Showing posts with label microbiome. Show all posts
Showing posts with label microbiome. Show all posts

Friday, December 30, 2016

This Month in Blastocystis Research (DEC 2016)

I would like to end the year by briefly highlight three of the most important/interesting papers in Blastocystis research published in 2016 (and not co-authored by me).

The first article that comes to my mind is one by Pauline Scanlan and colleagues, who took to investigating the prevalence of Blastocystis in US households (family units). The reason why I'm mentioning this article is not so much due to its approach; it's much more related to the fact that even when molecular methods are used (i.e., highly sensitive methods), the prevalence in this population was only 7%, and the vast majority of Blastocystis carriers were adults. The prevalence is much lower in this population (Colorado) than in a country such as Denmark. I'm interested in knowing the reason for this difference. Are people in Colorado less exposed or are they less susceptible than people in Denmark? I'm also interested in knowing why there was only one child among the carriers... we see similar trends elsewhere: Blastocystis is a parasite that emerges only in adolescence and adulthood. Meanwhile, we see a lot of Dientamoeba in toddlers and smaller children, with more or less all children being infected at some point - at least in Denmark; here, geographical differences may exist as well. Mixed infection with Blastocystis and Dientamoeba in adults is not uncommon, so it's not that they outcompete each other.

Next up, is the article by Audebert and colleagues who published in the Nature-affiliated Scientific Reports on gut microbiota profiling of Blastocystis-positive and -negative individuals. I already made a small summary of the article in this post.

While we gain valuable insight into gut microbiota structure, we also need to know what these microbes are able to do. We need to know about the interaction with the host and how they influence our metabolism. I hope to see more studies emerging on the metabolic repertoire of Blastocystis and how the parasite may be capable of influencing the diversity and abundance of bacterial, fungal and protist species in the gut. What would also be useful is a drug that selectively targets Blastocystis so that we can be able to selectively eradicate the parasite from its niche in order to see what happens to the surrounding microbiota and - if in vivo - to the host.

The last article is authored by my Turkish colleagues Özgür Kurt, Funda Dogruman-Al, and Mehmet Tanyüksel, who pose the rhetorical question: "Blastocystis eradication - really necessary for all?" in the special issue on Blastocystis in Parasitology International. For some time I have been thinking of developing a reply to the authors as a Letter to the Editor with the title "Blastocystis eradication - really necessary at all?" Nevermind, quite similar to what we did back in 2010, the authors review the effect of various drugs that have been used to try eradicate Blastocystis. Moreover, they acknowledge the fact that Blastocystis is often seen in healthy individuals, and that its role in the development of gut microbiota and host immune responses should be subject to further scrutiny. They even suggest that the role of Blastocystis as a probiotic should be investigated. It's great to see clinicians think along these lines, since this is an important step towards expanding the revolution lately seen in Blastocystis research, exemplified by studies such as that by Audebert et al. mentioned above.

So, wishing you all a Happy New Year and a great 2017, I'd like to finish by encouraging you to stay tuned; soon, I will be posting some very... interesting... neeeeeeewwwws...




References:

Audebert C, Even G, Cian A, Blastocystis Investigation Group., Loywick A, Merlin S, Viscogliosi E, & Chabé M (2016). Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Scientific Reports, 6 PMID: 27147260 

Kurt Ö, Doğruman Al F, & Tanyüksel M (2016). Eradication of Blastocystis in humans: Really necessary for all? Parasitology International, 65 (6 Pt B), 797-801 PMID: 26780545

Scanlan PD, Knight R, Song SJ, Ackermann G, & Cotter PD (2016). Prevalence and genetic diversity of Blastocystis in family units living in the United States. Infection, Genetics and Evolution, 45, 95-97 PMID: 27545648

Monday, June 13, 2016

This Month in Blastocystis Research (MAY 2016)

Very much belated, I'm back to give you the MAY entry of the 2016 "This Month in Blastocystis Research" blog series.

I'm basically just going to highlight a few papers and some other interesting things.

Ever since our metagenomics paper came out, it's as if the interest in Blastocystis in a gut microbiota context is exploding. If you put "Blastocystis microbiota" into the search box in PubMed, today you will get 20 hits, most of which papers are extremely interesting and of course very central to this type of research. Given the number of times I've addressed the relevance of studying Blastocystis in relation to gut microbiota diversity on this blog, I'll try not to flog it to death this time!

