Project:New studies to add: Difference between revisions
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Publications that describe symbiotic interactions that are not yet in the database. | Publications that describe symbiotic interactions that are not yet in the database. | ||
Please list the DOI, or link to the publication full-text if a DOI is not available. A full citation is not necessary as the publication metadata can be retrieved from CrossRef with the DOI. If necessary, comment briefly on what information in the publication should be added to the database. | Guidelines: | ||
* Please list the DOI, or link to the publication full-text if a DOI is not available. A full citation is not necessary as the publication metadata can be retrieved from CrossRef with the DOI. | |||
* If necessary, comment briefly on what information in the publication should be added to the database. | |||
* Preprints can be listed here, but should only be added as database entries when a peer-reviewed version is published | |||
* Remove entries from the list when the database has been updated. | |||
===Ciliates=== | ===Ciliates=== | ||
| Line 10: | Line 14: | ||
* https://doi.org/10.1186/s40168-024-01809-w large scale study of ciliate associated bacteria, from single-ciliate-cell amplification libraries, but doesn't appear to have a table of which bacteria is associated with which ciliate? | * https://doi.org/10.1186/s40168-024-01809-w large scale study of ciliate associated bacteria, from single-ciliate-cell amplification libraries, but doesn't appear to have a table of which bacteria is associated with which ciliate? | ||
* https://doi.org/10.1007/978-3-540-92677-1 Endosymbionts in Paramecium book | * https://doi.org/10.1007/978-3-540-92677-1 Endosymbionts in Paramecium book | ||
* https://doi.org/10.1007/978-3-540-92677-1_6 Diversity of Endosymbiotic Bacteria in Paramecium - in progress, stopped before section 5 | |||
* https://doi.org/10.1016/S0932-4739(11)80401-3 Endosymbionts in Paramecium calkinsi | |||
* [https://www.researchgate.net/profile/Giulio-Petroni/publication/228509435_Flagellated_endosymbiotic_bacteria_in_a_marine_Frontonia_spOligohymenophorea_Peniculida/links/0deec515f30f45986d000000/Flagellated-endosymbiotic-bacteria-in-a-marine-Frontonia-spOligohymenophorea-Peniculida.pdf link] flagellated endosymbionts in a Frontonia sp. | * [https://www.researchgate.net/profile/Giulio-Petroni/publication/228509435_Flagellated_endosymbiotic_bacteria_in_a_marine_Frontonia_spOligohymenophorea_Peniculida/links/0deec515f30f45986d000000/Flagellated-endosymbiotic-bacteria-in-a-marine-Frontonia-spOligohymenophorea-Peniculida.pdf link] flagellated endosymbionts in a Frontonia sp. | ||
* https://doi.org/10.1093/ismejo/wrae117 general review on ciliate symbioses | |||
* https://doi.org/10.1093/ismejo/wrae164 Methanogenic symbionts in anaerobic ciliates - no clear summary table, though, sequence data not yet public | |||
* https://doi.org/10.1128/aem.01900-23 Fluviibacteria endosymbionts in Euplotes octocarinatus | |||
* https://www.nature.com/articles/s41467-024-54047-x Relatives of Ca. Azoamicus detected in groundwater metagenomes, assembled as circular-contig MAGs (cMAGs). | |||
===Trichomonas=== | ===Trichomonas=== | ||
| Line 20: | Line 30: | ||
* [[Item:Q1742]] (no DOI, original URL defunct, archived at Internet Archive) - morphological description of Pelomyxa spp. symbionts | * [[Item:Q1742]] (no DOI, original URL defunct, archived at Internet Archive) - morphological description of Pelomyxa spp. symbionts | ||
