In June there was a paper out in Frontiers in Microbiology by Laura W Parfrey and co-workers identifying the diversity of intestinal microbial eukaryotic communities (IMECs) in humans and other mammals. It's probably one of the most interesting papers I've read for a long time; maybe because it expands on many of the things I've been blogging about - or at least intended to blog about (!) - over the past two years.
What the team did was to do comprehensive analysis of IMECs in both humans and mammals using broad specificity primers for PCR and next generation sequencing technology-based sequencing of the PCR products. While I'm not in a position to validate the analysis of the data, I'd just want to highlight the importance of the approach. It is very rare to see this type of analysis, despite the fact that it's probably the best currently available approach to studying the ecology, homeostasis and public health significance of IMECs. Some of these euks have probably co-evolved with humans and other animals over thousands and thousands of years and therefore may constitute part of the habitual/commensal flora; and so a current working hypothesis (Hygiene Theory) is that losing IMECs ('defaunation' due to Western life style (excessive hygiene and changes in diet)) may prove detrimental to human health and may be one of the most important reasons why we develop for instance allergies and other autoimmune diseases.
And indeed, what the authors found was that among 23 study individuals residing in agrarian communities in Malawi, Blastocystis and Entamoeba were almost obligate findings (not found in two infants, but apart from that almost a consistent finding), while none of the 13 (somewhat age-matched) study individuals from Boulder, Colorado, were infected with Blastocystis, and only two individuals had Entamoeba coli. I was surprised to read that Dientamoeba was not detected in any of the populations; it appears that there is a strong geographical component to the distribution of this parasite, but as the authors mention, specific tools are needed to confirm the absence.
The funny thing is that although this is not a paper specifically on Blastocystis, it is probably the most interesting surveys on Blastocystis coming from the US and a very valuable Blastocystis. Data on Blastocystis in this country is really scarce, but if the prevalence of the parasite is really as low as indicated in this study, then it's maybe quite understandable! And maybe (and this is a highly presumptuous 'maybe', I know) Blastocystis might even therefore an emerging pathogen in the US? When was the US experiencing the great IMECs wipe out? Can it be confirmed? Is there - within the US - also a strong geographical compoenent to the prevalence of IMECs?
Anyway, there are many interesting observations in the paper - and please visit the supporting files. Blastocystis ST11 was confirmed in an elephant (which also hosted Entamoeba moshkovskii! Probably first report of this parasite in an animal). ST13 was found in a Gazelle; not surprisingly, but nice to see independent data confirming what few researchers have found until now. ST4 was found in a sheep and in Okapis; when it comes to ST4, I'm hardly surprised about anything; it appears to be such a sporadic finding in a diversity of non-human hosts (i.e. low host specificity and incidental); one sheep also had ST8, a subtype almost exclusively seen in non-human primates (even South American monkeys rather than for instance African monkeys and apes), so this was surprising too. ST8 was moreover found in two kangaroos (not the first time), in an okapi (different from two first ones) which also hosted ST12, and in an armadillo!
Take home messages include:
1) The study is one of the first to virtually survey IMECs in human and non-human faecal samples using NGS tools.
2) The study confirms a very high prevalence of Blastocystis in some sub-Saharan African communities (for more on this, see a previous blog post), and interestingly, the prevalence and co-infection rate of (up to four species of) Entamoeba was comparably high.
3) Data suggest that IMECs in Western populations are highly reduced compared to rural African populations, but we still need to know more about the relative distribution of for instance fungi and whether these fungi are actually colonising the gut or just carry over from ingested food; right now, it seems as if there might be an inverse relationship between fungal and non-fungal IMECs... something that we can hopefully soon gather sufficient data on for publishing.
4) For those interested in Blastocystis subtype data, including host specificity and geographical distribution, there is a lot to look at in the paper (including supplementary files).
There's a lot more to be said about this paper, but I will sort of leave it here. But please go and read it!
Reference:
Parfrey, L., Walters, W., Lauber, C., Clemente, J., Berg-Lyons, D., Teiling, C., Kodira, C., Mohiuddin, M., Brunelle, J., Driscoll, M., Fierer, N., Gilbert, J., & Knight, R. (2014). Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity Frontiers in Microbiology, 5 DOI: 10.3389/fmicb.2014.00298What the team did was to do comprehensive analysis of IMECs in both humans and mammals using broad specificity primers for PCR and next generation sequencing technology-based sequencing of the PCR products. While I'm not in a position to validate the analysis of the data, I'd just want to highlight the importance of the approach. It is very rare to see this type of analysis, despite the fact that it's probably the best currently available approach to studying the ecology, homeostasis and public health significance of IMECs. Some of these euks have probably co-evolved with humans and other animals over thousands and thousands of years and therefore may constitute part of the habitual/commensal flora; and so a current working hypothesis (Hygiene Theory) is that losing IMECs ('defaunation' due to Western life style (excessive hygiene and changes in diet)) may prove detrimental to human health and may be one of the most important reasons why we develop for instance allergies and other autoimmune diseases.
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| Blastocystis virtually obligate finding in Malawi citizens? |
The funny thing is that although this is not a paper specifically on Blastocystis, it is probably the most interesting surveys on Blastocystis coming from the US and a very valuable Blastocystis. Data on Blastocystis in this country is really scarce, but if the prevalence of the parasite is really as low as indicated in this study, then it's maybe quite understandable! And maybe (and this is a highly presumptuous 'maybe', I know) Blastocystis might even therefore an emerging pathogen in the US? When was the US experiencing the great IMECs wipe out? Can it be confirmed? Is there - within the US - also a strong geographical compoenent to the prevalence of IMECs?
Anyway, there are many interesting observations in the paper - and please visit the supporting files. Blastocystis ST11 was confirmed in an elephant (which also hosted Entamoeba moshkovskii! Probably first report of this parasite in an animal). ST13 was found in a Gazelle; not surprisingly, but nice to see independent data confirming what few researchers have found until now. ST4 was found in a sheep and in Okapis; when it comes to ST4, I'm hardly surprised about anything; it appears to be such a sporadic finding in a diversity of non-human hosts (i.e. low host specificity and incidental); one sheep also had ST8, a subtype almost exclusively seen in non-human primates (even South American monkeys rather than for instance African monkeys and apes), so this was surprising too. ST8 was moreover found in two kangaroos (not the first time), in an okapi (different from two first ones) which also hosted ST12, and in an armadillo!
Take home messages include:
1) The study is one of the first to virtually survey IMECs in human and non-human faecal samples using NGS tools.
2) The study confirms a very high prevalence of Blastocystis in some sub-Saharan African communities (for more on this, see a previous blog post), and interestingly, the prevalence and co-infection rate of (up to four species of) Entamoeba was comparably high.
3) Data suggest that IMECs in Western populations are highly reduced compared to rural African populations, but we still need to know more about the relative distribution of for instance fungi and whether these fungi are actually colonising the gut or just carry over from ingested food; right now, it seems as if there might be an inverse relationship between fungal and non-fungal IMECs... something that we can hopefully soon gather sufficient data on for publishing.
4) For those interested in Blastocystis subtype data, including host specificity and geographical distribution, there is a lot to look at in the paper (including supplementary files).
There's a lot more to be said about this paper, but I will sort of leave it here. But please go and read it!
Reference:
