Ran Blekhman
@blekhman.bsky.social
Professor of Medicine at the University of Chicago. Decoding the human microbiome. http://BlekhmanLab.org
Pinned
Ran Blekhman
@blekhman.bsky.social
· Jan 22
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
if you're in line to sack drake maye, STAY IN LINE
February 9, 2026 at 2:15 AM
if you're in line to sack drake maye, STAY IN LINE
Work led by Katja Della Libera and Beth Adamowicz in my lab, in collaboration with Francesca Luca's lab at UChicago
February 4, 2026 at 2:22 PM
Work led by Katja Della Libera and Beth Adamowicz in my lab, in collaboration with Francesca Luca's lab at UChicago
Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 4, 2026 at 2:17 PM
Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
I can't talk about the details of the specific case you're describing, of course. But I think it's common that as a reviewer, one can find flaws in any paper, and list improvements that will make any paper "stronger". But the authors can disagree, and have the right to decide not do the work.
February 3, 2026 at 6:56 PM
I can't talk about the details of the specific case you're describing, of course. But I think it's common that as a reviewer, one can find flaws in any paper, and list improvements that will make any paper "stronger". But the authors can disagree, and have the right to decide not do the work.
This is not heartbreaking. Keep in mind that the authors perspective: they probably disagree that their paper "needs a lot of work". Instead they find another journal (and another set of reviewers) that agree with them, and save months of expensive, time consuming, unnecessary work.
It breaks my heart every time I review a paper that needs a lot of work, it gets rejected, and then I see it out in another journal with no changes whatsoever
February 3, 2026 at 12:25 AM
This is not heartbreaking. Keep in mind that the authors perspective: they probably disagree that their paper "needs a lot of work". Instead they find another journal (and another set of reviewers) that agree with them, and save months of expensive, time consuming, unnecessary work.
Work led by @pamferretti.bsky.social, with collaborators including Mattea Allert, Kelsey Johnson, Cheryl Gale, Ellen Demerath, Frank Albert, and David Fields.
See Pamela's thread below:
bsky.app/profile/pamf...
See Pamela's thread below:
bsky.app/profile/pamf...
Excited to share our new study out in Nature Communications. We mapped the composition of the human breast #milk #microbiome and showed that microbes present in breast milk directly contribute to the assembly of the #infant gut microbiome in the first months of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Client Challenge
www.nature.com
January 18, 2026 at 8:49 PM
Work led by @pamferretti.bsky.social, with collaborators including Mattea Allert, Kelsey Johnson, Cheryl Gale, Ellen Demerath, Frank Albert, and David Fields.
See Pamela's thread below:
bsky.app/profile/pamf...
See Pamela's thread below:
bsky.app/profile/pamf...
Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications
Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...
doi.org
January 18, 2026 at 8:35 PM
Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:
doi.org/10.1038/s414...
Reposted by Ran Blekhman
I just signed up and read the first of Ran's posts. Excellent stuff, highly recommended.
This is my new blog where I write about microbiome research and academic science. Would love to have you subscribe: blekhman.substack.com
Ran’s Substack | Ran Blekhman | Substack
My personal Substack. Click to read Ran’s Substack, by Ran Blekhman, a Substack publication. Launched a month ago.
blekhman.substack.com
January 6, 2026 at 8:27 AM
I just signed up and read the first of Ran's posts. Excellent stuff, highly recommended.
Indeed - the advantage here (as I write in the post) is that Scholar Labs gives you a link to the text of each paper, which you can read and evaluate. But so far, based on a few weeks of almost daily usage, it hasn't returned any noise.
January 1, 2026 at 5:49 PM
Indeed - the advantage here (as I write in the post) is that Scholar Labs gives you a link to the text of each paper, which you can read and evaluate. But so far, based on a few weeks of almost daily usage, it hasn't returned any noise.
