Saturday, 11 January 2014

The Story of the Sourdough Starter

As a food addict, I watch a lot of cooking programs on TV. One of my favourite celebrity chefs is master baker Paul Hollywood. Unfortunately, I recently heard the silver fox seemingly refer to yeast as 'Lactobacilius'. This broke my microbiologist heart into a thousand pieces, and I decided to help clarify. Before we go any further, let me stress that Lactobacillus (note the extra 'i' isn't necessary, Paul) is a group of Bacteria. Yeast are fungi. Totally different!

So I started doing some research, and it turns out that sourdough starters are fascinating!

Everybody knows that yeast is what bakers use to make their bread rise, and the increased popularity of artisan breads has introduced all of us to the concept of sourdough; made from a starter containing wild yeast, cultured in kitchens and larders the world over. It's super easy, if not lengthy, to get your starter going: you simply mix strong bread flour with water to a batter consistency, leave it somewhere to get contaminated, then feed it every few days with more flour to keep the microbes growing big and strong.

I always assumed that the yeast in a sourdough starter was Saccharomyces cerevisiae [sac-a-row-my-sees ser-eh-vis-ee-ay] (commonly known as bakers' yeast). This is the stuff you buy in the supermarket for bread baking. To the best of my knowledge, it comes in three forms: fresh, dried and fast action. It is also sometimes called Brewers' yeast, because it's the same species which ferments the sugars in grapes or malt to produce wine and beer. At home, we put this work horse of the food industry to good use often, with bread baking and home-brewing regularly on the go. As we all know, when bread is baked, the yeast digests sugars in the dough and produces carbon dioxide. This gas gets trapped in the strands of gluten in the dough, and expands as it heats in the oven. This is how bread rises and what gives the dough its tiny holes.
I'm a very lucky girl, to have a boyfriend who makes great beer and bakes delicious bread, using the yeast Saccharomyces cerevisiae. Shame none of it ever lasts long...

However, I was wrong in my assumption about the species found in a sourdough starter. It turns out that it's impossible to introduce S. cerevisiae into a sourdough starter, because it dies out after about a week. Instead, the wild yeast which most commonly falls into the flour and water mixture and becomes established is Saccharomyces exiguus, also called Candida holmii. So this S. exiguus lives happily in the batter, feeding on the carbohydrates from the flour. As the cells eat, they grow larger. Then when they've doubled in size they go through a process called binary fission; they split into two new cells. These smaller, new cells are called daughter cells. Each daughter then eats, grows, divides, and so it goes on...

Simple, right?

Actually, it's more complex than that!

The carbohydrates in the flour are often indigestible by the yeast, so it needs help to access the food locked up in the flour. That's where Paul Hollywood's Lactobacillus comes in. Sourdough starters are actually a mixed population of yeast and lactic acid Bacteria. The Bacteria break down the complex carbohydrates, turning them into smaller, simpler sugars which the yeast can sink their proverbial teeth into. The two species end up in a stable relationship, because if one grows a bit too quickly to out-compete their neighbour, they run out of food quickly and then their growth slows down, allowing their neighbour to catch up.

The most commonly cited lactic acid bacterium in a sourdough starter is Lactobacillus sanfranciscensis, which was discovered in a starter in, believe it or not, San Francisco! Luckily for the yeast, the way Bacteria digest their food is somewhat messy. Instead of taking the complex carbohydrates into their cells and breaking them down there, they secrete digestive enzymes into the environment to do the digesting outside the cells, and then they take up the products. This means that the long, complex carbohydrates in the flour get broken down while they're floating around in the batter, and the smaller sugars are left lying around for the yeast to gobble up. It's the same as the way my Mum used to cut up fish fingers for me when I was too young to use cutlery. Lactobacillus, like Saccharomyces, is also a genus with several applications in the food industry. For example, this group of Bacteria are used in the dairy industry to help convert milk into yoghurt and cheese. They do this by breaking down lactose, the sugar found naturally in milk. As a result of the break down of lactose, they produce lactic acid (yes, the same stuff your muscles produce when you push yourself hard at the gym). The lactic acid curdles the milk, making it thicker and more sour.

Cheese, made when Lactobacilli break down lactose and produce lactic acid (

Can you see where we're going here? We've got Lactobacillus in a sourdough starter. Yes! You see, that's where the characteristic flavour of sourdough comes from. Cool, huh?

