Photograph
of a glass SlipChip for growing microbes, shown next to a US quarter
(left). Fluorescent in situ hybridization image of the target organism
(right, top). Transmission electron microscopy image of a single cell of
the target organism (right, bottom). Credit: Liang Ma (Ismagilov group)
and Roland Hatzenpichler/Caltech
The world around us, and certainly within us, is full of bacteria.
Within our very guts are millions of individual strains that may have
beneficial functions for our bodies, be cause of disease, or simply be
resident microbes living peacefully in a hospitable environment.
Studying specific species among such a large set of bacteria is
difficult because some strains are considerably more numerous, eclipsing
others that are difficult to detect and isolate. This has greatly
impeded research into the gut’s microbiome. Researchers at Caltech have
developed a new method that relies on a microfluidic device, called
SlipChip, that can help isolate and culture specific bacteria for
laboratory work.
Fluorescence
images showing that RNA sequences from the target organism (red and
green) are present in every cell (blue, overlay). The overlay validates
that this is a pure culture of a single microbial species—and that the
single species is the target organism.
The SlipChip, also developed at Caltech, can help isolate specific
bacterial strains from a sample into separate compartments. Once there,
the researchers are able to split the contents of the compartments,
using one half to identify the strain using DNA sequencing, while the
other is kept alive for further cultivation and experimentation.
More info from Caltech:
To validate the new methodology, the researchers isolated
one specific bacterium from the Human Microbiome Project’s “Most
Wanted” list. The investigators used the SlipChip to grow this bacterium
in a tiny volume of the washing fluid that was used to collect the gut
bacteria sample from a volunteer. Since bacteria often depend on
nutrients and signals from the extracellular environment to support
growth, the substances from this fluid were used to recreate this
environment within the tiny SlipChip compartment—a key to successfully
growing the difficult organism in the lab.
After growing a pure culture of the previously unidentified
bacterium, Ismagilov and his colleagues obtained enough genetic material
to sequence a high-quality draft genome of the organism. Although a
genomic sequence of the new organism is a useful tool, further studies
are needed to learn how this species of microbe is involved in human
health, Ismagilov says.
In the future, the new SlipChip technique may be used to isolate
additional previously uncultured microbes, allowing researchers to focus
their efforts on important targets, such as those that may be relevant
to energy applications and the production of probiotics. The technique,
says Ismagilov, allows researchers to target specific microbes in a way
that was not previously possi
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