Posts Tagged microbes

Monday Micro – artificial sweeteners & a dose of bad science Siouxsie Wiles Sep 22

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Sugarcubes” by PallboOwn work. Licensed under Public domain via Wikimedia Commons.

There has been quite a bit of coverage of a recent Nature paper reporting a link between artificial sweeteners and high blood glucose levels (1) – an important finding if true, as high blood glucose levels are a step towards insulin resistance and type 2 diabetes. The study was carried out mostly in mice and was found to be mediated by the gut microbes. The paper isn’t open access so you’ll need $32 to read it if you don’t have a subscription to Nature.

The authors report that consumption of artificial sweeteners changes the microbes present in the gut of mice (and 4 out of 7 healthy human volunteers), with some microbes becoming more abundant and others less so or disappearing altogether, and that this is correlated with a rise in blood glucose levels. The effect disappears when mice are treated with antibiotics. The effect can also be transferred to animals who haven’t been fed artificial sweeteners by giving those animals a faecal transplant from animals with the altered gut microbiome.

The researchers first tested the effect of giving groups of mice access to drinking water spiked with three different artificial sweeteners currently used by people: saccharin (marketed as ‘Sweet’N Low’ in the USA), sucralose (marketed as ‘Splenda’) and aspartame (marketed as ‘NutraSweet’ and ‘Canderel’). The results of the blood glucose tests in mice are shown in Figure 1b of their paper, reproduced below. Despite not being widely used as an artificial sweetener in processed food and drinks anymore, saccharin was the sweetener the researchers chose to do the rest of their studies with, including feeding it to their 7 healthy volunteers.

So why did the researchers choose saccharin for their studies?

Let’s take a closer look at Figure 1b. It’s a graph that shows the area under curve of the data for the blood glucose tests for the mice. The higher the value, the higher or more prolonged the blood glucose levels. Each individual symbol is the value for an individual animal.


The first three groups of animals are the controls – the first were fed plain water (black circles), the second sucrose (black triangles) and the third glucose (black squares). The sucrose and glucose groups are an attempt to control for the sweet taste of the water containing artificial sweetener. The next three groups (blue) are the animals that have been fed the artificial sweeteners: saccharin (blue circles), sucralose (blue squares) and aspartame (blue triangles). The red and grey groups have been fed different antibiotics to knock down their gut microbes in addition to being either control animals or having had the artificial sweeteners.

What is immediately obvious to me is that there are about 4-5 animals in the saccharin and sucralose groups who have very high area under curve values – they look quite different from the rest of the animals in their groups. I think we can call these outliers. That doesn’t mean the effect isn’t real – just that they might not be quite representative of the rest of their cohort. When looking at the data for the rest of the animals, and for the aspartame group, there is quite a lot of overlap between the control groups and the groups fed the artificial sweeteners. I’d love to have access to this data to reanalyse it because I’m surprised the groups are significantly different from the controls, especially for aspartame. But this does explain why they chose saccharin – it showed the biggest difference when compared to the controls.

So could something else be going on with the saccharin group?

One of the things the researchers did was put the animals in ‘metabolic cages’. This allows the researchers to monitor the food and drink intake of the animals as well as how active they are. In their paper the authors state:

“Metabolic profiling of normal-chow or HFD-fed mice in metabolic cages, including liquids and chow consumption, oxygen consumption, walking distance and energy expenditure, showed similar measures between NAS- and control-drinking mice (Extended Data Fig. 3 and 4.)”

Let’s have a look at Extended Data Fig. 3, shall we?

extended fig

“Similar measures”? It looks to me like the saccharin group (and glucose group) drank more and ate less than the other groups. The saccharin group also looked like they expended more energy. Hmmmm. I think ‘similar measures’ is stretching the truth a little.

I’d love to know what the reviewers said about this paper. There’s far too much cherry-picking in it for my liking.

1. Suez J, et al (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature doi:10.1038/nature13793

Astrosquid! Siouxsie Wiles Mar 27


What is the value of blue-skies research?