So the yeast needs the Bacteria to help cut up its food for it; the yeast is required to produce the gas which makes the bread rise; and the Bacteria give the bread its delicious flavour. It's very clever! And the real beauty of all this is that it just happens by accident. The microbes are trying to get on and live their lives, and we've stumbled upon a way to use that to our advantage, again!

Tuesday, 2 July 2013

Superstition in Science

The Manchester Museum hit the spotlights recently thanks to a mysterious spinning statuette on display. The statuette in question has been filmed turning 180° over the course of several days, seemingly of its own accord. The story hit headlines all over the world, and news film crews showed up for several days on the trot to get a piece of the action. I have been working as a demonstrator at the Manchester Museum, which is part of the University of Manchester, for the past year or so, and since the media storm over this unexplained phenomenon, all my students who have visited to attend a science session have wanted to see the famous statue and speculate as to the explanation. Several teachers have even surreptitiously sidled up to me and quietly asked me what the trick is.

The Statuette showing us its prayer for beer and bread...
 The statuette, which by all accounts is nothing special, has only recently started turning, since it was moved a couple of metres from its previous position to a new display cabinet. Other objects in the same cabinet don’t move, and it only spins during daylight hours.

You can see the time-lapse video of the spinning statue and get more information here:

The University of Manchester’s resident ‘voice on all things physics’, Professor Brian Cox, quickly spoke out with his logical explanation for this mystery motion. He cites differential friction, between the stone surface and the glass of the shelf, which is causing the figurine of Neb-Senu to vibrate and therefore rotate, when visitors walk through the gallery. However, lots of tweeters, visitors and bloggers have asked how this can explain the fact that the statue only rotates half a turn, and doesn’t move in any other direction.

Regardless of what Brian Cox, or anyone else thinks about the explanation, one thing’s for sure: the buzz around the museum has been very tangible of over the recent week or two. The ‘mystery’ has sparked intrigue among some of our young visitors who might have otherwise rushed through the Ancient Worlds gallery to head to the more interesting snakes and frogs in the vivarium, or the stuffed polar bear in the Living Worlds gallery. It has probably also increased traffic through this jewel in Manchester’s crown. While some people have claimed this must be a publicity scam - if more people bother to go to the museum, isn’t that a good thing?

This got me thinking about the role of superstition in science, and in our lives in general. Although I’m a staunch scientist I’m also superstitious. It sounds contradictory, but I knock on wood if I’m hopeful that what I’m talking about will come true, and I always pick up a penny off the floor and hand it to whoever I’m with, since, as the saying goes, “Find a penny, pick it up, all day long you’ll have good luck. If you give it to a friend, then your luck will never end.”

Whilst I’ve never noticeably experienced any improvements to my day when I find a penny on the floor, my rationale is that at least the person I’m with ends up slightly richer than before, and no harm was done. My boyfriend, who is the most frequent recipient of my treasures, is used to me arriving home, rummaging in my pockets and retrieving a grubby 1p for him, with an expectant grin on my face. He graciously thanks me for the offering, and has learned not to ask what oily puddle it came from. On a good day, the coin is silver, and on rare occasions sometimes my beady eyes spot a £1 coin for him!

I decided to look into this issue of superstition and science a little more deeply. Unsurprisingly, there’s very little research out there into the crossover between scientific evidence and superstitious beliefs. The two are understood to be polar opposites, and proponents of one seem to be harsh critics of the other. There is, however, one brilliant book by Bruce M. Hood called ‘The Science of Superstition’. Hood begins the book by writing about houses which local authorities destroyed following revelations that horrific murders took place inside them. These unfortunate properties are notoriously difficult to sell at their actual value and are targeted by twisted fanatics who want to catch a glimpse of the site of such terrible events, and maybe even take a souvenir for themselves. I’d never thought about this issue before, but I certainly wouldn’t want to live in a house where victims had been tortured, killed and buried, and I don’t think many people would.

