Love this – The Aggie Transcript #UCDavis Undergraduate Life Sciences Journal

I just love things like this: The Aggie Transcript | An undergraduate life sciences journal at UC Davis.  From their site:

The Aggie Transcript is is a forum for undergraduate UC Davis students to share news, original writing, and art related to the life sciences.

Here are some recent posts:

What a great idea.

Everything (or, at least a lot) about Microbiology at UC Davis

Note – written in 2014 – in need of update

So – getting lots of calls and emails and having local meetings with people interested in microbiology at UC Davis.  Rather than continuing to answer each person separately I am just going to put everything together on this page. Departments and groups with a major focus on microbiology.

Departments with a lot of people working on microbiology

Continue reading “Everything (or, at least a lot) about Microbiology at UC Davis”

CAMERA metagenomics resource is shutting down

Just got this email and thought it would be of interest to many out there.

Thank you for being a CAMERA user during its operation as a resource for
environmental genomics. During the past few years, CAMERA has been able to
offer a number of important community resources, including an exceptionally
well curated environmental genomic database, the ability for researchers to
deposit molecular sequence datasets with associated environmental
parameters (metadata), open access to computational resources to enable
metagenomic comparisons, educational resources, and helpdesk services.
These efforts have been funded through the Gordon and Betty Moore
Foundation (GBMF) Marine Microbiology Initiative and the National Science
Foundation to serve the needs of the marine microbiology community and
other users.
In particular, the CAMERA compute resources, which include large-scale
BLAST capabilities and other workflow-enabled analysis capabilities
(RAMMCAP), were generously supported by the GBMF, the San Diego
Supercomputer Center, the NSF XSEDE program, and commercial Cloud computing
resource providers (CODONiS).
Due to the termination of GBMF support, CAMERA can no longer accommodate
the computational needs of the community. Therefore, starting July 1, 2014,
CAMERA will begin to shut down the CAMERA portal and will no longer accept
any new workflow submissions. The results of workflows submitted by July 1,
2014 will be available to users through July 15th. Urgent requests for the
temporary use of CAMERA workflow resources beyond July 1, 2014 will be
considered on a case-by-case basis.
If you are a current or prior CAMERA user and would like to retrieve
personal data from the system, we strongly encourage you to do so now.
As announced earlier this year, CAMERA will continue to maintain free and
open access to its rich collection of curated data and metadata via the
CAMERA Data Distribution Center (DDC), which includes links to the Marine
Microbial Eukaryote Transcriptome Sequencing Project. In conjunction with
the portal shutdown, CAMERA will also no longer accept user data
submissions past July 1st (but data submissions currently in progress will
be completed and made available via the DDC).
Please contact us at camera-info@calit2.net regarding matters pertaining to
the use of CAMERA.
Thank you so much for your support and participation!

The Conversation on China’s embracing #openaccess for Science but not the Humanities

Well, this is very interesting and exactly the type of topic that fits in well with our ICIS project:

Humanities left behind as China embraces open access science.

The article reports on how China as a whole is pushing open access in the sciences but how the humanities in China are pretty much the opposite. The writer Michael Hockx suggests that a big revolution could happen if China embraced green open access in the humanities. Really interesting points here.

Gulp – a good book for those into, well, our insides

On Saturday I went into downtown Davis, CA with my kids to get them haircuts and then to get a present for one of their friends for a birthday party. We decided to get a present at Avid Reader downtown. And after looking for the gift and for some books for my kids I decided I wanted to check out their science section. And I came up with a present for myself too

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And then started reading it. It is quite good.

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On top of reading the book I have been checking out some interviews with the author Mary Roach. Quite entertaining. For example I was pointed to one on Twitter:

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And I then remembered I had been pointed to another via email a while back by Steve Faith at UC Davis:  A Brief Tour Of The Alimentary Canal, From Spit To You Know What : Shots – Health News : NPR.
Still not done with the book but if you want a great read about our insides – I recommend Gulp by Mary Roach very highly.

Local elections in Davis, Yolo County and California are apparently a way for junk mail to be distributed. What a waste.

Well, the local elections in Davis, Yolo County and California are as far as I can tell mostly a way for junk mail to be distributed. What a waste. https://photos.gstatic.com/media/slideshow.swf

Registered for #ASM2014 but could not go; meeting sounded good; but annoyed ASM sold my info to advertisers

Very annoyed with the American Society for Microbiology right now as I have been collecting some of the junk mail I got associated with the meeting.  I presume that ASM sold my information to these advertisers.  I did not explicitly give permission for them to do that.  Not good.

