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Microbiota: hidden communities of friends and foes

Odd as it might sound, most of the average person isn’t human. Researchers have recently dismissed the often cited claim that there are 10 times more microbes than human cells in our bodies. Scientists in Israel who published new estimates in August say the ratio is closer to 4:3 in men and 11:5 in women.

These complex communities of tens of trillions of bacteria and other single-celled organisms that inhabit the gut, lungs, skin and other parts of the body are known collectively as the microbiota. They interact with the parts of our bodies that make up their environment in ways that can be beneficial, neutral or harmful to us. Particular genera or species of microorganisms are described as commensal, symbiotic or pathogenic depending on their known impacts on our health. 

Step change in our understanding Recent years have seen a rapid growth in our understanding  of the many ways these bugs influence our day-to-day functioning. They provide us with nutrients and energy by helping to break down food, and even produce chemicals that can influence our mood. Some believe their combined genomes – known as the microbiome – may exert a greater influence on our health than the genes we inherit from our parents. “There has been a step change in our understanding of the fundamental roles these microbes play in the development and functioning of the immune system in the last decade,” says Professor Fiona Powrie, Director of the Kennedy Institute of Rheumatology at the University of Oxford. 

Powrie, who carried out pioneering work on defining the roles of regulatory T cells in self-tolerance and autoimmune disease, has also long studied the interactions between the immune system and microbes in the gut. She has shown how specific species of bacteria promote the production of regulatory T cells and effector T cells (those that bring about an immune response), and described details of the roles they play in driving inflammation. “We don’t yet understand all of the pathways by which the microbiota influence regulatory T cell differentiation, but we do know that when certain microbes are deficient, those pathways can be diminished,” says Powrie.

Lung communities

While Powrie and most other scientists looking at the human microbiota have focused on the gut, others have shown that bacterial communities in different parts of the body have their own distinct characteristics and roles. After carrying out early landmark genetics studies on asthma, Professor Miriam Moffatt and colleague Professor William Cookson, both at Imperial College London, began to investigate the roles for microbes in the lungs and airways. At the time, medical students were taught that the lungs were sterile – something their previous work had led them to doubt.

The emergence and development of molecular techniques  has revolutionised microbiology, with the rapid increase in  speed and accuracy of genetic analysis tools based on highthroughput sequencing. Moffatt and Cookson used  16S rRNA gene sequencing, a technique previously employed to determine the relationships between organisms. It makes use of the highly conserved nature of the 16S rRNA gene to allow the identification of bacteria and other microbes, although often down to the genera rather than the species level. The Imperial team combined the technique with nextgeneration sequencing to characterise the microbiota in the airways of healthy people as well as in patients with asthma and chronic obstructive pulmonary disease (COPD).

“We showed that healthy airways are not sterile, but have a characteristic community of bacteria, and also identified specific groups of bacteria that are more abundant in those with asthma and COPD,” says Moffatt.

Earlier this year, along with their collaborators, Moffatt and Cookson published a study in which DNA sequencing of sputum from the lower airways identified marked differences in the make-up of the bacterial communities in the lower airways of severe asthmatics, non-severe asthmatics and healthy individuals. Certain species within the Firmicutes phyla were correlated with asthma severity and characteristics, for example. Moffatt acknowledges however that the study could not tell them whether the different levels of bacteria were causes of ill health, or the results of it.

Checkpoint blockages

Immunity in the gutAlong with greater understanding of the importance of microbes within the body to immune defences has come an appreciation of their roles in influencing the effectiveness of treatments for disease. Drug regulators have in recent years approved a number of cancer immunotherapy therapies that work by blocking inhibitory signals known as checkpoints that normally act to prevent inappropriate immune responses. These have been shown to be highly effective for some patients but ineffective in others. Scientists have been trying to find out why in order to improve patient outcomes.

A team from the University of Chicago showed last year that tumour growth in mice varies depending on the microbial composition of the gut, and that immune checkpoint blockade therapy became more effective in those prone to melanomas when they were given faeces from less susceptible mice. French scientists have also shown a treatment that acts on checkpoint target CTLA-4, an important regulator of T cell responses, doesn’t work in mice that are germ-free or have been treated with antibiotics.

Bacterial gut composition is also believed to explain why around 30% of patients given anti-CTLA-4 cancer immunotherapy get colitis as a side effect. “The pathways involved are not completely understood, but what we are learning is that the outcome of cancer immunotherapy, including both efficacy and side effects, are dependent on aspects of the microbiota,” says Powrie, who published a review of research on the impact of gut microbes on cancer immunotherapy in December last year.

Putting knowledge into practice

There is of course a big difference between understanding how the microbiota influence immune responses, and devising interventions to improve our health. As with many promising areas of biomedical science, some of the claims being made in this area, especially those with commercial interests at stake, are not necessarily backed up by the research evidence. Despite this, the value of the worldwide market in probiotics – yoghurts and food supplements containing so-called ‘friendly’ bacteria and yeasts – stood at $62.7 billion in 2014, according to one recent estimate.