To an extent we all value a connection between an emotion and an inanimate object. Perhaps your childhood teddy holds too many good memories to be thrown away. I’m sure that if da Vinci had dusted off an old canvas and painted an EXACT copy of the Mona Lisa a few years after the first, the duplicate - although identical in every respect - wouldn’t be nearly as valuable as the original is today. There’s a restaurant in Cornwall that sells food leftover by its famous patrons. Granted the sales are in aid of charity, but isn’t that a little bit disgusting? Hood calls this connection to objects, which we create in our minds, the ‘Supersense’. While on holiday in Peru last year, I saw a surprising number of people (all of them tourists) climbing onto or reaching to touch cordoned off Incan objects. Groups of hippies can be found meditating on the stones of Sacsayhuaman on a daily basis; guards must be employed to prevent wandering hands from touching the Intiwatana stone at Machu Picchu. It seems people love to feel the ‘energy’ of these important objects.

Ed and me, looking excited about reaching Machu Picchu!

There’s a great deal of superstition in the scientific practices going on around me in the lab. Some colleagues will only label tubes in a certain direction, or arrange equipment in a particular order. It’s not uncommon to inherit a protocol someone else has optomised, only to find that shaving out steps makes no difference to the outcome whatsoever.

Humans naturally place significance on objects or behaviour. The very fact that the statuette in Manchester Museum was found buried with a mummy makes it special and valuable. We wouldn’t have museums displaying these artifacts if we didn’t care about their connections. Just next to the Egyptology gallery is a room dedicated to objects relating to excavations of settlements of ancient humans in Britain. Take it from me, as someone who has pored over these cases for some time, most of the stuff on display is little more than rocks. If you squint, you can just about see how these inconspicuous lumps have been modified by ancient hands for a particular purpose, but if we applied nothing but pure, Vulcan logic to these stones, we wouldn’t care toffee for them. It’s all well and good for Prof Brian Cox to dismiss the mystery of the spinning statue with an explanation, but personally, I like that there are some things we can’t explain. As the French say, “C’est pour faire parler les curieux” (‘it’s to make the curious talk’). In other words, if the mystery can’t be reasoned but it excites a discussion, then it’s worth it.

Tuesday, 14 May 2013

Dental Flossing - A Microbiologist's Perspective on Dental Hygiene

I hate flossing! I’d put it up there with leg waxing and eyebrow plucking on my list of hated personal hygiene chores. Recently, I decided to look into what all the fuss was about, in order to try and scare myself into flossing my teeth and gums more regularly, and maybe even building the habit into my daily routine.
Image provided by mconnors (

The mouth is a pretty complex environment. It’s got soft parts, hard parts, moisture, fluctuating food and oxygen levels and there’s a constant movement of the contents in one direction or another. About a milliliter of saliva is produced every minute, most of which is swallowed quickly. Throughout the day, as we eat and drink, the surfaces of our mouths get covered in chewed up food, and mixed around with saliva which contains digestive enzymes. So, what’s actually going on in the mouth, from a microbiology perspective?

Firstly, let’s get to grips with the mouth itself. We all know about teeth and gums, but there’s more going on behind your lips than just that. There’s also the inside of the cheeks, the tongue and the roof of the mouth (or the palate) to think about.

All of these different surfaces represent different types of habitats for Bacteria. For example, gums are soft and fleshy with a strong blood supply. This means they’re easy for Bacteria to cling to, but there are white blood cells nearby to attack Bacteria. Teeth, on the other hand, are very hard and slippery – difficult for microbes to get hold of. The skin cells on the inside of cheeks are constantly being rubbed off as we talk and chew, so the Bacteria living there have to work hard to cling to their home. It’s hard to believe, but the surfaces of the cheeks and tongue are completely replaced every 48 hours! There are thousands of tiny nooks and crannies (or in science terms: niches) for Bacteria in the mouth to occupy, and the conditions in these niches can vary dramatically, with differences in moisture and oxygen levels, availability of nutrients and competition with neighbouring Bacteria. The tongue, for example, is covered in millions of taste buds, which give it a rough, bumpy texture – creating a huge surface area that can be covered in microbes. Like skin and lungs, the mouth is constantly being invaded by microbes; however, the mouth is a unique habitat because of the hard teeth, which don’t shed their outer layers on a regular basis.
Image provided by Alvimann (
The mouth of a healthy person contains a huge number of Bacteria: in fact, a normal mouth contains between 200 and 500 different species of Bacteria at any one time!! It has long been known that mechanical removal of these Bacteria is the most effective method of cleaning the teeth, but once you’ve brushed your teeth, there’s an almost immediate re-colonisation of the surface. This colonisation happens in a cycle, each time you brush your teeth.

