Chaos theory and theoretical modeling of Gut Microbiota.

Some old papers are just like the old pictures you get to find if you rummage in the garret during a rainy afternoon. Cluttered in a trunk just to be forgotten, they tell you about days gone by, but sometimes they can reveal facts you just couldn’t suspect. In the last decade, the research on the symbiotic interactions between mammals and bacteria made impressive steps forward. The so-called microbiota has been extensively studied, revealing his fundamental role in immunity, aging and several pathogenesis events. The last intriguing hypotesis links the composition of microbiota with autism, stating how can be crucial the role of microbes in our body.

For my very last exam, I had to study the composition of microbiota and his role in pathogenesis and immunity. We have been committed to choose a paper to make a small presentation. And as in the rainy afternoon in the old garret in front of a fucking trunk, I have found a picture from the past, a paper healing from the 90s, when no one had a clear idea on what those bacteria were doing around our body’s external surface. So, let me show you this old, but still very interesting picture.

The title immediately caught my attention:

Nonlinear dynamics, chaos-theory, and the” sciences of complexity”: their relevance to the study of the interaction between host and microflora

The article (PDF), dating 1997, is written by M.H.F. Wilkinson, a computer scientist from the University of Groningen, in Holland. After a concise and really clear explanation of non-linear dynamics, chaos theory and complex systems, the paper propose that gut and microbiota constitute a pseudo-chaotic complex system, thus showing a non-linear dynamic. With this assumption, a computer model of microflora has been built. The “organisms” are divided into aerobians and anaerobians and brought to compete for space and nutrients. IMHO, the result is quite striking. Several simulations of gut colonization confirm the interdependency between anaerobes and facultative anaerobes, but the most intriguing result is presented here:

chaos

If you check out the recently proposed dynamics for gut colonization of microbiota, from the birth till the very first weeks of life, you will find a very similar path. Facultative anaerobes, such as Firmicutes, take the stage as first to prepare the ground to strict anaerobes, such as Bacteroides, which overcome later to become the biggest population. Intriguingly, the theoretical modeling forecasted this years before the experimental approaches.

There is another important fact to highlight. This work gets the point when it remarks the semi-chaotic behavior of the system constituted by the intestine and the microbial community. As mentioned by the author, a semi-chaotic organization is really suitable for those systems who need a compromise between plasticity and stability, such as biological systems undergoing to evolutionary constraints.

An old picture, but still really interesting. A memory from a past in wich there were no mass sequencing, big data, proteomics and systems biology. To understand the complexity of biological systems, scholars made use of theoretical models developed in physics and math, such as chaos theory or fractal geometry. A theoretical modeling step that is quite often underestimated by genomic scientists and systems biologists, and wrongly forgotten in the post-genomic era.

Old pictures can be interesting.

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How vitamins auxotrophy has emerged in evolution?

After a long time off, due to my university commitments, I am really pleased to take my fingers back to the keyboard. As you may notice, I did a radical change in my blog template choosing an easier and cleaner one. Hope you like it, I kinda have a spot for minimalism. Today I am going to explore an issue that is both amazing and, in my opinion, too much understated. Even without a biological education, anyone is pretty aware of the importance of vitamins in daily diet. In biochemistry, vitamins are defined as small molecular weight organic compounds that are necessary for survival, but are not synthetized ex- novo. Basically, their role is linked to enzymatic activity, since they often play a co-factor role in catalyzed reactions. In many cases though, these compounds are not required by Protists, Plants, Bacteria and Archea, since they are able to synthesize them ex-novo. The question is how auxotrophy evolved among the different taxa.

My thesis project had an interesting turn as we realized that we could find some clues about the evolution of auxotrophy in B6 vitamins throughout bacteria. The auxotrophy for the pyridoxal- related compounds seems to emerge in all those ecological conditions that may be favorable to those organisms that need external organic compounds, such as commensalism or symbiosis.

Scanning the literature, we can see that Katherine Helliwell, from Cambridge, addressed specifically this issue several times. In a recent paper, Helliwell describes the general mechanisms underlying the loss of biosynthetic pathways for the most common vitamins, highlighting how the evolution of vitamins auxotrophy and the evolution of ecological interactions (predation, mutualism and commensalism) are interlinked.

In another paper, the Cambridge group explains how auxotrophy could have emerged in microalgae. The focus is on B12 vitamin. Citing the author, ‘Within the algal kingdom, approximately half of all microalgal species need the vitamin as a growth supplement, but there is no phylogenetic relationship between these species, suggesting that the auxotrophy arose multiple times through evolution.‘.

Favorable environmental conditions and the loss of at least one of the genes in the biosynthetic pathway, are usually the main reasons for the establishment of auxotrophy. We need vitamins and we know why, but the evolution of this necessity is still to explore.