{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T10:31:19Z","timestamp":1773484279124,"version":"3.50.1"},"reference-count":112,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T00:00:00Z","timestamp":1761782400000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UK Biotechnology and Bioscience Research Council Doctoral Training Partnership","award":["BB\/T008695\/1"],"award-info":[{"award-number":["BB\/T008695\/1"]}]},{"name":"UK Biotechnology and Bioscience Research Council Doctoral Training Partnership","award":["BB\/M011186\/1"],"award-info":[{"award-number":["BB\/M011186\/1"]}]},{"DOI":"10.13039\/501100000867","name":"Commonwealth Scholarship Commission","doi-asserted-by":"publisher","award":["CMCS-2019-109"],"award-info":[{"award-number":["CMCS-2019-109"]}],"id":[{"id":"10.13039\/501100000867","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000774","name":"Newcastle University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"UK Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BBSRC, BB\/W013630\/1"],"award-info":[{"award-number":["BBSRC, BB\/W013630\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Trichomonas species are a diverse group of microbial eukaryotes (also commonly referred to as protists) that are obligate extracellular symbionts associated with or attributed to various inflammatory diseases. They colonize mucosal surfaces across a wide range of hosts, all of which harbor a resident microbiota. Their evolutionary history likely involved multiple host transfers, including zoonotic events from columbiform birds to mammals. Using comparative transcriptomics, this study examines Trichomonas gallinae co-cultured with Escherichia coli, identifying a molecular toolkit that Trichomonas species may use to interact with bacterial members of the microbiota. Integrating transcriptomic data with comparative genomics and phylogenetics revealed a conserved repertoire of protein-coding genes likely acquired through multiple lateral gene transfers (LGTs) in a columbiform-infecting ancestor. These LGT-derived genes encode muramidases, glucosaminidases, and antimicrobial peptides\u2014enzymes and effectors capable of targeting bacterial cell walls, potentially affecting the bacterial-microbiota composition across both avian and mammalian hosts. This molecular toolkit suggests that Trichomonas species can actively compete with and exploit their surrounding microbiota for nutrients, potentially contributing to dysbiosis associated with Trichomonas infections. Their ability to target bacterial populations at mucosal surfaces provides insight into how Trichomonas species may have adapted to diverse hosts and how they could influence inflammatory mucosal diseases in birds and mammals.<\/jats:p>","DOI":"10.1093\/molbev\/msaf276","type":"journal-article","created":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:34:18Z","timestamp":1761744858000},"source":"Crossref","is-referenced-by-count":1,"title":["An Evolutionarily Conserved Laterally Acquired Toolkit Enables Microbiota Targeting by\n                    <i>Trichomonas<\/i>"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4092-2132","authenticated-orcid":false,"given":"Adam J","family":"Hart","sequence":"first","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2264-5799","authenticated-orcid":false,"given":"Lenshina A","family":"Mpeyako","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3290-2506","authenticated-orcid":false,"given":"Nick P","family":"Bailey","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7116-2451","authenticated-orcid":false,"given":"George","family":"Merces","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"Gray","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1286-6851","authenticated-orcid":false,"given":"Jacob","family":"Biboy","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4682-1037","authenticated-orcid":false,"given":"Manuel","family":"Banzhaf","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0408-8567","authenticated-orcid":false,"given":"Waldemar","family":"Vollmer","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]},{"name":"Centre for Superbug Solutions, Institute for Molecular Bioscience, University of Queensland , St Lucia, QLD 4072 ,","place":["Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3760-9958","authenticated-orcid":false,"given":"Robert P","family":"Hirt","sequence":"additional","affiliation":[{"name":"Biosciences Institute, Newcastle University , Newcastle-upon-Tyne NE1 7RU ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,10,30]]},"reference":[{"key":"2025111306113658100_msaf276-B1","doi-asserted-by":"publisher","first-page":"2391","DOI":"10.1093\/gbe\/evz164","article-title":"Multilocus analysis resolves the European finch epidemic strain of Trichomonas gallinae and suggests introgression from divergent trichomonads","volume":"11","author":"Alrefaei","year":"2019","journal-title":"Genome Biol Evol"},{"key":"2025111306113658100_msaf276-B2","doi-asserted-by":"publisher","first-page":"R19","DOI":"10.1186\/gb-2013-14-2-r19","article-title":"Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes","volume":"14","author":"Alsmark","year":"2013","journal-title":"Genome Biol"},{"key":"2025111306113658100_msaf276-B3","doi-asserted-by":"publisher","first-page":"D808","DOI":"10.1093\/nar\/gkad1003","article-title":"VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023","volume":"52","author":"Alvarez-Jarreta","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"2025111306113658100_msaf276-B4","author":"Andrews"},{"key":"2025111306113658100_msaf276-B5","doi-asserted-by":"publisher","first-page":"1471","DOI":"10.1016\/j.chembiol.2012.09.016","article-title":"Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion","volume":"19","author":"Bacik","year":"2012","journal-title":"Chem Biol."