Seconds after you put your toothbrush down and wipe away the toothpaste moustache, a layer called the ‘dental pellicle’ forms over the enamel surface of your teeth. This layer contains lots of glycoproteins, which select for the colonisation of some Bacteria, and inhibit the colonisation of others. The squeaky clean feeling you get after you’ve given your teeth a really good scrub is a result of this smooth pellicle layer.

So, who arrives first? Some of the early colonisers of clean teeth are Bacteria from the Streptococcus genus, particularly Streptococcus sanguis. These are relatives of the pathogen that causes ‘strep-throat’. Other Strep’ species are found all over the different surfaces of the body. Streptococci breakdown lactose in milk, producing lactic acid, so are vital workhorses in the cheese industry. What’s interesting is that Streptococcus sanguis colonisation of the teeth is encouraged by the pellicle, but Streptococcus salivarius is inhibited (despite what the name might suggest)! These Bacteria bind by interacting with the glycoproteins in the pellicle using receptors on their surface. Some Bacteria have tail-like projections from their surfaces that can be used to swim through saliva and interact with the pellicle to stick to teeth.

The colonising Bacteria multiply to big numbers, with 250,000-630,000 Bacteria per mm2 of tooth surface within the first four hours of colonisation! Although that sounds huge, these Bacteria actually grow relatively slowly, only dividing once every 4-6 hours on average. Microbiologists in general would scoff at this and tell you about the famous E. coli which has a doubling time of about 20 minutes under laboratory conditions. The reason these dental Bacteria multiply so slowly is probably because there’s (surprisingly) very little food available to them. The textured areas of the teeth used to chew are more likely to retain food, so of course these areas have higher numbers of Bacteria than the smooth sides of teeth.

Once a layer of these pioneer species has formed and grown, then another wave of invaders arrives. Instead of sticking to the pellicle, these ‘bridging species’ bind to the pioneer species to get a foothold on your teeth. This is not a random event; the guys who were first in the queue get to be very selective about who else can join the party. For example Fusobacterium nucleatum binds directly to Streptococci and the other Bacteria already on the teeth. It’s worth pointing out, at this stage, that the conditions on the surface of teeth are very different depending on whether you’re above or below the gum line. Above the gum line there’s lots of air and saliva, below the gum line there’s much less oxygen available. This means that the Bacteria found at these different sites are different, because they’re adapted to different conditions.

Bridging species start to grow and multiple, once they’ve made direct connections to the pioneer microbes on the teeth. As the numbers of microbial cells increase the original layer is cut off from the oxygen and food. The Bacteria produce and release all kinds of chemicals: to communicate with each other, to kill their competing neighbours and to secure their place in the growing biofilm – the plaque on your teeth. This plaque contains lots of waste products from the Bacteria, including acid from the breakdown of sugars, like the lactic acid produced by Streptococci. This is plaque acid, which erodes the hard, enamel surface of the teeth. After these bridging species have made a nice thick layer of cells and cell material, the final invaders start their assault. Species like Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia band together in a complex and bind to the Bacteria in the plaque biofilm, especially below the gum line. These three are known to be oral pathogens, they cause the gums to become inflamed and to shrink away from the teeth. This exposes more of the tooth’s surface, and allows the colonisation process to happen all over again.
Image provided by wax115 (

So, back to flossing; as I mentioned earlier, the best way to remove plaque from the teeth is by mechanical removal –mouthwash isn’t as effective at getting those slimey bugs off compared with a good scrub using a toothbrush and toothpaste. Although the cyclical colonisation of the teeth is completely natural and healthly, we all want to avoid gum disease, and to do that we need to wipe the slate clean and force the process to start all over again, before the likes of P. gingivalis have the opportunity to bed down in the gums and cause chaos. Brushing doesn’t clean between the teeth, and the surfaces which can’t be reached by brushes add up to a surprisingly big area, containing millions of Bacteria. Instead we need to use alternative, mechanical methods to clean out the bridging and climax species from those hard-to-reach areas on a regular basis. This is why flossing (or using those cute, inter-dental brushes) is so important. We can rely on the fact that the hundreds of Bacterial species that make up dental plaque take at least 24-48 hours to settle and grow into the worst form of harmful plaque, so we’ve got that window of opportunity each day to get rid of them. Once the layer of plaque is removed, saliva contains minerals to re-harden the tooth enamel, after plaque acid has gone.

