Brandon Seah

Environmental Microbiology • Genomics • Biodiversity

ORCiD | Google Scholar | PubMed | GitHub | Wikidata

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

I have previously worked as a staff scientist in the Thünen Institute for Biodiversity in Braunschweig, Germany; as a postdoc in the lab of Estienne Swart at the Max Planck Institute for Biology in Tübingen, Germany; and as a doctoral student in the team of Harald Gruber-Vodicka, under the Symbiosis Department headed by Prof Nicole Dubilier at the Max Planck Institute for Marine Microbiology in Bremen, Germany.

Highlights

Evolution of complex traits need not be a one-way street.
Developmental genome editing is a process that was formerly thought to be defining trait of the ciliates. We discovered ciliates that do not have genome editing, despite retaining other elements of their complex life cycles. (Seah et al,, 2024)
Organisms with “stop-less” genetic codes are not rare.
Some organisms use unusual genetic codes where the stop codons can function also as coding, depending on context, but they were formerly thought to be rare exceptions. We found that a diverse, successful group of marine ciliates all use such codes. (Seah, Singh and Swart, 2022)
Nutritional symbioses are possible even without autotrophy.
Many eukaryotes carry bacterial symbionts that fix CO2 autotrophically into biomass, which the hosts then consume as food. We found a symbiosis where the bacteria don't have autotrophic CO2 fixation pathways, but instead appear to grow by "upcycling" fermentation waste products. (Seah et al., 2019)

Projects

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. [More ...]

This picture of the ciliate genome shaped by developmental genome editing is based on a handful of model species. To better understand how this complex pathway has evolved and where IESs come from, my research looks at the germline genomes of less well studied ciliates.

The most surprising finding to emerge so far is that some ciliates have apparently lost genome editing. The ciliate Loxodes magnus has separate MIC and MAC that are different in morphology and chromatin organization, but they have more or less the same genome content. Unlike all other ciliates, there is no trace of IESs in their germline (Seah et al., 2024). If it is indeed possible to do without the costly exercise of genome editing, why do other ciliates retain it? We think that our results support the theory that genome editing is not a form of genome “defense”, as some characterize, but is instead held in place by a ratchet-like evolutionary mechanism.

In another ciliate which does have IESs, Blepharisma stoltei, we have previously documented how a substantial portion of its IESs are derived from the proliferation of a mobile element from a family called MITEs (Miniature Inverted-repeat Transposable Elements) (Seah et al., 2023).

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).

Biodiversity informatics

One persistent challenge when working with biodiversity is harmonizing taxon identifiers. Biologists traditionally use scientific names such as “Homo sapiens”, using the Linnaean system first established in the 18th century. However, taxonomists struggle to keep pace with describing the vastness of natural biodiversity. Errors and inconsistencies build up when names are used and transmitted through publications and databases. An apparently simple matter such as looking up a sequence record by taxon name can require specialist knowledge and curation to ensure that the intended taxon is retrieved. [More ...]

In my work, I took a systematic look at how errors creep in during taxon name matching between different databases. Beyond just data curation, I advocate for the use of the open knowledge graph Wikidata as a platform to crowdsource the linking of identifiers between various biodiversity databases, to avoid duplicated effort and also feed back into improving upstream databases (Seah, 2023).

Knowledge graphs like Wikidata distill information into a structured form, requiring an explicit data model of the entities and relationships represented in them. This makes them suitable for specific domains where queries should yield precise and verifiable answers. I built the Protist-Prokaryote Symbiosis Database to show how symbiotic interactions between microorganisms can be modeled as a knowledge graph interlinked with other open data sets.

Bioinformatics Tools

I am enthusiastic about open source software and have developed a number of software tools. [More ...]

Past Projects

Kentrophoros and its Bacterial Symbionts



The unusual ciliate Kentrophoros carries ectosymbiotic bacteria, and these ciliates 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”. [More...]

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, “upcycling” 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).

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 unfold 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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