},{"key":"2025111306113658100_msaf276-B6","doi-asserted-by":"publisher","first-page":"1242275","DOI":"10.3389\/fmicb.2023.1242275","article-title":"Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier","volume":"14","author":"Bailey","year":"2023","journal-title":"Front Microbiol"},{"key":"2025111306113658100_msaf276-B7","doi-asserted-by":"publisher","first-page":"e0004176","DOI":"10.1371\/journal.pntd.0004176","article-title":"The interplay of host microbiota and parasitic protozoans at mucosal interfaces: implications for the outcomes of infections and diseases","volume":"9","author":"B\u00e4r","year":"2015","journal-title":"PLoS Negl Trop Dis."},{"key":"2025111306113658100_msaf276-B8","doi-asserted-by":"publisher","first-page":"e1011563","DOI":"10.1371\/journal.ppat.1011563","article-title":"Nlpc\/P60 peptidoglycan hydrolases of Trichomonas vaginalis have complementary activities that empower the protozoan to control host-protective lactobacilli","volume":"19","author":"Barnett","year":"2023","journal-title":"PLoS Pathog."},{"key":"2025111306113658100_msaf276-B9","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","article-title":"Ilastik: interactive machine learning for (bio)image analysis","volume":"16","author":"Berg","year":"2019","journal-title":"Nat Methods."},{"key":"2025111306113658100_msaf276-B10","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2025111306113658100_msaf276-B11","doi-asserted-by":"publisher","first-page":"e0226266","DOI":"10.1371\/journal.pone.0226266","article-title":"Assessment of the role of Trichomonas tenax in the etiopathogenesis of human periodontitis: a systematic review","volume":"14","author":"Bisson","year":"2019","journal-title":"PLoS One"},{"key":"2025111306113658100_msaf276-B12","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1006\/jmbi.1994.1582","article-title":"The immunoglobulin fold. Structural classification, sequence patterns and common core","volume":"242","author":"Bork","year":"1994","journal-title":"J Mol Biol."},{"key":"2025111306113658100_msaf276-B13","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1097\/OLQ.0b013e3182631c79","article-title":"Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women","volume":"39","author":"Brotman","year":"2012","journal-title":"Sex Transm Dis"},{"key":"2025111306113658100_msaf276-B14","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1128\/jb.00608-08","article-title":"The peptidoglycan sacculus of Myxococcus xanthus has unusual structural features and is degraded during glycerol-induced myxospore development","volume":"191","author":"Bui","year":"2009","journal-title":"J Bacteriol"},{"key":"2025111306113658100_msaf276-B15","doi-asserted-by":"publisher","first-page":"D233","DOI":"10.1093\/nar\/gkn663","article-title":"The carbohydrate-active EnZymes database (CAZy): an expert resource for glycogenomics","volume":"37","author":"Cantarel","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2025111306113658100_msaf276-B16","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1126\/science.1132894","article-title":"Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis","volume":"315","author":"Carlton","year":"2007","journal-title":"Science"},{"key":"2025111306113658100_msaf276-B17","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"key":"2025111306113658100_msaf276-B18","doi-asserted-by":"publisher","first-page":"4836","DOI":"10.1128\/jb.182.17.4836-4840.2000","article-title":"Molecular characterization of the \u03b2-N-acetylglucosaminidase of Escherichia coli and its role in cell wall recycling","volume":"182","author":"Cheng","year":"2000","journal-title":"J Bacteriol"},{"key":"2025111306113658100_msaf276-B19","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1128\/cmr.15.3.329-341.2002","article-title":"Methods for cultivation of luminal parasitic protists of clinical importance","volume":"15","author":"Clark","year":"2002","journal-title":"Clin Microbiol Rev"},{"key":"2025111306113658100_msaf276-B20","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1097\/mib.0000000000000750","article-title":"Current understanding of dysbiosis in disease in human and animal models","volume":"22","author":"DeGruttola","year":"2016","journal-title":"Inflamm Bowel Dis"},{"key":"2025111306113658100_msaf276-B21","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nrg3055","article-title":"Controlling gene expression in response to stress","volume":"12","author":"de Nadal","year":"2011","journal-title":"Nat Rev Genet."