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What do you mean by repeatable? The gut microbiome is in constant flux; it constantly changes every day. A sample sent to 3 different companies on 3 different

What do you mean by repeatable? The gut microbiome is in constant flux; it constantly changes every day. A sample sent to 3 different companies on 3 different days would have 3 different results, even if their analysis was perfect. I've not had my stools analyzed. If I were to, the biggest thing I would look for would be the level diversity in my microbiome, as opposed to individual strains. I only have minor knowledge about this, so maybe I am missing something.

ipunchghosts 9y ago
> What do you mean by repeatable? This is a complicated question but let's break it down to the simplest problem i can think of. Suppose I do a study comparing the gut microbiota of CFS patients compared to controls. Then, another group does the same study. The control group better have reasonable overlap. If they do not, then both labs should process the raw samples and see if they get reasonable overlap. If not, start here to fix. > The gut microbiome is in constant flux; it constantly changes every day. It depends on who you talk to which is somewhat my point. Eric Alm's lab showed that the gut microbiome is relatively stable over time (they sample daily for over a year). Other labs have shown it varies daily. My own lab has shown that it varies greatly depending on where you take the sample (stool is actually quite heterogeneous in terms of bacterial populations). You could argue how you define "same" as a function of a scale, in this case taxon level. But the problem still remains. > A sample sent to 3 different companies on 3 different days would have 3 different results, even if their analysis was perfect. If the analysis was "perfect" (whatever that means), then why are they different. Can we model the differences? The real truth is that stool is quite heterogenous in terms of bacterial populations. Its quite easy to get an OOM difference between abundances in the same sample. > I've not had my stools analyzed. If I were to, the biggest thing I would look for would be the level diversity in my microbiome, as opposed to individual strains. Diversity on which level though? Most consumer sequencing companies do not go the strain level. Most are genus and you get about 50-75% of the species. > I only have minor knowledge about this, so maybe I am missing something. Appreciate your honesty. Science has done a sub par job (in my opinion) of emphasizing to the public that we (the community) understand what is going on. All we really know now, broadly speaking, is that the gut microbiota is different when compared to healthy controls be we really have no idea why. That doesnt mean we dont understand the metabolite profiles, but the simple fact that Provetella has been implicated in both sickness and in health should indicate that reproducibility would be very insightful.
- mswen 9y ago
  I upvoted your comment, but want to add a compliment. This kind of dialogue and knowledgeable comment are why I keep reading HN, often starting with the comments. Thank you for addressing the previous comment in a thorough manner while not talking down to him or the rest of us who are smart and interested but not educated in the specifics of this domain.
  - ipunchghosts 9y ago
    Thanks. In my mind, what gets done by berating someone in this context. The poster said they don't really know much so I assume they are part of the general public. Its up to science to educate the public on these matters. Also, I have run into quite a few microbiome zealots, all are what i call armchair scientists -- no college background and think they know everything from reading abstracts on pubmed. The kind of arguments they put up cannot be well addressed on the internet because they can find some study which proves their point. Which this proves my point -- the studies are inconsistant. I welcome thoughtful and engagine conversation about the matter and have problem being told I am wrong when evidence is presented.
- JacobJans 9y ago
  Thank you for the detailed response. I am part of the general public, so to speak, but am also interested in this research because I have a certain disease. I am treating this disease with diet modification, which seems to be working. (The Specific Carbohydrate Diet.) However, it seems like there are many questions as to why it works that is very much not understood. > The control group better have reasonable overlap. I wonder if there is enough understanding of what makes a "healthy" gut microbiome in order to properly assess what "overlap" means. Isn't a microbiome a complex system with many moving parts? For example, a study of successful businesses could include many successful businesses that are completely different from one another. Comparing these to "unhealthy" businesses would probably not be very useful. It seems like you're answering this question by saying the different labs should process the same samples, to at least see if the same samples are returning the similar results. Is that right? I wonder if there is a resource for further learning on this topic. Reading scientific studies, as you say, provides only limited value to a layman. The number of people with diseases affected by the gut microbiome is very, very large.

ipunchghosts 9y ago

> What do you mean by repeatable? This is a complicated question but let's break it down to the simplest problem i can think of. Suppose I do a study comparing the gut microbiota of CFS patients compared to controls. Then, another group does the same study. The control group better have reasonable overlap. If they do not, then both labs should process the raw samples and see if they get reasonable overlap. If not, start here to fix. > The gut microbiome is in constant flux; it constantly changes every day. It depends on who you talk to which is somewhat my point. Eric Alm's lab showed that the gut microbiome is relatively stable over time (they sample daily for over a year). Other labs have shown it varies daily. My own lab has shown that it varies greatly depending on where you take the sample (stool is actually quite heterogeneous in terms of bacterial populations). You could argue how you define "same" as a function of a scale, in this case taxon level. But the problem still remains. > A sample sent to 3 different companies on 3 different days would have 3 different results, even if their analysis was perfect. If the analysis was "perfect" (whatever that means), then why are they different. Can we model the differences? The real truth is that stool is quite heterogenous in terms of bacterial populations. Its quite easy to get an OOM difference between abundances in the same sample. > I've not had my stools analyzed. If I were to, the biggest thing I would look for would be the level diversity in my microbiome, as opposed to individual strains. Diversity on which level though? Most consumer sequencing companies do not go the strain level. Most are genus and you get about 50-75% of the species. > I only have minor knowledge about this, so maybe I am missing something. Appreciate your honesty. Science has done a sub par job (in my opinion) of emphasizing to the public that we (the community) understand what is going on. All we really know now, broadly speaking, is that the gut microbiota is different when compared to healthy controls be we really have no idea why. That doesnt mean we dont understand the metabolite profiles, but the simple fact that Provetella has been implicated in both sickness and in health should indicate that reproducibility would be very insightful.

mswen 9y ago
I upvoted your comment, but want to add a compliment. This kind of dialogue and knowledgeable comment are why I keep reading HN, often starting with the comments. Thank you for addressing the previous comment in a thorough manner while not talking down to him or the rest of us who are smart and interested but not educated in the specifics of this domain.
- ipunchghosts 9y ago
  Thanks. In my mind, what gets done by berating someone in this context. The poster said they don't really know much so I assume they are part of the general public. Its up to science to educate the public on these matters. Also, I have run into quite a few microbiome zealots, all are what i call armchair scientists -- no college background and think they know everything from reading abstracts on pubmed. The kind of arguments they put up cannot be well addressed on the internet because they can find some study which proves their point. Which this proves my point -- the studies are inconsistant. I welcome thoughtful and engagine conversation about the matter and have problem being told I am wrong when evidence is presented.
JacobJans 9y ago
Thank you for the detailed response. I am part of the general public, so to speak, but am also interested in this research because I have a certain disease. I am treating this disease with diet modification, which seems to be working. (The Specific Carbohydrate Diet.) However, it seems like there are many questions as to why it works that is very much not understood. > The control group better have reasonable overlap. I wonder if there is enough understanding of what makes a "healthy" gut microbiome in order to properly assess what "overlap" means. Isn't a microbiome a complex system with many moving parts? For example, a study of successful businesses could include many successful businesses that are completely different from one another. Comparing these to "unhealthy" businesses would probably not be very useful. It seems like you're answering this question by saying the different labs should process the same samples, to at least see if the same samples are returning the similar results. Is that right? I wonder if there is a resource for further learning on this topic. Reading scientific studies, as you say, provides only limited value to a layman. The number of people with diseases affected by the gut microbiome is very, very large.