The bugs are dead!!!

Being a scientist is all about blood, sweat & tears. Ok… maybe not blood… (shhhh… health & safety might be reading this…)

My latest scientific publication finally came out around 3 weeks ago. It culminates my last 2.5 years of hard working days and countless nights in the lab. It is entitled “Sample processing impacts the viability and cultivability of the sponge microbiome” and it was published in Frontiers in Microbiology, which is ranked as one of the top scientific journals in microbiology. Not too shabby…

Now if you’re not a scientist or you do not work in microbiology, you will probably not understand much if you try to read this paper (or any other scientific paper for that matter…). Fear not, my scientific enlightenment seeking friend! You are actually not meant to understand these intricate pieces of writing. Scientific publications are the way scientists communicate with each other. “Oh look, we’re so smart! We write stuff nobody else understands! Not even ourselves…” It’s kind of an intellectual masturbation, if you will…

So in this blog post I have set up a challenge to myself: explain what this work is about in a way that everyone is able to understand. Promise I will try my best to avoid being an intellectual wanker…

I work with sponges…


No… not that kind of sponges… This kind!

porifera marine sponges.jpg

Sponges are ancient organisms, thought to be the first animals with more than one cell to appear on our planet. They are presumed to have formed when tiny flagellated cells, wandering around feeling lost and lonely in the vast deep ocean, realised they would all have much more to gain if they joined together in a communist society.


Sponges and other animals have evolved from a common ancient organism that resembles the modern-day choanoflagellates. Beating of the flagella (their little tail) draws water through so that nutrients can be extracted and waste removed. Source:

Around 40 years ago, when my mum and dad didn’t even dream about me being born, a couple of marine biologists, Clive Wilkinson and Jean Vacelet, started to realise that sponge cells were not alone. They found that almost 40% (!!!) of the sponge could be formed of bacteria, living happily among the sponge cells and even some cheeky ones living inside the sponge cells! Hidden within the mess of cells that constitutes a sponge, there it was, an astonishingly large and previously undiscovered microbial world!

sponge bob bac

Where do they come from?
How did they get here?
What do they do?

Forty years have passed and, despite the many technological advances and scientific breakthroughs, these are the questions that marine sponge scientists are still trying to answer.

These days there are basically two ways you can study bacteria:

  • Cultivation, where you take a piece of the sponge and try to get all the bacteria out, put them on a petri dish or a test tube with their favourite food, so that they will grow and reproduce and then you can study each one of them individually.

Sponge bacteria growing and forming colonies on a Petri dish (personal picture)

  • Community analysis, where you study the bacteria as groups, rather than individually, and identify them without growing them in the lab. This is done using genetics and I will explain this a bit further.

Almost at the same time that sponge bacteria were being spotted, a couple of other smart people discovered that a particular gene, called the 16S rRNA gene, could be found in almost all bacteria and was different for each different bacteria. Because a gene is nothing more than a combination of the letters ACTG, with each one of these letters representing a group of molecules, if you determine this combination (or gene sequence), you can identify the bacteria! So in community analysis, you determine the sequences of virtually all the 16S genes to directly identify the bacteria that form part of that community.

Of course scientists started using these techniques to study the sponge bacteria and soon realised something was wrong. The bacteria that were found in the community were not the same ones that were obtained in the Petri dishes. Since bacteria do not magically appear and disappear, there was obviously a missing link. Some scientists argued that we were not able to get the bacteria out of the sponge and others said we were not giving them the right food or the right conditions (temperature, pH, light, shaking, etc…). Many bacteria are picky eaters and in some cases we’re not even sure what they eat or what other conditions they require and so we try to give them conditions as close as possible to what we think might be their natural environment.

In my work, I used community analysis to identify the bacteria that were initially present in the sponge and which ones were we able to squeeze out of the sponge. Because the methods we use to do this can be somewhat harsh, I also identified which of these bacteria were actually still alive. Then I tried to cultivate these bacteria using a massive array of different foods and conditions and identified the ones that were able to grow and reproduce.

What I found out in this work is that yes, we are unable to squeeze all the bacteria out of the sponge piece, and yes, in some cases we are not giving these bacteria the right food and so they do not grow and reproduce in our Petri dishes. But there was one other factor that up until now everyone had disregarded: the bugs are dead! By the time we put these bacteria on the Petri dish or in the test tube, they are already dead and so it does not matter how much we try and give them the right food and the right conditions to grow. The effort should now concentrate towards keeping these little creatures well and alive, from the sea to the lab.


Why is this important? Well, given that we can all (arguably) be sons and daughters of a sponge, and that in the past decade the relevance of bacteria in human health and in the environment has become increasingly evident, it is easy to understand the importance of studying this old relationship between sponges and bacteria and use these lessons to study other important bacterial systems.

Evolutionary Tree original

A simplified “Tree of Life” showing how all living organisms on Earth are related. Source:

Also, sponges and their bacteria have been found to produce new compounds that have a huge range of applications such as new antibiotics, anti-HIV and anti-cancer drugs, new biomaterials that can be used in bone regeneration, improve glass fibre production, provide stronger and more durable fibres, etc. Being able to successfully cultivate these producers in the lab will provide an endless source for these compounds.

Now that you all feel much more enlightened about the wonders of sponge microbiology and the world in general (hopefully!) and that I have surely pissed off at least a couple of hardcore academics (mission accomplished!), please excuse me as I have some knitting to do have another paper to write…


About The Knitting Scientist

I was born in a land where the sun shines bright, time passes by slowly and people take pride in what they do. My mom taught me my first stitches and I never put down my hook and needles again! Later I became a scientist, dwelling within the mysteries of life and the universe, using logic and analytic thinking, giving my humble contribution to human knowledge. Scientist during the day, knitter at night. Just like a super hero, creative hands on an analytic mind is my super power! That's me and this is my story lost among test tubes and balls of yarn!

One comment

  1. Hooray for bacteria! And it’s refreshing to read something where the humble bacteria isn’t being demonised or thought of as something to be killed…

    Now collect your reward and go knit! I mean, read a scientific paper or something.

    Liked by 1 person

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