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Overselling the microbiome award – many – for stories about placental vs. oral microbiomes

A few days ago on Twitter I was pointed to a news story about the human microbiome:

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I looked at the article and definitely agreed with Ed. So I responded

//platform.twitter.com/widgets.js And then a mini conversation happened

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And I pondered writing up an “overselling the microbiome award” but I got caught up in other things. And then today some people (including Jens Walter) pointed me to this New York Times article about the same topic: Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com. And I decided I had to write something up because too many news stories were not doing a great job with the science here.

So here goes. First, the Science news (UPDATE – NOTE this is the news part of Science magazine, not ScienceNewsOrg) story Ed Yong pointed to originally and the parts I have problems with.

  • Sentence 1Researchers have discovered a small community of bacteria living in a most unlikely place: the placenta, the organ that nourishes a developing fetus through the umbilical cord.  No – not really.  They did not discover this.  They did a more detailed characterization of the community.
  • Sentence 2The finding overturns the conventional wisdom that the placenta is sterile.  No – the study is another piece of evidence that argues against the “conventional wisdom”
  • Sentence 3 is OK.
  • Sentence 4.  Medical experts have long assumed that any bacteria found in the organ must have been picked up when it passed through the vagina after delivery.  Sure – some “experts” have assumed this.  But there has been growing evidence for many years that this is a bad assumption.  

I could go on and on.  Actually though I won’t.  Becuase every news story can have some limitations.  I don’t like inaccurate statements but it is a part of life I guess.  But the part that drives me batty in this story is the inclusion of a discussion about oral health.  Here are the two paragraphs that are the crux of my concern (with bold emphasizing the worst parts).

Surprisingly, the mix of bacteria in the placenta looked more like the microbiome in an adult human’s mouth than the vaginal, skin, gut, or other body microbiomes, Aagaard’s team reports today in Science Translational Medicine. The researchers think the microbes may get to the placenta from the mother’s mouth through her bloodstream, perhaps when she brushes her teeth and dislodges them into the blood. That possibility is intriguing, because there’s a well-known correlation between gum disease and preterm birth. Indeed, the array of bacteria in the placenta differed in women who gave birth early, before 37 weeks. 

“This reemphasizes the importance of oral healthduring pregnancy, Aagaard says. In fact, women may need to pay attention to their teeth even before they may become pregnant, because the placenta develops early in pregnancy, she says. That may be a challenge for low-income women who can’t afford dental care, Aagaard adds. The team also found a correlation between the composition of the placental microbiome and urinary tract infections, which suggests that such illnesses or antibiotics taken to treat them could alter the microbiome in unhealthy ways.

I have read and reread the paper (which I note – is not open access – making it hard to the public to actually dig into the paper if they wanted to).  And I see no evidence presented anywhere of the importance of oral health or any causal connection between oral health and the placental microbiome or risks to pregnancies. The claims made about this here in this news story are irresponsible.  Yes, there have been some other studies about dental health and birth issues.  But nothing in this paper.  And to imply otherwise is misleading at best.  And then to go on with “That may be a challenge for low-income women who can’t afford dental care” is really not appropriate.  And to then go on about UTIs and how treating them may “alter the microbiome in unhealthy ways” is also misleading and not supported.  
Where is the critical evaluation of such claims?  Certainly the paper is very interesting.  Among the findings of interest to me: (1) that low amounts of DNA from diverse microbes is found even in the placentas from healthy pregnancies and (2) that in their analysis these microbes were most similar to those from the mouth.  But how we get from those findings (and some others) to “the importance of oral health during pregnancy” and “such illnesses or antibiotics could alter the microbiome in unhelathy ways” is, well, not in the realm of scientific research.  This is in the realm of speculation.  And speculation is fine -IF YOU TELL PEOPLE YOU ARE SPECULATING.  If you don’t tell people you are speculating I have another term for it – it is called misleading.  I assume the researchers and reporter did not intend to be misleading but that is the end result of excessive speculation without making it clear what one is doing.