Over at Gut Microbiota For Health, a blog was posted a week ago summarising the recent findings of Audebert and colleagues and comparing them to data coming out from our lab. You can read the blog here. Using the Ion Torrent PGM sequencing platform, 16S rDNA gene sequencing was performed on genomic DNAs extracted from Blastocystis-positive and - negative stool samples. What Audebert hypothesised was that if Blastocystis is associated to intestinal disease such as for instance diarrhoea, one would expect to find a higher degree of microbiota perturbation (dysbiosis) in Blastocystis carriers than in non-carriers. Meanwhile, and similar to what we have have published, they reported that gut microbiota diversity is higher in Blastocystis carriers than in non-carriers, indicating that Blastocystis is generally a marker of a healthy gut microbiota rather than a perturbed one. Again similar to what we found in the metagenomics paper, Audebert et al. saw that the bacterial families Ruminococcaceae and Prevotellaceae were also more abundant in carriers than in Blastocystis-negative patients, while Enterobacteriaceae were enriched in Blastocystis-negative patients. What is also really interesting is the fact that the genera Faecalibacterium and Roseburia had a significantly higher abundance in Blastocystis-positive patients. These genera contain bacteria that produce butyrate which has a lot of important and beneficial functions. Loss of butyrate producers is seen for instance in patients with inflammatory bowel disease. The group used some of the same methods as we used in our study presented recently at ECCMID, including rarefaction analysis and calculation of Chao1 indices.

Together with colleagues at the Technical University of Denmark, we were lucky to have The European Journal of Clinical Microbiology and Infection publish our novel data on associations between common single-celled intestinal parasites--Blastocystis and Dientamoeba--and groups of intestinal bacteria, as evidenced by qPCR assays. We confirmed the findings from our metagenomics study, by finding a relatively lower abundance of Bacteroides in the parasite-positive samples than in the -negative ones.

By the way, on the Gut Microbiota For Health site you will find an e-learning course on Microbiota provided by the Gut Microbiota and Health Section of the European Society of Neurogastroenterology and Motility (ESNM) and developed for gastroenterologists.

Speaking of e-learning and gastroenterology: For a couple of years, I've had the immense pleasure of being part of the United European Gastroenterology e-learning task force. We host a resource - UEG Education - developed mainly for gastroenterologists, boasting e-learning courses, "Decide-on-the-Spot" series, "Mistakes in..." series, blogs, and other features. I have included a UEG widget in the right side bar of my blog - please click it!

Back to Blastocystis! Graham Clark and I published a personal view on the current status of Blastocystis in Parasitology International, in which we summarise the development and recent advances in Blastocystis research. The article is expected to form part of a special section/issue dedicated to Blastocystis to commemorate last year's 1st International Blastocystis Symposium in Ankara.

My colleague Juan-David Ramirez and his colleauges published data from a subtyping study from South America including 346 samples. More than 85% of the subtypes found belonged to either ST1, ST2, and ST3 as expected, while the rest belonged to ST4, ST5, ST6, ST7, ST8, ST12 and what they call a new subtype. I think this is the first time ST12 has been reported in humans. Despite the fact that the authors accounted for the databases that they used for subtype and allele calling, there is no mention on the criteria by which the subtypes were called in the NCBI database (i.e., in those cases where no hits could be found at the online Blastocystis database). For instance, what level of similarity was used to identify three samples as ST12? On the same note, which level of similarity was used to identify nine samples as belonging to a "novel subtype" (also, - was it the same sequence across the nine samples?). When dealing with a potentially novel subtype, usually the entire SSU rRNA gene is seqeunced and subjected to phylogenetic analysis, and sequences have not yet been made public in GenBank, so there is no possibility to work with the data so as to validate the findings (which are highly accurate, I'm sure). I think this information is critical to interpreting the data. Nontheless, the work that went into the sampling and the lab work should be highly accredited.

References:

Andersen LO, Bonde I, Nielsen HB, & Stensvold CR (2015). A retrospective metagenomics approach to studying Blastocystis. FEMS microbiology ecology, 91 (7) PMID: 26130823

Audebert C, Even G, Cian A, Blastocystis Investigation Group, Loywick A, Merlin S, Viscogliosi E, & Chabé M (2016). Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota. Scientific reports, 6 PMID: 27147260  

O'Brien Andersen L, Karim AB, Roager HM, Vigsnæs LK, Krogfelt KA, Licht TR, & Stensvold CR (2016). Associations between common intestinal parasites and bacteria in humans as revealed by qPCR. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology PMID: 27230509 

