The insides of humans are rife with viruses that feed on bacteria. What do they do?
The multitudes of bacteria and other microscopic organisms in our stomachs are known as the microbiome. It appears that the bacteria are infected with viruses, which has significant ramifications for them and us.
Introducing the phageome.
The human digestive system is home to billions, if not trillions, of these viruses, sometimes referred to as bacteriophages (Greek for “bacteria eaters”) or just “phages” by their pals. According to Breck Duerkop, a bacteriologist at the University of Colorado Anschutz School of Medicine, the field of phageome science has exploded recently, and scientists are finding it difficult to comprehend their immense diversity. Researchers believe that doctors may be able to enhance human health if they can identify and target the appropriate phages.
Paul Bollyky, a Stanford Medicine researcher and physician specializing in infectious diseases, predicts that there will be both beneficial and harmful phages. However, the exact number of phages in the gut is still unknown; it could be as little as one or as many as one for every bacterial cell. Phage genes can also be found in bacteria that don’t actively produce viruses; instead, the bacteria passively carry the phage DNA around in their genomes and go about their daily lives.
Furthermore, many phages remain unidentified. These are known as the phageome’s “dark matter” by scientists. The identification of these viruses and the bacteria that host them is a major focus of modern phage research. There are over 140,000 phages in the Gut Phage Database, but that number is undoubtedly underestimated. According to Colin Hill, an Irish microbiologist at University College Cork, “their variety is just extraordinary.”
By sorting through genetic sequences extracted from human fecal samples, scientists can identify phages. That’s where the most prevalent gut phage group, known as crAssphage, was discovered by researchers. (Given its name from the “cross-assembly” method used to extract their genes from the genetic jumble.) A lightbulb-shaped crAssphage with a 20-sided body and a stalk to inject DNA into host bacteria was described by Hill and colleagues in a recent study.
Although the impact of crAssphages on human health is unknown, Hill wouldn’t be shocked if it were the case considering that they infect Bacteroides, one of the most prevalent types of gut bacteria. The Gubaphage (gut bacteroidales phage) and the LoVEphage (many viral genetic elements) are two more prevalent types that also infect Bacteroides.
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Individual phageomes differ greatly from one another. In the 2023 Annual Review of Microbiology, Hill and colleagues detailed how they vary based on factors like as age, sex, nutrition, and lifestyle.
Although bacteria are occasionally killed by phages, the relationship between the two is more nuanced than that. “We used to think that phage and bacteria are fighting,” Hill explains, “but now we know that they’re dancing; they’re partners.”
Bacteria can gain from phages by absorbing new genes. A phage particle may occasionally cram bacterial genes into its protein shell in addition to its genetic material when it is building inside an infected bacterium. According to Duerkop, the inadvertently transferred genes may prove useful when they squirt those genes into a fresh host later on. They could offer the capacity to digest novel material or resistance to antibiotics.
According to Hill, bacteria are kept in shape by phages, which are always snapping at their heels. On their exterior surfaces, Bacteroides bacteria can exhibit up to twelve different types of sugary coatings. There are advantages to having multiple coats, such as being able to hide from the immune system or inhabit a different part of the digestive system. However, Hill notes that in the presence of crAssphages, Bacteroides have to continually switch coats to avoid being recognized by the phages. As a result, different coat types of Bacteroides are always present, allowing the population to fill a range of niches and adapt to novel situations.
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Phages also prevent the overgrowth of bacterial populations. Like the woods, the gut is an ecosystem, and phages are predators of bacteria just like wolves are of deer. Like the forests need wolves, the gut needs phages. The disease can arise from alterations in those predator-prey connections. Phageome modifications have been documented in inflammatory bowel syndrome (IBS), irritable bowel disease (IBD), and colorectal cancer. For example, the viral ecology of an IBS patient is frequently low in variety.
Individuals attempt to restore the gut microbiota through dietary changes or, in severe situations, fecal transplants. According to Hill, phage-based approaches may offer a more specialized strategy. For example, researchers are looking for phages that may be administered therapeutically to infect the bacteria responsible for stomach ulcers.
Maybe we should be appreciative of the trillions of phages that keep the ecosystem of the gut in check. Without them, a few types of bacteria may quickly take over, according to Hill, which could cause you to have gas and bloating and possibly be unable to digest certain foods.
