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Education, breastfeeding and gender affect the microbes on our bodies

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Trillions of microbes live in and on our body. We don’t yet fully understand how these microbial ecosystems develop or the full extent to which they influence our health. Some provide essential nutrients, while others cause disease. A new study now provides some unexpected influences on the contents of these communities, as scientists have found that life history, including level of education, can affect the sorts of microbes that flourish. They think this could help in the diagnosis and treatment of disease.

A healthy human provides a home for about 100 trillion bacteria and other microbes. These microbes are known as the microbiome, and normally they live on the body in communities, with specialised populations on different organs.

Evolution has assured that both humans and bacteria benefit from this relationship. In exchange for somewhere to live, bacteria protect their hosts from harmful pathogens. Past analysis of the gut microbiome has shown that, when this beneficial relationship breaks down, it can lead to illnesses such as Crohn’s disease, a chronic digestive disorder.

You’ve been swabbed

One of the largest research projects looking at the delicate connection between humans and their resident microbes is called the Human Microbiome Project (HMP). As part of the project, hundreds of individuals are being sampled for microbes on various parts of their bodies, with the hope that the data will reveal interesting relationships.

In the new study, published in Nature, Patrick Schloss at the University of Michigan and his colleagues set out to use data from the HMP to investigate whether events in a person’s life could influence their microbiome.

Their data came from 300 healthy individuals, with men and women equally represented, ranging in age between 18 and 40. Life history events, such as level of education, country of birth, diet, and recent use of antibiotics were among 160 data pieces were recorded. Finally, samples were swabbed from 18 places across the body to analyse their microbiome communities at two different time intervals, 12 to 18 months apart.

Those swabs underwent genomic analysis. A select group of four bacterial communities were selected to test what proportion of each was found on different body parts. That data was then compared with life history events. Only three life history events out of about 160 tested could be associated with a specific microbial community. These were: gender, level of education, and whether or not the subject was breastfed as a child.

This complicated issue may help diagnosis and treatment of illnesses. “If a certain community of bacteria is associated with a specific life history trait,” Schloss said, “it is not such a stretch to imagine that there may be microbiome communities associated with illnesses such as cancer.”

To be sure, these associations are only correlations. Neither Schloss nor hundreds of other scientists working on microbiome data can be sure why certain communities end up on certain body parts of only certain individuals. “We really don’t have a good idea for what determines the type of community you’ll have at any given body site,” Schloss said.

Lack of such knowledge means that Schloss cannot explain odd correlations, such as why women with a baccalaureate degree have specific communities in their vaginal microbiome. Because level of education is also associated with a range of other factors such as wealth and social status – we can’t know that it is only education affecting the vaginal microbiome. Janneke Van de Wijgert at the University of Liverpool said, “I think that it is impossible to tease out the individual effects of education, sexual behaviour, vaginal hygiene behaviour, ethnicity, and social status.”

Van de Wijgert believes the data has other limitations. “The study population of a mere 300 was homogenous and healthy – young, white women and men from Houston and St Louis – which likely means that much additional microbiome variation has been missed.”

With better tools, genomic data analysis has substantially improved since the project launched in 2008. Van de Wijgert thinks that future studies need to sample a lot more individuals and look for changes at shorter time intervals.

She is hopeful that microbiome data can be used to improve medicine, make it more tailored to individual. But before manipulations of the microbiome are used to treat illnesses, she said, it should be confirmed that the offending bacteria communities cause – and are not symptom of – disease. If the bacteria causes an illness, then efforts can be made – such as a change in diet or microbial transplant – to treat disease.The Conversation

Written with Declan Perry. First published on The Conversation. Image: NIAID

Scientists pinpoint when harmless bacteria became flesh-eating monsters

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Bacterial diseases cause millions of deaths every year. Most of these bacteria were benign at some point in their evolutionary past, and we don’t always understand what turned them into disease-causing pathogens. In a new study, researchers have tracked down when this switch happened in a flesh-eating bacteria. They think the knowledge might help predict future epidemics.

The flesh-eating culprit in question is called GAS, or Group A β-hemolytic streptococcus, a highly infective bacteria. Apart from causing flesh-eating disease, GAS is also responsible for a range of less harmful infections. It affects more than 600m people every year, and causes an estimated 500,000 deaths.

These bacteria appeared to have affected humans since the 1980s. Scientists think that GAS must have evolved from a less harmful streptococcus strain. The new study, published in the Proceedings of the National Academy of Sciences, reconstructs that evolutionary history.

James Musser of the Methodist Hospital Research Institute and lead researcher of the study said, “This is the first time we have been able to pull back the curtain to reveal the mysterious processes that gives rise to a virulent pathogen.”

Genetic gymnastics

Musser’s work required analysis of the bacterial genetic data from across the world – a total of about 3,600 streptococcus strains were collected and their genomes recorded. It revealed that a series of distinct genetic events turned this bacteria rogue.

First, foreign DNA moved into the original harmless streptococcus by horizontal gene transfer – a phenomenon that is common among bacteria. Such DNA is often provided by bacteriophages, viruses that specifically target bacteria. Picking up foreign genes can be useful because it can improve the bacteria’s survival.

