Hutlab

link.springer.comUsing the housekeeping gene cpn60 as a marker for microbial community profiling and viability assessment - MicrobiomeHigh-throughput sequencing has revolutionized microbiome research, yet distinguishing viable from nonviable microbes in complex communities remains challenging. Microbial viability underlines microbio...

New Paper Alert - Congrats to Lea and everyone in the lab for their new paper "Using the housekeeping gene cpn60 as a marker for microbial community profiling and viability assessment" 🎉🎉. Link - link.springer.com/article/10.1...

Hutlab reposted

Nature Microbiology

@natmicrobiol.nature.com

Out Now! Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning #MicroSky

go.nature.comPhylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learningNature Microbiology, Published online: 29 September 2026; doi:10.1038/s41564-026-02482-5This platform identifies phages capable of infecting specific bacterial strains using genome sequences alone and could enable rational phage-therapy design and precision microbiome engineering.

Jack Sumner @jacksumner22.bsky.social from the lab presented at the Microbiome Epidemiology Working Group (MEWG) yesterday at HSPH and presented on Virome ecology and function associate with disease severity in colorectal cancer!

Carter Merenstein from the lab recently presented at the Microbiome Epidemiology Working Group (MEWG) at HSPH and presented on Bacterial Genome-Wide Association Studies (GWAS) for Insights into Antibiotic Resistance Plasmid Ecology!

Curtis attended and presented at the Nordic Congress in Clinical Biochemistry in Denmark, at the microbiome session. While in Denmark, he also visited the LEGO House!

Jorden Rabasco @jordenrabasco.bsky.social earned their PhD at NC State with Ben Callahan, studying microbiome methods for kit contaminants to improve microbiome data processing. They joined the Hutlab as a postdoc in August and now model microbiome trajectories associated with autism development.

Erik Hasenoehrl, co-advised by Curtis, recently gave a talk titled, “Identification of the components of bacterial bilirubin metabolism in the gut and its role in inflammation” 🎉 This was part of the Microbiome Epidemiology Working Group (MEWG) series.

nature.comGut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk - Nature MetabolismIn the prospective, multicentre TEDDY study, distinct patterns of gut microbiome maturation are associated with differential risk of type 1 diabetes, with host genetics modifying the strength of this ...

New paper out now! Led by Danyue Dong, along with members from the Hutlab and Wang lab. Gut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk www.nature.com/articles/s42...

18 Sept

Curtis, @gfahurbottino.bsky.social and Jorden from the lab recently attended the first annual consortium meeting of Wellcome Leap FORM, hosted at Down Hall, UK. This work is aimed at investigating the link between the microbiome and neurodevelopmental challenges.

research.ubc.caEddie Goldenberg Research Chairs of CanadaThe Eddie Goldenberg Research Chairs of Canada program supports institutions in attracting world-leading researchers

10 Sept

We're excited to announce that Curtis was one of the inaugural recipients of the Impact+ “Eddie Goldenberg” Research Chair of Canada! He will be starting at the University of British Columbia's SBME and M&I departments in the summer of 2027 🎉 research.ubc.ca/federal-rese...

ubc.caThe University of British ColumbiaThe University of British Columbia is a global centre for research and teaching, consistently ranked among the top 20 public universities in the world.

10 Sept

We'll share more information about the Microbiome Centre to be launched there closer to that date, but in the meantime, let us know if you'd be interested in joining us in Canada next year! UBC - www.ubc.ca SBME - bme.ubc.ca M&I - mbim.ubc.ca Contact - huttenhower.sph.harvard.edu/contact-us/

10 Sept

@efranzosa.bsky.social kicked off BST 273, introduction to programming, with some new discussion about the value of learning to program in the "vibe coding" era. This included some more general discussion about why it's important to not outsource all of your thinking to AI.

3 Sept

Curtis gave a talk yesterday at the University of Puerto Rico on Finding Function in Microbial Community Dark Matter. Thanks to the Puerto Rico Center for Micriobiome Sciences for hosting!

Pics from the visit!

Welcome everyone to the new semester! Eric @efranzosa.bsky.social will be teaching BST 273 'Introduction to Programming' this fall. Excited to meet several @hsph.harvard.edu students there and at the lab!

gut.bmj.comMulti-kingdom signatures of the gut microbiome in Lynch syndrome: a prospective model for colorectal cancer evolutionRecent work in Gut has highlighted multi-kingdom interactions between gut bacteria and bacteriophage (‘phage’) as contributors to Crohn’s disease.1 Whether similar alterations characterise colorectal ...