There is evidence that probiotics can reduce the risk of infectious diarrhoea associated with antibiotic use by almost half, and be beneficial to those with ulcerative colitis and pouchitis, a complication of surgical treatment for ulcerative colitis. Faecal microbiota transplants have also been shown to be effective  in treating the recurrent hospital-acquired infection Clostridium difficile.

The evidence on whether probiotics improve outcomes for those with respiratory infections and colds is mixed. Claims that they can lower blood pressure and cholesterol, help with weight loss, prevent or improve skin conditions, anxiety, depression and urinary tract infections are not supported by strong evidence. Research has shown that those with a variety of different conditions including cardiovascular disease, type 2 diabetes, Alzheimer’s and Parkinson’s have differences in their microbiota compared to healthy people; however what is not clear is whether this is part of what has caused their ill health or just a consequence of it.

Cause or effect?

“Changes in the microbiota are important in a number of diseases, particularly inflammatory diseases of the gut,” says Professor Julian Parkhill, of the Wellcome Trust Sanger Institute. “What we don’t really know yet is whether the changes we see in the microbiota are cause or whether they are effect, and that’s a very difficult question to answer. I think there’s a lot of potential for some specific diseases, but there’s been a lot of hype around the microbiota and a lot of things that are currently touted as potential avenues of treatment may well not pan out.”

What we don't really know is whether the changes we see in the microbiota are cause or whether they are effect, and that's a very difficult question to answer

Parkhill, who studies pathogen diversity and variability using high throughput sequencing and phenotyping, says the methods being used by researchers to identify the beneficial and harmful bugs inside us are not yet advanced enough to come to definitive conclusions. “Our understanding of the microbiota is generally at species level, and we really know almost nothing about sub-species diversity, which can be enormous and have big effects in the real world,” he says.

Moffatt believes interventions to alter the microbiota that interact with the respiratory system are some way off. “We’ve still got a lot more to learn,” she says. “We have to be very careful because we don’t yet fully understand how we interact with our microbiome.” Moffatt believes interventions to alter the microbiota that interact with the respiratory system are some way off. “We’ve still got a lot more to learn,” she says. “We have to be very careful because we don’t yet fully understand how we interact with our microbiome.”

Revolution of molecular techniques

Molecular techniques, such as the 16S rRNA gene sequencing method used by Moffatt, have revolutionised standard microbiology and driven progress on the understanding of the microbiota. Whole microbial genome sequencing offers the comprehensive detail that can unlock an organism’s functions and roles, however it is still relatively costly and complex when there are large numbers of organisms to characterise. Advanced selective sequencing techniques are available, but organisms still need to be isolated and grown in the laboratory in order to study them in depth.

One of the major roadblocks to understanding the roles microbes play in the human body has been the idea that the vast majority of the bacteria in our guts cannot be cultured using traditional laboratory methods because they die when exposed to oxygen. “There’s this dogma in that 90% of the bacteria of the gut can’t be cultured, and that therefore the only way we can address them is bulk sequencing, but the problem with bulk sequencing is you have to know what you’re looking for before you can interpret the data,” says Parkhill.

The emergence and development of molecular techniques has revolutionised microbiology, with the rapid increase in speed and accuracy of genetic analysis tools based on high-throughput sequencing

Earlier this year a group led by Professor Trevor Lawley, also at the Sanger Institute, combined large-scale whole genome sequencing, phylogenetic analysis, computational modelling and targeted culturing to show that 50–60% of intestinal microbiota bacteria produce resilient spores that can survive outside the human body. The breakthrough, if confirmed, should allow researchers to culture the microbes that make up most of the gut microbiota and which were previously thought impossible to culture. This of course opens the door to far greater understanding of their roles in the human body.

Beyond the specific identities of the organisms involved, another approach being taken is to focus on their functions and the metabolites they generate that facilitate their roles. “Scientists are starting to scratch the surface of bacterial metabolites and understanding their functions in terms of immune cell activity,” says Powrie. It is known that gut bacteria are important in breaking down otherwise undigestible carbohydrates into short-chain fatty acids, which play important roles such as preventing dietinduced obesity and insulin resistance, for example.

Laying the foundations

Many scientists investigating the relationship between the microbiota and the immune system are keenly aware that overblown early claims have led to disappointments in other fields. Yet at the same time, it is hard to avoid the conclusion that the rapid advances in knowledge and experimental techniques of the last 5–10 years can lay the foundations for a host of major health benefits in the not too distant future.

“So many different technologies have come together in the last five years,” adds Powrie. “The advances in sequencing and the new approach to culturing components of the microbiota have come alongside advances in gene editing and stem cell technologies. We’re poised to bring these cross disciplinary approaches together, and move from model systems to human patients. It really is an exciting time to be working in immunology, and medical research in general.”

This article was written by Nic Fleming as part of the BSI's report '60 years of immunology: past, present and future'. This article is licensed under Creative Commons Attribution-NoDerivative Licence (CC BY-ND 4.0). Additional permissions may need to be sort from image licence owners.