Single-cell genome analysis for breakthroughs in microbiome research
and its microbial single-cell genome database
Whole-genome sequencing can provide valuable insights about the type and function of bacteria.
However, little whole-genome information can actually be accessed because only a small fraction of bacteria have been cultured.
We have developed a new analytical platform, bit-MAP®, which sequences individual bacterial cells to explosively uncover novel genomes through the high-throughput manner.
| Demo Data1: Gut Microbiome |
Demo Data2: Soil Microbiome |
bit-MAP® :
bitBiome Microbiome Analysis Platform
Hundreds of microbial whole genomes at a time
bit-MAP® eliminates conventional hurdles for microbiome research such as isolation, culture and complex data processing. This technology enables massively parallel whole-genome sequencing of diverse individual microbes to provide new insights into unknown strains.
Please refer to the sample dataset of gut microbiome.
High-quality genomic information from a single cell
In bit-MAP®, microbes are individually encapsulated, with multi-step biochemical reactions including cell lysis and DNA amplification occurring inside the capsules. Individual bacterial genomes are accurately sequenced by analyzing the DNA within each capsule.
Publications : Chijiiwa R et al. Microbiome. 2020. , Yoda T et al. Genome Resource Announcement. 2020. , Nishikawa Y et al. bioRxiv. 2020.
Bioinformatic analysis at single-cell resolution
Our unique bioinformatics platform accurately reconstructs microbial genomes at
the sub-strain level. It elucidates not only genetic and functional information of
individual bacteria, but also genetic differences between target and related strains.
Publications : Kogawa M et al. Scientific Reports. 2018.
Advantages of bit-MAP®
Towards a comprehensive understanding of target microbiomes
bit-MAP® achieves functional analyses of individual bacteria that would be difficult with existing technologies.
| Method | Isolation, Cultivation, and Sequencing |
16S rRNA Sequencing |
Shotgun metagenomics |
bit-MAP®: Single-cell genomics |
|---|---|---|---|---|
| Target | Isolated bacteria | Any microbial samples (incl. unculturable ones) | ||
| Pre-study | Required (over months) | Not required | ||
| Objective | Deep understanding of one type of bacteria |
Community-level analysis | Deep understanding of individual bacterial functions |
|
| Principle | Sequence the entire genome of a single microbe |
Sequence 16S rRNA | Sequence a mixture of microbial genomes genomes |
Individually sequence whole |
| Resolution | Strain | Genus | Species | Strain |
| Expected results | Whole genome sequences, I plasmid sequences, and gene lists of a single microbe |
Ratios of microbes present | Ratios of microbes and genes present |
Whole genome sequences, plasmid sequences, and gene lists of individual microbes |
| Potential bias | Small | Large | Small | Small |
| Contamination risk | Small | Large | Large | Small |
| Analytical load | Small | Small | Large | Controllable |
Case Study: Analyzing soil microbiome
Higher-quality microbial genomes even from complex microbiome samples
When compared to the shotgun metagenomic sequencing, our single-cell sequencing method discovered more than 10-fold unique genes from the same amount of sequencing data (~80Gbp). Notably, while the metagenomic method suffers from obtaining longer genes (>300 amino acid residues), bit-MAP® can robustly recover genes at any sizes, even longer than 600 residues.
Applications of bit-MAP®
Unearth ‘microbial dark matter’ to build proprietary database
bitBiome is accelerating the world of synthetic biology with our massive and highest-resolution microbial genome library obtained from a wide range of environments, such as soil, marine water or extreme environment microbiomes.
bit-MAP® can help unearth ‘microbial dark matter’, which would have enormous potential as industrial applications, such as synthetic biology and biocatalysis applications.
Using bit-MAP®, we have been busy accumulating microbial genome data at the single-cell level. So far nearly 100,000 microbial genomes (~100 million genes) were sequenced since our establishment.
By providing access to our proprietary microbial genomic database and/or building exclusive database for your own samples, we will support the swift development of your business in the synthetic biology or biocatalysis space.
