A recent study conducted by biological engineers at the Massachusetts
Institute of Technology (MIT) sheds light on how bacteria in the human gut
adapt their CRISPR defenses in response to viral threats. The human gut
microbiome, which is made up of trillions of bacteria from diverse species,
plays a crucial role in digestion, immunity, and overall health. However,
these bacteria are vulnerable to infections from viruses called
bacteriophages. One of the primary defense mechanisms against such viral
attacks is the CRISPR system, which allows bacteria to recognize and destroy
viral DNA.
Bacteria’s Ability to Adapt CRISPR Defenses
In laboratory conditions, bacteria can quickly adapt their CRISPR systems by
incorporating new viral recognition sequences known as spacers into their
genomes. This process helps bacteria "remember" past viral infections and
mount a stronger defense if the same virus invades again. These spacers can
accumulate in the hundreds within a bacterial cell and are passed down to
offspring. In some cases, they can even be transferred to neighboring bacteria
through horizontal gene transfer, spreading immunity within the bacterial
community.
Slow CRISPR Updates in the Human Gut
While bacteria in laboratory settings can acquire new spacers as often as once
a day, bacteria in the human gut update their CRISPR defenses at a much slower
rate. According to the study, gut bacteria acquire new viral spacers at an
average rate of one every three years. This finding is surprising, given the
constant viral exposure in the gut, both from the microbiome and external
sources like food. The study raises the question: why do gut bacteria update
their CRISPR defenses so much slower than those in the lab?
Research Methodology and Data Analysis
To explore this question, researchers analyzed two large datasets of microbial
genomic sequences from the human gut. The first dataset included over 6,000
genomic sequences from 52 different bacterial species, while the second
consisted of over 388 longitudinal metagenomes from four healthy individuals.
The analysis confirmed that spacer acquisition is a rare event in the human
gut microbiome, prompting researchers to investigate possible environmental
factors that could explain this slow process.
Factors Slowing Spacer Acquisition in the Gut
One key factor identified is the density of bacterial populations. In
laboratory environments, bacteria grow in high-density populations, making it
easier for them to interact with bacteriophages and incorporate new spacers.
However, in the human gut, food intake frequently dilutes bacterial
populations, flushing out bacteria and viruses multiple times a day. This
process reduces the frequency of interactions between bacteria and viruses,
diminishing the need for frequent CRISPR updates.
Spatial Distribution and Reduced Viral Exposure
Another factor contributing to slower spacer acquisition is the spatial
distribution of bacteria in the gut. Some bacterial populations reside in
areas less exposed to viruses, such as the mucus layer near the gut’s
epithelial lining. This separation reduces encounters with viruses, further
slowing the CRISPR update process.
Bifidobacterium longum: An Exception to the Rule
Despite the generally slow rate of spacer acquisition, researchers observed
that one bacterial species, Bifidobacterium longum, had recently
acquired multiple spacers targeting two types of bacteriophages. This suggests
that B. longum has been under significant viral pressure.
Interestingly, the acquisition of spacers in B. longum was primarily
driven by horizontal gene transfer, where bacteria "borrow" genetic material
from neighboring bacteria. This highlights the importance of
bacterial-bacterial interactions in the evolution of viral resistance.
Implications for Microbiome-Based Therapies
The study’s findings also have implications for microbiome-based therapies,
such as fecal microbiota transplants (FMT), which often show inconsistent
results. One potential reason for these inconsistencies is that transplanted
bacteria may struggle to survive or thrive in the recipient’s gut. By studying
how bacteria acquire viral resistance and identifying the prevalent viruses in
a patient’s microbiome, scientists may be able to design therapeutic microbes
better suited to resist local viral threats, improving treatment outcomes.
Conclusion: Insights into the Dynamics of the Human Microbiome
Published in Cell Genomics, this study provides valuable insights
into how the human microbiome defends itself against viral threats. The
research helps us understand the dynamics of CRISPR spacer acquisition in the
gut and the factors influencing microbial immunity in the human digestive
tract. Furthermore, it opens up new questions about the role of CRISPR in
microbial immunity and suggests that bacteria may use a range of immune
strategies, beyond CRISPR, to protect themselves from viruses. These findings
could lead to more effective therapies for promoting a healthy microbiome and
improving the success of microbiome-based treatments.