Navigating multi-omic integration methods for human microbiome research Gilbert, J. A. et al. Current understanding of the human microbiome. Nat. Med. 24, 392–400 (2018). Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). Marchesi, J. R. et al. The gut microbiota and host health: a new clinical frontier. Gut 65, 330 (2016). Xiong, R. et al. Multi-‘omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients. Cell Host Microbe 31, 273–287.e5 (2023). Wang, C. et al. Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk. Microbiome 10, 121 (2022). Ghaemi, M. S. et al. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics 35, 95–103 (2019). O’Sullivan, J. et al. Host–microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease. Gut Microbes 17, 2450207 (2025). Zhang, Y., Thompson, K. N., Huttenhower, C. & Franzosa, E. A. Statistical approaches for differential expression analysis in metatranscriptomics. Bioinformatics 37, i34–i41 (2021). Saenz, C., Nigro, E., Gunalan, V. & Arumugam, M. MIntO: a modular and scalable pipeline for microbiome metagenomic and metatranscriptomic data integration. Front. Bioinform. 2, 846922 (2022). Franzosa, E. A...

Navigating multi-omic integration methods for human microbiome research
->Nature | More on "Microbiome multi-omics integration methods" at BigEarthData.ai | #SoilHealth #Microbiome

Microbiome-Targeted Reduction of Circulating Trimethylamine N-Oxide Mitigates Ischemic Stroke Risk www.biorxiv.org/content/10.64898/2026.04...

A class of metallohydrolases expands bile salt hydrolase activity in the gut www.biorxiv.org/content/10.6...

Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids - Nature Microbiology Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of commensal bifidobacteria, inhibit pathogens and suppress inflammation in an organoid model.

A new probiotic in development? 🦠👶

Clostridium perfringens isolated from preterm infants metabolizes human milk oligosaccharide to promote commensal Bifidobacteria, inhibit pathogens and suppress inflammation in organoids
Interesting work from @stewartlab.bsky.social

www.nature.com/articles/s41...

This is kinda bonkers.

In addition, 20 amino acids were found on Ryugu, along with uracil and vitamin B3. These have been found in other instances, but since the samples from Ryugu were collected directly from the asteroid and delivered in sealed capsules, contamination on Earth could be ruled out.

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

Gut Bacteria May Drive Constipation…And Offer a Clue to Parkinson’s Disease Japanese researchers have identified two microbes that erode the intestine’s mucus lining, causing chronic constipation and offering a possible explanation for digestive symptoms seen in Parkinson’s.

Bacteria that cause constipation, with a surprising link to #ParkinsonsDisease. More at japanresearchreport.substack.com/p/gut-bacter.... #Neuroscience #Microbiome #GutHealth #JapanResearchReport

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Gut inflammation promotes adverse food reactions by disrupting the microbial metabolism of food triggers www.biorxiv.org/content/10.64898/2026.02...

Exploring #microbiome data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.

Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions Masi et al. synthesize how gut microbiome-derived functions shape obesity risk, metabolic dysfunction, and therapeutic response. The review highlights converging microbial signatures across dietary, s...

Here the authors advocate that integrating gut #microbiome data into clinical strategies may enable targeted interventions for specific #obesity subtypes, advancing prevention and personalized care. www.cell.com/cell-reports...

Emilie Glad Bak, PhD, is a microbiologist and translational science leader with over a decade of experience in microbiome research and product development. She is CSO and co-founder of Mastitia, where she leads the R&D strategy for a microbiome-derived medical device focused on the prevention of lactational mastitis. Emilie is an expert in translating microbiome science to industrial clinically-proven products.

🎤 Emilie Glad Bak, Co-founder & CSO at Mastitia, presents:
🧬 A Postbiotic-Based Medical Device Strategy for the Prevention of Mastitis
📍 Global Microbiome Congress 2026 | Boston
🗓 June 15–16, 2026
🔗 microbiomecongress.org/registrations/
#GMC2026 #MicrobiomeScience #Postbiotics #MastitisPrevention

Who out there likes to look at small molecule #drugs? You can explore all the ones FDA approved in 2025 using this interactive table in @cenmag.bsky.social (made by Shea Murphy): cen.acs.org/sections/dru...
#chemsky

Risk-Based vs Annual Breast Cancer Screening This randomized clinical trial examines whether risk-based screening is a safe and effective alternative to annual mammography for detecting breast cancer in women 40 years and older.