Now this brings me to other articles about this study.  There are many out there.  And most seem to have eaten up this oral health connection without questioning it.  For example, consider the artilce in the New York Times yesterday:Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com by Denise Grady.  Some issues I have with this article:

  • Let’s start with the title “Study Sees Bigger Role for Placenta in Newborns’ Health.”  Well, no – there was nothing in this study that showed any evidence about a new connection between the placenta and newborns’ health.  
  • NYTimes: “During pregnancy, the authors of the new study suspect, the wrong mix of bacteria in the placenta may contribute to premature births.” Sure – they suspect it.  Would have been good to point out they have no evidence for this.
  • NYTimes: Although the research is preliminary, it may help explain why periodontal disease and urinary infections in pregnant women are linked to an increased risk of premature birth.  Again, may help explain – sure.  But it also may have no connection whatsoever.  There is no evidence presented in the paper connecting periodontal disease and UTIs and the placental microbiome.  So this is pure speculation.  And it should have been met with some discussion of all the other ways that periodontal disease and UTIs could lead to risk of premature birth.  Like leading to increased inflammation in the mother.  Or affecting blood flow in the mother.  Or other things.  There is actually a TON of research in this area.  Below are some of the factors that affect preterm labor, as listed by the Mayo Clinic – are we now discounting the years and years of work on this and going whole hog into proposing a new cause without any evidence?
    • Previous preterm labor or premature birth, particularly in the most recent pregnancy or in more than one previous pregnancy
    • Pregnancy with twins, triplets or other multiples
    • Certain problems with the uterus, cervix or placenta
    • Smoking cigarettes, drinking alcohol or using illicit drugs
    • Certain infections, particularly of the genital tract
    • Some chronic conditions, such as high blood pressure and diabetes
    • Being underweight or overweight before pregnancy, or gaining too little or too much weight during pregnancy
    • Stressful life events, such as the death of a loved one
    • Domestic violence or any form of abuse during pregnancy
    • Multiple miscarriages
    • Red blood cell deficiency (anemia), particularly during early pregnancy
    • Too much amniotic fluid (polyhydramnios)
    • Pregnancy complications, such as preeclampsia
    • Vaginal bleeding during pregnancy
    • Presence of a fetal birth defect
    • Little or no prenatal care
    • An interval of less than six months since the last pregnancy
    • Also, having a short cervical length or the presence of fetal fibronectin — a substance that acts like a glue between the fetal sac and the lining of the uterus — in your vaginal discharge might be linked to an increased risk of preterm labor. 
  • I note – the authors even say in their paper “Although this study is not able to address the relationship between periodontal disease and the placental microbiome, we, as a community of obstetricians, have appreciated for decades the association between periodontal disease and preterm birth”. Clearly the paper received more scrutiny that the quotes and the news stories. 
  • NYTimes: The new study suggests that babies may acquire an important part of their normal gut bacteria from the placenta. No.  Nothing in this study showed any connection between what is in the placenta and what is in the babies guts.  None.
  • NYTimes: If further research confirms the findings, that may be reassuring news for women who have had cesareans. Some researchers have suggested that babies born by cesarean miss out on helpful bacteria that they would normally be exposed to in the birth canal.  Again – there is no evidence that babies pick up microbes from the placenta.  So speculating that this may reassure women who have C- sections is way way way too premature.
  • NYTimes: “I think women can be reassured that they have not doomed their infant’s microbiome for the rest of its life,  said Dr. Kjersti Aagaard.  Wow. Now we have gone from “if further research confirms” to just flat out reassuring women who have had C-sections that there are no effects on the microbiome.
  • NYTimes: It didn’t make a whole lot of sense to us,” she said. “It’s not like babies are hanging out in the vagina. They come shooting out pretty fast.” Also, she said, they emerge covered in a waxy substance called vernix, which most likely helps keep bacteria from latching on. Wow.  So babies come shooting out of the vegina and therefore cannot get microbes from the vagina.  This despite the massive amounts of evidence that they in fact do get microbes from the vagina and that C-section born babies get a different community (see for example this).  (UPDATE 5/26 – see UPDATE below with some comments / papers about C-sections vs. vaginal birth and how my use of “massive” here may be an overstatement itself).
I could go on and on.  But I won’t.  I am pleased the reporter talked to Martin Blaser who puts some damping on the speculation:

Dr. Martin J. Blaser, director of the human microbiome program at NYU Langone Medical Center, and the author of a recently published book, “Missing Microbes,” said that Dr. Aagaard’s study was important, but preliminary, and that it did not provide information that could be used in treating pregnant women. 

Thank you Martin.  But even with this, these articles leave me very frustrated.  The best I can do I guess is give out an award or two. So, for their reporting on the topic I am giving Denise Grady of the New York Times and Jocelyn Kaiser of Science News an Overselling the Microbiome award since they oversell the potential connection between oral health and infant health as mediated by the placenta.  And I am also giving this award to  Kjersti Aagaard, the first author of the paper, for her comments on the topic.

For more examples of “Overselling the Microbiome” awards see my page here.


