{"entity": "researcher", "timestamp": "2026-08-13T18:21:36.495Z", "family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5"}}, "publications": [{"entity": "publication", "iuid": "97a9599da59641ebb05e5b7a8fe6ad45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97a9599da59641ebb05e5b7a8fe6ad45"}}, "title": "The expanded genome of Hexamita inflata, a free-living diplomonad.", "authors": [{"family": "Akdeniz", "given": "Zeynep", "initials": "Z", "orcid": "0000-0002-5279-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6a7222e2d3487db2b50842f74e173e.json"}}, {"family": "Havelka", "given": "Michal", "initials": "M"}, {"family": "Stoklasa", "given": "Michal", "initials": "M"}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "\u017d\u00e1rsk\u00fd", "given": "Vojt\u011bch", "initials": "V"}, {"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Kol\u00edsko", "given": "Martin", "initials": "M"}, {"family": "Provazn\u00edk", "given": "Jan", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Tachezy", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2025-02-01", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "12", "issue": "1", "pages": "192", "issn-l": "2052-4463"}, "abstract": "Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.", "doi": "10.1038/s41597-025-04514-x", "pmid": "39893204", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11787283"}, {"db": "pii", "key": "10.1038/s41597-025-04514-x"}], "notes": [], "created": "2025-03-07T09:59:16.550Z", "modified": "2025-04-03T08:27:54.918Z"}, {"entity": "publication", "iuid": "72f3a3d242e74c4099a9732a095b6219", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3a3d242e74c4099a9732a095b6219.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3a3d242e74c4099a9732a095b6219"}}, "title": "Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.", "authors": [{"family": "Aguilera-Campos", "given": "Karla Iveth", "initials": "KI", "orcid": "0000-0003-1299-341X", "researcher": {"href": "https://publications.scilifelab.se/researcher/331e2dcabae64ae281c9c354bb4a259d.json"}}, {"family": "Boisard", "given": "Julie", "initials": "J", "orcid": "0000-0002-6191-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3ceb5d8238e4855a09ea93d10f74f1c.json"}}, {"family": "T\u00f6rnblom", "given": "Viktor", "initials": "V", "orcid": "0009-0008-8017-8402", "researcher": {"href": "https://publications.scilifelab.se/researcher/295329ac66314e54882a8feaa4528309.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Behnck\u00e9-Serra", "given": "Ada", "initials": "A", "orcid": "0009-0007-8632-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ba0c2817d14321bfb4a3e3d83f1fe7.json"}}, {"family": "Cotillas", "given": "Elena Aramendia", "initials": "EA"}, {"family": "Stairs", "given": "Courtney Weir", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "19", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.", "doi": "10.1093/ismejo/wraf171", "pmid": "40795332", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12453579"}, {"db": "pii", "key": "8228259"}], "notes": [], "created": "2025-11-28T10:49:37.264Z", "modified": "2025-11-28T10:49:37.595Z"}, {"entity": "publication", "iuid": "a39f01f3a62f42d88d88d1a5f418c3b7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a39f01f3a62f42d88d88d1a5f418c3b7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a39f01f3a62f42d88d88d1a5f418c3b7"}}, "title": "A unique symbiosome in an anaerobic single-celled eukaryote.", "authors": [{"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}, {"family": "Gallot-Lavall\u00e9e", "given": "Lucie", "initials": "L", "orcid": "0000-0001-6763-3388", "researcher": {"href": "https://publications.scilifelab.se/researcher/7790fd356f5c4d29a58c22c708e7d886.json"}}, {"family": "Salas-Leiva", "given": "Dayana E", "initials": "DE", "orcid": "0000-0003-2356-3351", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a8a3928d494986b64ea03f66df2057.json"}}, {"family": "Curtis", "given": "Bruce A", "initials": "BA"}, {"family": "Z\u00e1honov\u00e1", "given": "Krist\u00edna", "initials": "K", "orcid": "0000-0002-5766-0267", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a88cec1dc4398865f4f840535ec9d.json"}}, {"family": "\u010cepi\u010dka", "given": "Ivan", "initials": "I", "orcid": "0000-0002-4322-0754", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f2c1a48df3e4f3f957907c1e547070c.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Pipaliya", "given": "Shweta", "initials": "S"}, {"family": "Dacks", "given": "Joel B", "initials": "JB", "orcid": "0000-0003-4520-5694", "researcher": {"href": "https://publications.scilifelab.se/researcher/97c30e7e0487483d894192c2c7c76368.