From Reads to Function Workshop at ISME Lat 2025
A Workshop on an Accessible Metagenomics Toolkit for Decoding Microbial Contributions to Biogeochemical Cycles
Welcome!
Here you will find the agenda and resources for the From Reads to Function Workshop at the 4th Latin American Congress of Microbial Ecology (ISME Lat 2025), hosted by the Organizing Committee in Mérida, Mexico on August 4 and 5.
Aquí encontrará la agenda y recursos para el Taller De la Reads a la Función en el 4th Congreso Latinoamericano de Ecología Microbiana (ISME Lat 2025), auspiciado por el Comité Organizador en Mérida, México el 4 y 5 de agosto.
Seminario sobre un conjunto de herramientas metagenómicas accesibles para descifrar la contribución microbiana a los ciclos biogeoquímicos.
- Acceso a KBase / Access to KBase: kbase.us
- Crear su cuenta KBase / Set up a KBase account: https://docs.kbase.us/getting-started/sign-up/step-by-step
- KBase YouTube Channel: http://www.youtube.com/@DOEKBase
- Antes del seminario de ISME Lat 25, práctica en KBase y entonces cargue y ensamble sus reads metagenómicas / Before the workshop, practice in KBase and then upload and assemble any metagenomic reads for the workshop.
- Introducción actividad / Introduction activity: https://narrative.kbase.us/narrative/214949
- Cargue y ensamble sus reads metagenómicas / Upload, Import & Assemble Metagenomic Reads: https://narrative.kbase.us/narrative/220565
Workshop Agenda
Agendas para cada día.
Agendas for each day below.
Reads to Metagenome-Assembled Genomes (MAGs)
Lecturas de genomas ensamblados en metagenomas (MAG)
Local Time – Activity / Topic (Lead)
Hora local – Actividad / Tema (Principal)
9:30 Lecture: Intro to workshop, GROW, and Lake Yojoa data (Borton & Hall)
10:00 Lecture: Intro to omics data and analysis (Servìn)
10:45 Live Demo: Assembly QA/QC to binning in KBase (Dow & Rodriguez)
11:15 Live Demo: Exploration and evaluation of bin quality (Dow & Jurgensen)
11:45 Open Discussion / Q&A
12:00-13:30 Almuerzo / Lunch
13:30 Live Demo: Taxonomic assessment of communities (reads and bins) (Dow & Rodriguez)
14:00 Live Demo: Explore taxonomic representation (Dow & Jurgensen)
14:30 Lecture: Microbial metabolism annotation with DRAM (Jurgensen & Rodriguez)
15:00 Break
15:30 Live Demo: Comparative analysis of community representation and function (DRAM outputs) (Borton & Jurgensen)
16:30 Lecture: Sample metadata and data management (Rodriguez)
17:00 Lecture: Publishing with KBase (Dow & Rodriguez)
17:30 Recap, final Q&A, evaluation
18:00 End of Workshop Day 1
Lecture = Conferencia
Live Demo = Demostración
Narrative / Narrativa: https://kbase.us/n/223320/4/
Open Office Hours
Local Time – Activity / Topic (Lead)
9:00 Activity: Hands-on work with support & Help Desk (All)
Please have your data assembled and ready to go!
Cargue y ensamble sus reads metagenómicas
Utilice esta Narrativa para hacer lo siguiente: https://narrative.kbase.us/narrative/220565 (inglés: https://narrative.kbase.us/narrative/219108)
Instrucciones
- Cargue e importe sus reads de secuenciación a KBase
- Control de calidad de lecturas con FastQC y Trimmomatic
- Generación de ensambles de reads
- Comparación de ensambles (o contigs)
2:00 End of Workshop Day 2
Activity = Actividad
Resources & Helpful Links
Participant Resources
Slide Decks / Diaspositivas
Data: Hall et al. 2024
Protocol: Chivian et al. 2022
DRAM Outputs
Narrative Workflow / Flujo: https://kbase.us/n/223320/4/
Workshop Data and Project Paper
Fadum JM, Borton MA, Daly RA, Wrighton KC, Hall EK. 2024. Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9:e01059-23. doi: 10.1128/msystems.01059-23
Borton MA, McGivern BB, Willi KR et al. 2025. A functional microbiome catalogue crowdsourced from North American rivers. Nature 637:103–112. doi: 10.1038/s41586-024-08240-z
KBase GROWdb US River Systems Narrative – https://doi.org/10.25982/109073.30/1895615
GROW Org in KBase – https://legacy.narrative.kbase.us/#org/grow
NMDC GROWdb – https://data.microbiomedata.org/details/study/nmdc:sty-11-5tgfr349
People
Colorado State Microbiome Network
Mikayla Borton – Workshop Lead and Microbial Ecosystems Lab co-PI, Colorado State University
Ed Hall – Associate Professor, Data Curation and Microbial Limnology Laboratory PI, Colorado State University
Sophie Jurgensen – Research Associate, Microbial Ecosystems Lab, Colorado State University
KBase
Ellen Dow – KBase Educators Program Lead, Lawrence Berkeley National Laboratory
Elisha Wood-Charlson – KBase User Engagement Lead, Lawrence Berkeley National Laboratory
NMDC Champion
Josue Rodriguez – Postdoctoral Researcher, Pacific Northwest National Laboratory
International Society for Microbial Ecology – ISME Workshop Hosts
Luisa Falcon – PI, National Autonomous University of México (UNAM), Ecology Institute
Wendy Escobedo-Hinojosa – Professor, UNAM, Faculty of Chemistry in Sisal
Luis Servín – Professor, UNAM, National School of Higher Education in Morelia
Julian Wissner – PI, UNAM, Biotechnology Institute
Kelly Wrighton – Microbial Ecosystems Lab PI, Colorado State University
Teaching Assistants
Pablo Suarez Moo – Postdoctoral researcher, UNAM, Faculty of Chemistry
Andrés Sánchez Quinto – Postdoctoral researcher, San Diego State University, Forest Rhower Lab
