2021–present
Gut Microbiome Tree of Life (GMToL)
Gut microbiomes across the animal kingdom, curated for even coverage of host phylogeny, diet, ecology and geography.
17,000samples
828host species
2025–present
Microbiome Metadata Crisis (MMC)
A decade-scale audit of the field's own record-keeping: most published microbiome data is public, but not reusable.
3,300studies
1M+samples
450students, 19 institutions
2024–present
Human Microbiome Tree of Life (HMToL)
The human-focused successor: a global collection that deliberately reaches the populations the literature has left out.
16,956samples
70countries
The Microbiome Metadata Crisis Consortium: 450+ members
UC San DiegoNorthwesternJohns HopkinsDukeHarvardYaleColumbiaNew York UniversityUCLAMichiganVirginiaIllinois Urbana-ChampaignArizona StateDartmouthBaylorFlorida InternationalHarvey MuddSoonchunhyangEast Jefferson General Hospital
A large-scale citizen science effort
450undergraduates, grads, postdocs & professors
19institutions
3main projects
8undergraduate-led subprojects
1publication
2preprints
2submissions under review
News
Publications
8 May 2026An expansive animal gut microbiome dataset elucidates major compositional shifts across bilaterian evolution
GMToL's second paper, and the one the dataset itself is built on. Degregori, Patel, Xu, Iter, Weng, Huang, Martel, Kisselev, Zhao, Allaband, Ackermann, González, McDonald, Amato and Knight.
- 18 February 2026
Sample Size Reporting in Human Cancer Microbiome Research is Inconsistent and Unstandardized
Led by David Kobobel, with Degregori, Gonzalez, Wright, Richie, Han, Gu, Huang, Martel, Garcia Reyes, Kisselev, Song and Knight.
- 2024
Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices
GMToL's first paper. Degregori, Wang, Kommala, Schulhof, Moradi, MacDonald, Eblen, Jukovich, Smith, Kelleher, Suzuki, Hall, Knight and Amato — eight of the fourteen authors were undergraduates on the project.
PhD Program Acceptances!
Zoey Hall Zoey Hall — Epidemiology, UNC Chapel Hill
Accepted to the PhD programme in epidemiology.
Luis Xu Luis Xu — Bioinformatics, UC San Diego
Accepted to the bioinformatics PhD programme.
Masters Program Acceptances!
Kaiyuan Du Kaiyuan Du — ScM in Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health
Graduated from Johns Hopkins as an undergraduate in May 2026 and starts the ScM programme this autumn.
Randima Bellana Randima Bellana — MSE in Computer Science, Johns Hopkins University
Accepted to the residential master's programme.
Tyra Gravesande Tyra Gravesande — MSPH in Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health
Accepted to the master's programme.
Saleem Sabeer Saleem Sabeer — Applied Science in Computer Science (MSc), University of Pennsylvania
Accepted to the master's programme.
Xaolin (Diego) Wang Xaolin (Diego) Wang — MPhil in Finance and Economics, University of Cambridge
Accepted to the MPhil programme.
Medical School Acceptances!
Emily Kelleher 2026Emily Kelleher — University of Northern Colorado
Accepted to the programme.
Sadaf Moradi 2024Sadaf Moradi — Washington University School of Medicine
Accepted to medical school.
Conferences
5 June 2026Analysis of Transnational and Cross-Continental Collaboration Trends in Microbiome Papers
Ariadne García Reyes presented the MMC collaboration work — how often microbiome research crosses borders, and which countries are left out of it. With Vudatha, Kisselev, Kobobel, Degregori and Knight.
People
Sam DegregoriDirectorPostdoctoral fellow, UC San Diego
Katherine AmatoAdvisorAssociate professor, Northwestern University
Rob KnightAdvisorProfessor, UC San Diego
Project leads
GMToL interns
HMToL interns
MMC interns
Institutions
UC San DiegoNorthwesternJohns HopkinsDukeHarvardYaleColumbiaNew York UniversityUCLAMichiganVirginiaIllinois Urbana-ChampaignArizona StateDartmouthBaylorFlorida InternationalHarvey MuddSoonchunhyangEast Jefferson General Hospital
MMC Consortium
- Jake A
- Gail Ackermann
- Tomisin Adebari
- Emanoel Agbayani
- Aniqa Ahmed
- Ben Alfinito
- Celeste Allaband
- Mariya Alsaiari
- Katherine Amato
- Madison Ambre
- Jack Anderson
- Blessing Anyangwe
- Fnu Babita
- Maya Balakumaran
- Efe Mert Balkanli
- Chaya S Bangalore
- Randima Bellana
- Amanda Birmingham
- Jeffrey Bohrer
- Melody Borg
- Alisa Bryantseva
- Sidhaarth Bulusu
- Rohan Butani
- Solana Callaway
