Dear all,

This is to remind you that the 3rd International Blastocystis Conference (http://blastocystis2021.com) will take place virtually between 2nd to 4th of June 2021 and currently both the registration (http://blastocystis2021.com/registration/) and the abstract submissions are open (http://blastocystis2021.com/abstract-guidelines/), with the deadlines for abstract submission and early-bird registration approaching soon: April 15th, 2021.

Participants from LMICs will receive a 20% discount in their registration fees. Please contact the Conference Secretariat (synedrio@topkinisis.com) to register at the discounted rate.

 For frequent updates, please follow us on twitter: @Blastocystis21 . Please do also spread the word! 

We look forward to seeing you (even virtually) in June 2021.

 

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.

More on Blastocystis and Gut Bacteria...

As an appropriate follow-up on yesterday's post, I feel like guiding your attention to the paper by Laforest-Lapointe and Arrieta from University of Calgary, Canada with the title 'Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies', which elaborates on some of the issues that we have already been highlighting several times in the past.

Nevermind, in their article, which just appeared in the ASM-based journal "mSystems", they speculate that the reason for the observed link between Blastocystis colonisation and increased bacterial diversity (which was mentioned several times in the paper that I referred to yesterday) might be due to predation by Blastocystis on bacteria, a process which selects for higher diversity. They argue that

"In the absence of Blastocystis, a strong bacterial competitor dominates the community, which limits species richness and community evenness; when [Blastocystis is] present, its predation on abundant bacterial taxa lowers the competition for nutrients and space, which leads to an increase in bacterial richness and community evenness."

Since predation on bacteria by Blastocystis has only been documented once (I believe) to date, the authors are right in encouraging colleagues to study engulfment of bacteria by Blastocystis.

Those of us who take a special interest in the public health impact of common intestinal parasites and who work in the field of clinical microbiology and infectious diseases might benefit from taking some lessons from experts in 'food web theory' and micro- and macroecology.

The article can be accessed here.

This Month in Blastocystis Research - Interactive Edition

What are your thoughts on Blastocystis carriage and age?

More and more data suggest that the prevalence of Blastocystis carriage increases by age - at least to a certain point.

Some intestinal parasites, such as Cryptosporidium, may not be that uncommon in infants/very young toddlers, while they are much less common in older children and adolescents. Other parasites appear to peak in prevalence around the age of 7, e.g., Dientamoeba fragilis.

Meanwhile, Blastocystis appear to increase in prevalence by age until mature adulthood... why is that? And what does it tell us? Please comment! I'm not having all the answers to these questions myself, and if some interesting suggestions pop up, I'll post them! You only need a Google account to be able to comment. If you don't have one, please send your comment using

crs[at]blastocystis.net 

For those interested in Blastocystis carriage in association with age, I have listed a couple of relevant recent studies below.

References:

Forsell J, Granlund M, Samuelsson L, Koskiniemi S, Edebro H, & Evengård B (2016). High occurrence of Blastocystis sp. subtypes 1-3 and Giardia intestinalis assemblage B among patients in Zanzibar, Tanzania. Parasites & Vectors, 9 (1) PMID: 27356981  

Poulsen CS, Efunshile AM, Nelson JA, & Stensvold CR (2016). Epidemiological Aspects of Blastocystis Colonization in Children in Ilero, Nigeria. The American Journal of Tropical Medicine and Hygiene, 95 (1), 175-9 PMID: 27139454

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   

This Month in Blastocystis Research (DEC 2015)

The potential pathogenicity of Blastocystis is something that has kept me preoccupied for more than a decade. Nonetheless, what I find perhaps even more interesting, is the overall role of Blastocystis in both health and disease.

And so, what do I mean by that?

Well, we just published a MiniReview in Journal of Clinical Microbiology (JCM) with the title: "Blastocystis in Health and Disease--Are we Moving from a Clinical to A Public Health Perspective?" I guess we were a bit lucky to get the paper published as a review, since it's probably more likely to be viewed upon as an Opinion paper, and so it would perhaps have been more suitable for a journal such as Trends in Parasitology. However, we would like medical doctors to be aware of our thoughts, and that's one of the reasons why we approached JCM.

Practically all Blastocystis research has focussed on identifying a role for the parasite in disease. Pathogenic properties have been identified for many other intestinal parasites since long; for Blastocystis, however, we still have no rockhard and reproducible evidence of

• Outbreaks
• Virulence-assoicated properties including invasiveness, phagocytosis, or adhesion to other cells
• Symptom relief upon parasite eradication

Meanwhile, no one has really tried to looked into what Blastocystis may tell us about human health. Together with partner labs, our lab has produced data suggesting that Blastocystis carriage is extremely common, and probably also extremely long lasting. We have also shown that the parasite is associated with certain gut microbial communities and that it is more common in healthy individuals than in patients with IBD, IBS, etc. We have even identified intriguing data that suggest that Blastocystis may be less common in obese individuals compared with lean.

