Hello QIIME 2 Developer Community! 
Below is the list of guaranteed interface changes, plugin API changes, and environment file updates for the 2026.4 QIIME 2 release. You can use the linked environment files for each distribution to ensure compatibility with any plugin you're developing against the relevant distribution it should be tested/used within. Note that these 'seed' environment files won't change between now and the 2026.4 release, but the full environment files that conda will resolve at any given installation will change. This shouldn't impact your development process, as all of the core dependencies in these 'seed' files will remain the same.
Interface Changes 
Plugin API Changes 
Environment File Changes 
TINY
linux environment file
macos environment file
- biom-format=2.1.17
- h5py=3.15.1
- hdf5=1.14.6
- networkx=3.6.1
- numpy=2.4.2
- pandas=2.3.3
- parsl=2026.2.23
- python=3.12
- r-base=4.5.2
- r-reticulate=1.45.0
- scikit-bio=0.7.2
- scikit-learn=1.7.1
- scipy=1.17.1
- tzlocal=5.3.1
- unifrac-binaries=1.5.1
- unifrac=1.5.1
AMPLICON (plus all changes from tiny)
linux environment file
macos environment file
- blast=2.17.0
- fastp=1.0.1
- matplotlib=3.10.8
- ncbi-datasets-pyclient=18.18.0
- patsy=1.0.2
- pillow=12.1.1
- r-vegan=2.7_3
- rpy2=3.6.4
- samtools=1.22.1
- seaborn=0.13.2
- sepp=4.5.6
- statsmodels=0.14.6
- tqdm=4.67.3
MOSHPIT (plus all changes from tiny*)
linux environment file
macos environment file
*NOTE: The required r-base version for these updates led to a downgrade from 4.5.2 (used in tiny and amplicon) to 4.4.2. The only overlapping plugin affected in both amplicon and moshpit is q2-quality-control (via decontam). The decontam versions from both r-base releases were reviewed and showed no breaking changes, bugs, or meaningful behavioral differences, so usage of q2-quality-control should remain consistent between amplicon and moshpit.
- bigscape=2.0.2
- biopython=1.86
- bowtie2=2.5.5
- das_tool=1.1.7
- eggnog-mapper=2.1.12
- entrezpy=2.1.3
- matplotlib=3.9.1
- metabat2=2.18
- multiqc=1.33
- ncbi-datasets-pyclient=18.18.0
- pyarrow=16.1.0
- pysam=0.23.3
- r-base=4.4.2
- samtools=1.22.1
- seaborn=0.13.2
- semibin=2.2.0
- sepp=4.5.6
- spades=4.2.0
- tqdm=4.67.3
- vamb=5.0.4
PATHOGENOME (plus all changes from tiny)
linux environment file
macos environment file
- genomad=1.11.2
- matplotlib=3.10.8
- prodigal=2.6.3
- pyarrow=16.1.0
- seaborn=0.13.2
- screed=1.0.4
- spades=4.2.0
- tqdm=4.67.3