The Fraunhofer Institute for Interface and Bioprocess Engineering (IGB) carried out a comprehensive metagenomic study of the gut microbiome of Antarctic krill (Euphausia superba) as part of the BioProMare: KiGuMi project, funded by the German Federal Ministry of Education and Research (BMBF) from 1 February 2020 to 31 January 2023. The project was organized into six work packages led by principal investigators R. Rabus, K. Sohn, H. Wilkes, and B. Meyer. Work package 1 focused on isolation of microorganisms, package 2 on diversity analysis, package 3 on integrated meta‑omics, package 4 on cultivation‑dependent proof‑of‑concept studies, package 5 on feeding scenario experiments, and package 6 on synthesis and dissemination.

Technically, the study combined short‑read Illumina sequencing, long‑read Oxford Nanopore MinION sequencing, and Sanger sequencing of isolates. Seventy‑two krill samples were processed, including stomach, gland, and whole digestive tract material. DNA was extracted, amplified for the V4 region of the 16S rRNA gene, and sequenced on Illumina platforms after dual‑indexing and AMPure XP bead clean‑ups. Whole‑genome libraries were also sequenced on Nanopore to generate a hybrid assembly. The hybrid assembly pipeline produced a high‑quality, near‑complete metagenome that revealed a dominant taxonomic group of Alteromonadales, with most contigs assigned to this order. Because whole‑genome shotgun sequencing of the gut material was not feasible, the team relied on amplicon data for taxonomic profiling and on the hybrid assembly for functional inference.

Functional annotation of the assembled contigs identified 374 non‑redundant enzyme commission (EC) numbers, indicating a broad enzymatic repertoire. Two bacterial strains isolated from the krill gut were shown to possess strong hydrolytic activity in plate‑based assays, and their genomes were added to a newly created database of hydrolytic enzymes. The database, curated with the same annotation pipeline, links each enzyme to its EC number and to potential substrate specificity, providing a resource for future biotechnological exploitation of krill‑derived enzymes.

The integrated meta‑omics approach also included transcriptomic and proteomic layers, although the transcriptome data were not fully published in the report. Functional assays on the biobank of isolates confirmed the presence of enzymes capable of degrading complex marine polymers, supporting the hypothesis that krill gut bacteria contribute to the host’s nutrient acquisition. The study’s findings were disseminated through a biobank of krill gut isolates, a database of hydrolytic enzymes, and a series of peer‑reviewed publications.

Overall, the project delivered a high‑resolution view of the Antarctic krill gut microbiome, revealing a dominant Alteromonadales community, a rich set of hydrolytic enzymes, and two promising bacterial strains with potential industrial applications. The collaborative effort between IGB, the BMBF, and partner scientists such as B. Meyer and H. Wilkes ensured that both the technical and translational aspects of the research were addressed within the project’s three‑year timeframe.