* https://doi.org/10.1186/s12866-016-0906-1 Acanthamoeba isolates containing chlamydia | * https://doi.org/10.1186/s12866-016-0906-1 Acanthamoeba isolates containing chlamydia | ||
* https://doi.org/10. | * https://phaidra.univie.ac.at/detail/o:1356651.pdf Unpublished Masters thesis on chlamydial intranuclear symbiont of Naegleria clarki ("Pn") | ||
* https://doi.org/10.1038/s41467-024-54102-7 (preprint version: https://doi.org/10.1101/2023.03.03.530753) Desulfobacteraceae associated with Anaeramoeba in "symbiosome", deep cell surface invaginations, formerly thought to be intracellular (https://doi.org/10.1016/j.protis.2017.07.005) | |||
* https://doi.org/10.1016/j.protis.2017.07.005 Original publication re Anaeramoeba | |||
* https://doi.org/10.1101/2024.11.01.621453 (preprint) Chlamydia in wild Dictyostelium isolates | |||
===Forams=== | ===Forams=== | ||
| Line 31: | Line 44: | ||
===Termite gut flagellates=== | ===Termite gut flagellates=== | ||
* https://doi.org/10.1083/jcb.94.3.697 Motility symbiont(s) of a devescovinid flagellate | * https://doi.org/10.1083/jcb.94.3.697 Motility symbiont(s) of a devescovinid flagellate | ||
* https://doi.org/10.1371/journal.pone.0233065 ASV study of gut protist associated microbes in Reticulitermes flavipes | * https://doi.org/10.1371/journal.pone.0233065 ASV study of gut protist associated microbes in Reticulitermes flavipes | ||
* https://doi.org/10.1111/j.1574-6941.2000.tb00750.x Spirochaete ectosymbionts of termite gut flagellates | |||
* https://doi.org/10.1111/j.1574-6941.2000. | |||
* https://doi.org/10.1111/j.1550-7408.2011.00564.x EM study of symbionts from Barbulanympha and Urinympha from Cryptocercus punctulatus; intracellular localization observed | * https://doi.org/10.1111/j.1550-7408.2011.00564.x EM study of symbionts from Barbulanympha and Urinympha from Cryptocercus punctulatus; intracellular localization observed | ||
* https://doi.org/10.1128/mbio.00826-24 Endomicrobia comparative genomics, but no information on protist hosts; their table S3 lists bacterial MAGs, but termite host names are in separate Table S1, and no systematic information is provided on the protist hosts | |||
* https://doi.org/10.1111/brv.13038 Review of protist symbionts of termites | |||
* https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=18ac2be7fd364d7871888f06b24b0d15223c7b9f#page=40 TEM study of symbionts in Joenia annectens; the intranuclear symbiont appears not to have been reported elsewhere | |||
* https://doi.org/10.1099/mic.0.2007/009217-0 Endomicrobia in termite gut flagellates; unfortunately it is not clearly reported which symbiont phylotype comes from which flagellate | |||
===Other=== | ===Other=== | ||
* https://www.jstor.org/stable/43336527 https://doi.org/10.1111/j.1438-8677.1982.tb01611.x https://doi.org/10.1111/j.1438-8677.1983.tb01673.x Apparent "symbionts" of Chrysostephanosphaera and Lepochromulina in extracellular matrix, described as "refractive bodies" elsewhere (https://doi.org/10.1111/j.1756-1051.1998.tb01545.x), probably not bacteria | * https://www.jstor.org/stable/43336527 https://doi.org/10.1111/j.1438-8677.1982.tb01611.x https://doi.org/10.1111/j.1438-8677.1983.tb01673.x Apparent "symbionts" of Chrysostephanosphaera and Lepochromulina in extracellular matrix, described as "refractive bodies" elsewhere (https://doi.org/10.1111/j.1756-1051.1998.tb01545.x), probably not bacteria | ||
* [[Item:Q1104]] - Check that examples listed in their table are included in DB | * [[Item:Q1104]] - Check that examples listed in their table are included in DB | ||