},{"key":"2025111306113658100_msaf276-B22","doi-asserted-by":"publisher","first-page":"e016959","DOI":"10.1136\/bmjopen-2017-016959","article-title":"Prevalence of Trichomonas vaginalis infection and protozoan load in South African women: a cross-sectional study","volume":"7","author":"de Waaij","year":"2017","journal-title":"BMJ Open"},{"key":"2025111306113658100_msaf276-B23","doi-asserted-by":"publisher","author":"Dmitry","DOI":"10.1101\/2021.09.03.458852"},{"key":"2025111306113658100_msaf276-B24","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-Seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2025111306113658100_msaf276-B25","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2025111306113658100_msaf276-B26","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2025111306113658100_msaf276-B27","doi-asserted-by":"publisher","first-page":"e110943","DOI":"10.1371\/journal.pone.0110943","article-title":"An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease","volume":"9","author":"Fettweis","year":"2014","journal-title":"PLoS One"},{"key":"2025111306113658100_msaf276-B28","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1136\/sextrans-2013-051052","article-title":"The villain team-up or how Trichomonas vaginalis and bacterial vaginosis alter innate immunity in concert","volume":"89","author":"Fichorova","year":"2013","journal-title":"Sex Transm Infect"},{"key":"2025111306113658100_msaf276-B29","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1093\/infdis\/147.1.87","article-title":"Phagocytosis and killing of Neisseria gonorrhoeae by Trichomonas vaginalis","volume":"147","author":"Francioli","year":"1983","journal-title":"J Infect Dis."},{"key":"2025111306113658100_msaf276-B30","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1038\/nrmicro2009","article-title":"Swimming with protists: perception, motility and flagellum assembly","volume":"6","author":"Ginger","year":"2008","journal-title":"Nat Rev Microbiol."},{"key":"2025111306113658100_msaf276-B31","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1016\/0003-2697(88)90468-x","article-title":"Separation and quantification of muropeptides with high-performance liquid chromatography","volume":"172","author":"Glauner","year":"1988","journal-title":"Anal Biochem"},{"key":"2025111306113658100_msaf276-B32","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1093\/molbev\/msp259","article-title":"SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building","volume":"27","author":"Gouy","year":"2010","journal-title":"Mol Biol Evol."},{"key":"2025111306113658100_msaf276-B33","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1177\/0956462418809767","article-title":"Trichomonas vaginalis virus: a review of the literature","volume":"30","author":"Graves","year":"2019","journal-title":"Int J STD AIDS"},{"key":"2025111306113658100_msaf276-B34","doi-asserted-by":"publisher","first-page":"1096","DOI":"10.1107\/s090744490000857x","article-title":"Structure of jack bean chitinase","volume":"56","author":"Hahn","year":"2000","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2025111306113658100_msaf276-B35","doi-asserted-by":"publisher","first-page":"21","DOI":"10.4103\/0975-7406.106559","article-title":"Chitinases: an update","volume":"5","author":"Hamid","year":"2013","journal-title":"J Pharm Bioallied Sci"},{"key":"2025111306113658100_msaf276-B36","doi-asserted-by":"publisher","first-page":"643422","DOI":"10.3389\/fmicb.2021.643422","article-title":"Role of vaginal microbiota dysbiosis in gynecological diseases and the potential interventions","volume":"12","author":"Han","year":"2021","journal-title":"Front Microbiol."},{"key":"2025111306113658100_msaf276-B37","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1186\/s13071-019-3660-z","article-title":"Characterization of the BspA and pmp protein family of trichomonads","volume":"12","author":"Handrich","year":"2019","journal-title":"Parasit Vectors"},{"key":"2025111306113658100_msaf276-B38","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1016\/S0022-2836(95)80059-X","article-title":"The refined crystal structure of an endochitinase from Hordeum vulgare L. seeds at 1.8 \u212b resolution","volume":"248","author":"Hart","year":"1995","journal-title":"J Mol Biol"},{"key":"2025111306113658100_msaf276-B39","doi-asserted-by":"publisher","DOI":"10.1128\/iai.00141-19","article-title":"Cooperative interactions between Trichomonas vaginalis and associated bacteria enhance paracellular permeability of the cervicovaginal epithelium by dysregulating tight junctions","volume":"87","author":"Hinderfeld","year":"2019","journal-title":"Infect Immun"},{"key":"2025111306113658100_msaf276-B40","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1136\/sextrans-2013-051105","article-title":"Trichomonas vaginalis virulence factors: an integrative overview","volume":"89","author":"Hirt","year":"2013","journal-title":"Sex Transm Infect"},{"key":"2025111306113658100_msaf276-B41","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1017\/S0031182019000647","article-title":"Mucosal microbial parasites\/symbionts in health and disease: an integrative overview","volume":"146","author":"Hirt","year":"2019","journal-title":"Parasitology"},{"key":"2025111306113658100_msaf276-B42","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.mib.2014.11.018","article-title":"Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites","volume":"23","author":"Hirt","year":"2015","journal-title":"Curr Opin Microbiol"},{"key":"2025111306113658100_msaf276-B43","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1097\/QCO.0000000000000128","article-title":"Trichomonas vaginalis origins, molecular pathobiology and clinical considerations","volume":"28","author":"Hirt","year":"2015","journal-title":"Curr Opin Infect Dis."