This is a question often asked by politicians and the public. Why should public money be spent funding science that seems to have no obvious benefit beyond generating scientific knowledge? The simple answer is that it can be almost impossible to predict what new avenues that scientific knowledge will open up. Take the Hawaiian bobtail squid, for example. What could studying this little nocturnal hunter possibly lead to? Take a guess. No ideas? Let me help you out.

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It lead to the discovery that bacteria are able to communicate with each other, including how they sense when the time is right to turn on genes needed to cause disease. I’m not sure anyone could have seen that coming! Importantly, this research has provided scientists with another potential weapon with which to fight antibiotic resistant superbugs. In a world rapidly running out of antibiotics, we need all the weapons we can get.

This animation was produced with the support of a public engagement grant from the UK Society for Applied Microbiology, to engage the services of graphic artist Luke Harris and his team. Dr Siouxsie Wiles (@SiouxsieW) is a microbiologist and bioluminescence enthusiast who heads up the Bioluminescent Superbugs Group at the University of Auckland in New Zealand. She and her team make nasty bacteria glow in the dark to help understand and combat infectious diseases.

What we couldn’t fit into 3 minutes…

The Hawaiian bobtail squid, Euprymna scolopes, is just 3 cm in length and lives in the shallow moonlit waters off Hawaii. It spends its days sleeping buried in the sand, emerging at night in search of food. It has a very cunning trick to hide its shadow from fish looking for a meal, or from creatures like shrimp that it feeds on. It houses a colony of glowing bacteria (Vibrio fischeri) in a special organ on its underside. These bioluminescent bacteria shine their light down so that to any creatures looking up, the squid just looks like the moon. What is even more clever is that the squid uses its ink sac to match the intensity of moonlight hitting its back, dimming the light from the glowing bacteria as needed. This is important not just for cloudy nights but as the squid moves through different depths of water.

Baby squid are born without V. fischeri or a light organ. Instead they just have a small opening in their mantle (the bulbous bit of their body) that is bathed by sea water. What is incredible is that only V. fischeri can colonise this opening – once they do, the squid cells start to change and the light organ forms. The ability to glow is crucial though – scientists have made versions of V. fischeri which can’t glow and they aren’t able to colonise either.

Adult squid have an ingenious way of ensuring that there is plenty of V. fischeri floating around in the water to colonise baby squid. Each morning, before they settle down in the sand to sleep for the day, they expel 99.9% of the bacteria from their light organ into the sea. This serves another purpose too, ensuring the bacteria left behind in their light organ are constantly growing and have plenty of nutrients. Bacteria that run out of nutrients start to shut down to save energy. Producing light takes quite a bit of energy and the last thing the squid wants is a mantle full of lazy dim bacteria!

When scientists first identified V. fischeri and grew it in the lab they noticed something quite interesting. The bacteria only switch on their light when they have reached a critical population size. This makes perfect sense. There is no point going to all the trouble of making light if it isn’t bright enough to be seen. Each bacterium produces a chemical, called the autoinducer, that diffuses out of the bacterial cell. The more bacteria there are, the more autoinducer is produced. If those bacteria are growing in a confined space like a flask, or the light organ of the squid, the autoinducer will accumulate. Once it reaches a critical concentration, the autoinducer triggers the bacteria to switch on the genes for producing light*. This phenomenon is called quorum sensing.

Scientists then used the bioluminescence reaction to see if other species of bacteria produce autoinducers. Surprise, surprise, it turns out that lots of different bacteria use quorum sensing to signal to each other that they are in the right numbers or environment to do something, which is not worth doing otherwise. From the bacterial form of sex, to swimming, to switching on the genes needed to cause disease in plants, animals and humans. Now we just have to find a way of exploiting this to our advantage!

You can hear me chatting about the squid and quorum sensing on Radio New Zealand’s Nine to Noon programme with Kathryn Ryan here (13’12”):

*For those who really want to know, the autoinducer is the product of the luxI gene. When it reaches a critical concentration, it interacts with the product of the luxR gene, and together this complex binds to a region of DNA upstream of the genes under their control called the lux box which then triggers their transcription.