Ramírez JD, Sánchez A, Hernández C, Flórez C, Bernal MC, Giraldo JC, Reyes P, López MC, García L, Cooper PJ, Vicuña Y, Mongi F, & Casero RD (2016). Geographic distribution of human Blastocystis subtypes in South America. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 41, 32-5 PMID: 27034056

Stensvold CR, & Clark CG (2016). Current status of Blastocystis: A personal view. Parasitology international PMID: 27247124   

Wednesday, July 1, 2015

This Month in Blastocystis Research (JUN 2015)

I started developing this blog more than three years ago. After a bit more than a year, I collected a bunch of the posts, edited them and published them as a book on Amazon. Recently, I logged into my Amazon profile to see how the book was doing, and I was very pleased to notice that there were no less than four reviews of the book, and very positive ones too! Thank you to everyone who read/browsed it.

Blastocystis research is currently a quickly moving field, and I'm please to be able to inform you that one of the most interesting contributions to Blastocystis research coming out from our intstitute has just been published in Fems Microbiology Ecology. The article appearing in this journal was first-authored by PhD student Lee O'Brien Andersen (Statens Serum Institut) and post doc Ida Bonde (Danish Technical University) and describes how Lee and Ida took a retrospective approach to analysing metagenomics data originally generated by the MetaHIT Consortium and published in the often cited paper by Arumugam et al. (2012).

The abstract reads as follows:
Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in co-abundance gene groups, which are groups of genes that co-vary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD), and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities.

As far as we know this is the first study to sift out data on Blastocystis from data originally intended for analysis of bacterial communities only, and in the paper we describe how this was done. We believe that this approach has imminent potential for quickly advancing our knowledge on Blastocystis in a gut ecology context, including knowledge on the role of Blastocystis in terms of impacting/manipulating one or more types of intestinal bacteria.

I have a feeling that this is the first study in a string of similar studies that will soon hit PubMed, and within a year or two, we should be able to with confidence to hypothesise on the relationship between the structure and function on of the gut microbiota and Blastocystis, and–hopefully–other intestinal micro-eukaryotes.

Lastly, it was very interesting to note the article by Paramsothy et al. on donor recruitment for faecal microbiota transplantation (FMT; never heard of this? Watch the video below to learn more), recently appearing in the journal Inflammatory Bowel Disease. The study is interesting because it shows that most FMT donors are seemingly ineligible due to a variety of reasons, including colonisation by intestinal parasites such as Blastocystis... Given emerging data suggesting that Blastocystis is more common in healthy invididuals than in patients with gastrointestinal disease, the question remains whether Blastocystis-positivity should be a limiting factor for stool donation?



References:

Andersen LO, Bonde I, Nielsen HB, Stensvold CR. A retrospective metagenomics approach to studying Blastocystis. Published online 30 June 2015. DOI: http://dx.doi.org/10.1093/femsec/fiv072

Paramsothy S, Borody TJ, Lin E, Finlayson S, Walsh AJ, Samuel D, van den Bogaerde J, Leong RW, Connor S, Ng W, Mitchell HM, Kaakoush N, & Kamm MA (2015). Donor Recruitment for Fecal Microbiota Transplantation. Inflammatory bowel diseases, 21 (7), 1600-6 PMID: 26070003

Thursday, April 30, 2015

This Month in Blastocystis Research (APR 2015)

#ECCMID2015 took place in Copenhagen. It was a great venue with a lot of interesting sessions. My favourite presentation was by Dr Paul D Cotter. We have had the pleasure of doing some work together with Dr Pauline D Scanlan as the main driving force. In his talk, Dr Cotter highlighted the emergence of research exploring whether certain organisms are pathobionts or probionts; among these, Blastocystis. Among many things, Dr Cotter reviewed the two recent Blastocystis-specific publications by Scanlan et al. focusing on the commonness and stability of Blastocystis colonisation [1] and on the need to use subtype-specific PCRs to detect and identify mixed subtype colonisation/infection [2].

Based at TEAGASC - Ireland, the Cotter/Scanlan group is one of the teams interested in looking into the ecology of Blastocystis (and other microbial eukaryotes of the gut), including its influence of the parasite on gut microbiota/microbiome (structure and function of our all gut organisms) and vice versa, and I'm sure that there will be a lot of interesting data coming out from their lab in the near future.

