBCs appear as blue puncta under a dissecting microscope, confirming bacterial invasion during urinary tract infection.
02:54
Exposing a Synthetic Oral Bacterial Community to Simulated Phases of Digestion
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2025
Source: Arroyo, M. C., et al. Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface. J. Vis. Exp. (2018)This video demonstrates the viability assessment of a synthetic oral microbial community during simulated oral, gastric, and intestinal digestion. Bacterial survival is quantified after each phase, revealing a progressive decline due to digestive stress.
02:56
Isolation of Mouse Bladder Epithelial Cells Containing Intracellular Bacterial Communities
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2026
Source: Yang, E., et al. Isolation of Single Intracellular Bacterial Communities Generated from a Murine Model of Urinary Tract Infection for Downstream Single-cell Analysis. J. Vis. Exp. (2019)This video demonstrates the manual isolation of single epithelial cells containing intracellular bacterial communities from infected mouse bladder using mouth micropipetting, enabling downstream single-cell analysis of viable host-associated E. coli populations in urinary tract infection...
07:34
Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing
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Cited by 1 •
2023
Here, we present a protocol to describe amplicon metagenomic for determining the bacterial community of Traminette grapes, fermenting grapes, and final wine.
FAQs
16S rRNA profiling focuses on amplified taxonomic marker genes, providing a targeted way to characterize bacterial populations. Total-community DNA sequencing examines DNA from the entire community rather than one selected marker. This distinction affects the type of sequence information available and helps researchers choose between a targeted community survey and a broader assessment of sample DNA.
After sequencing, bioinformatics assigns sequences to bacterial taxa and compares how frequently different sequence groups occur within each sample. These analyses support estimates of community composition and relative abundance, while diversity measures summarize how varied the bacterial population is. Together, the outputs allow researchers to compare community structure across samples or experimental conditions.
Comparing profiles can reveal shifts in bacterial populations associated with disease, environmental change, diet, or treatment. The resulting patterns may also help connect community structure with ecosystem function or host biology. In biology, this makes profiling useful not only for listing taxa, but also for examining how bacterial communities vary alongside changes in their environment or host.
A typical workflow begins with a biological, clinical, or environmental sample, followed by extraction of community DNA. Researchers then amplify a marker such as 16S rRNA or sequence total community DNA. Finally, bioinformatics assigns sequences to taxa and supports comparisons of composition, diversity, relative abundance, and overall community structure among samples.
Researchers may select this approach for biodiversity surveys, microbiome investigations, pathogen monitoring, or evaluation of interventions that alter bacterial communities. It is also useful when a study asks whether disease, diet, environmental conditions, or treatment corresponds with a change in community structure. The appropriate application depends on whether the goal is ecological, clinical, or host-related.
Bacterial community profiles can show whether populations differ between samples and whether particular conditions coincide with changes in diversity or relative abundance. In environmental studies, those patterns can be examined in relation to ecosystem function. In host-focused research, they can be compared with disease, diet, or treatment to investigate associations between bacterial communities and host biology.