Monday Micro – roller derby micro! Siouxsie Wiles Mar 18


There were a smorgasbord of micro stories to choose from this week, but how could I pass up a story which combines microbes, open access and gorgeous women on roller skates?!

James Meadow and colleagues, from the Institute of Ecology and Evolution at the University of Oregon, have just published a paper looking at the effect of contact sports on the microbial communities living on the skin of the participants. This is where the roller skates come into the story, as the contact sport James and his colleagues studied was roller derby*.

This great picture by Emily Thomas AKA Mummy'sLittleMonster sums up roller derby perfectly!

This great picture by Emily Thomas AKA Mummy’sLittleMonster sums up roller derby perfectly!

James’ paper is one of the first to be published in new online open access journal PeerJ which launched recently. More on this new journal below, but one feature I do want to point out is that authors can elect to make the review history of the article public, which James and his colleagues did. It makes for fascinating reading!

But back to the paper. James and colleagues hypothesised that close contact between people would create shifts in the microbial communities living on the skin. And that’s pretty much what they found. Here is a nice plot showing the microbial composition of the skin of each team member before and after playing. Each symbol represents a player, each colour represents a different team (they looked at three teams: the Emerald City Roller Girls, the DC Roller Girls and the Silicon Valley Roller Girls) and the coloured ellipses show the standard deviations around the community variances from each team. Before they started, the skin microbiomes of members of each team clustered nicely together – presumably because they train together and therefore often come into contact with each other. After playing you can see that the skin microbiomes have changed and become much more similar between the teams – they’ve shared their microbes!

Variation in skin microbial community composition is significantly explained by team identity.

Variation in skin microbial community composition is significantly explained by team identity.

The authors concluded that:

“contact sports provide an ideal setting in which to evaluate dispersal of microorganisms between people.”

Certainly looks that way!

Meadow et al. (2013) Significant changes in the skin microbiome mediated by the sport of roller derby. PeerJ 1:e53

Conflict of interest statement: I am a PeerJ academic editor but did not handle or review this manuscript.

* For details see the official Women’s Flat Track Derby Association (WFTDA) rules. Two competing teams, each composed of up to 4 ‘blockers’ and 1 ‘jammer’, simultaneously circle the track while the jammers, who start behind the pack, try to score points by lapping players of the opposing side. The catch is that the blockers can use their bodies (arms from shoulder to elbow, torso, hips, booty** and legs from mid to mid to upper thigh) to try to stop the jammers from lapping the pack. There is some great footage of some teams in action on You Tube:

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**Official WFTDA nomenclature..

***PeerJ was founded by Peter Binfield (formerly at PLOS ONE) and Jason Hoyt (formerly at Mendeley) and is backed by O’Reilly Media. PeerJ aims to be a biological and biomedical version of PLOS ONE, with papers judged solely on their scientific and methodological soundness, rather than potential ‘impact’,. Like PLOS ONE, PeerJ papers are freely available to read and published under a Creative Commons licence which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Like PLOS ONE the costs are covered by the researcher but in the form of membership fees per author, rather than article processing charges. a one off payment of $99 allows an author to publish one paper per year for life, while $299 allows an author unlimited publications per year.

Monday Micro – extremophiles & 50 shades of … immunity! Siouxsie Wiles Mar 11

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In last week’s Monday Micro I mentioned horizontal gene transfer (HGT), the process by which bacteria acquire new genes from other microbes in their environment. HGT is one of the primary ways that genes for antibiotic resistance are able to spread between different bacteria. It is also how plenty of bacteria pick up genes for things like toxins which help them cause disease. But it’s not all bad. A few years ago, a team of scientists reported in the journal Nature that the gut microbes of Japanese people had picked up the ability to digest the unique carbohydrates present in seaweed through HGT from a seaweed chomping microbe called Zobellia galactanivorans (1).