So, although it’s hateful, I’m determined to make a much better effort to floss everyday. Knowing the good it does, maybe you should too.


Human Oral Microbial Ecology and Dental Caries and Periodontal Diseases (W.F. Liljemark and C. Bloomquist, 1996)

The efficacy of interdental brushes on plaque and parameters of periodontal inflammation: a systematic review(DE Slot, CE Dörfer, GA Van der Weijden, 2008)

Defining the healthy "core microbiome" of oral microbial communities (Egija Zaura, Bart JF Keijser, Susan M Huse and Wim Crielaard, 2009)

Role of the Oral Microflora in Health (Philip D. Marsh, 200)
Dental plaque formation (Burton Rosan and Richard J Lamont, 2000)
Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia: the ‘red complex’, a prototype polybacterial pathogenic consortium in periodontitis (Stanley C. Holt, Jeffrey L. Ebersole, 2005)

Saturday, 20 April 2013

The Germs In Your Kitchen - Should We Care?

Feedback is incredibly important. No one can hope to get better at anything without some way to measure how they’re doing. I’m a great believer in feedback; I regularly contribute to Trip Advisor and hang around in shops to speak to managers about how great a job one of their employees did at serving me (much to my boyfriend’s embarrassment). So, when I read an article ( about the Bacteria in your kitchen in the NY Times blog recently, the need for feedback kicked in.
Image provided by sjfranks (
It’s a piece by Anahad O’Connor, about a study conducted by NSF International. This study investigated different parts of the kitchen to identify potentially dangerous Bacteria lurking in the heart of every home.

Now, don’t misinterpret me. I’m not saying that the post made me angry, or even livid to the point of scarlet, incendiary rage. I’m not saying that I shrieked in horrified rage across the quiet mutter of conversation at my local pub last Friday evening when I read the article. I’m not saying that at all. In fact, there are some brilliant aspects to this piece, which I’ll mention as we go on. However, there are also a couple of areas that I’d have written very differently. Be clear, this isn’t meant to be a criticism of the article, or of its creator (an immeasurably better science writer than me – I’ve never written a book!). This isn’t smack talk, or beef. I’m trying to open up the topic of environmentally and clinically important Bacteria from my own personal perspective, hopefully to create a little scientific debate. This article is a springboard to talk about issues, which I think, many writers and journalists are getting wrong when it comes to microbes.

O’Connor should be congratulated for bringing the issue of microbes in the kitchen to the public’s attention. For someone who runs home to tell my family and friends about the millions of Bacteria we encounter on a daily basis, it’s exciting when these underrepresented but crucial little critters get a big stage appearance. I’m saddened though, that there’s no mention of the obvious limitations to the study. Looking for potentially dangerous Bacteria isn’t like looking for life on other planets. Take a deep breath – there you found some potentially dangerous microbes, and now they’re in your lungs. I’m typing this on a keyboard – eurghhh that means I’m touching potentially dangerous Bacteria! You see what I’m getting at. If you set out to find food-borne Bacteria in a place where food is prepared, stored and eaten, you’ll definitely find what you’re looking for.

On a more important note, is it healthy to spread the perception that ‘nasty germs’ live in the kitchen?  Should we be cracking open the bleach every morning before we prepare breakfast?
Image provided by pegesus (
The Hygiene Hypothesis is the idea that as standards of living have risen since the industrial revolution, so standards of cleanliness in the home have improved, which has, in turn, lead to a dramatic increase in immune disorders such as hay fever and asthma. This hypothesis has been around for as long as I have and in that time, researchers have made huge leaps towards understanding the effects of a more ‘clean’ domestic environment on human health. The bottom line is: a diverse and healthy population of microbes in the body, from birth to death, is how our immune system keeps itself in check. Scientists are now starting to realize that we humans are ‘superorganisms’ because we are made up of more than just human cells. Bacterial cells outnumber human cells in our bodies, and not just by a slim margin, by ten to one. So for every skin cell, brain cell or blood cell, in your body, there are ten times more Bacteria. These microbes are much smaller than our own cells, but they’re as much a part of you as your own cells. These microbes make up what’s called the human ‘microbiome’.

