Single-Microbe Genomics: High Throughput for Gut Microbiome Strain
Summary
In an intricate exploration of the human gut microbiome, researchers have unveiled the nuanced genomic structure of microbial communities, emphasizing the significance of strain-level distinctions. The novel method, Microbe-seq, harnesses an integrated microfluidic approach to encapsulate and sequence individual microbes, offering strain-resolved insights. Contrasting the clarity of reference genomes in mammalian systems, the human gut microbiome, with its myriad species, presents a challenge. To address this, a sophisticated computational framework was devised, amalgamating sequencing reads to produce a comprehensive set of reference genomes. This meticulous process illuminated the coexistence of multiple strains within species and their genomic interplay. Applying Microbe-seq to specific gut samples, the team discerned 76 species-level genomes, revealing intricate horizontal gene transfers and notable associations between microbes and bacteriophages. In culmination, Microbe-seq, a synergy of microfluidic techniques and advanced bioinformatics, offers a transformative lens into the genomic intricacies of microbial communities, holding promise for broader applications and deeper insights into human health interplays.
Fig.1 Microbe-seq overview1.
Research Criteria
In the realm of biology, Zheng and his team introduced a cutting-edge method named Microbe-seq, focusing on individual bacterial cells from microbiomes. Through microfluidics, this process isolates these cells within droplets, then extracts, amplifies, and barcodes their DNA, leading to combined Illumina sequencing. When applied to human fecal specimens, it produced barcoded data for numerous single amplified genomes in each sample. By grouping these genomes from identical bacterial types, a clearer understanding of differences at the strain level emerged, highlighting phage relationships and restrictions on gene transfer between strains.
Sample Type
Bacterial cells from human fecal samples
Result—Sample Preparation at High Throughput Using Droplet-Based Microfluidic Devices
In an intricate procedure delineated in Fig.2 A, individual microbes are isolated using a microfluidic apparatus, encapsulating them within droplets infused with lysis agents. Post-encapsulation, these droplets undergo incubation, ensuring the DNA of each microbe remains confined to its respective droplet. Subsequent stages involve the reinjection of these droplets into successive microfluidic devices, facilitating the merging of each droplet with others containing amplification, fragmentation, and adapter addition reagents. The culmination of this meticulous process involves the integration of a barcoding bead—a hydrogel microsphere adorned with DNA barcode primers, generated via combinatorial barcode extension. These primers, bifurcated into a droplet-specific barcode sequence and another that anneals to the previously incorporated adapters, are affixed to the fragmented DNA molecules within each droplet through polymerase chain reaction (PCR). Post PCR, the droplets are dissolved, sequencing adapters appended, and a sequencing procedure is executed. The resultant raw data comprises sequencing reads, bifurcated into a shared barcode sequence and a microbe genome sequence, with the assemblage of microbial sequences linked to a singular barcode epitomizing a SAG.
Fig.2 Microbe-seq pipeline diagram and use in a community of known bacterial strains1.
Result—Genomes of Microbial Species in the Human Gut Microbiome
In an intricate exploration of data from droplet-based methods, researchers discerned the contents of Single Amplified Genomes (SAGs) by contrasting them with known genomes. When dealing with human gut microbiome samples, the absence of a comprehensive set of genomes from all major strains posed challenges. The study introduced a novel method that amalgamates genomic information from multiple SAGs to coassemble genomes, facilitating the identification of individual SAGs. This method involved extracting signatures from each SAG's genome, employing hierarchical clustering, and iterating the process to refine the data bins. Despite initial challenges with bins containing multiple taxa, the team managed to refine and coassemble genomes, yielding 76 species with high or medium quality. These species, predominantly from the human gut microbiome, were then cross-referenced with a public database, revealing a diverse array of phyla. Remarkably, the coassembled genomes closely mirrored the "gold standard" genomes derived from isolates, underscoring the method's precision and potential in advancing microbiome research.
Fig.3 Coassembled genomes of 76 bacterial species from a single human donor's gut microbiome1.
Creative Biolabs' Service
Single Microbe Genome Sequencing
Creative Biolabs introduces a revolutionary single bacteria DNA sequencing platform. Achieve high-throughput microbial genome sequencing with unmatched resolution. Our technology enables strain-level identification, horizontal gene transfer analysis, and uncovers uncultured strains. Dive deep into microbial genomics with precision and efficiency. Choose Creative Biolabs for unparalleled insights into the microbial world, one cell at a time.
Learn moreCreative Biolabs offers a high-throughput platform for single microbe genome sequencing, enabling high-throughput single-cell microbial whole genome sequencing. This technology addresses the limitations of metagenomic resolution, marking the first time that high-throughput and high-resolution strain-level identification have been achieved simultaneously. Our breakthrough approach allows for the analysis of horizontal gene transfer (HGT) between strains, host-phage association information, and the discovery of uncultured novel strains. With Creative Biolabs, you're not just getting a service; you're unlocking a world of unparalleled microbial insights. Trust in our expertise for comprehensive and precise bacterial genomics, one cell at a time.
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Reference
- Zheng, Wenshan, et al. "High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome." Science 376.6597 (2022): eabm1483.