25 Aug

Congratulations to Nanako, @longnguyen.bsky.social and the whole team for their new paper out today 🎉🥳 - Multi-kingdom signatures of the gut microbiome in Lynch syndrome: a prospective model for colorectal cancer evolution Link - gut.bmj.com/content/earl...

nature.comGetting over ANOVA: estimation graphics for multi-group comparisons - Nature MethodsNature Methods - Getting over ANOVA: estimation graphics for multi-group comparisons

25 Aug

HutLab took to the water last Friday! 🛶🌊 A great day of kayaking and sunshine.

Hutlab reposted

Nature Methods

@natmethods.nature.com

7 Aug

DABEST 2.0: Estimation graphics for multi-group comparisons. www.nature.com/articles/s41...

21 Aug

Kelsey and Xochi from the lab attending ISME @isme-microbes.bsky.social in New Zealand! 🇳🇿

14 Aug

Congratulations to Yiqing Wang on receiving an NIH/NIA K99/R00 Pathway to Independence Award! 🎉🎉

sciencedirect.comHarmonized Metagenomic Signatures of the Gut Microbiome Reveal Robust Species, Functions, and Strain Links to Inflammatory Bowel DiseaseCoupled with well-characterized host genetic and environmental risk factors, alterations of gut microbial communities contribute to risk and severity …

14 Aug

Congrats to Kelsey, @longnguyen.bsky.social and the whole team on the new IBD meta-analysis paper!! Harmonized Metagenomic Signatures of the Gut Microbiome Reveal Robust Species, Functions, and Strain Links to Inflammatory Bowel Disease - www.sciencedirect.com/science/arti... @hsph.harvard.edu

youtube.comDay in the Life at an Academic Conference! Cornell PhDYouTube video by Sithija Manage

7 Aug

Curtis and @sithijamanage.bsky.social from the lab attended and presented their work at JSM. Sithija presented on nonparametric regression for tree-structured data, while Curtis presented on applications of statistical methods in microbiome. Vlog on it from Sithija! - www.youtube.com/watch?v=CDvs...

29 July

More pics from the bioBakery course last week! We had an incredible time discussing all things microbiome with students/scientists from all over the country and beyond. Grateful to @broadinstitute.org for hosting the course, and to Kelsey and @efranzosa.bsky.social for organizing and running it!

22 July

Our weeklong course on metagenomic community analyses using bioBakery tools has begun, with students from all over the country and beyond! 🎉 Some pics from the first couple of days, held at Broad Institute @broadinstitute.org @efranzosa.bsky.social @jacksumner22.bsky.social @chahat.bsky.social

huttenhower.sph.harvard.edubiobakerycourses – The Huttenhower Lab

16 July

Excited to meet all course participants on Monday for a week of microbiome analysis together!

Hutlab@hutlab.bsky.social

EXCITING NEWS 🚨 - Are you interested in microbial community analysis? Join us in Cambridge, MA (July 20–24) for a week-long, hands-on bioBakery course on multi-omics and statistics. Hosted by the Huttenhower Lab & HCMPH. No prior experience needed. Link - huttenhower.sph.harvard.edu/biobakerycou...

15 July

Askarbek @orakov.bsky.social and Guilherme @gfahurbottino.bsky.social from the lab attended the Boston Bacterial Meeting @bostonbacteria.bsky.social at Boston University @bostonu.bsky.social. Askarbek's daughter was probably the youngest attendee of the meeting👶😁. Guilherme won a best poster award 🎉

Hutlab reposted

Nature Biotechnology

@natbiotech.nature.com

14 July

The July issue is live nature.com/nbt/volumes/... On the cover, @ycongzhang.bsky.social @efranzosa.bsky.social @hutlab.bsky.social introduce FUGAsseM, a method that uses microbial community data to infer the functions of previously uncharacterized gene products go.nature.com/435C4lp rdcu.be/ftNUV

10 July

@gfahurbottino.bsky.social , a joint Research Scientist in the lab, recently gave a workshop in Brazil on metagenomic pipelines for the USP Microbiome Center (University of Sao Paulo) @uspoficial.bsky.social 🎉

9 July

Summer vacation pics 🌴🥾 - Crater Lake, Hoh Rainforest, Seattle Chihuly Garden and Glass. Pic courtesy - Curtis!

cell.comLong-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancerNogal et al. profile the gut microbiome and metabolome of individuals with a history of colorectal adenoma resection, revealing microbial and metabolic alterations detectable more than a decade after ...

