New technique combines single-cell and metagenomic analyses to
characterize microbes
Researchers develop an integrated single-cell metagenomics framework that
can improve the accuracy and resolution of microbial characterization

Date:
October 13, 2021
Source:
Waseda University
Summary:
Metagenomic analysis has greatly advanced our understanding
of the complex human microbiome without the need for extensive
bacterial isolation and culturing. However, metagenome-assembled
genomes may be imprecise and insufficiently differentiate closely
related species. Now, researchers have developed a novel integrated
framework that combines conventional metagenomics and single-cell
genomics and can complement the lacunae in each approach, thus
yielding better genome recovery and accurate resolution of complex
microbial populations.



FULL STORY ==========================================================================
The microbial inhabitants of the human body, collectively known as the
"human microbiome," play an integral role in maintaining the health of
the body. These microbes often reside in harmony, while also aiding normal physiological processes. However, any imbalance in their populations can trigger various pathological conditions. Understanding these host-microbe relationships in health and disease is therefore crucial.


========================================================================== Metagenomics, an advanced DNA sequencing technique, enables the direct extraction and in silico(or computer-simulated) characterization of
genetic material from mixed microbial populations at once, while bypassing
the cumbersome task of isolating and culturing different bacterial species
from the mixture. While this technique is useful in getting a broader
picture regarding the microbiome, finer details across closely related
species can be missed, thereby contributing to bias and inaccuracy.

Single-cell (sc) genomics is a promising alternative approach that
enables the recovery of genomes from individual cells. In the larger
picture, however, this approach can result in incompleteness of the
assembled genomes given the smaller DNA fragment sizes, compared to the conventional metagenomics approach.

In a pioneering collaborative study between Waseda University, Japan,
and bitBiome, a startup initiative from Waseda University, a team of researchers including Associate Professor Masahito Hosokawa tested a
hybrid approach combining conventional metagenomics with sc-metagenomics
that can bridge the gaps in both the techniques. "Bacterial genomes reconstructed from metagenomic analyses alone are imperfect and contain
errors. We have developed a novel single cell metagenomics integration framework, termed SMAGLinker, which determines the genome sequence of
each cell individually. Using this method, we aim to obtain accurate
bacterial genomes comprehensively, which has been a challenge in the
past," explains Hosokawa, who is also the founder of bitBiome.

They first generated single-cell amplified genomes (SAG) using
microfluidic technology (an advanced DNA amplification technique), for
the human gut and skin microbiota, as well as for a "mock" microbial
community containing known bacteria for validation purposes. Next,
they analyzed and clustered the sequences, using a method called "contig binning." They integrated this analysis with metagenome-assembled genomes
(MAG) to improve the overall coverage and binning accuracy.

On comparing the integrated approach with the conventional metagenomics approach, they found that the former showed higher accuracy and precise
binning along with a notably higher genome recovery rate (including rRNA,
tRNA and plasmids), compared to the conventional approach.

Using SMAGLinker, the researchers could construct a large number
of high- quality genomes from the gut and skin microbiota. Moreover,
genomes obtained using this integrated approach spanned a larger number
of bacterial genera compared to the conventional approach, indicating
better coverage of bacterial diversity.

Diving deeper, the researchers also obtained better resolution of
intra-species diversity using SMAGLinker. While the conventional
metagenomic approach revealed only one genome of the bacterium
Staphylococcus hominis, contaminated with other Staphylococcusspecies
genomes, the integrated approach revealed two independent strains
harboring distinct plasmids from the same skin microbiota sample. They
were also able to successfully validate their findings using the mock
microbial sample.

In summary, SMAGLinker is a powerful tool that can improve the accuracy
and quality of genome recovery and resolution of closely related genomes
in complex microbial mixtures. The authors are excited about the potential ramifications of their findings. "Human commensal bacteria are deeply
related to human health and understanding host-microbe interactions is important for designing novel medical treatments as well as for industrial
and environmental applications. We are hopeful that this technology can
be extended across diverse research disciplines for accurate microbial characterization," concludes Hosokawa.

========================================================================== Story Source: Materials provided by Waseda_University. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Koji Arikawa, Keigo Ide, Masato Kogawa, Tatsuya Saeki, Takuya Yoda,
Taruho Endoh, Ayumi Matsuhashi, Haruko Takeyama, Masahito Hosokawa.

Recovery of strain-resolved genomes from human microbiome through
an integration framework of single-cell genomics and metagenomics.

Microbiome, 2021; 9 (1) DOI: 10.1186/s40168-021-01152-4 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/10/211013104625.htm

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