The Gut's Friendly Viruses Revealed

Published online 14 July 2010 | Nature | doi:10.1038/news.2010.353

The gut's 'friendly' viruses revealed
DNA sequencing reveals a new world of bacterial viruses in our intestines.

Amy Maxmen


In the gut, viruses that normally prey on bacteria seem to live in harmony them.
DR. HAROLD FISHER, VISUALS UNLIMITED /SCIENCE PHOTO LIBRARYIn the latest exploration into the universe of organisms inhabiting our bodies, microbiologists have discovered new viral genes in faeces. They find that the composition of virus populations inhabiting the tail ends of healthy intestines (as represented in our stools) is unique to each individual and stable over time. Even identical twins — who share many of the same intestinal bacteria — differed in their gut's viral make-up.

More than 80% of the viral genetic sequences found, which included sequences characteristic of both animal and bacterial viruses, have never been reported previously. "This is a largely unexplored world," says Jeffrey Gordon at Washington University in St Louis, Missouri, and an author on the paper, which is published in Nature today1. "We are truly distinct lifeforms — sums of microbial and human parts."

More than 10 trillion bacteria normally inhabit the gastrointestinal tract, where they synthesize essential amino acids and vitamins, produce anti-inflammatory factors and help break down starches, sugars and proteins that people could not otherwise digest. Within and among these bacteria live bacterial viruses, or bacteriophages, which affect bacterial numbers and behaviour as they either prey on bacteria or co-exist with them, shuttling genes from one bacterium to another.

This microscopic dynamic ecosystem affects our lives in ways we still do not fully understand. Indeed, the rise in the incidence of food allergies in Western societies has led to hypotheses that extreme hygiene disrupts the ability of microbes to colonize human guts, resulting in a lack of tolerance to usually harmless foods.

“This study is looking into the genesis of the human body by seeing what viruses within it are up to.”

To explore this provocative hypothesis, researchers must first understand the complete composition of the microbial ecosystem of the healthy body. To this end, Gordon's group and others are beginning to catalogue the human 'microbiome', all the microorganisms living in the human body, using advanced DNA sequencing technologies. Until now, however, such attention has primarily focused on the bacteria rather than viruses.

"This is a wonderful study," says David Relman, a microbiologist at Stanford University in California, who is involved with the US National Institute of Health's Human Microbiome Project. "It could be that viruses are the real drivers of the system because of their ability to modify the bacteria that then modify the human host," he says. "So this study is in some ways looking into the genesis of the human body by seeing what viruses within it are up to."

Microbial truce
According to the new study, bacterial viruses in the terminal gut or colon seem to exist in a more stable state than do similar communities in the environment, such as in the oceans. Faeces from each individual — four pairs of identical twins and their mothers — carried a distinct viral community that varied by less than 5% over the course of a year. The bacterial viruses also appeared to mainly be lying low as 'prophages' rather than multiplying and killing the bacteria they infect.

"In oceans, the modality of viruses has tended to be predatory," comments Edward DeLong at the Massachusetts Institute of Technology in Cambridge. "Now the interesting thing here is that the system in the faecal microbiota seems to be driven by prophages, which tend to basically integrate their genetic material into the host genome and hide there — it's a much more stable situation."

"This kind of stability implies that there is a symbiosis between bacteria and viruses," comments Martin Blaser at New York University Medical Center. "This is different from a predator-prey, or an arms race, situation. This is a picture of a more settled existence, in which the different populations are working together."

The team found genes encoding proteins never detected before in bacterial viruses. When in bacteria, these proteins are part of pathways responsible for carbohydrate metabolism and amino-acid synthesis. Viruses carrying such genes might alter them and insert them into gut bacteria, potentially changing a person's metabolism.

Because human nutrition partly depends on the relationship between bacteria and their viruses, understanding the dynamics of that relationship might yield treatments for obesity, allergies and other maladies. "This human ecosystem is quite important because it determines what we can do and what we can eat," says DeLong. "That's why we should care about this."

http://www.nature.com/news/2010/100714/full/news.2010.353.html

Glynis

Very interesting - thanks Glynis - another piece to reveal more in our "jigsaw"

Thanks Glynis ...

What an interesting idea ... I found this while googling good viruses ... it's well worth reading. I copied in a small paragraph that I thought was interesting ...

http://www.cosmosmagazine.com/node/1024

Is it possible that our chronic viruses are really the result of viruses trying to control bad bacteria ? .... x

Thank you, Enid,

as you will probably know, I have been looking at d-lactic acid in CFS, and wondered whether a virus could somehow cause changes to the gut flora, so that d-lactic acid producing bacteria become dominant, as per KDM/Sheedy's paper. I wonder whether the mechanism is in the paper as it says "The team found genes encoding proteins never detected before in bacterial viruses. When in bacteria, these proteins are part of pathways responsible for carbohydrate metabolism and amino-acid synthesis. Viruses carrying such genes might alter them and insert them into gut bacteria, potentially changing a person's metabolism."

As d-lactic acidosis is caused by carbohydrates being fermented by d-lactic acid producing bacteria, in short bowel patients with a gut bacterial overgrowth, and given the gut symptoms in CFS patients, I wonder how relevant this might be.

Glynis x

Hi Xchocoholic,

Thanks for the link, I was thinking the same, that a certain virus has taken control over the gut bacteria, and that the bacteria then overgrow and cause d-lactic symptoms.

I have put a thread on d-lactic acid, if you are interested. Here is the link, however the info is a bit disorganised!

http://forums.aboutmecfs.org/showthread.php?8022-D-Lactic-Acidosis-in-CFS

After I read the KDM/Sheedy paper in which d-lactic acid producing bacteria were found to be higher in CFS patients than in healthy controls, and that the 2 conditions are said to be strikingly similar, I looked online to see whether this study was being taken forward. I have discovered that at Melbourne Uni, a study is just starting to see whether d-lactate can be detected in CFS patients' blood. Given the similarities of CFS/d-lactic acidosis, this may be exciting, time will tell.

This paper on d-lactic acid has a graph of symptoms, you will see how similar the symptoms are to CFS, hope you find it of interest.

http://hkjpaed.org/details.asp?id=577&show=1234

Best Wishes

Glynis x

Glynis, the symptoms are indeed so very familiar (including my loss of consciousness twice as well as the ME "black holes" over a very unpleasant period and severe cognitive difficulties over a long period - all starting 10 years ago. I have always had bowel problems off and on. Rethinking timing though makes me a little confused because I was not using Probiotics then - that's not to say the the culprits were not building up in the bowel. I rushed to check my current P's which seem to be controlling stools - more solids and not dark - and the makeup is (a BioCare mix) - fructooligosaccharides 200mg, lactobacillus acidophilus 80mg plus bifidobacterium bifidum/lactis 12mg. And yet the culprit or the mix has eased things. There's no doubt that the lining of the gut was way out kilter, and so many of us have it. I tested positive high on Kenny Meileir's Neurotoxic Metabolite Test (NHS found no problem) so all is a mystery. Sorry to give you all the details. Any research in that area has to be good for us too - very much in the news. This relates to the article on over use of Probiotics (esp acidophilus) being a "cause".