In this case, the foreign DNA that was incorporated in the host’s genome allowed the streptococcus cell to produce two harmful toxins. A further mutation to one of these toxin genes made it even more virulent.

According to Musser, another horizontal gene transfer event made a good disease-causing pathogen into a very good one. The additional set of genes allowed it to produce proteins that suppress the immune system of those infected, making the infection worse.

Marco Oggioni of the University of Leicester said, “Because this study used data of the entire genome, all the genetic change could be observed. This makes it possible to identify molecular events responsible for virulence, as you get the full picture.”

Musser could also accurately date the genetic changes in GAS by using statistical models to, as it were, turn back the clock on evolution. They say the last genetic change, which made GAS a highly virulent bacteria, must have occurred in 1983.

Continental drift

That timing makes a lot of sense. “The date we deduced coincided with numerous mentions of streptococcus epidemics in the literature,” Musser said. Since 1983, there have been several outbreaks of streptococcus infections across the world. For example, in the UK, streptococcus infections increased in number and severity between 1983 and 1985.

It is the same story for many other countries, with Sweden, Norway, Canada and Australia falling victim to what is now an inter-continental epidemic. The symptoms ranged from pharyngitis to the flesh-eating disease, necrotizing fasciitis.

“In the short term, this discovery will help us determine the pattern of genetic change within a bacteria, and may help us work out how often bacterial vaccines need to be updated,” Musser said. “In the long term, this technique may have an important predictive application – we may be able to nip epidemics in the bud before they even start.”

What Musser is suggesting is that if enough bacterial genomes are regularly recorded and monitored, there is a chance that mutations or gene transfers, such as those GAS experienced, could be found ahead of time.

But Oggioni is sceptical. “While making such predictions may not be possible, this research will have other applications,” he said. “Knowing which genetic changes happen when can help tailor drug discovery research in a certain direction.”

Oggioni added that Musser’s work with GAS is only a model. Using Musser’s methods to record the evolutionary histories of other pathogens could be quite useful to tackle the diseases they cause now and, perhaps, even those that they may cause in the future.The Conversation

Written with Declan Perry. First published on The Conversation. Image credit: Zappys Technology

Massive asteroid may have kickstarted the movement of continents

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Earth was still a violent place shortly after life began, with regular impactors arriving from space. For the first time, scientists have modelled the effects of one such violent event – the strike of a giant asteroid. The effects were so catastrophic that, along with the large earthquakes and tsunamis it created, this asteroid may have also set continents into motion.

The asteroid to blame for this event would have been at least 37km in diameter, which is roughly four times the size of the asteroid that is alleged to have caused the death of dinosaurs. It would have hit the surface of the Earth at the speed of about 72,000kmph and created a 500km-wide crater.

At the time of the event, about 3.26 billion years ago, such an impact would have caused 10.8 magnitude earthquakes – roughly 100 times the size of the 2011 Japanese earthquake, which is among the biggest in recent history. The impact would have thrown vapourised rock into the atmosphere, which would have encircled the globe before condensing and falling back to the surface. During the debris re-entry, the temperature of the atmosphere would have increased and the heat wave would have caused the upper oceans to boil.


AGU

Donald Lowe and Norman Sleep at Stanford University, who published their research in the journal Geochemistry, Geophysics, Geosystems, were able to say all this based on tiny, spherical rocks found in the Barberton greenstone belt in South Africa. These rocks are the only remnants of the cataclysmic event.

According to Simon Redfern at the University of Cambridge, there are two reasons why Lowe and Sleep were able to find these rocks. First, the Barberton greenstone belt is located on a craton, which is the oldest and most stable part of the crust. Second, at the time of the event, this area was at the bottom of the ocean with ongoing volcanic activity. The tiny rocks, after having been thrown into the atmosphere, cooling, and falling to the bottom of the ocean, then ended up trapped in the fractures created by volcanic activity.

This impact may have been among the last few major impacts from the Late Heavy Bombardment period between 3 and 4 billion years ago. The evidence of most of these impacts has been lost because of erosion and the movement of the Earth’s crust, which recycles the surface over geological time.

However, despite providing such rich details about the impact, Lowe and Sleep are not able to pinpoint the location of the impact. It would be within thousands of kilometres of the Barberton greenstone system, but that is about all they can say. The exact location may not be that important, Lowe argued: “With this study, we are trying to understand the forces that shaped our planet early in its evolution and the environments in which life evolved.”

One of the most intriguing suggestions the authors make is that this three-billion-year-old impact may have initiated the the movement of tectonic plates, which created the continents that we observe on the planet.

The continents ride on plates that make up Earth’s thin crust; the crust sits on top of the mantle, which is above a core of liquid iron and nickel. The heat trapped in the mantle creates convection, which pushes against the overlying plates.

All the rocky planets in our solar system – Mercury, Venus, Earth and Mars – have the same internal structure. But only Earth’s crust shows signs of plate motion.

A possible reason why Earth has moving plates may be to do with the heat trapped in the mantle. Other planets may not have as much heat trapped when they formed, which means the convection may not be strong enough to move the plates.

However, according to Redfern: “Even with a hot mantle you would need something to destabilise the crust.” And it is possible that an asteroid impact of this magnitude could have achieved that.The Conversation

First published on The Conversation.

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