/More than 140,000 different viruses live in the human gut

More than 140,000 different viruses live in the human gut


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The most comprehensive database to date ‘maps out’ the multitude of bacteriophages — bacteria-eating viruses — in the human gut.
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  • Our gut is teeming with bacteriophages, which are a type of virus that infects bacteria.
  • Bacteriophages play a vital role in regulating gut bacteria, which, in turn, have a wide range of effects on our health.
  • Scientists have now compiled the most comprehensive database of human gut bacteriophages to date.
  • In the coming years, the Gut Phage Database will help to shed light on the contribution of bacteriophages to human health.

The community of bacteria, viruses, and other microorganisms that make their home in the human intestines is known as the gut microbiota.

Scientists know that gut bacteria are intimately involved in health and disease. These bacteria have effects on the metabolism, the immune system, and the nervous system. In some cases, they play a role in a wide range of illnesses and conditions, including malnutrition, heart disease, obesity, and multiple sclerosis.

Scientists know much less about gut bacteriophages, which are the viruses that prey on these bacteria, though their effect on a person’s health is likely to be equally profound.

In addition to regulating the population sizes of different bacterial species in the gut, bacteriophages drive evolutionary change in bacteria by transferring genes between species.

However, the diversity of viruses living in the human gut, their prevalence, and their effects on human health remain largely unknown.

To close this knowledge gap, scientists at the Wellcome Sanger Institute and the European Bioinformatics Institute, both in Hinxton, United Kingdom, have built up what they believe to be the most comprehensive collection of human gut phage genomes in the world.

They identified and classified viral DNA in 28,060 human gut “metagenomes,” which are the collective genetic sequences of entire communities of organisms living inside individuals. The metagenomes came from all over the world.

They also analyzed the genomes of 2,898 distinct strains of isolated and cultured human gut bacteria.

Their Gut Phage Database currently contains over 140,000 distinct viral genomes, more than half of which were previously unknown to science.

Most of the samples that the team analyzed were from healthy individuals. The viruses the team identified mostly use DNA as their genetic material, unlike pathogens, such as SARS-CoV-2 or Zika, that use RNA.

“It’s important to remember that not all viruses are harmful but represent an integral component of the gut ecosystem,” says one of the researchers, Dr. Alexandre Almeida, a postdoctoral fellow at European Bioinformatics Institute and the Wellcome Sanger Institute.

“It’s fascinating to see how many unknown species live in our gut and to try and unravel the link between them and human health,” he adds.

The study appears in the journal Cell.

Other scientists will be able to use the new database to investigate how viruses affect the “gut microbiome” — the collective genome of all the microorganisms in the gut — and hence human health. For example, it could lead to the development of bacteriophage-based therapies that target disease-causing gut bacteria.

“High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments, such as antimicrobials from bacteriophage origin,” explains first author Luis F. Camarillo-Guerrero from the Wellcome Sanger Institute.

The database is a further step towards identifying associations between the gut microbiome and individuals’ lifestyle, age, and diseases.

A study reported by Medical News Today in 2020 found that the communities of viruses in the gut are highly variable and probably unique to each individual.

The new research suggests that the composition of gut phages also varies by lifestyle. The scientists discovered that phages from people living in urban areas tended to target a bacterial genus called Bacteroides. In contrast, those from people in nonurban areas (among rural and hunter-gatherer communities) favored a family of bacteria called Prevotellaceae.

The study also revealed that while the majority of gut bacteriophages can only infect a single bacterial species, around 36% are likely to infect many different species.

These broad tastes may allow them to transfer bacterial genes between distantly related species in the human gut, say the authors. This could facilitate the rapid spread of evolutionary adaptations through the microbiome.

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