Brandon Seah

Eukaryotic Microbiology • Microbial Symbiosis

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I am a research scientist at the Thünen Institute for Biodiversity in Braunschweig, Germany.

Previously, I worked on ciliate genomics as a postdoc in the group of Estienne Swart at the Max Planck Institute for Biology in Tübingen, Germany, and on microbial symbiosis as a doctoral student at the Max Planck Institute for Marine Microbiology in Bremen, Germany, in the team of Harald Gruber-Vodicka, under the Symbiosis Department headed by Prof Nicole Dubilier.

Projects

My research interests lie in protists (microbial eukaryotes), microbial symbiosis, and in applying bioinformatics to tackle problems in genomics, phylogenetics, and organismal biology.

Ciliate Genomics

Ciliates are microbial eukaryotes (protists). As their name suggests, they are covered in cilia, but what actually makes them unique is the intricate genomic ballet they perform during their sexual life cycle. Each cell has two types of nuclei: germline micronuclei (MIC) which are like inactive “backup copies” of the genome, and somatic macronuclei (MAC), “working copies” where gene expression typically occurs. MICs participate in meiosis and sexual recombination, and some of the resulting daughter nuclei differentiate into MACs. This process involves eliminating thousands of interspersed segments from the genome called internally eliminated sequences (IESs), as well as chromosome fragmentation, rearrangement, and copy number amplification. The genome content of a MAC is hence a subset of what is found in the MIC.

This picture of the ciliate genome is based on a handful of model species. To better understand how this complex developmental pathway has evolved and where IESs come from, my research looks at the germline genomes of less well studied ciliates, which entails developing new methods to assemble and reconstruct germline genomes (Seah and Swart, 2021). In the heterotrich Blepharisma (Seah et al., 2023), we found that miniature inverted-repeat transposable elements (MITEs), a type of small mobile element, make up a substantial fraction of the IESs, including one family that appears to have proliferated recently.

Another research theme is ambiguous genetic codes with context-dependent stop/sense codons, where a stop codon can either terminate translation or encode an amino acid. We showed that they are not isolated or rare phenomena, but that such a code is used by a group of ciliates comprising over a hundred described species, the karyorelicts (Seah, Singh, and Swart, 2022).

Kentrophoros and its Bacterial Symbionts


The unusual ciliate Kentrophoros and its ectosymbiotic bacteria were the focus of my doctoral research. Kentrophoros are found in marine sediment (muds, fine sand) of coastal areas around the world. The bacterial symbionts are attached to the ciliate’s surface, and use chemical energy from the environment (e.g. from oxidation of sulfide) to build up biomass, a process known as chemosynthesis. The ciliates then harvest them for food, and so the symbionts have been called a “microbial kitchen garden”.

My research showed that the symbionts are a distinct lineage of Gammaproteobacteria, which we called “Candidatus Kentron”, that are uniquely associated with these Kentrophoros ciliates (Seah et al. 2017). However, unlike all other chemosynthetic symbioses known to date, these symbionts do not encode metabolic pathways for autotrophic CO2 fixation (Seah et al. 2019). Instead of being a “garden” for their hosts, they are assimilating organic molecules from the environment like acetate and propionate, “recycling” these low-value waste products of fermentation into high-value biomass that their hosts then consume.

This makes it an exception to the usual textbook explanations of such symbioses as autotrophic CO2-fixing factories. Instead, alternative carbon sources and metabolic flexibility in storing and mobilizing resources are important for Kentrophoros, and other symbiotic systems too (Jäckle et al. 2019).

Bioinformatics Tools

Several software tools that I have been involved in developing have been packaged for use by the wider community. These include:

Publications and Data

Links to associated data or software are provided for publications where I was the first or corresponding author; first-author publication titles in bold. Preprints are open-access but not peer-reviewed. Click on triangles to show details and links to supplements.

Diamond open access logoGold open access logoGreen open access logo open-access | pencil preprint | * joint authorship | + corresponding

Teaching and Outreach

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