Unlocking microbial diversity with targeted sequencing

The challenge of analyzing complex microbial communities

Microbial communities play crucial roles in human health, the environment, and ecological systems, and by studying them, we can learn how to prevent disease, protect agriculture, and preserve biodiversity. When studying microbes from environmental samples, host tissues, or clinical specimens, however, the dominance of host DNA or RNA in samples can overwhelm the microbial signals of interest making comprehensive analysis difficult.

Traditional approaches like whole-genome shotgun sequencing require extremely deep sequencing to recover sufficient data from low-abundance microbes, resulting in excessive costs and computational burdens. Meanwhile, PCR-based amplicon methods can introduce biases and can miss important microbial taxa due to primer mismatches. Additionally, these methods often struggle with the sheer complexity of microbial samples, which can contain thousands of species in varying abundances. Targeted next-generation sequencing has emerged as a powerful solution for researchers seeking to explore microbial diversity more effectively and efficiently.¹

Elevating microbial research: targeted sequencing with hybridization capture

Next-generation sequencing reaches new levels of efficiency through targeted sequencing – an approach that focuses analysis on specific genomic regions of interest. This targeted technique enables scientists to obtain significantly higher read depth while simultaneously reducing experimental costs.

Targeted next-generation sequencing can be conducted using a variety of methods, but hybridization capture stands out as a particularly robust and adaptable technique, well-suited for microbial community analysis. Hybridization capture uses biotinylated nucleic acid probes to selectively enrich microbial sequences of interest from complex samples, significantly increasing the proportion of relevant reads.

The key advantages of hybridization capture include:

• Enhanced detection sensitivity for low-abundance microbes
• Reduced sequencing costs compared to shotgun metagenomic approaches
• Greater taxonomic resolution than traditional amplicon-based methods
• Efficient recovery capability for highly divergent molecules

These advantages highlight why hybridization capture is increasingly becoming the premier tool for accurately profiling microbial community diversity.

myBaits®: a cutting-edge solution for microbial sequencing

Arbor Biosciences’ myBaits hybridization capture system is a powerful tool for targeted microbial sequencing, offering exceptional versatility across research applications. This technology enables researchers to selectively target specific pathogens, functional genes, complete pathways, or entire microbial communities with customized probe designs tailored to each unique project. The system’s adaptability extends to sample compatibility, performing effectively across diverse specimens from clinical tissues to complex environmental matrices.

At the core of the myBaits technology is its ability to dramatically enhance sequencing depth, consistently achieving over 100-fold enrichment of microbial genomes compared to conventional shotgun approaches. This superior efficiency makes targeted sequencing particularly valuable for challenging samples where microbial signals are overwhelmed by host DNA or RNA, transforming previously impossible analyses into routine procedures.

Versatility unleashed: how researchers leverage myBaits technology

Researchers across diverse applications are leveraging Arbor Biosciences’ myBaits technology, demonstrating the impact of targeted sequencing on microbial research:

Pathogen genome recovery: When conventional methods fail due to overwhelming host DNA, hybridization capture excels at enriching microbial genomes from complex samples. In one study using myBaits, researchers achieved ~ 2,500-fold enrichment of Vibrio cholerae genomic DNA from complex river water samples, enabling researchers to detect and characterize pathogens even at extremely low levels of abundance.²

16S rRNA metagenomic profiling: Targeted capture of 16S regions strikes an optimal balance between traditional amplicon sequencing and shotgun metagenomics. This method provides comprehensive taxonomic profiles without the substantial costs of deep metagenomic sequencing while avoiding the primer biases inherent to PCR-based approaches.³

Ancient DNA studies: The ability to retrieve fragmented, degraded DNA makes hybridization capture invaluable for paleomicrobiological research, enabling reconstruction of ancient pathogen genomes. From a 400-year-old mummy sample, the myBaits system helped one group to retrieve trace genomic fragments and fully reconstruct a smallpox genome.⁴

Host-pathogen interactions: The multi-target capability of hybridization capture allows simultaneous enrichment of vector, host, and pathogen sequences from a single sample. This integrated approach provides comprehensive insights into disease transmission dynamics through one unified workflow, replacing multiple specialized assays that would otherwise be required.⁵

Antimicrobial resistance monitoring: Targeted sequencing enables comprehensive “resistome” profiling with dramatically reduced sequencing effort. With myBaits, one lab demonstrated that this approach not only identifies known resistance determinants but also uncovers novel antimicrobial resistance genes.⁶

Unlocking microbial discovery

Targeted next-generation sequencing represents a powerful approach for exploring microbial diversity across diverse research applications. By overcoming the limitations of traditional methods, technologies like Arbor Biosciences’ myBaits system enable researchers to gain deeper insights into microbial communities with greater efficiency and cost-effectiveness.

As microbial research continues to advance our understanding of human health, environmental processes, and evolutionary biology, targeted sequencing provides an essential tool for unlocking the full complexity of the microbial world.

Interested in learning how myBaits can enhance your research? Explore our myBaits custom DNA and RNA targeted next-generation sequencing kits.

References

1. Beaudry, M. et al. Enriching the future of public health microbiology with hybridization bait capture. Clinical Microbiology Reviews. (2024) Nov; 37(4). doi: 10.1128/cmr.00068-22
2. Vezzulli L. et al. Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. Microbial Ecology. (2017) Apr; 73(3):734-738. doi: 10.1007/s00248-016-0902-x
3. Beaudry, M. et al. Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment. Frontiers in Microbiology (2021) Apr; 12: doi:10.3389/fmicb.2021.644662
4. Duggan, A. et al. 17^th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology. (2016) Dec 19;26(24):3407–3412. doi: 10.1016/j.cub.2016.10.061
5. Campana, M. et al. Simultaneous identification of host, ectoparasite and pathogen DNA via in-solution capture. Molecular Ecology Resources. (2016) Sep;16(5):1224-39. doi: 10.1111/1755-0998.12524.
6. Guitor, A. et al. Capturing the Resistome: A Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrobial Agents and Chemotherapy. (2019) Dec 20; 64(1): doi: 10.1128/AAC.01324-19.

Daicel Arbor Biosciences launches myReads Extractions, an in-house DNA extraction service for plant and animal samples, designed to optimize yield and reliability from the start.

We are excited to continue our journey, and our ongoing commitment to empowering researchers.

International Plant & Animal Genome in San Diego, CA