These are some of the most important reasons why I think that research into the public health significance of Blastocystis should be supported. We need to know much about what it means physiologically, microbiologically, and immunologically to be colonised, including 'what happens to our intestinal ecosystem when we are exposed to and colonised by Blastocystis?' Can we identify any benefits from colonisation, and if yes, which are these and can this knowledge be exploited with a view to producing drugs/probiotics that mimic any beneficient properties of Blastocystis? What does it mean to become colonised at an early age vs. only later in life?

In this regard, future areas of research could include studies on the ability of Blastocystis to

• induce changes in bacterial communities in vitro and in vivo
• assist in the metabolisation of food items (e.g., short-chain fatty acid metabolism)
• promote stabilisation of gut microbiota
• produce immunomodulatory and/or pro-/antibiotic substances, etc.

Happy New Year everone!

Reference:

Andersen LO & Stensvold CR (2015). Blastocystis in Health and Disease–Are We Moving from a Clinical to a Public Health Perspective? Journal of Clinical Microbiology PMID: 26677249
doi: 10.1128/JCM.02520-15

This Month in Blastocystis Research (NOV 2015) - Persian Gulf Edition

Today is the first time an Airbus A380 will be landing in Copenhagen Airport, Denmark. Flying in from Dubai, it will mark the inauguration of a runway that was recently refurbished to enable accommodation of a plane of this size.

I therefore thought I'd make a tribute to this particular day by dedicating the "This Month in Blastocystis Research" post to studies on Blastocystis recently published by researchers based along the Persian Gulf. Three surveys on Blastocystis from this region recently made it to parasite/microbiology research journals. The studies are important since they represent examples of studies employing molecular tools for screening and molecular characterisation of parasite isolates identified in regions where such data are extremely scarce. Some of these data will enable us to better understand host specificity, differences in geographic distribution, clinical and public health significance, and transmission patterns.

 The first study was on Blastocystis in Qatar and published in Acta Tropica; it was already mentioned in my September blog entry.

I was lucky to be involved in the second study, which was a study carried out in Sharjah, United Arab Emirates, and designed by Ali ElBakri and colleagues. In this study, we screened a total of 133 samples from ex-pats living in Sharjah, subtyping the samples positive for Blastocystis using partial small subunit (SSU) ribosomal RNA gene sequencing. Fifty-nine (44.4%) samples were positive, of which 39 were successfully sequenced and subtyped. The ST distribution was as follows: ST3, 58.9% (23/39); ST1, 28.2% (11/39); and ST2, 7.6% (3/39). This study is the first to provide data on the prevalence of Blastocystis and the distribution of various STs in the UAE. As usual, ST4 was absent, while ST1, ST2, and ST3 were all common in this geographical region; a situation similar to most other regions outside of Europe.

The third study was from the city of Baghmalek in Southwestern Iran, and was published by Khoshnood and colleagues in Jundishapur Journal of Microbiology. This team used microscopy to identify Blastocystis in 1,410 stool samples from patients presumably suffering gastrointestinal symptoms. A very low prevalence was identified, about 3%. This low figure most likely reflects the use of microscopy, which is an extremely insensitive diagnostic method. From Blastocystis-positive samples, DNA was extracted and submitted to PCR and sequencing targeting the (SSU) ribosomal RNA gene. It says in the article that the subtypes identified in the study included "ST3, ST4, ST5, and ST7 with the most prevalent being ST4 (40.9%)", and the main conclusion is that, unlike the situation in other countries in the Middle East, ST4 was identified as the most prevalent subtype.

There are at least two conspicuous situations here: The first one pertains to the rather unusual subtype distribution reported, which appears quite dissimilar to the ones reported from neighbouring countries. The next one is even more odd and pertains to the fact that the sequences (AB915194 - AB915214) generated in the study, and from which the subtype data must have been inferred, do not BLAST to other nuclear ribosomal RNA genes in GenBank, of which there are thousands! In fact, AB915194 represents a protein-coding gene, translating into  

S P Y L L S I S T E E S Y T D S H Y Y G E C T T I A Q S I Y H Q S S K S V E A S I W D C V Y Met T L I Y E G V T D L T Y D E M K A S Y T D P V E T L T V L G K Y P G A D I S G I S L D L V F G Y I G R G I P V I S R I N D G R Y V L I V S Y N S E A V R Y Y D P V L D E Q V R K Q

... which is a Clostridium hypothetical protein with a peptidase domain! This may either reflect an error linked to the accession numbers, or it may reflect a situation where for some reason non-ribosomal DNA sequences were uploaded to GenBank. Given the appearance of the phylogeny included in the article, it could easily be suspected that the sequences produced and used were in fact non-Blastocystis DNA sequences, in which case the paper should be retracted. Before this mystery has been solved, the results of the Iranian study cannot be fully appreciated, and the relevance of citing the study appears very limited for now.