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM", "orcid": "0000-0001-7255-780X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc225404ccd7449b95d00245b7d5df38.json"}}, {"family": "Roger", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0003-1370-9820", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf086d9bf6d45d2941c6ba5e8a0e838.json"}}], "type": "journal article", "published": "2024-11-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9726", "issn-l": "2041-1723"}, "abstract": "Symbiotic relationships between eukaryotes and prokaryotes played pivotal roles in the evolution of life and drove the emergence of specialized symbiotic structures in animals, plants and fungi. The host-evolved symbiotic structures of microbial eukaryotes - the vast majority of such hosts in nature - remain largely unstudied. Here we describe highly structured symbiosomes within three free-living anaerobic protists (Anaeramoeba spp.). We dissect this symbiosis using complete genome sequencing and transcriptomics of host and symbiont cells coupled with fluorescence in situ hybridization, and 3D reconstruction using focused-ion-beam scanning electron microscopy. The emergence of the symbiosome is underpinned by expansion of gene families encoding regulators of membrane trafficking and phagosomal maturation and extensive bacteria-to-eukaryote lateral transfer. The symbionts reside deep within a symbiosomal membrane network that enables metabolic syntrophy by precisely positioning sulfate-reducing bacteria alongside host hydrogenosomes. Importantly, the symbionts maintain connections to the Anaeramoeba plasma membrane, blurring traditional boundaries between ecto- and endosymbiosis.", "doi": "10.1038/s41467-024-54102-7", "pmid": "39521804", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11550330"}, {"db": "pii", "key": "10.1038/s41467-024-54102-7"}, {"db": "figshare", "key": "10.6084/m9.figshare.24033777"}, {"db": "figshare", "key": "10.6084/m9.figshare.20375619"}, {"db": "figshare", "key": "10.6084/m9.figshare.20375601"}, {"db": "figshare", "key": "10.6084/m9.figshare.22193497"}, {"db": "figshare", "key": "10.6084/m9.figshare.27108724"}, {"db": "figshare", "key": "10.6084/m9.figshare.27108751"}, {"db": "BioProject", "key": "PRJNA634776"}], "notes": [], "created": "2024-11-19T12:30:44.514Z", "modified": "2025-09-12T09:08:56.147Z"}, {"entity": "publication", "iuid": "53fbc4d093de4ad3b1e17fcca31fca04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53fbc4d093de4ad3b1e17fcca31fca04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53fbc4d093de4ad3b1e17fcca31fca04"}}, "title": "A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).", "authors": [{"family": "Onu\u021b-Br\u00e4nnstr\u00f6m", "given": "Ioana", "initials": "I", "orcid": "0000-0002-7723-8629", "researcher": {"href": "https://publications.scilifelab.se/researcher/e51e62ab66244945889efc4669d2d853.json"}}, {"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Campos", "given": "Karla Iveth Aguilera", "initials": "KIA"}, {"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Keeling", "given": "Patrick J", "initials": "PJ"}, {"family": "Bass", "given": "David", "initials": "D"}, {"family": "Burki", "given": "Fabien", "initials": "F", "orcid": "0000-0002-8248-8462", "researcher": {"href": "https://publications.scilifelab.se/researcher/c386a8e440344f25bea35d570450b09b.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "3", "issn-l": "1759-6653"}, "abstract": "Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.", "doi": "10.1093/gbe/evad022", "pmid": "36790104", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9998036"}, {"db": "pii", "key": "7039708"}, {"db": "figshare", "key": "10.6084/m9.figshare.21206669.v1"}, {"db": "figshare", "key": "10.6084/m9.figshare.21206807.v1"}, {"db": "figshare", "key": "10.6084/m9.figshare.21770576.v1"}], "notes": [], "created": "2023-11-27T21:52:34.646Z", "modified": "2024-01-16T13:48:33.882Z"}, {"entity": "publication", "iuid": "d50103cc28a443cbb19050234fc11364", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d50103cc28a443cbb19050234fc11364.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d50103cc28a443cbb19050234fc11364"}}, "title": "Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.", "authors": [{"family": "Stairs", "given": "Courtney W", "initials": "CW", "orcid": "0000-0001-6650-0970", "researcher": {"href": "https://publications.scilifelab.se/researcher/618e83e896494c7bb6cbe06350baf0a5.json"}}, {"family": "Kokla", "given": "Anna", "initials": "A"}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1"}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}], "type": "journal article", "published": "2019-03-01", "journal": {"volume": "17", "issn": "1741-7007", "issue": "1", "pages": "19", "title": "BMC Biol.", "issn-l": "1741-7007"}, "abstract": "Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive.\n\nTo investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis.\n\nWhile oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.", "doi": "10.1186/s12915-019-0634-8", "pmid": "30823887", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-019-0634-8"}, {"db": "pmc", "key": "PMC6397501"}], "notes": [], "created": "2019-12-03T12:58:12.091Z", "modified": "2021-06-16T14:41:22.388Z"}]}