Important new, large (N>28,000 women) randomized clinical trial of breast cancer screening: age-based vs risk-based by polygenic risk score, genomics
"opportunity to modernize screening"
jamanetwork.com/journals/jam...

First page of Opinion piece: "Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism"

The link between the gut #microbiome and autism is not backed by science, researchers say.

Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA

@wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social

@bravo-abad.bsky.social , not recently active on Bluesky, on the use of #Quantum Computing for #Genomics:
journals.aps.org/prxlife/abst...

From #drug cabinet → gut #microbiome: screening 312 therapeutic compounds, we mapped 4.6 million microbial protein-level responses to reveal how our drugs don’t just target us, they hit our gut microbes too.

rdcu.be/eMmcT

💡 30 scientific recommendations from the #CHINAGUT Conference!
👩‍🔬 63 experts joined forces to shape the future of:
🦠 #Probiotics
💊 Live biotherapeutic products
💩 #FMT
The goal: standardization, regulation & precision in #microbiome-based therapies.
🔗 doi.org/10.1002/imt2...

Woman in a pink top stands in front of an open fridge holding a bowl of salad in one hand and a plate of fried chicken in the other.

#Hypertension in middle-aged women may be linked to gut #microbiome changes that boost inflammation. Altered tryptophan metabolism could be a key target for improving heart health. Read more in APS Publications AJP-Heart: https://ow.ly/jCL750Xc0yK #ArticlesInPresS #WomensHealthResearch 🧪

Using cross-species co-expression to predict metabolic interactions in microbiomes In microbial ecosystems, metabolic interactions are key determinants of species’ relative abundance and activity. Given the immense number of possible interactions in microbial communities, their expe...

New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...

Causal relationships between gut microbiome and hundreds of age-related traits: evidence of a replicable effect on ApoM protein levels | Aging Aging | doi:10.18632/aging.206293. Federica Grosso, Daniela Zanetti, Serena Sanna

🧫 Gut microbiome and ageing

Using genetic data, researchers tested 55k links between gut microbes and age-related traits. They found 91 causal relationships, including effects on protein levels tied to inflammation and metabolism.

🔗 doi.org/10.18632/agi...

#SciComm #Microbiome #Ageing 🧪

The Apple "Reasoning Collapse" Paper Is Even Dumber Than You Think We're this far into reasoners and neither hypesters nor skeptics really understand their significance. Also: Read Toulmin.

While framed as a critique of Apple’s recent paper, I found this article mostly interesting because it made me think about reasoning in general: mikecaulfield.substack.com/p/the-apple-...

Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects Fecal microbiota transplants (FMTs) may not always effectively restore small bowel microbiota due to regional differences in gut environments, potentially causing unintended effects on metabolism and ...

The unintended consequences of a gut microbiome transplant
www.cell.com/cell/abstrac...

Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, fr...

Cool study:

Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters www.tandfonline.com/doi/full/10....

The potential risk of age-related macular degeneration with GLP-1 drugs in people with diabetes
jamanetwork.com/journals/jam...

📣 Happy to share our review on host-microbiome genomics!

We synthesize the growing field exploring interactions between human genetics and the microbiome, building a roadmap for mapping the dialogue between our genes and microbes

Out now in Nature Reviews Genetics👇

www.nature.com/articles/s41...

Microbiome–metabolome dynamics associated with impaired glucose control and responses to lifestyle changes - Nature Medicine A map of microbiome–metabolome dynamics in people with type 2 diabetes identifies over 500 blood metabolites associated with impaired glucose control, with approximately one-third linked to an altered...

Our gut microbiome and its metabolites play a critical role for our glucose regulation, as does diet and exercise for improving it, through modulating the gut microbiome
@naturemedicine.bsky.social
www.nature.com/articles/s41...

Good resource: Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions www.cell.com/molecular-c...

logos of the 12 companies reviewed

The business of promoting longevity and healthspan through extensive medical testing. A review of 12 companies and why this is a flawed, expensive model without evidence.
erictopol.substack.com/p/the-busine...

Out now in #NatureMetabolism 📢

Leveraging four large, longitudinal, prospectively-followed mother–child cohorts, this study shows that a western diet in early–mid-pregnancy is associated with neurodevelopmental disorders in the offspring.