One thing that many people don’t realize, is that by having a complete layer of Bacteria on every surface of your body, you’ve got a ready made, primary defense mechanism against other microbes. Colonisation of the gut by Bacteria is almost impossible if the existing population is healthy, even if the would-be colonizers are usually found in the gut; treat your microbiome well, and it will fiercely defend you and kill off foreign attackers - even if those attackers are harmless and would love to live in your gut. The chance of being colonized by an individual bacterial cell that happens to have grown on your blender is slim. To be fair, we’re constantly being bombarded with Bacteria, and sooner or later at least one will make it past the bacterial doorkeepers and the immune system, so I’m not encouraging anyone to live in a house of squalor. A common sense approach to cleanliness is key. Besides, who didn’t realize that the vegetable draw and the water dispenser would be full of Bacteria and mould??

Another aspect of this article that I found disappointing, was the heavy talk about E. coli and Salmonella; every journalist’s ‘go-to’ nasties when it comes to food poisoning. Did you know, however, that the most common cause of bacterial gastroenteritis (food poisoning) is a bacterium called Campylobacter jejuni? Few people have heard of the Campylobacter family, but they cause more infections of the digestive system, worldwide, than E. coli and all the Salmonella species combined!! Campylobacter causes acute infection of the digestive tract (with all the horrifying symptoms you’d expect), and can result in a paralysis disorder called Guillain Barré Syndrome. Infection with C. jejuni is nasty, and every year up to 2 million Americans are left pinned to the bathroom floor, unsure of which end they should point towards the bowl, by it. This number isn’t dropping either. I’m not trying to scare you about food poisoning, instead I’m trying to highlight the fact that lazy journalists go back to E. coli and Salmonella time and time again, perpetuating the idea that these Bacteria are the ones we should be worried about. The only reason journalists got to hear of them in the first place is because there have been a handful of highly publicized outbreaks of dangerous versions of these species – while C. jejuni infects people at a fairly constant rate, so that doesn’t count as news for some reason. C. jejuni isn’t mentioned in the NSF report either, and that’s because it’s a microaerophile, meaning it can only grow in a low oxygen environment and dies quickly when exposed to normal, atmospheric levels of oxygen. It is found naturally in the guts of chickens, so is commonly found in chicken meat. This isn’t a problem, as long as you cook your poultry produce properly because the cooking process kills the Bacteria.

Infectious Bacteria are like people – the vast majority will never bother you or have any direct impact on your life at all; the ones you do encounter will mostly be nice; but very occasionally you’ll come across a rotter. Poor old E. coli, and it’s cousins the Salmonella species are generally decent, upstanding Bacteria, harmlessly going about their business without any damage to us humans, but they get hounded! The truth is, your body is made up of more E. coli cells than human cells, and every gram of solid waste (poo) you produce contains 1000000000000 E. coli cells!!! Every single person’s intestines are crammed full of E. coli, which is great because those tiny cells help to digest our food, and are also producing up to 70% of the vitamin K we absorb. If we tried to avoid E. coli, we wouldn’t get very far. Of course sometimes a stray E. coli cell wanders off to the urinary tract, or develops toxins which cause disease, but those are the evil psychopaths of the microbial world, not the Average Joes.

On a side note, biologists use a binomial nomenclature for naming all organisms scientifically and this system comes with a couple of rules. The first part of a scientific name is always the genus; it starts with a capital letter and can be abbreviated to just the first letter. The second part is the species name, which is always in lowercase letters. Since they’re both in Latin, they have to be italicized. So, for Anahad O’Connor’s benefit, E. coli was almost right, but you didn’t put it in italics, and Salmonella needed a capital S and italics, because it’s the genus and not the species name. I’m sure a physicist would cringe if I were to write Einstein’s famous equation as E=MC2, right?

For more information about the different roles Bacteria play in our body, a good place to start is the excellent review paper by Stig Bengmark called ‘Gut microbiota, immune development and function’ (Pharmacological Research Volume 69, Issue 1, March 2013, Pages 87–113).

Thursday, 28 March 2013

SGM Spring Conference - My Experience

The Society for General Microbiology came to town this week. Their annual Spring conference was held in Manchester this year, which was very convenient. This post summarises my experiences from the first two days of the meeting.

So, aside from almost barging into a Professional Hairdressers Conference, which was going on at the same time (and I know I'm not the only person who almost made that mistake), getting registered and getting our bearings was very smooth and straightforward. I was planning to stay resolutely fixed to the symposium entitled "Metabolic Interactions at the Host-Pathogen Interface"; and for the most-part, I did. So, even though neither metabolism nor the host-pathogen interface are particularly pertinent to my research, I was ready to learn all about them.