Cotter mentioned that Blastocystis has been subject to bad science. This may be due to a number of reasons. When developing hypotheses, we have a tendency of opting for dichotomous outcomes - either it is this or that, - maybe that's the very nature of hypotheses. If the clinical significance of Blastocystis is dependent on a number of different things such as co-colonising microbes (cross-talk), differences in host immunity response, Blastocystis subtype, and host diet for instance, then the true tapestry of physiological/biological/clinical mechanisms is likely to be extremely difficult to uncover. Moreover, despite the fact that so many people are curious about the public health significance of Blastocystis, apparently very little funding for targeted Blastocystis research exists. This means that mostly minor and not so significant studies ("cheap studies") on Blastocystis are available. Relatively little seminal research has been done in the clinical field (including the field of gastroenterology), and most studies on Blastocystis are cross-sectional and descriptive and usually not very well designed/carried out (use of diagnostic tools with limited sensitivity, for instance).

Maybe things will change when more and more people realise that we might be able to use Blastocystis as a biomarker/surrogate marker of intestinal homeostasis...

In my opinion the following topics would make for good research projects:

1) Large studies of both diseased cohorts and healthy individuals, including Blastocystis subtype data and data on accompanying protists, bacteria and fungi (16S/18S/ITS profiling).
2) Manipulaton studies where Blastocytsis (cysts) are introduced in ecosystems (in vitro or in vivo) to monitor potential changes.
3) Animal models using cyst challenge (to look at microbiota profile changing upon challenge, and, if in vivo colitis models are used, impact on host immunity)
4) Longitudinal microbiome studies of patients with and without Blastocystis.
5) Investigation of Blastocystis as a biomarker/surrogate marker of microbiota profiles and gut microbiome homeostasis... similar to my recent blog post: 'Show me your gut bacteria, and I'll tell you if you have Blastocystis!'
6) Comparative genomics (virulence gene identification for instance).
7) Identification of Blastocystis-specific signatures in metagenomics data sets.
8) Identification of drugs that have anti-Blastocystis properties, since currently, there is no drug regimen that consistently enables eradication of Blastocystis.

Speaking of which: We just published data in Journal of Ethnopharmacology on the anti-Blastocystis activity of 24 plant parts from 21 medicinal plants from Ghana [3]. We performed in vitro challenge of 48 h Blastocystis cultured cells (subtype 4) using ethanolic, warm and cold water plant extracts. Screening of these 24 different plant parts showed significant anti-Blastocystis activity of six of the ethanolic extracts: Mallotus oppositifolius, IC50, 24h 27.8 µg/mL; Vemonia colorata, IC50, 24h 117.9 µg/mL; Zanthoxylum zanthoxyloides, cortex IC50, 24h 255.6 µg/mL; Clausena anisata, IC50, 24h 314.0 µg/mL; Z. zanthoxyloides, radix IC50, 24h 335.7 µg/mL and Eythrina senegalensis, IC50, 24h 527.6 µg/mL. The reference anti-protozoal agent metronidazole (MTZ) had an IC50, 24h of 7.6 µg/mL. Since cultures were xenic, antimicrobial activity was tested against two Gram-positive and two Gram-negative bacteria for all 24 plant parts at a final concentration of 1 mg/mL. Only C. anisata showed antimicrobial activity at a concentration of 800 µg/mL.

Hence, M. oppositifolius showed nearly as good activity as the reference anti-protozoal drug MTZ. Historically, the active plants found in this study have been used against dysentery, diarrhoea or other stomach disorders. Nowadays they are not used specifically for dysentery, but they are being used as medicinal plants against various stomach disorders.

Our book 'Biology of Foodborne Parasites' is out and available for ordering.

Incidentally, Blastocystis earned a designated chapter in the book 'Biology of Foodborne Parasites' which is now out and available for ordering here. It was fun writing it up, and hope that the chapter will be of interest to health care professionals and students around the world. The book also contains  introductions to the public health importance of foodborne parasites, molecular biological techniques in studies of foodborne parasites, and detection of parasites in foods.

References:

[1] Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HG, De Vos WM, O'Toole PW, & Cotter PD (2014). The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS Microbiology Ecology, 90 (1), 326-30 PMID: 25077936   

[2] Scanlan PD, Stensvold CR, & Cotter PD (2015). Development and application of Blastocystis subtype-specific PCR reveals that mixed subtype infections are common in a healthy human population. Applied and Environmental Microbiology PMID: 25841010

[3] Bremer Christensen C, Soelberg J, Stensvold CR, & Jäger AK (2015). Activity of medicinal plants from Ghana against the parasitic gut protist Blastocystis. Journal of Ethnopharmacology PMID: 25773490

Tuesday, March 31, 2015

This Month in Blastocystis Research - MAR 2015

"Show me your gut bacteria and I'll tell you if you're infected with Entamoeba"

One of my 'partners in crime', science reporter Jop de Vrieze, made me aware of a study just published now by Elise R Morton and colleagues. The study appeared in bioRxiv—The Preprint Server for Biology, operated by Cold Spring Harbor Laboratory. The study is totally in line with one of the research foci in our lab.