UPDATE: Some other news stories where the headline alone is painful


UPDATE 2: Some articles that discussed placental microbes before this story came out

and many more


UPDATE 3: Paper on placental – mother – infant connection not even mentioned

Just found this paper from a Google Scholar search:  Probiotics Modulate Host-Microbe Interaction in the Placenta and Fetal Gut: A Randomized, Double-Blind, Placebo-Controlled Trial.  Seems like it is of direct relevance.  Abstract is below;

Abstract
Background: Early host-microbe interaction provides important maturational stimuli for the developing immune system. The role of prenatal microbial contact remains elusive. Objectives: Our aim was to investigate whether microbes in placenta or amniotic fluid affect fetal innate immune gene expression during late pregnancy and whether innate immune gene expression profiles in the placenta and the fetal gut may be modulated by dietary supplementation with specific probiotics. Methods: Altogether 43 pregnant women were randomized to receive (1) Bifidobacterium lactis, (2) B. lactis in combination with Lactobacillus rhamnosus GG (LGG) or (3) placebo for 14 days before elective cesarian section at full term in a double-blind clinical trial. Bacteria in amniotic fluid and placenta were detected by quantitative (q)PCR. The expression of Toll-like receptor (TLR)-related genes in the placenta and meconium samples was assessed by qPCR. Gene expression patterns in meconium were interpreted to reflect immune physiology in the fetal gut. Results: The study was completed by 29 mother-infant pairs. Bacterial DNA was detected in all placenta samples. Microbial DNA in amniotic fluid and placenta was associated with changes in TLR-related gene expression in the fetal intestine. Maternal probiotic supplementation significantly modulated the expression of TLR-related genes both in the placenta and in the fetal gut. Conclusions: Microbial contact in utero is associated with changes in fetal intestinal innate immune gene expression profile. Fetal and placental immune physiology may be modulated by maternal dietary intervention using specific probiotics.

This paper was not mentioned or cited as far as I can tell in the current study.


UPDATE 4: This paper also seems relevant

Microbial contact during pregnancy, intestinal colonization and human disease.  Abstract:

Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host–microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host–microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host–microbe interaction to reduce the risk of disease in the child.


UPDATE 5 – more misleading quotes

  • From Time’s misleadingly named article “The New Way to Predict When Pregnant Women Will Deliver“: “By focusing on oral health, we may actually be optimizing the health of the pregnancy and limiting the risk of pre-term birth,” says Aagaard. After paying so much attention to the more obvious ways to make a pregnancy healthy, it may be time to consider the less obvious – and less visible ones
  • That quote is just so inappropriate … uggh

UPDATE 6: May 24.  Some  Made a Storify with some of the Tweets related to this post.


UPDATE 7: May 26 – some other papers of relevance to birth mode and infant microbiomes and placentas

A key question to me I guess is the following – how do differences between the microflora in babies born by C-Section vs. vaginal birth arise if the microbes in placentas have a big role in colonizing infants?  Perhaps the differences between C-section babies and vaginal birth babies are small — I do not know — need to dig into this more.

What the fungi do I do with my ITS library? (Part 2)

What the fungi do I do with my ITS library (Part 2)
Originally posted on jennomics.com on May 22, 2014

Previously, I expressed some concern about size variation in my environmental fungal ITS PCR libraries. I’m still concerned about that, but I have an additional concern. The ITS region can’t be aligned, and I’m partial to phylogenetic approaches to pretty much everything. So maybe ITS is not for me?

So, I asked Twitter again…

In summary, I don’t think that I can use ITS given the size variation that I see, and I’m not sure that I want to, given the fact that you cannot align it to do phylogeny-based analyses.

28S (or LSU) is a reasonable alternative to ITS that has two big downsides: 1) the reference database is much smaller than the ITS reference database and 2) it does not provide the fine-scale taxonomic resolution that ITS does.

Rachel Adams referred me to Amend et al, in which they use both. I’ll have to look into this approach…

Quick Post – Interview of me is up on the Story Exchange re: #WomenInSTEM especially at conferences

Thanks to the Story Exchange and Candice Helfand for featuring me and the issue of Women in Science on their blog.  Here is a link to the interview she did with me a few days ago that she just posted:  Welcoming Women at STEM Conferences – and Beyond | The Story Exchange.  The interview discusses not only some of the reasons to care about diversity in science and at science meetings, but also how I got interested in the topic in the first place.

For some other background on my work and posts in this area see this page with a compilation of my Posts on diversity (gender, etc) in science.

Some selected ones are below: