Education, breastfeeding and gender affect the microbes on our bodies

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

The greatest mass extinction may have been the doing of microbes

The worst time to be alive in Earth’s history is unarguably the end-Permian, about 250 million years ago. It is the period when the greatest-ever extinction event recorded took place, killing 97% of all species, an event so severe it has been called The Great Dying.

This event has generally been blamed on massive volcanic eruptions that took place at the same time. But now, in a new analysis, researchers at the Massachusetts Institute of Technology (MIT) argue that the mass extinction event may have been instigated by microbes. These microbes led to a perturbation of the carbon cycle that caused environmental shocks, such as global warming and ocean acidification. The shocks wiped out species in great numbers over a period of tens of thousands of years – a blip on geological scales.

Felt like the end of time

The end-Permian extinction, which took place about 250 million years ago, is the most severe of five known mass extinction events. It killed off the last of the trilobites – a hardy marine species that had survived two previous mass extinction. While land plants survived, almost all forests disappeared. Worse of all, it is the only known extinction event where even insects weren’t spared.

For an event of this size to take place, a lot of things would have had to go wrong. At the time the world was made up of a single supercontinent called Pangea. This large landmass, by altering the dynamics of how carbon is cycled with subducting plates, may have pushed global temperatures to the highest they had ever been.

Then, over the course of about a million years, huge eruptions in Siberia created basalts that cover an area that was about seven times the size of France. This may have pushed the environment past a tipping point by sending even more carbon dioxide into the atmosphere. That would have caused the oceans to acidify, killing more marine life, and heat up, releasing frozen methane. The upshot of all this would have been a “runaway” climate that kept heating up and removing more oxygen from the environment.

The mighty microbe

But Daniel Rothman of MIT thinks that the numbers don’t add up. “The changes in the carbon cycle globally are difficult to reconcile with only volcanic activity in Siberia,” he said.

His calculations, just published in the Proceedings of the National Academy of Sciences, were hinting that something else must have caused the runaway event. One hypothesis was that microbial life may have been responsible for that.

“This hypothesis is not as outrageous as it seems. After all, about 2.4 billion years ago, it was microbes in the form of cyanobacteria that gave our atmosphere all of its oxygen,” Rothman added. That period, called the Great Oxygenation Event, also killed most organisms that were adapted to the lack of oxygen and began one of the longest cold periods in Earth’s history. So microbes can certainly have global impact.

With colleagues at MIT, Rothman looked at the evolutionary history of Earth and spotted the rise of a particular type of microbe that occurred around the time of the Great Dying. That microbe, called Methanosarcina, had the ability to digest organic matter to produce methane. (Molecular biologists at MIT have shown that Methanosarcina evolved this ability thanks to the transfer of a single gene from the Clostridia class of bacteria.)

Rothman knew that the chemical process involved in creating the methane relied on the metal nickel. He went looking for evidence that Methanosarcina was thriving at the time in the sedimentary layer of the Meishan region of China. If the environment at that time had any more nickel than normal, then the sediments would hold the record of it.

Rothman chose the Meishan region to look for nickel because it is a particularly well-studied region. Its sedimentary layers have been used to mark and standardise different periods of Earth’s geological history, and they span the period of the Great Dying.

The search was successful. There was indeed a higher amount of nickel in the sediments deposited during that period. Methanosarcina would not have just been effective at creating methane – they would have flourished.

The nickel, Rothman suggests, would have been added to the oceans, where Methanosarcina lived and grew, by the continuous volcanic activity occurring in Siberia. The growing amount of nickel, transported by ocean currents, would have allowed more Methanosarcina to convert organic matter into methane, which would be converted to carbon dioxide through reactions with oxygen. This would have meant increased global temperatures and acidification of the oceans. The latter would have combined with the loss of oxygen (used up in creating the carbon dioxide) to accelerate the extinction in the oceans. And the dead organisms would have provided Methanosarcina with more organic matter to digest.

In short, a microbial innovation may have tipped over the balance to cause the Great Dying.

Marc Reichow at the University of Leicester remains sceptical of these results. He argues that there is no evidence that the increased nickel came from Siberian volcanoes. Rothman agrees that current data cannot identify the source of the nickel.

“This is an interesting hypothesis, but I think that Great Dying was the doing of many ‘kill mechanisms’ rather than just a single mechanism suggested here,” Reichow said.

There is also doubt over the exact period in which Methanosarcina actually evolved. Current techniques for estimating its origins based on DNA sequence differences have a huge error margin, which means it could have been well before or after the Great Dying.

Rothman concedes that there are limitations. “We believe that volcanism alone could not have caused this extinction event. Instead, what we have done is broadened the conversation by suggesting that it is possible that microbes may have caused it to happen.”

“The implications for today are that there many ways in which natural fluctuations can happen in Earth’s carbon cycle. When studying the changes happening to the carbon cycle now, we should try to take into consideration as many of those as possible to make future predictions.”The Conversation

This article was originally published on The Conversation. Image credit tjt195 (CC-BY-NC).