Showing posts with label bacteria. Show all posts
Showing posts with label bacteria. Show all posts

Wednesday, January 8, 2014

2014 Prospects

Happy New Year!

So, what's in store for us in 2014?

Difficult to say, but as least I can try and say a little about what is going on in our lab. Firstly, we are trying to publish what we are think are very interesting data on how gut bacteria may select for Blastocystis colonisation, a hypothesis we have developed based on studies of metagenomic data.

We are also working with the assembly and annotation of mitochondrial and nuclear genomes in collaboration with our international colleagues; something that will definitely take a while, since we have so few people in our lab to do it (literally one-two persons) but oceans of data (!!) - it's a pity that we cannot speed this up, since genomes are expected to hold keys to some of the great gates of Blastocystis enlightenment. Of course, a constant aim is to attract funding that can help us employ one or more PhD students/post docs interested in genomics and parasites. As always, I encourage my readers to come up with suggestions for funding.

Funding-wise we are also going to try and establish a Marie Curie ITN-network on the roles of intestinal microbial eukaryotes in health and disease and we are also awaiting decisions on other applications; hopefully, we will get some money for gut microbiome and immunological host profiling in experimental animals challenged with Blastocytis cysts. There may also be some work in our lab dealing with the impact of Blastocystis on bacterial communities in in-vitro studies.

Epidemiological data are produced as we speak; luckily, quite a few colleagues in different parts of the world are taking an interest in characterisation of Blastocystis in various cohorts so that we will know more about its epidemiology.

Those are the seminal things. Of course, there will be some exciting conferences, which I've mentioned before, and I'm also looking forward to putting together a Blastocystis review.

Thursday, March 14, 2013

Extremophilic Eukaryotes

My recent post Blastocystis aux Enfers was my "literary take" on biological adaptation of intestinal parasitic protists, using Blastocystis as an example. As a parasitologist you'd come across many peculiar and shrewd biological adaptations and life cycles, and I hope to be able to give some examples in a future post. Actually, there is a parasite which is quite common in humans, maybe even just as common as Blastocystis, which is also single-celled, but which may have a much more complicated life cycle than Blastocystis, namely Dientamoeba fragilis; a colleague of mine is currently doing his PhD on Dientamoeba and he has collected multiple sources of evidence to confirm the hypothesis that this parasite is transmitted by a vector, namely pinworm, probably along the same way that Histomonas meleagridis – the cause of blackhead disease in especially turkeys – is transmitted by heterakids (which again are transmitted by parathenic hosts such as earthworms, which get eaten by turkeys, chickens, etc.). Anyway, I’ll probably get back to Dientamoeba, once his data are out.

Meanwhile, Blastocystis comes out of a very heterogeneous group of organisms called Stramenopiles, many of which are algae. Algae are photosynthetic organisms found in habitats as diverse as glacial ice and hot springs.One of these algae is named Galdieria sulphuraria, which is a remarkable unicellular eukaryote inhabiting hostile environments such as volcanic hot sulfur springs where it is responsible for about 90% of the biomass; indeed this certainly qualifies as "Galdieria aux enfers"!

Saturday, February 23, 2013

Blastocystis aux Enfers

We tremble at the thought of being devoured by a ferocious animal, - of ending our days in a narrow, suffocating slimy tube covered in acidic, nauseating glaze! Remarkably, for some eukaryotic beings, this is the only way forward if they want to carry on with their lives! Intestinal protists such as Blastocystis are in a state of hibernation when outside our bodies and the only thing that may rouse these Sleeping Beauties to action is the passage through low pH enzyme ponds. They thrive, grow and raise their progeny only in the swampy Tartarus of our large intestines; they bequeath to their offspring the affinity for this gloomy, filthy slew; this murky, densely populated, polluted channel, and when the pool of poo becomes all too arid, they know it’s time to buckle up, shut down, and prepare themselves for the great unknown which can potentially mean death to them if eventually they are not lucky enough to be gulped down by another suitable host.

Source
And yet, despite their remarkable modesty and humble requirements these little buggers are being bullied by their inhospitable human hosts; we’d throw anything at them to force them out, organic and inorganic compounds meant to arrest or even kill them. But the whelps of Blastocystis appear extremely resilient, which may hold the key to part of their success; they stay afloat on the Styx of our bowels. In order to eschew Flagyl, perhaps they bribed Phlegyas?

I think it's sometimes useful to put things into a completely different perspective. In any event, from an evolutionary biology standpoint it is highly interesting that a genus which is genetically related to water molds such as those causing potato blight and sudden oak death, has so successfully adapted to a parasitic, anaerobic life style, capable of protractedly colonising a plethora of very diverse host species including members of primates, other mammals, birds, reptiles, amphibians and arthropods and thereby evading innate and adaptive immune defenses from such a diverse range of hosts. One could be inclined to say: Well done! But which is it? Parasitism? Commensalism? Mutalism? Symbiosis? And what will happen to Blastocystis in the future? Will this successful crusader eventually succumb to our avid but maybe imprudent war strategies? And if so, what will happen to us after removing such a common player from our intestinal ecosystems?

