Parasite Course: Concepts in Parasitology (Australia)

For those interested:

There will be a two-week specialist course for PhD students and earlycareer researchers (ECRs), 

run by the Australian Society for Parasitology (ASP) called Concepts in Parasitology.
  
The course is running again this year from the 25^th of November to the 8^th of December 2019 in New South Wales (Kioloa Coastal Campus), and the deadline for applications is the 13^th of July 2019. 

Details of the course are here.

OPPORTUNITY!

For those interested in and working with
1) new technological and bioinformatic approaches to detecting and differentiating intestinal parasites
2) the role of Blastocystis and other common luminal intestinal parasitic protists
 there are currently a few interesting calls:

Mark van der Giezen (with whom I've had the pleasure of working with on a couple of projects) recently tweeted:

Funded #PhD studentship available in my new lab @UniStavanger to study the role of the #eukaryotic microbial #microbiome (the #eukaryome) on #InflammatoryBowelDisease. A collaboration between the University and Academic Hospital in #Stavanger in #Norway.https://t.co/k9YcuGvyZk

— Mark van der Giezen (@MitoRem) April 28, 2019

For more information, please go here.

He also tweeted:

Interested in your own personal fellowship and work on #mitochondrial #evolution and #microbial #eukaryotes in my new lab @UniStavanger in beautiful #Norway? Then check out the just announced Marie Skłodowska-Curie Individual Fellowships!https://t.co/8ISNs3EiF1

— Mark van der Giezen (@MitoRem) April 26, 2019

Moving on to special issues in journals, I would like to highlight that Parasite Epidemiology and Control (PEC) is planning to publish two special issues of particular interest to our community:


Special Issue: 2nd International Blastocystis Conference

As the readers of this blog will know, the 2nd International Blastocystis Conference took place in Bogotá, Colombia only half a year ago. A special issue in PEC will be dedicated to this conference. It welcomes papers on Blastocystis also from those of our colleagues who could not attend the conference. You can read more here.

Guest editors: Juan David Ramirez Gonzalez (Editor of PEC), Funda Dogruman-Al and myself.


Special Issue: Novel Technologies and Approaches for Detecting Intestinal Parasites

Together with Juan David Ramirez Gonzalez I look very much forward to editing a special issue on new technologies and approaches to detecting intestinal parasites. I'm thinking metagenomics, amplicon-based sequencing, etc. Of course, also papers describing non-DNA-based methods are welcome. You can read more here.


Special Issue: Recent Advances in the Controverisal Human Pathogens Pneumocystis, Microsporidia, and Blastocystis

Finally, I'd like to highlight a special issue call from Frontiers in Microbiology on Pneumocystis, microsporidia, and Blastocystis - the odd ones out. Please go here for more information. The special issue is edited by Olga Matos, Lihua Xiao, and myself.

Blastocystis PhD position available with Tasos

Hi all,

Just spreading the word: 

There is a funded PhD opportunity (!!!) in Dr Tsaousis' lab on Blastocystis:

'Identifying the parasitic or passenger role of Blastocystis, in patients with gastrointestinal disease'

available for September 16th start!  

 

Deadline for applications is 22 April.

Find more info here

Special issue on Blastocystis, Pneumocystis and microsporidia in 'Frontiers'

The online journal 'Frontiers in Microbiology - Infectious Diseases' will be publishing a special issue on Blastocystis, Pneumocystis and microsporidia as opportunistic eukaryotes and controversial pathogens.

Please go and see the call for papers here.

Topics editors include Olga Matos, Lihua Xiao and myself.

(Blastocystis images towards the right courtesy of Marianne Lebbad)

Eukaryome - upcoming conference in Paris

Just a heads-up regarding the 'Eukaryome' conference in Paris later this year... looks interesting!

You can find the website here.

The role of Blastocystis and other 'apathogenic' gut parasites in health and disease - how to proceed?

If you're interested in reading my most recent paper

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges

published recently in Parasitology, you can read it for free here.

Thank you for taking an interest.

