Future trend: More detailed analysis of intestinal microbial strains and diseases and health

Every day, the billions of bacteria that are parasitic in your digestive system change; the food you eat, the medications you take, and the bacteria you come into contact with will make some bacteria more likely to breed than others

In the past ten years, scientists have generally described a person's microbiome by describing the types and numbers of bacteria present-the collection of microorganisms found in the human intestine

Bacterial strains are a bit like dog breeds or tomato breeds-they are part of the same species, but different from each other

The researchers found that, in some cases, the abundance of a bacterium remained constant between two time points, but the strains in that species changed dramatically

More meaningful microbial research

In your gut, bacteria may not only digest food

Since each type of bacteria has its own genetic code, scientists rely on DNA sequencing to discover which bacteria inhabit the microbiota of a particular person

So far, identifying genetic differences in microbiome samples requires high-performance computing power and cloud storage, which most laboratories cannot do

"The algorithm for analyzing genetic sequences was developed for the human genome," said Pollard, a professor at the University of California, San Francisco and a researcher at the Chen Zuckerberg Biological Center

Pollard and her colleagues know that long-term genome sequences are common in many bacterial species or strains

The researchers analyzed more than 100,000 publicly available high-quality genomes of about 900 bacteria commonly found in the human intestine

"With the proliferation of newly sequenced genomes in the gut microbiota and other environments, we can now create detailed genetic maps for thousands of bacteria.

This field of research has previously been limited because only a few laboratories in the world have funds or computer hardware to analyze microbiome data at strain resolution

Pollard said: "Our new algorithm opens the door for everyone to achieve this level of resolution on a personal computer

Before and after antibiotics

One of the questions that microbiome researchers have been trying to answer in recent years is how much change will happen to the microbiome in a person over time
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This issue has been discussed at the species level; scientists have tracked how the species composition of the human microbial community changes with changes in diet, disease, or the environment
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However, the results of the study failed to explain how the microbiota acquired new functions, such as antibiotic resistance or the ability to inactivate chemotherapy drugs, while the species composition remained stable every month
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Pollard and her colleagues hope to investigate this issue in depth by analyzing bacterial strains, not just species
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They repurposed a method used to sequence human single cells and used it to barcode bacterial DNA molecules
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This allowed the research team to track a single bacterial strain in a person during a five-month study
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In 5 months, the team sequenced the microbiome of a healthy individual approximately once a week
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During this time, the subject was unexpectedly diagnosed with Lyme disease and received a two-week antibiotic treatment-as we all know, antibiotics can destroy many types of bacteria, including those living in the human intestine
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Goode, assistant professor of applied physics at Stanford University, said: “Our hypothesis is that many microorganisms will become less abundant after antibiotics and then recover, but the final microbiome will be more or less similar to the microbiome at the beginning.

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In some cases, this is true-certain types and strains of microorganisms have remarkable adaptability, with almost no changes in their genomes at the beginning and end of the 5-month period
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But in other cases, the strain that emerged after the antibiotic was genetically different from the beginning of the antibiotic, even if the abundance of the species did not change
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Importantly, if the research team only analyzed the species in each microbiome sample, these differences would be ignored
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Although the GT-Pro algorithm cannot be used in this research yet, Pollard said it will make similar research easier and cheaper in the future
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Map new paths for microbiome research

The bacteria in your body is like a jungle-a living, ever-changing ecosystem coexisting with organisms in a delicate balance
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When looking at satellite images from above, ecologists can monitor the deepest and most dramatic changes in the jungle, but they miss the finer complexities that shape the environment
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Similarly, those who study the microbiome by observing changes in species have gained a high-level perspective on this network, seeing only the most obvious links to health and disease
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But with GT-Pro and new perspectives on microbial strains, new connections will become apparent
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"There is still a lot of work to be done to understand the functional consequences of different microbiota," Pollard said
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"But until now, we haven't had the right measurement tools to ask these questions-now we have
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research about

Paper "Fast and accurate metagenotyping of the human gut microbiome with GT-Pro" on December 23, 2021, published in " Nature Biotechnology on" magazine
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The paper "Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment" was published in the August 2021 issue of " Genome Research "
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