Tag: human microbiome

Yes Virginia, even the cervix has a #microbiome ……….. or does it?

Just read over the following paper: PLoS ONE: The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

It is interesting and has lots of tidbits worth looking at in more detail including

  • An analysis of methods for classifying sequence reads as to which organism they likely come from
  • comparison of amplification and sequencing methods
  • long time period covered in the sampling
  • and much more
But what struck me more than anything is that, well, they referred to the microbial community that they were sampling as the “cervical microbiome.”  And though what they discuss here is fascinating in many ways, I am beginning to wonder if every site on the human body (or sites on other organisms) should have its own microbiome.    Or, another way of looking at this is – where do we draw the line between niches?  Is there a eyebrow microbiome?  A left elbow microbiome?  A testicle microbiome?  Certainly, I view the microbes that live in and on people as part of an ecosystem.  But I think just as biomes in the world around us should be defined by – well – something bigger than just GPS coordinates – so too microbiomes should probably be a bit bigger than just the microbes found in a particular body site.  Starting to wonder if we are going to see a proliferation of microbiomes just as we have seen a proliferation of OMIC words.  Ooh — this could give me something new to give an award for.  
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Episode of Radio New Zealand "This Way Up": "Meet your microbes" discussion w/ me

Did an interview over the phone with Simon Morton for Radio New Zealand’s “This Way Up.”  Discussing microbial diversity and in part as a follow up on my TEDMED/TED talk.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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"Life on Man" – amazing book on human associated microbes

Just got this book by Theodor Rosebury in the mail: The Tree of Life Store – Life on Man.

I ordered it a few days ago after someone named Richard Montgomery posted a comment about it in relation to my “Human microbiome” talk that is posted at TED.

Just starting the book but it is awesome so far.  Definitely worth trying to get a copy.  Though it is out of print, I found many copies online … //ws-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&OneJS=1&Operation=GetAdHtml&MarketPlace=US&source=ac&ref=tf_til&ad_type=product_link&tracking_id=thtrofli-20&marketplace=amazon&region=US&placement=0670427934&asins=0670427934&linkId=UY6Y5ADMTK4HG6FI&show_border=true&link_opens_in_new_window=true

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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My "human associated microbes" talk now available on TED site (w/ transcripts too).

My TedMed talk is now on Ted.Com. See below. Some interesting comments too – have been trying to respond to most — even the unusual ones.

http://video.ted.com/assets/player/swf/EmbedPlayer.swf

Plus there is now a transcript available in English and German. And the transcripts are hot linked to the portions of the video …

Thanks to Tedmed for allowing this and to TED to posting the talk.  Plus the folks at TED re-edited the talk and added some more camera angles for the part where I tossed giant stuffed microbes into the crowd …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Nice feature on the human microbiome in the SF Chron w/ a little Toxoplasma error

Nice article in the SF Chronicle by Erin Allday on human microbiome related topics.  It features some Bay Area scientists working on the issue – David Relman, Janet Jansson, Les Dethlefsen, and Michael Fischbach.  See:100 trillion good bacteria call human body home – SFGate.

It has some nice pictures of Relman in the lab (though I think he could use some new lighting in there …).  There is one microbial error in there

At least one bacterium – toxoplasmosis gondii – has been shown to affect behavior. The bacterium reproduces only in cats, and studies have shown that when mice or rats are infected with it, the bacterium makes them less afraid of cats, and they are, therefore, more likely to be eaten by them.

Alas toxoplasmosis is caused by a microbial eukaryote known as Toxoplasma gondii (it is a relative of the causative agent of malaria Plasmodium falciparum).  But otherwise the article is a good read.  I like the end

Fischbach at UCSF is perhaps facing the most difficult challenge: caring for his days-old daughter and nurturing her infant microbiome. He’s in the tough position of having both too much and not nearly enough information. 