This week, in a paper just out in the journal Science, Gerald Schönknecht, Wei-Hua Chen and colleagues report that HGT is the secret to the success of the extremophile Galdieria sulphuraria, an algae that is able to thrive in hot, acidic springs, like those found in Iceland or the Yellowstone National Park. When the researchers sequenced the genome of G. sulphuraria, they found it had acquired at least 5% of it’s protein-coding genes through HGT (2). These genes give G. sulphuraria the ability to detoxify heavy metals, deal with high concentrations of salt, and to consume a variety of unusual food sources.

Galdieria sulphuraria growing on a rock in an  Icelandic hot spring near Reykjavik.  CREDIT: Christine Oesterhelt

Galdieria sulphuraria growing on a rock in an Icelandic hot spring near Reykjavik.
CREDIT: Christine Oesterhelt

And finally, also leading on from last weeks description of the CRISPR system, Michael Criscitiello and Paul de Figueiredo have written a piece in the open access journal PLOS Pathogens challenging the dogma that is the black and white existence of the innate and adaptive immune systems*. Playfully nodding to the Fifty Shades phenomenon, their piece is entitled Fifty Shades of Immune Defense, and lays out the immune system as a continuum (3).

Different immune mechanisms with adaptive properties are being discovered in species originally considered to only possess innate immunity. Taken from (3)

Different immune mechanisms with adaptive properties are being discovered in species originally considered to only possess innate immunity. Taken from (3)

*We are generally taught that the immune system has two parts to it: the innate immune response, in which cells recognise and respond to pathogens in a generic way, but can’t confer long-lasting protection to the host, and the adaptive immune response, in which cells respond in a specific way, and confer long lasting protection to the host.

1. Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature, 464 (7290), 908-912 DOI: 10.1038/nature08937
2. G. Schonknecht, W.-H. Chen, C. M. Ternes, G. G. Barbier, R. P. Shrestha, M. Stanke, A. Brautigam, B. J. Baker, J. F. Banfield, R. M. Garavito, K. Carr, C. Wilkerson, S. A. Rensing, D. Gagneul, N. E. Dickenson, C. Oesterhelt, M. J. Lercher, A. P. M. Weber. Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote. Science, 2013; 339 (6124): 1207 DOI: 10.1126/science.1231707
3. Criscitiello MF, de Figueiredo P (2013) Fifty Shades of Immune Defense. PLoS Pathog 9(2): e1003110. doi:10.1371/journal.ppat.1003110

Monday Micro – just who are we? Siouxsie Wiles Feb 04

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Hi, I’m Siouxsie. I’m 5 ft 2 inches tall (short?), on the rather rotund side, and have green eyes. I sport an abundance of pink/red hair although I’m naturally a brunette. That’s me. Or is it?

Because what I like to think of as me, my Homo sapiens cells, is outnumbered 10:1 by the microbes that live in and on my body. There are trillions of them. It’s not that I don’t like to bath or shower. On the contrary. No, these microbes are my microbiome. Only over the past few years have scientists come to realise just how important our microbiome is. It performs essential functions like digesting food and synthesising vitamins. It also keeps pathogenic microbes at bay, and regulates our immune system. In fact, our microbiome is thought to be responsible for many gut disorders, as well as eczema and chronic sinusitis, and may also play a role in our mood and behavior.

So wouldn’t you like to know more about this important part of you? Well, now you can. The uBiome project, on the crowdfunding platform Indiegogo, is offering to sequence your microbiome. Just US$79 (NZ$94) and you get your gut microbes. Or you can spend US$335 (NZ$395) for your gut, mouth, skin, nose and genital microbes. If you have the cash, you can really splash out with the Delta^5 deal (US$1,337/NZ$1,582), which will allow you to sample five different areas of your body on five occasions. Want to see how changing your diet affects your microbiome? Then this is the one for you!

