Discover and read the best of Twitter Threads about #microbiome

Most recents (17)

On red meat: "this is sure to be controversial"
5 systematic reviews, including 100's of studies, millions of participants, RCTs, show little evidence for adverse #cancer or cardiovascular outcomes
annals.org/aim/fullarticl…
@AnnalsofIM ★editorial- 6 papers
@aaronecarroll @DrTiff_
@AnnalsofIM @aaronecarroll @DrTiff_ @IUMedSchool The 6 papers/guidelines are all #openaccess
annals.org/aim/latest
This does indeed fulfill the Dunning–Kruger effect
(The less people know, the more they actually think they know) owing, in part, to poor methodology/analysis/bias of #diet studies
@AnnalsofIM @aaronecarroll @DrTiff_ @IUMedSchool What a wacky day for #diet research:
1. Red meat may not be so bad for health risk, after all? (I haven't had for ~40 yrs)
2. ⬆️vegetarian diet by increasing choices; see @PNASNews by @eegarnett89 @MarteauTM
3. Cooked plant food ->⬆️ gut #microbiome diversity @NatureMicrobiol
Read 5 tweets
Happy to announce our latest work where we combined and analysed over 280,000 genomes from the human gut microbiome: biorxiv.org/content/10.110…. A great collaboration between the teams of @robdfinn, @kyrpides, @nsegata, @PhilHugenholtz, Katie Pollard and @fstrozzi #microbiome
We generated a unified genome and protein catalogue comprising 4,644 microbial species and over 170 million non-redundant proteins, representing a comprehensive picture of the currently known diversity of the human gut microbiome
Our analyses revealed a nice overlap between the recent large-scale datasets of MAGs from @nsegata (bit.ly/2krlJFk), our team (go.nature.com/2kw9OGq) and @kyrpides (go.nature.com/2mqEtp9), reinforcing the results from each of the original studies
Read 7 tweets
Cross-sectional surveys have generated exciting hypotheses for how our bacteria influence our health and well-being. Next phase in #microbiome research requires that we develop a personalized model of the gut ecosystem and test hypotheses more directly with bacterial isolates.
Here, we unveil the @broadinstitute @OpenBiome Microbiome Library (BIO-ML) a resource of thousands of human gut bacterial isolates paired with whole genome sequences and longitudinal multi-omic data (broadinstitute.org/bio-ml).
Read 10 tweets
"You don't see radio changing gradually and suddenly become radar. #Darwin's theory doesn't work for #technology, and we have to make a new observation."

- W Brian Arthur at SFI today

#evolution #innovation #invention
"Novel technologies are constructed from existing technologies. These offer themselves as components for the construction of further technologies."

- W Brian Arthur at SFI today

#evolution #innovation #invention #technology #engineering #design
Unlike the two-parent #inheritance typical to (but not ubiquitous among) #complex organisms, #technology inherits features from n parents - a "vast ancestral #network" more like horizontal gene transfer networks in #bacteria.

