Extensive, Highly Curated Data

BioCyc integrates genome data with a comprehensive body of additional data including metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings.

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Portion of Genome Browser

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Clostridioides difficile Pathway/Genome Databases

Clostridioides difficile infections are a growing public health threat. Use of broad-spectrum antibiotics in health care settings can disrupt the normal gut microbiota and allow C. difficile to thrive. Current treatment options are limited and include additional courses of antibiotics, surgical removal of the colon, and fecal transplants.

This website contains 17 Clostridioides difficile genomes (show list) and associated metabolic pathways. This site is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button (above) to explore the available databases.

This site includes extensive retrieval, visualization and analysis tools, including a genome browser and a metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Vibrio cholerae and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.

What people are saying

See more BioCyc testimonials

"BsubCyc is a tool of the utmost value."

Penn State

Paul Babitzke
Prof. of Biochemistry
& Molecular Biology

"My lab uses these resources on a daily basis."

University of Wisconsin

Patricia Kiley,
Professor and Chair,
Dep't. of Biomolecular Chemistry

"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."

University of Minnesota

Arkady Khodursky
Assoc. Prof. Biochemistry

"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."

Pacific Northwest National Lab

William Cannon, Team Lead
Computational Biology

Learning Library

Tutorial Videos

Tutorial #1: Introduction to BioCyc
Tutorial #2: Introduction to SmartTables
The following Tutorial will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below.
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
This tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms.
Tutorial #4: Omics Data Analysis
This tutorial will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools.
Tutorial #5: Pathway Collages
Pathway collages are multi-pathway diagrams that you can customize by, for example, overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. Learn how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways.
Tutorial #6: Creating a Pathway/Genome Database
Tutorial #7: Using the Structured Advanced Query Page
An introduction to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. You'll learn about:The basic steps of setting up an advanced query; Four examples of increasingly complex queries, including how to query across multiple databases; Where to learn more about the structure of BioCyc databases.