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How to keep up with microbial ecology and the built environment: microBEnet is your place

Comment
Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting
My posts:
Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams - post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD
Brent Stephens of the Illinois Institute of Technology

Calling attention to poor speaker gender ratio - even when it hurts

Comment
So I saw this Tweet earlier today


And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)
  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)
If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don't think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now - do I know who the possible speakers were for this symposium?  No - I don't really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note - I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias - whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.



UPDATE 3/25 11:29 AM

The meeting organizers have responded on Twitter

Storify of some responses here


Treponema are not "ancient" but absence from some human's guts is very interesting

Comment
So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:





These refer to a sadly inappropriate headline in Science



What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:
As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
And then some further detail in the paper:
Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 
So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.


In a similar way, we could say that Westernized humans have "lost" the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But "losing skinnyness" does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like "do not show an ancestral trait" (the ancestral trait here being skinnyness) and to not use "lost" until we know more about what is going on.  Similarly, I think saying some human populations have "lost" these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these "missing" Spirochaetes is definitely worth paying attention to.

In addition, I note - the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.



Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments

The ChuckNorrisMicrobiome will get you, and you, and you ...

Comment

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen

Comment

Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:
Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you're back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.
This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence ...

Then there is a discussion that makes the microbome sound like the master controller of all that is human:
Our bodies are cohesive entities, yes, but within each there are several languages spoken. 
The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).
And then there is evidence free claims about fatigue and the microbiome
I've found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says
Whenever someone critiques "conventional" medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  
So - if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

Some silly microbome ideas from @DeepakChopra and @rudytanzi

Comment
Well, just got to reading this: Big Idea 2015: Medicine, Wellbeing, and the Microbiome | Deepak Chopra MD. Yes, it was from December 2014 but I could not get up to reading it then because I saw some of the comments online about it and it seemed off.  But anyway I caught up to it today.  It has many inaccurate and misleading statements about microbes and microbiomes I just felt like I had to post something.  Some of the problemmatic parts are below with comments.

Let's start gently.  As with many other stories on the microbiome, this article quotes the oft cited "fact" of a 10:1 ratio of microbial cells to human cells.
By some estimates the body has between 35 and 100 trillion cells with only 1 in 10 belonging to tissues and organs and the rest belonging to the microbiome.
This has been refusted by a great article in the Boston Globe by Peter Andrey Smith in September 2014 (long before this was published): Is your body mostly microbes? Actually, we have no idea.  Yes, I and many others cited this 10:1 ratio before the Globe.  But seeing it cited in this from December 2014 suggests Chopra and Tanzi aren't really paying attention to microbiome science.

The next comment I find a bit off is the follwing:
Our personal human genome also determines the composition of our microbiome, which in turn can influence metabolism and propensity for weight gain.
Sure.  Our genes influence out microbiome.  But "determines the composition" is way to strong a statement.

But the things that got to me most were many of the comments supposedly about evolution.  I list some of them below:
  • This varying ecosystem isn't populated by foreign invaders and pathogens but by colonies closely connected to human evolution.
    • I don't even know what this is supposed to mean.  These are not "colonies" first of all.  And second, what does "connected to human evolution" even mean?  And wouldn't pathogens be connected to human evolution?
  • The microbiome interfaces between the human body and the outside world in complex ways, but the gist is that human DNA has evolved in cooperation with microbial DNA. This fact is more important than the interactions that cause diseases created by invading bacteria and viruses.
    • Re "human DNA has evolved in cooperation with microbial DNA".  Well, sure.  Some of the microbes we live with are mutualists. But most likely only a limited number of mutualistic interactions are going on.  This sounds like a Gaia type of model, with no evidence.  
    • And then "This fact is more important than the interactions that cause diseases created by invading bacteria and viruses."  Really?  More important than the plague?  Than malaria? Aids?  Cholera.  TB? Worms? And more.  This sounds really silly.
  • Mitochondria actually have their own genomes inherited from the mother without change.
    • Umm - no mitochondria mutate and change, well, all the time.
  • Some of the most archaic microorganisms on Earth survive today in our microbiome.
    • This is without any justification.  First of all - what does "most archaic" mean?  And second, if it means what I think it means (organisms that have features like those from billions of years ago) - well - no - the human microbiome does not have a lot of such organisms.  This is just complete hooey.  
  • It would appear that the genome and the microbiome cross-talk, a conversation that has been continuing for billions of years with no signs of stopping.
    • What does this even mean?  In what way has the human microbiome been interacting with the human genome for billions of years.  In what way have human ancestors been interacting with microbiomes for billions of years?

Yes, the microbiome is important.  But this "essay" is filled with nebulous pseudoscientific comments about the microbiome all, apparently, to sell an upcoming book and related activities

"In an upcoming book we are co-authoring, Super Genes, we will present the latest findings as well as a lifestyle program devoted to what we call Self-Directed Biological Transformation"

Right now, I don't think Chopra and Tanzi show any evidence they really understand the microbiome .. doesn't bode well for their book and lifestyle program.

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Comment
Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

"got asked by another reporter to comment on this

so - have seen the paper 
it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "
I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 
Without seeing the alignments I offer multiple alternative hypothesis for their findings
  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.
Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.
Reporter asking what other analyses could they do
So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 
In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.
Reporter asking about initial impressions:
I see little here that is particularly convincing evidence for HGT ...
My follow up email
Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 
For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

Some related links:
Also here are some presentations from many years ago with some discussion of HGT




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السبت، 28 مارس 2015

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting
My posts:
Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams - post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD
Brent Stephens of the Illinois Institute of Technology
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الأربعاء، 25 مارس 2015

Calling attention to poor speaker gender ratio - even when it hurts

So I saw this Tweet earlier today


And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)
  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)
If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don't think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now - do I know who the possible speakers were for this symposium?  No - I don't really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note - I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias - whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.



UPDATE 3/25 11:29 AM

The meeting organizers have responded on Twitter

Storify of some responses here


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Treponema are not "ancient" but absence from some human's guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:





These refer to a sadly inappropriate headline in Science



What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:
As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
And then some further detail in the paper:
Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 
So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.


In a similar way, we could say that Westernized humans have "lost" the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But "losing skinnyness" does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like "do not show an ancestral trait" (the ancestral trait here being skinnyness) and to not use "lost" until we know more about what is going on.  Similarly, I think saying some human populations have "lost" these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these "missing" Spirochaetes is definitely worth paying attention to.

In addition, I note - the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.



Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments
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الأحد، 22 مارس 2015

The ChuckNorrisMicrobiome will get you, and you, and you ...

Some Saturday fun ...



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السبت، 14 مارس 2015

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen


Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:
Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you're back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.
This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence ...

Then there is a discussion that makes the microbome sound like the master controller of all that is human:
Our bodies are cohesive entities, yes, but within each there are several languages spoken. 
The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).
And then there is evidence free claims about fatigue and the microbiome
I've found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says
Whenever someone critiques "conventional" medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  
So - if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

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Some silly microbome ideas from @DeepakChopra and @rudytanzi

Well, just got to reading this: Big Idea 2015: Medicine, Wellbeing, and the Microbiome | Deepak Chopra MD. Yes, it was from December 2014 but I could not get up to reading it then because I saw some of the comments online about it and it seemed off.  But anyway I caught up to it today.  It has many inaccurate and misleading statements about microbes and microbiomes I just felt like I had to post something.  Some of the problemmatic parts are below with comments.

Let's start gently.  As with many other stories on the microbiome, this article quotes the oft cited "fact" of a 10:1 ratio of microbial cells to human cells.
By some estimates the body has between 35 and 100 trillion cells with only 1 in 10 belonging to tissues and organs and the rest belonging to the microbiome.
This has been refusted by a great article in the Boston Globe by Peter Andrey Smith in September 2014 (long before this was published): Is your body mostly microbes? Actually, we have no idea.  Yes, I and many others cited this 10:1 ratio before the Globe.  But seeing it cited in this from December 2014 suggests Chopra and Tanzi aren't really paying attention to microbiome science.

The next comment I find a bit off is the follwing:
Our personal human genome also determines the composition of our microbiome, which in turn can influence metabolism and propensity for weight gain.
Sure.  Our genes influence out microbiome.  But "determines the composition" is way to strong a statement.

But the things that got to me most were many of the comments supposedly about evolution.  I list some of them below:
  • This varying ecosystem isn't populated by foreign invaders and pathogens but by colonies closely connected to human evolution.
    • I don't even know what this is supposed to mean.  These are not "colonies" first of all.  And second, what does "connected to human evolution" even mean?  And wouldn't pathogens be connected to human evolution?
  • The microbiome interfaces between the human body and the outside world in complex ways, but the gist is that human DNA has evolved in cooperation with microbial DNA. This fact is more important than the interactions that cause diseases created by invading bacteria and viruses.
    • Re "human DNA has evolved in cooperation with microbial DNA".  Well, sure.  Some of the microbes we live with are mutualists. But most likely only a limited number of mutualistic interactions are going on.  This sounds like a Gaia type of model, with no evidence.  
    • And then "This fact is more important than the interactions that cause diseases created by invading bacteria and viruses."  Really?  More important than the plague?  Than malaria? Aids?  Cholera.  TB? Worms? And more.  This sounds really silly.
  • Mitochondria actually have their own genomes inherited from the mother without change.
    • Umm - no mitochondria mutate and change, well, all the time.
  • Some of the most archaic microorganisms on Earth survive today in our microbiome.
    • This is without any justification.  First of all - what does "most archaic" mean?  And second, if it means what I think it means (organisms that have features like those from billions of years ago) - well - no - the human microbiome does not have a lot of such organisms.  This is just complete hooey.  
  • It would appear that the genome and the microbiome cross-talk, a conversation that has been continuing for billions of years with no signs of stopping.
    • What does this even mean?  In what way has the human microbiome been interacting with the human genome for billions of years.  In what way have human ancestors been interacting with microbiomes for billions of years?

Yes, the microbiome is important.  But this "essay" is filled with nebulous pseudoscientific comments about the microbiome all, apparently, to sell an upcoming book and related activities

"In an upcoming book we are co-authoring, Super Genes, we will present the latest findings as well as a lifestyle program devoted to what we call Self-Directed Biological Transformation"

Right now, I don't think Chopra and Tanzi show any evidence they really understand the microbiome .. doesn't bode well for their book and lifestyle program.
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الخميس، 12 مارس 2015

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

"got asked by another reporter to comment on this

so - have seen the paper 
it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "
I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 
Without seeing the alignments I offer multiple alternative hypothesis for their findings
  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.
Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.
Reporter asking what other analyses could they do
So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 
In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.
Reporter asking about initial impressions:
I see little here that is particularly convincing evidence for HGT ...
My follow up email
Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 
For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

Some related links:
Also here are some presentations from many years ago with some discussion of HGT




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