Wednesday, December 5, 2012

My Microbes - Share Your Microbiota!

Many people are told by their GPs or specialists that they are infested by Blastocystis. What these people might not always be aware of is the fact that our intestine is home to billions of organisms, most of which are bacteria. Some bacteria are good for you and help you metabolise food items and synthesise compounds that you cannot produce yourself, while others are associated with disease. Some bacteria are supposed to be there and some are not. Blastocystis is very successfully parasitising on the human intestine, but to our knowledge, there is still no convincing pathogenomic evidence of it causing disease. So, what does it do and why is it there? Does it cause disease at all? How do we get it? We are are trying to find out...

Meanwhile, a lot of effort is being put into collecting stool samples from the background population. There is a project called My Microbes, there's the uBiome project and the American Gut Project, just to mention some. For instance, for less than $100 you can have your entire bacterial intestinal microbiome seqeunced and identified. Maybe, you will even get to know your "enterotype"?!

Below is a brief introduction to the enterotypes (courtesy of My.microbes) that I've been blogging about previously:



My.microbes from Anna Pesavento on Vimeo.

It is, however, debatable whether these enterotypes are clear-cut or represent a continuum/gradient. Nevertheless, the prospects of these stupendous microbiome projects are numerous, and once we add the intestinal eukaryotic microbiome to this field and probe into the ecological interplay between eukaryotes, bacteria and the host, new pathways of knowledge will probably lead to many answers to old conundrums, but also to new questions of course. We will get a better impression not only of which bacteria that are beneficial, but also whether - or to which extent - common "scroungers" like Blastocystis are in fact benevolent along some of the lines presented in this recent blogpost.

By the way: Behold the video still: All set for setting up PCR!

Literature:

O’Toole, P. (2012). Changes in the intestinal microbiota from adulthood through to old age Clinical Microbiology and Infection, 18, 44-46 DOI: 10.1111/j.1469-0691.2012.03867.x  

Gosalbes, M., Abellan, J., Durbán, A., Pérez-Cobas, A., Latorre, A., & Moya, A. (2012). Metagenomics of human microbiome: beyond 16s rDNA Clinical Microbiology and Infection, 18, 47-49 DOI: 10.1111/j.1469-0691.2012.03865.x  

Baquero, F., & Nombela, C. (2012). The microbiome as a human organ Clinical Microbiology and Infection, 18, 2-4 DOI: 10.1111/j.1469-0691.2012.03916.x  

Salonen, A., Salojärvi, J., Lahti, L., & de Vos, W. (2012). The adult intestinal core microbiota is determined by analysis depth and health status Clinical Microbiology and Infection, 18, 16-20 DOI: 10.1111/j.1469-0691.2012.03855.x

Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D., Fernandes, G., Tap, J., Bruls, T., Batto, J., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E., JunWang, ., Guarner, F., Pedersen, O., de Vos, W., Brunak, S., Doré, J., Consortium, M., Weissenbach, J., Ehrlich, S., & Bork, P. (2011). Enterotypes of the human gut microbiome Nature, 474 (7353), 666-666 DOI: 10.1038/nature10187

O’Toole, P. (2012). Changes in the intestinal microbiota from adulthood through to old age Clinical Microbiology and Infection, 18, 44-46 DOI: 10.1111/j.1469-0691.2012.03867.x  

Gosalbes, M., Abellan, J., Durbán, A., Pérez-Cobas, A., Latorre, A., & Moya, A. (2012). Metagenomics of human microbiome: beyond 16s rDNA Clinical Microbiology and Infection, 18, 47-49 DOI: 10.1111/j.1469-0691.2012.03865.x  

Baquero, F., & Nombela, C. (2012). The microbiome as a human organ Clinical Microbiology and Infection, 18, 2-4 DOI: 10.1111/j.1469-0691.2012.03916.x  

Salonen, A., Salojärvi, J., Lahti, L., & de Vos, W. (2012). The adult intestinal core microbiota is determined by analysis depth and health status Clinical Microbiology and Infection, 18, 16-20 DOI: 10.1111/j.1469-0691.2012.03855.x

Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D., Fernandes, G., Tap, J., Bruls, T., Batto, J., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E., JunWang, ., Guarner, F., Pedersen, O., de Vos, W., Brunak, S., Doré, J., Consortium, M., Weissenbach, J., Ehrlich, S., & Bork, P. (2011). Enterotypes of the human gut microbiome Nature, 474 (7353), 666-666 DOI: 10.1038/nature10187

Sunday, August 19, 2012

The Potential Role of Our Microbiome Ecosystems

For those who like these pop-sci articles on the still somewhat conjecture-like but very inspiring theories about the role of our intestinal microbiome in health and disease, here's a link to an article from The Economist (18 AUG 2012):

The Human Microbiome: Me, myself, us

And let me reiterate: We still don't know much about mikro-eukaryotes in all this... do they play a role as well? And how do they cope with different types of microbiomes?

Anyways, enjoy!