* https://www.nature.com/articles/s41598-021-82369-z presence of intracellular bacteria briefly mentioned | * https://www.nature.com/articles/s41598-021-82369-z presence of intracellular bacteria briefly mentioned | ||
* https://doi.org/10.1126/science.adk1075 argues that UCYN-A should be considered an organelle, rather than an endosymbiont | * https://doi.org/10.1126/science.adk1075 argues that UCYN-A should be considered an organelle, rather than an endosymbiont | ||
* https://doi.org/10.1146/annurev-micro-090817-062650 review of cyanobacterial symbionts of microalgae | * https://doi.org/10.1146/annurev-micro-090817-062650 review of cyanobacterial symbionts of microalgae -- the reference numbering in the supplementary table appears to be incorrect, I cannot trace the cited studies | ||
* https://doi.org/10.1371/journal.pone.0301343 Potential bacterial symbionts of Alexandrium catenella | * https://doi.org/10.1371/journal.pone.0301343 Potential bacterial symbionts of Alexandrium catenella | ||
* https://doi.org/10.3354/ame01440 Heterotrophic ?diazotrophs associated with dinoflagellate-cyanobacteria consortia | |||
* https://doi.org/10.1038/s41579-022-00754-5 Add giant viruses? | |||
* https://doi.org/10.1016/j.cub.2024.04.085 large scale survey of published eukaryotic genome data for mirusviruses, using major capsid protein sequence as marker; three assemblies found with circular viral genomes | |||
* https://doi.org/10.1128/microbiolspec.funk-0056-2016 Endohyphal symbionts of fungi | |||
* http://www.phi-base.org/ PHI-Base, gene-centric pathogen-host interaction database | |||
* https://doi.org/10.1016/j.cub.2024.09.009 "Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean" | |||
Latest revision as of 12:30, 3 December 2024
Publications that describe symbiotic interactions that are not yet in the database.
Guidelines:
- Please list the DOI, or link to the publication full-text if a DOI is not available. A full citation is not necessary as the publication metadata can be retrieved from CrossRef with the DOI.
- If necessary, comment briefly on what information in the publication should be added to the database.
- Preprints can be listed here, but should only be added as database entries when a peer-reviewed version is published
- Remove entries from the list when the database has been updated.
Ciliates
- https://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-443d0e0e-63a9-4de1-8030-60c431e77f83 Endosymbionts in Blepharisma japonicum (full text not yet found)
- https://doi.org/10.1186/s40168-024-01809-w large scale study of ciliate associated bacteria, from single-ciliate-cell amplification libraries, but doesn't appear to have a table of which bacteria is associated with which ciliate?
- https://doi.org/10.1007/978-3-540-92677-1 Endosymbionts in Paramecium book
- https://doi.org/10.1007/978-3-540-92677-1_6 Diversity of Endosymbiotic Bacteria in Paramecium - in progress, stopped before section 5
- https://doi.org/10.1016/S0932-4739(11)80401-3 Endosymbionts in Paramecium calkinsi
- link flagellated endosymbionts in a Frontonia sp.
- https://doi.org/10.1093/ismejo/wrae117 general review on ciliate symbioses
- https://doi.org/10.1093/ismejo/wrae164 Methanogenic symbionts in anaerobic ciliates - no clear summary table, though, sequence data not yet public
- https://doi.org/10.1128/aem.01900-23 Fluviibacteria endosymbionts in Euplotes octocarinatus
- https://www.nature.com/articles/s41467-024-54047-x Relatives of Ca. Azoamicus detected in groundwater metagenomes, assembled as circular-contig MAGs (cMAGs).