“My wife and I have tried to pledge to each other that this is going to be our baby, not our experimental subject,” Fischbach said with a laugh. “At the same time, my thinking is influenced by the things going on around me. The cast of characters in her is changing dramatically week to week, day to day. I do wonder, where are most of the bacteria that she’s got in the gut coming from?”

And as a bonus there is an interview with Relman too:  Sequencing of human microbiome fills knowledge gap

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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The human #microbiome project (HMP): new papers and news stories

Just collecting here the new papers from the Human Microbiome Project and some news stories discussing them.

Main papers in Nature

PLoS Collection (all free)

Other paper out in Nature on the topic though not from the HMP

Some news stories:

Some previous posts of mine in this general area

Some other good recent posts or articles worth looking at on the topic
Related links
And of course – a gratuitous embed of my recent TEDMED talk
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Crowdsourcing help needed: how many microbes are brought into human GI tract via food? #microbiome

Quick but somewhat complex question here that came up at a recent meeting I went to – someone wanted to know:

How many microbes come into the human GI tract from outside sources (e.g., food)?

Other related questions:

  • How many cells /day?
  • How many are alive?
  • How many kinds come in?
  • How much flow through is there vs. digestion vs. colonization?

Note – I know there have been many studies of pathogens on food and how they get into the GI tract, but what about non pathogens?

Any references or #s would be very helpful.

Thanks

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Crowdsourcing some facts for my upcoming #Tedmed talk on #microbes on #humans

OK all I am looking for some help here is finding out some latest pieces of information about the microbes that live in and on people for my Tedmed talk next week Some things I could use

  • 1. What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)? 

  •  2. What is the number of species of known human pathogens (that are microbes) 

  •  3. What human ailments are now thought to be possibly caused by disturbances in the microbiome? 

  •  4. How many viruses (kinds and numbers) are found in the human microbiome? 

  •  5. What is a good source of open (e.g., creative commons) images of the microbes found in / on people? 

 I am going to post these each as a comment below so people can respond to each one … Thanks
UPDATE 6/4/2012 – Embedding the talk I gave for TEDMED

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Draft post cleanup #4: Gut microbes and cancer

Yet another post in my “draft blog post cleanup” series.  Here is #4:

Interesting article in the Scientist August 1, 2011:
Sharing the Bounty | The Scientist by Michelle Rooks and Wendy Garrett.

It is based on an article from the journal F1000 reports by the same authors.

The article in essence reviews other studies that suggest a possible link between microbes in one’s gut and the risk of development of certain cancers.  It is worth a look.

See abstract below:

Abstract:

Gut microbes are essential components of the human organism—helping us metabolize food into energy, produce micronutrients, and shape our immune systems. Having a particular pattern of gut microbes is also increasingly being linked to medical conditions including obesity, inflammatory bowel disease, and diabetes. Recent studies now indicate that our resident intestinal bacteria may also play a critical role in determining one’s risk of developing cancer, ranging from protection against cancer to promoting its initiation and progression. Gut bacteria are greatly influenced by diet and in this review we explore evidence that they may be the missing piece that explains how dietary intake influences cancer risk, and discuss possible prevention and treatment strategies.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Carl Zimmer on "Who Owns Your Microbes"?

There was an interesting piece by Carl Zimmer in the New York Times a few days ago: Our Microbiomes, Ourselves – NYTimes.com
In the piece Zimmer discusses the issue of who owns your microbiome. This can be considered an extension of the concept of “Who owns your cells?” such as has been discussed in the context of Rebecca Skloot’s HELA book.
My favorite line(s):

Monitoring the bacteria flushed into the sewer system of a town, for instance, might reveal a lot about the entire town’s health. But a regulation requiring permission from every resident of the town would stop the study dead in its tracks

Personally I think none of us own our microbes – since we get them from the world around us and likely share them with millions of others. It would be akin to saying we own genes found in all humans. But there very well may be some person specific alleles in microbes that could in a way be akin to person specific cell lines. Not sure.

Anyway – I think I am going to name all my microbes as a first step in protecting my rights to them …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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