This is my new blog where I write about microbiome research and academic science. Would love to have you subscribe: blekhman.substack.com
Ran’s Substack | Ran Blekhman | Substack
My personal Substack. Click to read Ran’s Substack, by Ran Blekhman, a Substack publication. Launched a month ago.
blekhman.substack.com
January 1, 2026 at 5:07 PM
This is my new blog where I write about microbiome research and academic science. Would love to have you subscribe: blekhman.substack.com
I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post:
substack.com/home/post/p-...
substack.com/home/post/p-...
Google's New AI Tool Can't Do Much. That's Exactly the Point
Finally, an AI research tool that doesn't hallucinate papers
substack.com
January 1, 2026 at 4:56 PM
I'm usually skeptical about AI research tools. But Google's new tool for literature search is fantastic - because it does less, not more. New post:
substack.com/home/post/p-...
substack.com/home/post/p-...
December 30, 2025 at 12:23 AM
December 30, 2025 at 12:22 AM
My favorite Chicago photos of 2025
December 30, 2025 at 12:21 AM
My favorite Chicago photos of 2025
another one bites the dust
iRobot files for bankruptcy
iRobot files for bankruptcy
But your Roomba will still work, for now
buff.ly
December 15, 2025 at 7:31 PM
another one bites the dust
I usually don't, because with figures a lot of choices are a matter of style, but I comment if there's a real issues (the data are not presented clearly or accurately)
December 15, 2025 at 7:31 PM
I usually don't, because with figures a lot of choices are a matter of style, but I comment if there's a real issues (the data are not presented clearly or accurately)
Reposted by Ran Blekhman
Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social
rdcu.be/etIRy
rdcu.be/etIRy
Genomics of host–microbiome interactions in humans
Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...
rdcu.be
December 15, 2025 at 4:59 PM
Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social
rdcu.be/etIRy
rdcu.be/etIRy
Reposted by Ran Blekhman
Excited to share our new @natecoevo.nature.com
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
December 3, 2025 at 4:00 PM
Excited to share our new @natecoevo.nature.com
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8)
www.nature.com/articles/s41...
Due to the shutdown, NIH cancelled >370 study sections, impacting >24,000 applications
Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed"
grants.nih.gov/grants/guide...
Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed"
grants.nih.gov/grants/guide...
NOT-OD-26-012: Updated Guidance on Reopening of NIH Extramural Activities Following the October 1, 2025 - Lapse in Appropriations
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Updated Guidance on Reopening of NIH Extramural Activities Following the October 1, 2025 - Lapse in Appropriations NOT-...
grants.nih.gov
November 24, 2025 at 6:55 PM
Due to the shutdown, NIH cancelled >370 study sections, impacting >24,000 applications
Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed"
grants.nih.gov/grants/guide...
Rescheduled meetings will only discuss 30-35% of applications, have simplified summary statements (no narrative paragraph), and a new category - "competitive but not discussed"
grants.nih.gov/grants/guide...
Seriously someone should write about the scientific evidence supporting the alleged health benefits of each of these items - I bet it's 99% nonsense
November 21, 2025 at 11:21 PM
Seriously someone should write about the scientific evidence supporting the alleged health benefits of each of these items - I bet it's 99% nonsense
Great example of what I call a "grift bag"
And yes, the swag bags. Attendees received MAHA-branded tote bags with:
- Packets of creatine
- Beef tallow potato chips ($79 for a 6-pack!!)
- Mouth tape
- RFK Jr's biography
- Beef protein bars
- Packets of creatine
- Beef tallow potato chips ($79 for a 6-pack!!)
- Mouth tape
- RFK Jr's biography
- Beef protein bars
November 21, 2025 at 11:20 PM
Great example of what I call a "grift bag"
Yes -- this is actually the same parallel the authors use in the review!
November 20, 2025 at 5:18 PM
Yes -- this is actually the same parallel the authors use in the review!
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field
open.substack.com/pub/blekhman...
open.substack.com/pub/blekhman...
The Autism-Microbiome Hypothesis Is Falling Apart
Why this new review paper should be required reading for every microbiome researcher
open.substack.com
November 19, 2025 at 5:12 PM
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field
open.substack.com/pub/blekhman...
open.substack.com/pub/blekhman...