Bacterial Genome Integration
Bacterial Genome Integration - Related Videos
09:31
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Cited by 56 •
2016
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
06:33
A Rapid Protocol for Integrating Extrachromosomal Arrays With High Transmission Rate into the C. elegans Genome
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Cited by 59 •
2013
This protocol describes a rapid and low material consuming procedure for the integration of transgenic extrachromosomal arrays into the Caenorhabditis elegans genome using ultra violet (UV) irradiation. Furthermore, this protocol is particularly well suited for transgenic lines that transmit extrachromosomal arrays at a high rate.
10:44
Generating Whole Bacterial Genomes from Clinical Samples using a Target Enrichment Workflow
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Cited by 1 •
2025
Here, we present a protocol to enable whole-genome sequencing of bacterial sexually transmitted infections from clinical samples using target enrichment. This novel, syndromic panel-based method overcomes challenges of abundant human DNA and low bacterial loads, facilitating genomic surveillance for Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and Mycoplasma genitalium.
08:31
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
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Cited by 2 •
2013
Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.
10:41
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Cited by 34 •
2018
Here, we describe an optimized high-throughput ChIP-sequencing protocol and computational analyses pipeline for the determination of genome-wide chromatin state patterns from frozen tumor tissues and cell lines.
FAQs
Homologous recombination depends on matching DNA sequences between the introduced construct and the bacterial chromosome, allowing the foreign segment to align with a corresponding genomic region. Site-specific recombination instead uses a recombinase that recognizes defined attachment sites. The choice therefore reflects whether integration should be guided by sequence similarity or by a specified recognition site.
Chromosomal placement can make an inserted genetic program more stable as bacteria grow and divide, while also reducing variation associated with plasmid copy number. This distinction matters when interpreting gene-function experiments or engineered phenotypes, because differences between cells are less tied to fluctuating numbers of plasmid copies. The approach supports more consistent biological comparisons.
CRISPR-assisted targeting can improve insertion accuracy by directing the integration process toward a selected chromosomal location. In the context of bacterial genome integration, it complements rather than replaces the underlying recombination logic: the system still depends on either matching DNA sequences or defined attachment sites. Its value is greater positional control when constructing engineered strains.
A planning workflow begins by selecting the genomic targeting logic: matching sequences for homologous recombination, defined attachment sites for a site-specific recombinase, or CRISPR-assisted targeting when improved insertion accuracy is desired. Researchers then relate that choice to the intended use, such as gene-function analysis or strain engineering. These decisions connect mechanism with experimental purpose.
Researchers can place foreign or engineered DNA in the chromosome to examine how a genetic element contributes to bacterial traits while maintaining it through cell growth and division. This is useful for comparing strains in which the added sequence remains part of the genome rather than being carried on a plasmid with variable copy number. It connects genomic construction to functional biology.
For metabolic pathway engineering, chromosomal integration allows pathway genes to be incorporated into a bacterial strain for biotechnology or synthetic biology. The resulting design emphasizes persistence and reduced copy-number variation, features that help researchers evaluate the engineered pathway as part of the chromosome. This makes the method relevant when building microbial strains intended to carry defined genetic programs.
In biosensor development, integration can anchor genetic components within the bacterial chromosome, supporting stable inheritance as cells proliferate. This provides a genomic foundation for engineered strains whose sensing functions are studied over continued growth. More broadly, the approach links molecular genetics with applied biology by enabling microbial systems that retain designed DNA while serving biotechnology and synthetic biology goals.