The morning was heavy on intra-cellular pathogens, such as Listeria, Salmonella and Plasmodium. I tend to get up on my soapbox when academics talk about the importance of Salmonella, because public perception of food poisoning is often that Salmonella and E. coli are the biggest players in disease, but I was pleased to see that Paul Barrow gave Campylobacters their just credit! After these talks, we all headed to the auditorium for the Colworth Prize Lecture, delivered by Jeffrey Almond. His talk was about vaccine development, and was certainly very interesting from a business perspective. Academics can sometimes forget that if there's not enough market interest in a product, then no one can afford to spend the money developing it.

After the delicious (although bijou) lunch, it was back to Charter 1 for more metabolic interactions. This time, the most interesting talks for me were given by Tyrrell Conway and David Clarke, because there was some 'real' microbiology! Tyrrell's presentation was about his research into colonisation of the gut by E. coli, which is a very buzz topic at the moment. Conversely, David told us all about a very funky bacterium called Photorhabdus, which glows bright green (for no apparent reason) and which has a very intricate relationship with a nematode worm. Between these two some of the details were positively stomach turning (lots of poo and exploding worms!). Campylobacter jejuni finally made an appearance in John Kendall's talk at the end of the session.

The highlight of the day, for me was David Bhella's Peter Wildy Lecture. David, who is clearly well rehearsed at talking to groups of fidgeting students with poor attention spans, kept me captivated the entire way through his presentation with mesmeric videos of spinning viral particles and DNA models. I have to admit, though, that watching one of his videos did feel like the closest I'll ever get to an LSD trip! At the end of his talk, I felt very really fired up to get back into the public domain and spread the word about microbes in a fun and engaging way!

Another bonus of the day was chatting to Vicki Symington at the SGM stand about the range of resources the SGM can provide members for educational purposes.

With the rumours of biscuits at coffee time I was re-enthused and ready for the morning session. The talks in the Metabolics section seemed more intensive than Monday's, but I thoroughly enjoyed listening to Graham Stafford talking about sialic acid use by Tannerella forsythia, which lives in the gap between the teeth and the gums.

The SGM Prize Medal Lecture was given by (HRH) Harald zur Hausen - yes, the Nobel Prize winner! He talked about cancers caused by viruses which affect different parts of the world at different levels. The topic was somewhat bleak, and there were mutters as we left the auditorium about whether to eat beef in future. Despite the sobering nature of the lecture, it was really great to hear about real-life, applied virology and the impact virologists are having on the lives of humans around the world.

After lunch (with much more appropriate food levels - thanks SGM), it was back to the Metabolic Interface. The afternoon talks seemed to take a decidedly molecular turn and I was rapidly struggling to keep up, so I headed for the Co-Infection session at a convenient moment. All the talks I heard there were focused on Candida albicans (a fungus) and a bacterial partner in crime, bringing us back to the gore, with details about hospital-aquired infections, pictures of rotten tongues and nasty stories of systemic diseases. We even saw a video of a patient who'd be given a voicebox implant, and then were presented with information about how these implants can fail because of microbes which colonise their surface. My throat was closing up at the mere thought of it!

The last talk of the day was the Hot Topic Lecture, delivered by Paul O'Toole. This presentation made the entire meeting for me; I was frantically scribbling notes from start to finish! Paul was discussing the human microbiome, the population of microbes that each and every one of us carries around with us throughout our entire lives. These 'fellow travellers', as Paul called them, are hugely important for our bodies. I learned that 70% of the Bacteria living on our bodies cannot be cultured in the lab. That is staggering! It's only recently, since we've been able to study these microbes by getting sequence data from them, that we've been able to detect them at all, and yet they are as much a part of our bodies as our hearts or our skin!!

After the lecture, I was dying to ask Paul a question, but I was too far away, at the back of the auditorium, so I didn't dare put my hand up and yell all the way to the front. I didn't get to catch him in the drinks session afterwards, either, which is a big shame (for me - probably not so much for him!), but he was undoubtedly being swamped by adoring groupies! I did, however, bump into a former lecturer, Charles Penn, from my undergraduate days at the University of Birmingham - as well as some other familiar faces. I also managed to trap David Bhella into a conversation, while trying not to melt into a nonsensical, starstruck wreck! The conference, for me, ended with a girly gossip and catch up with a fellow Birmingham escapee who I used to attend aerobics classes with (of course!).