W Brian Arthur on sumulating #invention on a chip:
Read 18 tweets
"Digital Orthodoxy," aka Deep Phenotyping or High-dimensional human data, is a great research tool w/ many proven advances, but has NO commercial/clinical validation and may be harmful
thelancet.com/journals/lance…
Our latest @TheLancet Digital Medicine essay
@EvanMuse @ScrippsRTI
@TheLancet @EvanMuse @ScrippsRTI The multi-modal testing may someday be validated to benefit, but until that time we raise concerns about the practice, ethics and safety for companies to be charging individuals for such data accumulation.
@TheLancet @EvanMuse @ScrippsRTI In @TheLancet essay we briefly touched on advances that deep phenotyping of people has made in biomedical research. I'm going to briefly review 5
1. Pre-diabetes-> #diabetes
2. Individualized diet
3. Colon #cancer+ microbiome
4. Gut #metagenomics sequence Δ
5. Tumor microbiome
Read 8 tweets
Just published: Team uses mNGS + culture-based techniques + negative controls 👉 Identify fungi + bacteria in complex communities in the first pass meconium (stool) of infants☝️Indicates that the neonatal gut microbiome starts to form in the womb: biorxiv.org/content/10.110…
2/2 The organisms they identified colonizing the fetal #intestine prior to birth 👉 were identified in the meconium of both term-born and #preterm newborns☝️And machine learning suggested that #fungal gut communities develop in complexity w/ advancing gestational age at birth.
3/3 Quote from paper 👉 “The demonstration of live #microorganisms in the #newborn gut represents a monumental shift from the sterile #womb hypothesis that dominated perinatal biology for the last century...”
Read 7 tweets
Whoa. The gut #microbiome of elite athletes (marathon runners) has a bacterium that enhances performance, makes mice run longer, and this is mediated via lactate metabolism @NatureMedicine
nature.com/articles/s4159…
(file under more #microbiome amazing stuff)
Will the future of doping be crapsules for enhanced athletic performance? ;-)
In other gut #microbiome discovery news today, @BostonChildrens and @BrighamWomens investigators identified a pathway associated with food allergy and a bacterial therapy that might protect against them
nature.com/articles/s4159…
Read 4 tweets
The human gut #microbiome never ceases to amaze me. Now a discovery of a bacterium that coverts Type A or B blood to type O, with big implications for blood transfusion.
nature.com/articles/s4156… @NatureMicrobiol by @PRahfeld Steven Withers and colleagues @UBC
Our gut #microbiome is a treasure for discovery. More coming out on this later this week that is mind-blowing.
BTW, another example of a striking finding that has not garnered coverage by any media. Surprising, in light of the public's interest in science.
Read 5 tweets
Today new data marks an advance towards the individualized diet
1. We knew our glucose response to food was highly variable and unique
(work form @WeizmannScience @segal_eran and colleagues, reviewed here
nytimes.com/2019/03/02/opi…
2. At #ADA2109 and #Nutrition2019, @timspector and colleagues reported the same for triglycerides and insulin levels in a large cohort of twins. The variability was also noteworthy in identical twins.
nytimes.com/2019/06/10/hea…
@NYTScience by @cagraber @nicolatwilley
3. The results summarized, emphasizing that the variability in response to food in these 3 metabolic metrics is striking, that they don't track each other, and that much of the heterogeneity is not genetically determined. The gut #microbiome is an important driver.
Read 4 tweets
Holobiont activity in chronic disease 👉In this analysis of #cardiovascular-disease-related proteins in human blood☝️genetics contributed most to immune-related proteins, while #microbiome contributed most to proteins tied to metabolism + intestinal health:nature.com/articles/s4158…
Worth noting that the team largely assumed that the proteins identified in #blood were derived from the gut microbiome 👉 but some #proteins could have been derived from organisms in the blood itself and/or organisms persisting in #microbiome communities outside the gut
Overall takeaway 👉 “This study provides important evidence for a joint genetic and microbial effect in #cardiovascular disease and provides directions for future applications in personalized medicine”
Read 3 tweets
Not to mention that factoring the #microbiome/virome (+ the #pathogens that end up persisting in these communities!) into #ME/CFS 👉 allows “unique #infectious history” to factor into disease progression (w/ #chemical exposures/stress etc facilitaring pathogen persistence)
Also keep in mind pathogens can persist in #latent forms 👉 Eg: here Zika was shown capable of persisting in the #cerebrospinal fluid + lymph nodes of monkeys for months after the #virus had been cleared from peripheral blood and urine: sciencedirect.com/science/articl…
Ok that’s it for now 😅 Thanks for reading!
Read 3 tweets
No need for skepticism of #microbiome + virome involvement in #ME/CFS 👉 But we must factor in the activity of organisms (bacteria, viruses, phages, fungi etc) that often persist + interact outside the gut☝️And many such organisms are not “good” but are pathogens/#pathobionts
In fact, Komaroff asked if anyone has a model for #ME/CFS that links together many findings recently presented at #MECFSatNIH19 👉 Well, that’s what my recent paper on ME/CFS does!...w/ #microbiome + virome activity central to how separate findings connect:frontiersin.org/articles/10.33…
That is b/c 👉 Humans are now understood to be #holobionts: our activity is controlled by the human genome, our microbial/#viral genomes and their respective proteins + metabolites working in tandem (together!): nph.onlinelibrary.wiley.com/doi/full/10.11…
Read 10 tweets
Today, I am watching Episode 5 of the #Interconnected #microbiome series, called "Leaky gut - leaky brain - leaky kids".
interconnectedseries.com/episode5syo
Note: link will be disappear after 24h; after that you will have to pay.
My tweets will stay and are free!
The first part of the episode is mainly about the gut-brain connection. The main message is that you need to eat good food (fiber, vegetables) to send good signals to your brain. This is good information that can help many people.
But the summary of the first part, as given by the presenter on this slide, has some errors that should have been edited out.
1. "Enteroception" appears to be a vague term that only occurs 3 times in Pubmed, so there is no widespread scientific support for it.
Read 38 tweets
Here is my report from episode 4 of the #Interconnected #microbiome series. The title is: "Trouble With Toxins".
See: interconnectedseries.com/episode4rve.
The episode starts off with making us scared. The presenter says:
"We will look at the elephant in the room: The billions of pounds of toxins that are suffocating ourselves and our health. "
I am not sure how to fact check this, but this seems very hyperbolic.
At about 2m, we hear: "Since 1980, we have up to a 7-fold increase in type 2 diabetes. We've seen our population gone up from a very small percentage, maybe 10% obese, to now over 30% obese and 70% overweight."
Let's fact check.
Read 16 tweets
Earlier this week, I tweeted about Episode 1 of the #Interconnected series on the human #microbiome. See
Let's take a look at some other episodes (new thread).
The series features a mix of microbiome scientists, many of whom I have collaborated with and respect a lot, functional medicine doctors, and chronic disease patients. So, the documentary has a lot of great information, some inspiring stories, and some #FakeNews.
The problem with the series is that it is hard to distinguish between the correct and the incorrect information, especially if you are not a scientist.
By watching this series, you might learn a lot and be inspired, but please proceed with caution.
Read 22 tweets
V. thought provoking seminar today @TRI_info by Prof John Huss entitled ‘Ecological medicine & medical ecology’. Discussed were ecological strategies for #coral remediation and the #microbiome. But more interesting was unpacking the #philosophy of biological research!.... (1/12)
The field of microbiome #research is still very young, and it’s hard to get a handle on what is established and where exactly the field will progress (2/12)
However, there seem to be two different concepts thrown around when people talk about the microbiome:
a) Micro-biome: a biome of microbes, an ecological conception.
b) Microbi-ome: the microbial genome, a molecular conception.
(3/12)
Read 13 tweets
This #WorldOceansDay I'm inspired by all the dedicated people working everywhere to understand and protect the dominant geographic feature of our planet. So today I'm going to be tweeting about just a few of those people to spread the news of their good deeds
1st up @HeatherKoldewey. Heather is at @OfficialZSL & has done incredible work with @projectseahorse, @Nets2Carpet and the Chagos MPA with @Bertarelli_fdn. Any one of those would be huge, but all three is just amazing. zsl.org/users/heather-…
Nxt @CoralReefFish Luiz Rocha, originally from Brazil, is leading a team of folks @calacademy discovering new fish diversity in the gloom beyond regular SCUBA depths, using rebreathers. Every bit as hard as space walking, maybe harder. calacademy.org/explore-scienc…
Read 11 tweets

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