Five answers to the question ‘why microbes?’

Last month, Amelia gave us five great reasons to love plants. But plants aren’t the only species worked on at the John Innes Centre that lack the respect they deserve.


As a microbiologist I thought it was only fair to come up with my own ‘five answers’ – and show that microorganisms aren’t just here to cause us harm. In fact, they are essential for many processes, and have great potential for many more.


1. Antibiotics

The world is facing a crisis: antibiotic resistance. The best way to fight this is to treat antibiotics with a bit more respect – stop prescribing them when unnecessary, and follow treatment schedules properly. Until we solve this problem, however, we need to go out and find more to battle the strains that are multi-drug resistant.


Antibiotics are produced in nature as a defence against bacteria in the environment – such as streptomycin produced by Streptomyces, found in the soil. We are in a ‘drought’ of antibiotic discovery, with few breakthroughs in the past few decades. Scientists are now searching far and wide for new bacterial strains that can produce novel antibiotics to compete in the ‘arms race’ between humans and their pathogens.


We have barely scratched the surface with microbe discovery – and there may be more hiding away that we are unable to culture, or in environments we barely know. Examples of these are in deep sea trenches or the guts of insects. Some people even think there may be bacteria on Mars – and I’m sure if we do find them, people will be looking for antibiotics there too.


2. Genetic engineering

Microbes can be easily manipulated, and so have huge potential for genetic engineering. The best example of this is for the production of human insulin for treatment of diabetes.


Initially, diabetics were treated with insulin derived from animals – which often came with side-effects. As biology progressed the structure of insulin could be characterized (earning Fred Sanger a Nobel Prize), and entirely synthetic human insulin could be produced. Further developments meant that yeast could be engineered to produce human insulin – and this is how medical insulin is now produced.


Another example of a medicine produced by microbes is human growth hormone. Before we engineered microbes to make this, it would come from human cadavers!


Other potential uses for bacteria include developing them to clean up pollution (‘bioremediation’), fight tumours or detect arsenic in drinking water.


3. Food

If you say the words ‘microbes’ and ‘food’ to most people, they would probably think of food poisoning. However, some of our favourite foods wouldn’t exist without microbes.


Many industries rely on ‘fermentation’ – the ability of microorganisms to break down chemicals. Both brewing and baking require yeast fermentation (specifically Saccharomyces cerivisiae) to produce the gas bubbles that we need for beer and bread. Another example of fermentation is in the production of yoghurt, which uses a bacteria that converts lactose sugar in milk to lactic acid, giving yoghurt its sharp taste.


Bacteria aren’t the only microbes that are used in the food industry. Quorn, the popular meat alternative is produced from mycoprotein – produced from the fungus Fusarium venenatum.


Another use for fungi in food production is in cheese-making. Blue cheeses are treated with moulds which grow within, creating veins full of flavour. Soft cheeses such as brie have a bacteria growing on their outsides, allowing them to age from the outside in and allowing the interior to become runny.


4. Fuel

Our fossil fuel reserves are running out, and the race is on to find alternative sources of energy to sustain us.


Scientists are looking to bacteria for help. Like all organisms, bacteria are able to convert chemical energy (such as glucose) to other forms of energy (such as movement). In 1911 a scientist was able to produce an (albeit very small) electric current from E. coli. So the concept of microbial fuel cells was born.


Humans respire using oxygen, converting fuel (sugars) to energy, producing carbon dioxide and water. Many bacteria are able to respire without oxygen, and so instead of producing water in this reaction, produce protons and electrons. If we can harvest these electrons, then we have bacteria that produce electricity – a microbial fuel cell.


It is hoped that these fuel cells can be developed to be more efficient, and to use waste products such as those from industry as their fuel. If this can be achieved, it could have a huge impact on electricity production, as well as waste processing.


5. Symbiosis

The soil is a world full of microbes of all shapes and sizes – from bacteria to fungi to oomycetes. Although some aren’t friendly and can cause plant disease, many of them play quite the opposite role. Plants and specialised fungi can live together in harmony, and even help each other out. These beneficial relationships are known as symbioses.


There are two cases of soil symbioses that are particularly well-studied. The first of these (and the field in which my PhD falls) is the rhizobia-legume symbiosis – where bacteria convert nitrogen from the air into a form that plants can use in return for plant sugars.


The second is the case of mycorrhizal fungi, which associate with plant roots to get direct access to sugars. In return, the fungi scavenge through the soil for important nutrients and minerals such as phosphates.


There are many other cases of symbiosis that shape the world we live in – see this post from last year if you want to read more about rhizobia and some of our other favourite mutualistic relationships.


Interactions with plants aren’t the only case of bacteria living in harmony with other species. Our guts are full of bacteria with a wide range of benefits. They help us digest our food, stimulate cell growth, protect us from harmful microbes and help train our immune system to protect itself.

So, next time you think of microbes, don’t tarnish them all with the same brush. There is huge diversity across the microbe world – and huge potential for their use in many different areas of science.

To see Amelia’s answers to the question ‘why plants?’, click here

Izzy is a John Innes Centre PhD student. She’s on Twitter as @isabelwebb.

Photo: Alex Indigo/Flickr

Scientists in live public discussion today about what ‘natural’ really means

We’ve all seen it. Whether it’s on labels in supermarkets or in adverts on our TVs, the word ‘natural’ is often used to sell products.

Foods may be ‘naturallly’ farmed or contain only ‘natural’ colours and flavours. Or you may have used a ‘natural’ remedy to help you recover from an illness.

But why do products sold in this way appeal to us as consumers? Why are we so keen for our food to be grown ‘naturally’ while we strive for technological advances in other aspects of our lives? And does ‘natural’ in this context really mean what we think it does – if anything at all? Continue reading

Photo: Skånska Matupplevelser/Flickr.

EU’s rules on genetically improved crops a ‘threat’ to developments in agriculture, say MPs

A report out today is calling for the equivalent of Nice – the National Institute for Health and Clinical Excellence – for developments in crop technologies. The House of Commons Science and Technology Committee also says the government should encourage more public debate around developments in crop technologies

It recommends forming a ‘citizens council’ for considering the social and ethical impacts of new crops. Nice has a similar role producing advice on new medicines, which is used by the NHS to make funding decisions.

In its report, the committee criticises the model used for regulating genetically modified organisms in the European Union. The system “threatens to prevent such products from reaching the market both in the UK, in Europe and, as a result of trade issues, potentially in the developing world,” according to the committee of MPs. Continue reading

A global approach to achieving food security

Last month, 13 developing countries received recognition from the UN’s Food and Agriculture Organization (FAO) for their progress towards eradicating hunger and improving food security. At the ceremony, the FAO’s director general, José Graziano da Silva, congratulated them for turning political commitment into actions and demonstrating the will to achieve and surpass the millennium development goals.

Achieving food security – that is, guaranteeing that all people have access to sufficient and nutritious food to lead an active and healthy life – is the ultimate goal of the FAO’s work. The organisation’s activities range from creating indexes of agricultural productivity to supporting collaborations between public and private parties. It is also a neutral forum for international discussions and agreements so that global productivity may be increased through sustainable agriculture.

Improving crop productivity around the world requires actions on a number of fronts: political, social, economic and scientific. Small farmers in developing countries must be supported and their contribution to food security acknowledged. We need to enhance the capacities of breeders, scientists and workers in the seed industry. High-yielding and resistant crop varieties need to be bred. And key traits underlying adaptation to changing environments need to be identified – as is being done here at the John Innes Centre!

Continue reading

Genetically modified foods: would you eat a purple tomato?

In the past week there has been a lot of press coverage about genetically modified foods. The first of these was a proposal made by Rothamsted Research in Hertfordshire to carry out field trials on plants engineered to produce the omega-3 oils that are usually found in fish. The second of these was a farm in Canada who had produced 1,200 litres of juice from‘purple tomatoes’ – a genetically modified tomato developed here at the John Innes Centre. With all the buzz around these genetically modified foods, it made sense to write a post about the potential that genetic modification (GM) has for increasing the benefit of our foods.

GM is a type of plant breeding that has been used to improve crops, and has been in global commercial use for 18 years. These GM organisms, or GMOs, contain a DNA sequence that does not occur naturally in its own genome and has not been created by conventional breeding. GM has been used to create more efficient and improved crops, for instance increasing food production or creating herbicide-resistant plants.

Genetic modification is usually carried out using one of two systems. Both systems begin with identification of a desired gene. The gene is then inserted into a circular piece of DNA called a plasmid. This plasmid is then transferred into a bacterium which reproduces to create several copies of the gene. The gene is then transferred to the plant by one of two ways. The first is to attach the DNA sequence to particles of gold or tungsten and firing the particles into plant tissue. The second is to use an infective soil bacterium called Agrobacterium tumefaciens which has been modified so that it takes the chosen gene into the plant tissue but does not become active once inside the plant. These processes are usually done involving an antibiotic marker to allow detection of successful GMOs, although new technologies are being developed that work without an antibiotic marker1.

The first commercial GMOs were grown in North America in the late 1990s. Globally over 12% of arable land is now used for GM crops. Soya is the world’s leading GM crop imported for both feed and human products, with GM maize, oilseed rape and cotton being other important GM crops.

Most GM crops that are commercially grown are modified to improve their yields or pest/disease resistance. However, in more recent years, the potential of GM has been directed to improving the crops to make them more beneficial to health or to provide nutrients that are more difficult to get into the diet otherwise. Here I will briefly highlight three examples of this to show the potential that this technology can have.

Golden Rice vs Normal Rice
(Image from Wikimedia Commons)

Golden Rice:
Golden rice is a strain of rice that has been engineered with higher levels of vitamin A than normal rice. It was developed to combat childhood vitamin A deficiency – a common problem in developing countries such as India, which can lead to a compromised immune system and even blindness. This golden rice was developed with the aim that it would be freely available to developing countries without the demand for payment or licences which they simply could not afford. Engineering this sort of crop could make a huge difference to the lives of children in developing countries, and golden rice has had a lot of positive publicity behind it2.

If you are more interested in Golden Rice, there is an event at JIC this week, which will be streamed online and open to questions on twitter. More information here.

purple tomatoes

Only the purple tomatoes are GM.
The rest are natural varieties

Purple tomatoes:
These tomatoes produced here at the Norwich Research Park have two new genes from the snapdragon plant. These genes increase the levelsof anthocyanins in the tomatoes. These anthocyanins are the antioxidants found in blackberries and cranberries, and it is thought that these anthocyanins offer protection against some cancers, cardiovascular disease and age-related diseases. Considering that in 2012 32% of UK deaths were caused by circulatory disease, and 29% from cancer, developing foods that could combat these diseases is a top priority3. Tomatoes and their by-products such as tomato sauce are a widely produced and consumed food in the UK, and are more commonly consumed than the berries with naturally high anthocyanins. These purple tomatoes have been shown to extend the lifespan of cancer-susceptible mice4, leading to possible application in human cancer treatment/prevention. As mentioned previously, a farm in Canada has recently grown and juiced a crop of these tomatoes. This juice can now be used for further research on its benefits, as well as used to attract new investors. To find out more about the new advances in this, check out this video or this press release
People may be put off by the purple colour of the tomatoes – but humans have been breeding to change the colour of vegetables for centuries. Ancestral carrots were once purple – but the Dutch bred them to be orange, and those are the carrots we eat today.

Many people take fish oil capsules as a supplement (Image from Wikimedia Commons)

Omega-3 oils in plants:
Some fatty acids that we need in our diet are found in oily fish – which gain these oils by consuming marine algae. Eating these fish allows the fatty acids into our diets, and there are also dietary supplements that can be bought. Increasing omega-3 oil consumption is putting pressure on rapidly diminishing fish stocks, and fish farming relies on feeding fish existing omega-3 oils rather than the marine algae that they would get them from in nature adding furtherpressure on the industry. Researchers at Rothamsted Research in Hertfordshire have inserted algal genes into oil-producing crops (such as Camelina sativa, or false flax) to enable them to produce these oils in a more sustainable setting5. The crops that they have produced are currently awaiting approval for field trials of these GM crops.

As you can see from these three examples, there is a huge potential for using genetic modification to improve the crops that we grow and improve our diets for the better (and possibly cheaper too!). GM still has its skeptics, as well as a large amount of regulation at the EU and government level. We won’t be growing any of these crops for consumption here in the UK in the near future, but as even more developments come in the science, maybe changes will be made in the regulation and we might finally get the chance to try these exciting new products. I’d certainly like to try a purple tomato – would you?

To read about our experiences talking about GM at Science Festivals, check out our post from a few months ago here


  2. Am J Clin Nutr 2009; 89:1776–83; 7. Nature Biotechnology 26, 1301 – 1308 (2008)
  3. Deaths Registered in England and Wales (Series DR), 2011, ONS
  4. Nature Biotechnology 26, 1301 – 1308 (2008)
  5. Plant Biotechnology 7: 704-716 (2009)

By Izzy Webb – a second year PhD student in Phil Poole’s group