Season's Greetings and Best Blastocystis Paper of the Year

The year of 2018 is coming to an end, and what a BLASTO year we had!

The 2nd International Blastocystis Conference was so much more than a worthy sequel to the conference in Ankara in 2015, - it was also the conference that initiated the tradition of having a conference on Blastocystis every three years! And as most of you probably know, the next conference will be in Crete in 2021. More info to follow.

We also had a specific Blastocystis session in ICOPA 2018 in Daegu, South Korea, and I expect that this is also something that we'll see more of in future conferences.

Most exciting Blastocystis-related paper of the year for me is probably the one published by Raul Tito and colleagues in the journal Gut, which is available for free download here. The paper is a good example of the opportunity we have to study Blastocystis across geographical regions and taxonomic kingdoms. I would very much like to re-congratulate Raul on his fantastic work! His work sets an example for all of us.

Everyone, please remember that we have founded the International Blastocystis Network, which is a memeber of World Federation of Parasitology. Please help us come up with ideas as to what it can be used for.

To those of you who celebrate Christmas: Happy Christmas!
And a Happy New Year to everyone!

Rune

Is this a new Blastocystis subtype? Maybe not! Here's Why!

The genetic diversity of Blastocystis is becoming comparable to the universe! Seventeen subtypes (which are likely separate species or even genera) have been acknowledged so far, but quite a few more have been mentioned.

However, before assigning new Blastocystis subtype numbers to your SSU rDNA sequences, you'd need to do some QC work on your data. Sometimes we notice sequences deposited in the NCBI Database or included in articles that may look like new Blastocystis subtypes.... but they're most likely not!

I asked Prof Graham Clark from London School of Hygiene and Tropical Medicine, who has more than 20 years' experience in the Blasto business, to give a couple of examples, explaining where issues may arise. He says:

'One of the tasks I do when I have a few minutes to spare is to look at new Blastocystis sequences that have been deposited into GenBank. I am always hoping to stumble across some exciting new subtypes or new hosts that will expand our understanding of diversity in Blastocystis. Only rarely does this happen, however. I do, occasionally, come across sequences that are problematic and it is these that I want to focus on.

Chimaeras: This problem occurs during PCR amplification when one primer binds to a Blastocystis subtype DNA and the other primer binds to a different source of DNA. In the first case I came across the other source was a different Blastocystis subtype, meaning that the sequence at one end of the PCR product matched one subtype and the sequence at the other end matched a different subtype. This observation is mentioned in the paper describing barcoding of Blastocystis (Scicluna et al, 2006). Since then I have seen other chimaeric sequences: one recently was a mixture of Blastocystis plus a plant while another was Blastocystis plus a free-living protist.

Chimaeras are produced when there is incomplete replication of a DNA strand during a cycle. After denaturation in the next cycle, the single stranded partial product can bind to another single stranded product from a different source and synthesis results in a product combining sequences from two sources. The conservation of ribosomal RNA genes means there can be sufficient similarity to allow binding between sequences from distantly related organisms.

Chimaeras are generally only found when the sequences are from cloned ribosomal RNA gene sequences obtained by PCR, although they also occur in some forms of Next Generation  Sequencing. When mixed PCR products are sequenced directly the sequence obtained is the average of all the products in that reaction, and so chimaera sequences will usually be ‘diluted out’ by the major product of the reaction. Only when a single sequence from that mixture is isolated and studied will chimaeras be detected.

If the ‘alien’ region makes up a significant percentage of the sequence then the result of BLAST analysis will show a percentage divergence from known subtypes that indicates it may represent a new subtype. A quick way to evaluate this is to compare the BLAST results using the first and last thirds of the sequence. If it is a new subtype the results should be similar. In a recently detected chimaera, the first third was a 100% match to a known Blastocystis subtype while the last third was a 95% match to asparagus. This approach is an easy way to check whether there is something to get excited about.

A chimaera sequence can sometimes be detected because of its impact on phylogenetic trees. The sequence will be on its own branch, often at the base of a clade containing the subtype found at the Blastocystis-matching end.