The last study highlights the importance of making sequence data publicly available; if these data had not been available for critical appraisal, the conclusions made in this article could easily have been accepted without any further ado!

References:

Abu-Madi M, Aly M, Behnke JM, Clark CG, & Balkhy H (2015). The distribution of Blastocystis subtypes in isolates from Qatar. Parasites & Vectors, 8 PMID: 26384209

AbuOdeh R, Ezzedine S, Samie A, Stensvold CR, & ElBakri A (2015). Prevalence and subtype distribution of Blastocystis in healthy individuals in Sharjah, United Arab Emirates. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases PMID: 26611823 

Khoshnood S, Rafiei A, Saki J, & Alizadeh K (2015). Prevalence and Genotype Characterization of Blastocystis hominis Among the Baghmalek People in Southwestern Iran in 2013 - 2014. Jundishapur Journal of Microbiology, 8 (10) PMID: 26587213 

This Month in Blastocystis Research (OCT 2015)

I'm actually going to skip the small review I do each month for a variety of reasons. Instead, I'm just going to upload a presentation I gave in Tilburg, The Netherlands, a bit more than a week ago, before attending the UEG Week in Barcelona.

I uploaded it to Google Drive, hoping that it will be easy to download for everyone interested. I have not included any notes, hoping that the slides will be pretty much self-explanatory.

I think there is even a bit of Danish in there, - hope you don't mind! Also, the preview option does not work very well, so make sure you download it.

If the presentation left you wondering a bit and wish for more, why not look up my publications listed in PubMed? They are available here.  Some of them can be downloaded for free.

Thank you for your attention.

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 

This Month In Blastocystis Research (APR 2014)

Due to all sorts of activities I have not been able to update myself with 'novelties' in the scientific Blastocystis literature lately.

Instead, I would like to highlight two review/opinion papers on the use of PCR-based methods for diagnosis of intestinal parasitic infections in the clinical microbiology laboratory.

Both papers have been published very recently (actually one is still 'in press'). The first is co-authored by Jaco J Verweij and myself, and appears in the April issue of 'Clinical Microbiology Reviews'. This paper aims to provide a relatively systematic review of the extent and relevance of PCR- and sequencing-based methods for diagnosis and epidemiology studies of intestinal parasites, and is as such an inventory of all sorts of DNA-based diagnostic and typing modalities for individual protists and helminths.

The second one is authored solely by Jaco J Verweij and is currently in the 'first online' section in the journal 'Parasitology'. This paper offers a discussion of the application of PCR-based method as a supplementary tool or a substitute for conventional methods (microscopy, antigen detection, etc.). Dr Verweij deals with central questions such as 'Is Molecular Detection Good Enough?' and 'Is Molecular Detection Too Good To Be True?'.

And so these two papers complement each other quite well. For those interested in the very low prevalence of intestinal helminth infections in the Western world, the latter paper has a table which summarizes some quite stunning data.

Although DNA-based methods currently in use do have quite a few limitations, I do believe that for a long while the application of species- and genus-specific PCR methods (real-time PCR, conventional PCR + sequencing, etc.) will appear relevant and state-of-the-art. Dr Verweij, I and a few of our colleagues around the world are currently discussing to which extent next generation sequencing methods can be used to

• generate data that can assist us in identifying the role of pro- and eukaryote microbial communities in health and disease
• serve as a tool to generate sequences that can be processed by designated software and thereby identify patterns of microbial communities associated with various disease and health conditions

To this end, at the Laboratory of Parasitology, Statens Serum Institut, we are currently assisting in the development of a software called BIONmeta. BION meta is an open-source package for rRNA based pro- and eukaryote community analysis. Like Qiime and Mothur it is open source but with a growing number of advantages. The package has so far been developed mostly by Niels Larsen (DK), one of the original Ribosomal Database Project authors. It is as yet unpublished, but has been selected for in-house trial-use by companies and institutions that also partly sponsor its development.When relevant, I'll post more information on this software.

References:

Verweij JJ, & Stensvold CR (2014). Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections. Clinical Microbiology Reviews, 27 (2), 371-418 PMID: 24696439

Verweij, JJ. (2014). Application of PCR-based methods for diagnosis of intestinal parasitic infections in the clinical laboratory Parasitology, 1-10 DOI: 10.1017/S0031182014000419