The paper is called 'Variation in rural African gut microbiomes is strongly shaped by parasitism and diet', and can be downloaded here. The backbone in this type of research is the recognition that studies revealing a large contrast between the microbiomes of populations in developing countries and those of populations in urban industrialised areas have shown that geography is an important factor associated with the gut microbiome, but that such studies yet have to disentangle the effects of factors such as climate, diet, host genetics, hygiene and parasitism.

It's very refreshing that for once, 'parasitism' is included in such considerations. As mentioned in one or more of my previous blog posts, we have metagenomics data stongly indicating that Blastocystis colonisation is associated with certain microbial communities. As of yet, we have no idea about cause and effet, but the idea alone is immensely intriguing.

A large and a small cyst of Entamoeba coli. Courtesy of Dr Marianne Lebbad.
Now, Morton et al. have produced data that suggest that the presence of Entamoeba—another gut-associated eukaryotic genus comprising multiple species of varying pathogencitiy—is strongly correlated with microbial composition and diversity. They showed that an individual's liability to being infected by Entamoeba could be predicted with 79% accuracy based on gut microbiome composition.

The authors used 16S PCR and Illumina-based sequencing of 16S amplicons, and I could have wished that molecular assays, e.g., the 18S PCR that we have developed in our lab + associated software, had also been used to test the faecal samples from the 64 individuals enrolled in the study in order to obtain more precise data, not only on Entamoeba but also on other human-associated gut protists, such as Blastocystis.

While alpha (intra-host) diversity of Entamoeba-positive individuals was significantly higher than that of Entamoeba-negative individuals, analysis of the beta (inter-host) diversity revealed that gut communities across Entamoeba-positive individuals were more similar than across Entamoeba-negative individuals, suggesting that, as alpha diversity increases, there are fewer potential stable states for individual gut communities, or that infection by Entamoeba drives changes in the microbiome that are dominant over other factors.

Right—this is Entamoeba, I know, but in principle, the type of analyses that were performed in the present study could be applicable to Blastocystis, Dientamoeba, and other gut parasites, which may help us understand their role in health and disease. Are these parasites able to influence gut microbiota? Can they be used for gut microbiota manipulation? Or do they only infect people with certain microbiota profiles? Time will show... maybe.

For those of you who would like to read more about what is shaping our microbiomes and how the gut microbiota may impact on our gastrointestinal health, I recently did a couple of blog posts for United European Gastroenterology (UEG) Education that might be of some interest:

Are we finally saluting the fungal kingdom as a co-ruler of GI health and disease?

The intestinal microbiome—Rosetta Stone or Tower of Babel?


Reference:

Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekham R, Segurel L.
Variation in rural African gut microbiomes is strongly shaped by parasitism and diet. bioRxiv doi





Sunday, August 24, 2014

This Month in Blastocystis Research (AUG 2014)

Some August highlights in Blastocystis research:

1) The PRE-IOPCA Molecular Parasitology Workshop took place from the 7-10 August at CINVESTAV, Mexico City. Top-motivated students from some 10-15 countries worked hard from 7 am to 7 pm in dry+wet lab sessions, and we all had a really great time, thanks to both participants and fantastic organisers. There was a 4 h session on Blastocystis molecular epidemiology, and I was pleased to learn that some of the participants currently work with (or plan to work with) Blastocystis. I look forward to doing something similar in Ankara, Turkey on the 27th of May next year (www.blastomeeting2015.com - did you bookmark it?).

Most of the task force of the Molecular Parasitology Workshop (ICOPA 2014).
2) At the actual ICOPA conference, I chaired a session on Blastocystis in the context of IBS, with talks delivered by Ken Boorom, Pablo Maravilla, Pauline Scanlan and myself. In the audience I was honoured to see and meet Dr Hisao Yoshikawa, who has been a main contributor to Blastocystis research over the past 25 years or so (you can look up the publications by Dr Yoshikawa here). Considering the focus of this post, I guess that Pauline's talk was of particular interest, since she presented the data that we just published in FEMS Microbiology and Ecology:

3) The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. That's the title of the paper appearing in FEMS Microbiology and Ecology. The study, led by Pauline, showed that Blastocystis was present in 56% of 105 healthy adults, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected and Blastocystis was present in a subset of individuals sampled over a period of time between six and ten years, indicating that it is capable of long-term host colonisation. These observations show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine. And one of the interesting things here is: Why do we see this great divide? Why does half of the population appear colonised while the other half not? What are the factors driving successful Blastocystis colonisation? Would some people be refractory to colonisation or does it really boil down to some sort of enterotype-driven phenomenon as previously indicated?

