Ran Blekhman

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

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...

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.

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...

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...

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...

Thanks Willem!

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.

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.

This is my new blog where I write about microbiome research and academic science. Would love to have you subscribe: blekhman.substack.com

Google's New AI Tool Can't Do Much. That's Exactly the Point Finally, an AI research tool that doesn't hallucinate papers

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-...

2023 edition:

bsky.app/profile/blek...

2024 edition:

bsky.app/profile/blek...

My favorite Chicago photos of 2025

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)

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...

Review: Genomics of host–microbiome interactions in humans by @pamferretti.bsky.social ocial, Kelsey Johnson, @sambhawa.bsky.social & @blekhman.bsky.social
rdcu.be/etIRy

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...

One month later

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...

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"

Yes -- this is actually the same parallel the authors use in the review!

The Autism-Microbiome Hypothesis Is Falling Apart Why this new review paper should be required reading for every microbiome researcher

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...

Analyzing human gut microbiome data from global populations: challenges and resources Research on the human gut microbiome is expanding rapidly; yet, most published studies focus on populations from high-income regions such as North America and Europe. Underrepresentation of population...

Our contribution to this special issue: a review on data analysis of human gut microbiome data from global populations

www.cell.com/trends/micro...

Amazing journal cover for the new Trends In Microbiology special issue on geographic diversity in microbiology

www.cell.com/trends/micro...

This project was brilliantly led by Sabrina Arif, and is a close collaboration with @fluca2406.bsky.social's lab, and the Global Microbiome Conservancy (Mathieu Groussin and Mathilde Poyet)

3. Specific microbes like Bifidobacterium adolescentis (influenced by dairy intake) directly affected metabolic gene expression.

2. High-diversity microbiomes elicited a stronger host transcriptional response, while low-diversity microbiomes triggered epithelial restructuring & glycolysis – a stress response that characterizes several chronic inflammatory diseases.