Non-Blastocystis Blastocystis sequences: Like chimaeras these are often PCR artefacts, most commonly encountered when amplifying from stool DNA, especially if the stool is non-human. There is an expectation that Blastocystis-specific primers will only amplify Blastocystis DNA but, sadly, that is not always the case. I have personally seen this many times - if Blastocystis DNA is a minority of the eukaryotic DNA in the sample then the likelihood of artefacts increases greatly. These are generally identified easily if the sequence is compared using BLAST against the full nr/nt nucleotide collection in GenBank. However, there is a temptation to limit the search to the genus Blastocystis to speed up the identification process, because that is what you expect it to be. Again because of the conservation of ribosomal RNA genes, if ribosomal RNA genes are amplified there will be a match to Blastocystis, and the divergence will likely suggest, again, a new subtype.  Comparing against the full nucleotide collection will always show whether the sequence is of Blastocystis origin.

Both chimaeras and non-Blastocystis products are easily identified if the correct steps are taken. In conclusion, be suspicious of anything that is significantly divergent to known Blastocystis – it could be an indication of an artefact.'

Fig. 1. A 'Blastaragus' (a chimaera of a Blastocystis and an asparagus)

Fig. 2. An example of a chimaeric DNA sequence (the 'Blastaragus' from Fig. 1). Notice how the consensus sequence starts out as Blastocystis ST14, shifts to asparagus, and then shifts back again to Blastocystis ST14.

I thank Graham, and I really hope that this information will be picked up by many of our colleageus. And please share! Research into Blastocystis is rapdily expanding, and we should all take on the responsibility of QCing our data.

Thanks for listening!

By the way... if you're interested in tutorials on Blastocystis subtyping from our recent workshop in Colombia, please look up Workshop Session 4 in the manual available at this link. 

Hope to be back before Christmas!

2nd International Blastocystis Conference Wrap-Up - Part III

I asked around for some more take-home messages from a couple of the keynote speakers present at the 2nd International Blastocystis Conference last month in Bogotá. Here's a summary:

Kevin Tan:

• Blastocystis is a species complex and as such, it is difficult to generalize on its roles in health and disease.
• Studies are revealing that intra-subtype variations are associated with different phenotypes, so it is likely that we will require more resolution (allelic) when studying the effects of Blastocystis on the host.
• Recent metagenomics studies on stools of healthy individuals associate the presence of Blastocystis with a diverse bacterial microbiota, but more studies are required on diseased groups to identify their possible associations with rare/ pathogenic isolates (e.g. ST7 isolates).
• Recent work on rodent models are shedding light on possible pathogenic effects of acute Blastocystis infections.
• More studies on the cell and molecular biology of Blastocystis are required to better understand the molecular basis for Blastocystis-host interactions (identify virulence factors, adaptation strategies etc).
• It is very likely that more surprises are in store for the curious and observant Blastocystis researcher!

Kevin Tan giving his keynote

Kevin Tan taking questions - here probably expanding on Blastocystis ploidy...

Andrew Roger:

• We shouldn’t try to generalize about characteristics of ‘Blastocystis’ based on studies of individual isolates. This is a category error — Blastocystis comprises many many different organisms with different genetic makeups. There is variation not just between subtypes, but within subtypes. So we shouldn’t say “Blastocystis is a commensal/parasite” because different Blastocystis isolates could be commensals or parasites depending on the host, the genetic makeup of the parasite and the microbiota with which they interact.
• In microbiome studies, colonization with Blastocystis in general seems to correlate with a different composition of the prokaryotic microbiota in hosts.
• We know virtually NOTHING about the basic cell biology of Blastocystis (Kevin Tan’s group is making important inroads into understanding this).
• We know virtually NOTHING about how Blastocystis interacts with (or responds to) other microbes and the host immune system.
• There may be an important impact of host diet on Blastocystis colonization and ‘behaviour'.
• The diversity of Blastocystis in humans and animals is huge — new lineages are being continuously revealed.

Andrew Roger about to give his keynote

Andrew Roger taking questions from the audience