4) I would like to reiterate the paper by Klimes et al. published a study in Genome Biology and Evolution (GBE) on a striking finding in the Blastocystis nuclear genome. Stop codons created by mRNA polyadenylation have been seen so far in mitochondrial genomes only and not in nuclear genomes; however, the authors observered this feature in Blastocystis's nuclear genome. Partly due to limitations of currently available annotation software, this finding ostensibly calls for reannotation of the genome currently available in GenBank (ST7). The paper was highlighted in a separate article in GBE that can be accessed from here.

5) Speaking of Blastocystis genomes: The genome of Blastocystis ST4 (WR1 strain) is now available on-line and can be accessed here.

6) Wang and colleagues studied the location and pathogenic potential of Blastocystis in the porcine intestine. They studied a total of 28 pigs from a commercial piggery, a small animal farm, and a research facility, and all pigs were positive (for ST5, and mixed subtypes were also seen in some). Post-mortem analyses showed that all pigs were consistently found to harbour Blastocystis in the colon, and approximately 90% of the caeca and rectums examined were positive. Some of the pigs were immunosuppresed (Dexamethasone), and interestingly, Blastocystis was occasionally detected in the small intestine, notably in immunosuppressed pigs, suggesting that immunosuprression may alter host-agent relations and predispose to small intestinal colonisation. Histopathological analysis saw the presence of vacuolar and granular forms of Blastocystis, but there was no evidence of attachment or invasion of the intestinal epithelium. The lack of pathology, including inflammation, epithelial damage, mucosal sloughing, and lamina propria oedema, confirmed the trend from a previous study carried out by Ron Fayer's group (see reference below). The study adds to the string of papers finding no evidence in support for Blastocystis causing primary intestinal damage.

6) Lastly, I want to extend a cordial thank you to Shashiraja Padukone and Subhash Chandra Parija, Department of Microbiology, Jipmer, Puducherry, India, for writing up a review of my 'Thoughts on Blastocystis' available on Amazon for the price of only one US$ or so. The review was published recently in Tropical Parasitology and can be accessed here.

And, for those who are worried about researchers 'overselling' microbiome research, there is a small comment in Nature calling for sound scepticism to be applied to research dealing with the relationship between the microbiome and different types of diseases. There is much to be agreed upon, and what I find particularly important, is to take the reductionist approach where possible - in terms of Blastocystis there are lots of ways to study the impact of Blastocystis on bacteria in vitro, and also host microbiota, physiology and immunology in vivo; ways that can be controlled quite diligently. Also, I think that simple validation of methods applied to map e.g. intestinal microbiota is key. This is for some reason something that is generally being utterly and completely ignored. Why?

References 

Fayer R, Elsasser T, Gould R, Solano G, Urban J Jr, & Santin M (2014). Blastocystis tropism in the pig intestine. Parasitology Research, 113 (4), 1465-72 PMID: 24535732

Hanage, W. (2014). Microbiology: Microbiome science needs a healthy dose of scepticism Nature, 512 (7514), 247-248 DOI: 10.1038/512247a

Klimeš V, Gentekaki E, Roger AJ, & Eliáš M (2014). A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biology and Evolution, 6 (8), 1956-61 PMID: 25015079

Scanlan PD, Stensvold CR, Rajilić-Stojanović M, Heilig HG, De Vos WM, O'Toole PW, & Cotter PD (2014). The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota. FEMS Microbiology Ecology PMID: 25077936 

Venton, D. (2014). Highlight: Not Like a Textbook--Nuclear Genes in Blastocystis Use mRNA Polyadenylation for Stop Codons Genome Biology and Evolution, 6 (8), 1962-1963 DOI: 10.1093/gbe/evu167

Wang W, Bielefeldt-Ohmann H, Traub RJ, Cuttell L, & Owen H (2014). Location and pathogenic potential of Blastocystis in the porcine intestine. PloS One, 9 (8) PMID: 25093578