So how does it work? It’s pretty easy. They send you a kit, you take a sample (a bit of poo for gut microbes, a swab up your nose for those microbes, you get the picture) and answer a health survey. You then send your sample back to be sequenced and when the data is ready, they send you a link to their website. Here they will you what’s in your sample and how it correlates to other people in the project (you can opt out of having your data included but the more people opt in the better for science).

So far, the campaign has raised over US$250,000 (NZ$300,000) with 2 weeks left to run. This project is inspired. The NIH funded Human Microbiome Project is looking at the microbiomes of 600 healthy individuals and the scientific questions addressed reflect the interests of the researchers. The uBiome project is opening up the technology to everyone. There is even a ‘Philanthropist’ supporter level, where you pay for someone in the developed world to have their microbiome sequenced. To date, over 1,800 people have contributed to the campaign and nearly 1,100 of those have opted to sampled some bit of their microbiome. That’s almost double the number of people sampled in the Human Microbiome Project.

Even more excitingly, the uBiome team want to involve the public in analyzing the data and generating and testing hypotheses. The data of those people who opt in will be open to the world, anonymised of course! Is this the future of science? I can’t wait to find out.

So watch this space, I hope to be posting my gut microbiome for all to see later in the year. And if you fancy joining me, then hop on over to uBiome and choose which bit of your microbiome you want to get to know better!

Monday Micro Siouxsie Wiles Dec 10

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Just a brief Monday Micro today as it will soon be Tuesday!

First up, what looks like quite a neat paper just out in the [Elsevier] journal Cell. Alas, its not open access so I’ve just read the abstract and write up on Science Daily. Marcus Stensmyr and colleagues at the Max Plank Institute for Chemical Ecology have found that fruit flies (Drosophila melanogaster) have a dedicated neural circuit to detect rotten food.

Because fruit flies feed primarily on yeast growing on fermenting fruit, they need to be able to distinguish fruit with safe yeast from fruit containing toxic microbes. Turns out they do this by sniffing out geosmin, a chemical produced by harmful bacteria and fungi.

What I like about this paper is the fact that the authors have made real efforts to communicate their science beyond the actual publication. They have made a short video explaining their results which is available to view on their institutions webpage here. It’s a little too full of jargon for my liking but a great effort nonetheless. Marcus also appears to be a dab hand at modelling clay and has made some great graphical representations of the work such as this below:

Copyright Marcus Stensmyr


Marcus C. Stensmyr, Hany K.M. Dweck, Abu Farhan, Irene Ibba, Antonia Strutz, Latha Mukunda, Jeanine Linz, Veit Grabe, Kathrin Steck, Sofia Lavista-Llanos, Dieter Wicher, Silke Sachse, Markus Knaden, Paul G. Becher, Yoichi Seki, Bill S. Hansson. A Conserved Dedicated Olfactory Circuit for Detecting Harmful Microbes in Drosophila. Cell, 2012; 151 (6): 1345 DOI: 10.1016/j.cell.2012.09.046

Monday Micro Siouxsie Wiles Dec 03

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Welcome back to Monday Micro. Last week’s Monday was lacking in microbiology factoids as I was at the New Zealand Microbiology Society‘s annual meeting*. This year it was at the University of Otago in Dunedin. Highlights for me were keynotes by Rob Knight (microbiomes and Next Gen Sequencing), Eric Ruben (TB) and Steven Wilhelm (cyanobacterial blooms). Tweets of some of the talks are here.

Highlights for me:

Finding that lots of people flush public toilets with their feet, that cyanobacteria are a bad food source “like ordering pizza and only eating the box”** and that “we are all accidents of history”***.

Moving on, Round 3 of the SciFund Challenge is in full swing so if you fancy supporting some microbiology projects Amy Truitt wants so study butterflies and their sexually transmitted diseases, Will Helenbrook is studying the effects of infectious diseases on Mantled howler monkeys and Andy MacDonald is working on Lyme disease.

* The slides for my talk (Fireflies and superbugs: when science and nature collide) are up on slideshare. I started my talk with my Meet the Lampyridae animation….

** Steven Wilhelm
*** Unknown kilted MC of conference dinner :)

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