All in all, my first SGM conference was a great experience. It had the right blend of learning, networking and re-motivating me to get back into the lab and produce some groundbreaking research. I'm very much looking forward to going again next year...

Tuesday, 19 March 2013

Why is Microbiology Important?

What am I doing, banging on about microbes? Why do microbes matter?

The field of microbiology is relatively old, as science goes; the ancient Romans knew that some invisible life forms sometimes caused disease. However, unlike some other disciplines, the huge bulk of discoveries in microbiology have come about in the past 200 years. This rapid acceleration in learning was kick started in the 1600s when scientists like Kircher and van Leeuwenhoek used lenses to magnify, enabling us to see tiny microscopic creatures. Before this time, the only evidence we had of microbes was the effects they had on the world around us.

So, what are microbes?

A microbe (or micro-organism) is a living creature which is very very tiny. No, really - they're tiny!! Microbes are microscopic, which means they can't be seen with the naked eye; they can only be seen under a microscope.
Image provided by Ardelfin (

To put this in context: the species of Bacteria which I research, called Campylobacter concisus, is roughly 3 micrometres long - in other words three millionths of a metre, or 0.000003 metres. In some very quick (quite literally done on the back of an envelope) maths, I calculate that approximately 140000 bacterial cells could fit into the full stop at the end of this sentence.

Microbes are often unicellular (or single-celled) organisms. All living creatures are made of cells; complex animals like humans are made from trillions of cells which are specialised to do different jobs (like brain cells, blood cells and kidney cells). For unicellular microbes, each individual cell is a complete organism, and it must do everything required to survive: eat, move, sense danger and everything else they might require. Some microbes a multicellular; but even these are very small. The term 'microbe' covers things like Bacteria and Fungi, as well as unicellular animals like amoebae and algae. Microbes have evolved to live in almost every niche on the planet, and some are able to survive in extremely challenging environments.
Tiny cells, big business

Although the numbers are hard to find (and it's tough to get my brain to work after a day helping undergrads in the lab!), I estimate that microbes are worth many hundreds (if not thousands) of billions of pounds every year!!

 A big claim, but here's my logic:

  • According to a report published by The Brewers of Europe, european beer sales were worth 106 billion Euros (£93.1 billion) in 2010 (
  • ReportLinker says that the Vitamin and Supplements industry is worth $68 billion (£59.8 billion)
  • US Drug companies represented by PhRMA (Pharmaceutical Research and Manufacturers of America) invested $49.5 billion (£32.8 billion) in 2011 (
Since these industries, and many others, are intrinsically underpinned by microbes, the total yearly economic value of those teeny, tiny bugs works out as mega bucks! There's also the food industry which produces things like bread, quorn and Marmite with microbes; agriculture which relies on nitrogen-fixing Bacteria in the soil to grow crops; even your body needs microbes to keep your immune system in check and to stop harmful disease-causing microbes from colonising the body.

Image provided by Jusben (

So, next time you're washing your hands, think carefully about those tiny, invisible, living organisms circling the plughole in a a swirl of soapy suds.


Monday, 25 February 2013


Inspired by the recent success of Prof Brian Cox's latest foray into broadcasting science, I have decided to try my hand at communicating science.

So, what makes me qualified to do this?

Well, I'm a PhD student at the University of Manchester, working in Microbiology. In practical terms, this means that my day job is to research something interesting in Bacteria. In addition to my lab research, I also spend a considerable amount of time in a beautiful gothic museum attached to the university, called The Manchester Museum, helping to develop and deliver science workshops to groups of adults and school students. These workshops cover a wide range of topics including Human Evolution and Forensic Science.

(Not so) Secretly, my real interest is in the Industrial Exploitation of Microbes. That covers things like brewing beer and making bread using bakers' yeast (a fungus called Saccharomyces cerevisiae), producing antibiotics and vitamins (using Bacteria like Escherichia coli), and fermenting milk to create cheese and other dairy foods (with the likes of Lactobacillus acidophilus).

I will try to use this blog to explain some concepts which we microbiologists assume the rest of the world knows. I will also aim to use this space to bring other people's interesting ideas to the fore. I hope you find the entries interesting (and dare I say it, enjoyable).

Thanks for joining me,

Hard at work, in the lab!