- Kaicheng Cao
- Jake Castillo
- Victor Ceballos
- Ritvik Chand
- Stephanie Chang
- Kriti Chauhan
- Hebe Chen
- Dingjun Chen
- Alex Chen
- Monalia Sadia Rahman Chowdhury
- Weil Chu
- Trisha D
- Afolake Dairo
- Sam Degregori
- Laya Devulapalli
- Arnav Dhole
- Odia Diallo
- Pieter C. Dorrestein
- Kaiyuan Du
- Jack Elder
- Emiley A. Eloe-Fadrosh
- Eve
- Suya Fang
- Rachel Fernandes
- Lynn Fetcinko
- Andre Fortes
- Claudio Franc
- Nathalia Franco
- Eric Gan
- Bansal Gandhi
- Aryan Gautam
- Jack Gilbert
- Saanvi Gireesh
- Írena Héðinsdóttir Gonzalez
- Antonio González
- Elijah Gordon
- Tyra Gravesande
- Harrison Gu
- Yueyi Guan
- Zoey Hall
- Ariana Hampton
- Vyasa Hari
- Kai Henrikson-Brandt
- Erica Hong
- David Hong
- Max Hong
- Zaima Hossain
- Isabella Huang
- Annie Huang
- Qihong Huang
- Emily Hung
- Daniel Hutcherson
- Michael Iter
- Nidhi Iyengar
- Unnati Jain
- Keshav Jha
- Amelia Joseph
- Sophia Jukovich
- Sreyas Kanaparti
- Ishanvi Karthikeyan
- Ashar Keeys
- Emily Kelleher
- Julia Kelliher
- Soumya Khadye
- Avnish Khandeshi
- Akshita Kikkuru
- Jonathan Kirkland
- Kirsha
- Dmitry Kisselev
- Rob Knight
- David Kobobel
- Akhil Kommala
- Belgin Kozanoğlu
- Ananya Krishnan
- Aditi Lagad
- Shloka Lakka
- Sonija Lam
- Emily Lam
- Seoyeong Lee
- Yoonseo Lee
- Luz Letona
- Yangxi Li
- Alan Li
- Felix Liang
- Weili Lu
- Lia Lucas
- Chloé Légé
- Maggie Ma
- Zinia Mahabub
- Sahithi Malleboyina
- Ammar Mandviwalla
- Harrison Martel
- Aryan Masaldan
- Jeffrey Mathew
- Daniel McDonald
- Julia Messing
- Saurabh Methta
- Micah
- Akshaya Mohan
- Julia Moosikasuwan
- Sadaf Moradi
- Christopher J. Mungall
- Saketh Nallapaty
- Alex Nath
- Khanh Nguyen
- Calis Nguyen
- Truc Nguyen
- Noah O'Connor
- Aarushi Pandey
- Lucas Patel
- Dev Patel
- Vedant Patel
- Anjali Phadnis
- Anoushka Prabhu
- Mohak Prakash
- Mike Qiu
- Joy Qui
- rama
- Ariadne García Reyes
- Nicolas Rodrigo
- Giacomo Rossi
- Jack Ryzman
- Aditya S
- Saleem Sabeer
- Robert Sallash
- Karishmaa Sampath
- Paul Sandhu
- Simriya Sandhu
- Noah Schulhof
- Michael Schweitzer
- Iman Sharif
- King Shi
- Nadine Shill
- Camille Sicat
- Aditya Sinha
- Siddarth Sivalanka
- Emma Smith
- Cynthia Sofia
- Emily Song
- Lindy Stadtlander
- Alexandra Streaker
- Serena Strode
- Malleeka Suy
- Kota Suzuki
- Taichi A. Suzuki
- Ana-Laura Tamez
- Sarah Tan
- Ellen Tang
- Sarah Tasnim
- Zihan Tian
- Nour Touqatqa
- Khue Tran
- Kian Vargo
- Eduard Flores Ventura
- Sneha Verma
- Anjali Vinodh
- Ritvik Vudatha
- Christian Walter
- Xaolin (Diego) Wang
- Rex Wang
- Derek Wang
- Yuhan Weng
- Christine Wong
- Christine Woo
- Sterling Wright
- Kevin Wu
- AMY XIA
- Bree Xie
- Luis Xu
- Victoria Xu
- Vanessa Yang
- Nicolas Zepeda
- Jianshu Zhao
- David Zhao
- 温博栋
The Gut Microbiome Tree of Life
The Gut Microbiome Tree of Life visualized across multi-dimensional space
Host phylogeny
Composition across the host tree
Diversity
How diversity varies across host classes
Papers
- Preprint · bioRxiv, 8 May 2026 · under review at Science
- Biological Reviews 100(2):748–763, 2024
Reusability
3,145 clinical human microbiome studies that we meticulously surveyed, shown at the sample level
Over time
Volume climbs; reusability does not follow
Method
16S is still how most of the literature was sequenced
Papers
- Preprint · in revision at Access Microbiology, 18 February 2026
Led by the MMC Consortium
The Human Microbiome Tree of Life
European and North American subjects still dominate the human gut microbiome literature. HMToL is the human-focused successor to GMToL: 16,956 gut microbiomes drawn from public data spanning 124 studies and 70 countries, harmonised onto one phylogeny so that geography, development and age can be compared without the study-to-study noise that usually swamps them.
Summary
What has been collected, and from where
Succession
Genus trajectories across the lifespan
Westernization
Distance from the industrialised gut
HDI gradient
That distance tracks development, not age
Core microbiome
There is barely a global core microbiome
Papers
- A dataset paper is in preparationNo preprint yet — nothing to link
Status. HMToL is unpublished. The ordination, the maps and the trajectories above are real HMToL results; the tree component's two ring encodings are placeholder values carried over from the report prototype it came from, kept only to show the interaction.