Trichomonas
- https://doi.org/10.3389/fmicb.2017.01188 Mycoplasma and Ureaplasma spp associated with Trichomonas vaginalis, detected by PCR from T. vaginalis cultures
Amoebae
- Item:Q1742 (no DOI, original URL defunct, archived at Internet Archive) - morphological description of Pelomyxa spp. symbionts
- https://doi.org/10.1186/s12866-016-0906-1 Acanthamoeba isolates containing chlamydia
- https://phaidra.univie.ac.at/detail/o:1356651.pdf Unpublished Masters thesis on chlamydial intranuclear symbiont of Naegleria clarki ("Pn")
- https://doi.org/10.1038/s41467-024-54102-7 (preprint version: https://doi.org/10.1101/2023.03.03.530753) Desulfobacteraceae associated with Anaeramoeba in "symbiosome", deep cell surface invaginations, formerly thought to be intracellular (https://doi.org/10.1016/j.protis.2017.07.005)
- https://doi.org/10.1016/j.protis.2017.07.005 Original publication re Anaeramoeba
- https://doi.org/10.1101/2024.11.01.621453 (preprint) Chlamydia in wild Dictyostelium isolates
Forams
- https://doi.org/10.1038/s41598-019-48166-5 bacteria related to sulfur cycling enriched in forams
- https://doi.org/10.1016/j.marmicro.2017.09.001 Review of prokaryotes associated with benthic forams, see their table 1
- https://doi.org/10.1073/pnas.2200198119 Desulfobacteraceae associated with denitrifying forams Globobulimina spp. (10 species studied, also associated with other bacteria, only metagenomics applied, no FISH or TEM; have to check which MAGs linked to which foram; list of MAG accessions is in their Table S7)
- https://doi.org/10.4319/lo.2014.59.6.1879 intracellular bacteria in Ammonia beccarrii under anoxic conditions
Termite gut flagellates
- https://doi.org/10.1083/jcb.94.3.697 Motility symbiont(s) of a devescovinid flagellate
- https://doi.org/10.1371/journal.pone.0233065 ASV study of gut protist associated microbes in Reticulitermes flavipes
- https://doi.org/10.1111/j.1574-6941.2000.tb00750.x Spirochaete ectosymbionts of termite gut flagellates
- https://doi.org/10.1111/j.1550-7408.2011.00564.x EM study of symbionts from Barbulanympha and Urinympha from Cryptocercus punctulatus; intracellular localization observed
- https://doi.org/10.1128/mbio.00826-24 Endomicrobia comparative genomics, but no information on protist hosts; their table S3 lists bacterial MAGs, but termite host names are in separate Table S1, and no systematic information is provided on the protist hosts
- https://doi.org/10.1111/brv.13038 Review of protist symbionts of termites
- https://citeseerx.ist.psu.edu/document?repid=rep1&type=pdf&doi=18ac2be7fd364d7871888f06b24b0d15223c7b9f#page=40 TEM study of symbionts in Joenia annectens; the intranuclear symbiont appears not to have been reported elsewhere
- https://doi.org/10.1099/mic.0.2007/009217-0 Endomicrobia in termite gut flagellates; unfortunately it is not clearly reported which symbiont phylotype comes from which flagellate
Other
- https://www.jstor.org/stable/43336527 https://doi.org/10.1111/j.1438-8677.1982.tb01611.x https://doi.org/10.1111/j.1438-8677.1983.tb01673.x Apparent "symbionts" of Chrysostephanosphaera and Lepochromulina in extracellular matrix, described as "refractive bodies" elsewhere (https://doi.org/10.1111/j.1756-1051.1998.tb01545.x), probably not bacteria
- Item:Q1104 - Check that examples listed in their table are included in DB
- https://www.nature.com/articles/s41598-021-82369-z presence of intracellular bacteria briefly mentioned
- https://doi.org/10.1126/science.adk1075 argues that UCYN-A should be considered an organelle, rather than an endosymbiont
- https://doi.org/10.1146/annurev-micro-090817-062650 review of cyanobacterial symbionts of microalgae -- the reference numbering in the supplementary table appears to be incorrect, I cannot trace the cited studies
- https://doi.org/10.1371/journal.pone.0301343 Potential bacterial symbionts of Alexandrium catenella
- https://doi.org/10.3354/ame01440 Heterotrophic ?diazotrophs associated with dinoflagellate-cyanobacteria consortia
- https://doi.org/10.1038/s41579-022-00754-5 Add giant viruses?
- https://doi.org/10.1016/j.cub.2024.04.085 large scale survey of published eukaryotic genome data for mirusviruses, using major capsid protein sequence as marker; three assemblies found with circular viral genomes
- https://doi.org/10.1128/microbiolspec.funk-0056-2016 Endohyphal symbionts of fungi
- http://www.phi-base.org/ PHI-Base, gene-centric pathogen-host interaction database
- https://doi.org/10.1016/j.cub.2024.09.009 "Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean"