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
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.