1/ You have a precancerous colon polyp (adenoma) removed to lower your cancer risk. So why does that risk stay elevated for years later? Our new paper in @cp-cellhostmicrobe.bsky.social, led by Ana Nogal, a joint postdoc with the Song lab @hsph.harvard.edu, investigated: www.cell.com/cell-host-mi...

6/ The metabolome carried disease-specific signals too, including associations between Bilophila wadsworthia and alanine-containing dipeptides, pointing to microbe-metabolite interplay specific to adenoma cases.

7/ Bottom line: an altered microbiome and metabolome are still detectable years after a polyp is removed. Cutting out the polyp may not reset the microbial environment around it. (Cross-sectional, so causality stays open)

4/ To see how these changes relate to colorectal cancer (CRC), we compared these microbial alterations against 14 independent CRC case-control studies (2,112 metagenomes). Adenoma-associated shifts partially resemble those observed in CRC cases.

5/ 31 microbes were altered in both adenoma and CRC, including Faecalibacterium prausnitzii and Flavonifractor plautii. In women with a past adenoma, these shared microbes correlated with diet and lifestyle more strongly than in controls.

2/ Unlike earlier work that sampled around the time of removal, we took the long view: stool metagenomes from 354 women ~12 years after adenoma removal, each matched 1:1 to an adenoma-free control, plus fecal metabolomes in 184 pairs.

@apcmicrobiomeirel.bsky.social

3/ The gut microbiome and metabolome of women with a past adenoma differed from their matched controls, even after ~12 years.

Hutlab reposted

APC Microbiome Ireland

26 June

How do you classify a new phage? A new paper in 𝐏𝐋𝐎𝐒 𝐂𝐨𝐦𝐩𝐮𝐭𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐁𝐢𝐨𝐥𝐨𝐠𝐲 shares 10 tips on genome completeness, ANI, marker genes and structure. @colinhillucc.bsky.social @plos.org @uccmicrobiology.bsky.social 📰 buff.ly/XNE0S3X #Microbiome #Phage #Bacteriophage #Virome #Phagesky

25 June

bioBakery Course SOLD OUT 🎉. Thank you everyone for your interest in the course this year, we are really excited for it to start in a few weeks! If you were not able to register this year or if you would like to be on the email list for future events, please email us at biobakerycourses@gmail.com

18 June

Bocce-ball with the lab!

18 June

Thank you to ASM @asm.org for an incredible conference yet again this year. Curtis gave two talks there - on HVP and FUGAsseM. Dongyu @dongyuwang.bsky.social from the lab also presented her work!

18 June

Thank you @ihmc2026seoul.bsky.social for organizing IHMC this year at Seoul and inviting Curtis to speak. Also pictured are Cherry and Yan who are lab alumni and also attended the conference!

10 June

Jacob @jnearing.bsky.social presented MaAsLin3 at the Microbiome ANCHOR conference in Nova Scotia!

9 June

Team Biobakery participated last weekend in the Take Steps, organized by @crohnscolitisfdn.bsky.social in Boston aimed at fundraising and outreach to improve quality of life for those living with inflammatory bowel disease.

5 June

Wendy gave an amazing keynote address at ASM yesterday!

takesteps.crohnscolitisfoundation.orgLet’s Go There — toward cures for inflammatory bowel disease (IBD)I'm participating in Take Steps, the Crohn's & Colitis Foundation's largest fundraising campaign. Every dollar raised accelerates breakthroughs in IBD research, delivers trusted resources, and improve...

2 June

Boston friends! Our lab is joining the Crohn’s & Colitis Foundation’s Take Steps walk this Saturday to support IBD research, patient resources, and the search for cures. We'd love to have you on our team! Come walk with us 💜🚶‍♂️🚶‍♀️ Join here: takesteps.crohnscolitisfoundation.org/teams/22016

Cell - a Cell Press journal

29 May

Congratulations to all Biology in Public Health (BPH) graduates who graduated this week! A special shoutout to Jordan Jensen from the lab who graduates with a PhD🎉🎉 @hsph.harvard.edu

Hutlab reposted

@cp-cell.bsky.social

31 Mar

Now online! Phages communicate across species to shape microbial ecosystems

dlvr.itPhages communicate across species to shape microbial ecosystemsGallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of phage infections, mixed lysogenic communities, and polylysogens. Our results demonstrate that crosstalk is an important mechanism that drives phage interactions in microbial communities.

18 May

Wendy and Curtis wrap up the talks part of the symposium. Congratulations to all speakers for an incredible day of microbiome science. Now on to the poster session!

18 May

Michael Fischbach @mfgrp.bsky.social from Stanford gave an excellent talk on Commensal Vaccines. #HCMPH2026