},{"key":"2025111306113658100_msaf276-B44","doi-asserted-by":"publisher","first-page":"mgen001086","DOI":"10.1099\/mgen.0.001086","article-title":"Cazy_webscraper: local compilation and interrogation of comprehensive CAZyme datasets","volume":"9","author":"Hobbs","year":"2023","journal-title":"Microb Genom"},{"key":"2025111306113658100_msaf276-B45","doi-asserted-by":"publisher","first-page":"4889","DOI":"10.1111\/j.1742-4658.2006.05487.x","article-title":"Crystal structure and enzymatic properties of a bacterial family 19 chitinase reveal differences from plant enzymes","volume":"273","author":"Hoell","year":"2006","journal-title":"FEBS J"},{"key":"2025111306113658100_msaf276-B46","doi-asserted-by":"publisher","first-page":"e01492","DOI":"10.1128\/mBio.01492-17","article-title":"Dysbiosis and its discontents","volume":"8","author":"Hooks","year":"2017","journal-title":"mBio"},{"key":"2025111306113658100_msaf276-B47","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1038\/s41392-022-00974-4","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct Target Ther."},{"key":"2025111306113658100_msaf276-B48","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1159\/000181181","article-title":"Bacterial peptidoglycan degrading enzymes and their impact on host muropeptide detection","volume":"1","author":"Humann","year":"2009","journal-title":"J Innate Immun"},{"key":"2025111306113658100_msaf276-B49","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/nrmicro.2017.137","article-title":"Functional horizontal gene transfer from bacteria to eukaryotes","volume":"16","author":"Husnik","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2025111306113658100_msaf276-B50","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1097\/OLQ.0000000000000026","article-title":"Prevalence and factors associated with Trichomonas vaginalis infection among high-risk women in Los Angeles","volume":"40","author":"Javanbakht","year":"2013","journal-title":"Sex Transm Dis."},{"key":"2025111306113658100_msaf276-B51","doi-asserted-by":"publisher","first-page":"19978","DOI":"10.1038\/s41598-020-76821-9","article-title":"Changes in the diversity and composition of gut microbiota in pigeon squabs infected with Trichomonas gallinae","volume":"10","author":"Ji","year":"2020","journal-title":"Sci Rep"},{"key":"2025111306113658100_msaf276-B52","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1007\/bf01963936","article-title":"In vitro phagocytic interaction between Trichomonas vaginalis isolates and bacteria","volume":"10","author":"Juliano","year":"1991","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"2025111306113658100_msaf276-B53","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2025111306113658100_msaf276-B54","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichia coli","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat Rev Microbiol."},{"key":"2025111306113658100_msaf276-B55","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1097\/OLQ.0b013e3181cfcd8c","article-title":"Trichomonas vaginalis prevalence, incidence, risk factors and antibiotic-resistance in an adolescent population","volume":"37","author":"Krashin","year":"2010","journal-title":"Sex Transm Dis."},{"key":"2025111306113658100_msaf276-B56","doi-asserted-by":"publisher","first-page":"2260","DOI":"10.1091\/mbc.E17-05-0285","article-title":"Electrostatic interaction between polyglutamylated tubulin and the nexin-dynein regulatory complex regulates flagellar motility","volume":"28","author":"Kubo","year":"2017","journal-title":"Mol Biol Cell"},{"key":"2025111306113658100_msaf276-B57","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","article-title":"Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool","volume":"52","author":"Letunic","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"2025111306113658100_msaf276-B58","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nri.2017.7","article-title":"Dysbiosis and the immune system","volume":"17","author":"Levy","year":"2017","journal-title":"Nat Rev Immunol."},{"key":"2025111306113658100_msaf276-B59","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.resmic.2012.01.002","article-title":"Characterization of endolysin from a Salmonella typhimurium-infecting bacteriophage SPN1S","volume":"163","author":"Lim","year":"2012","journal-title":"Res Microbiol"},{"key":"2025111306113658100_msaf276-B60","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1093\/bioinformatics\/btt688","article-title":"RNA-Seq differential expression studies: more sequence or more replication?","volume":"30","author":"Liu","year":"2014","journal-title":"Bioinformatics"},{"key":"2025111306113658100_msaf276-B61","doi-asserted-by":"publisher","first-page":"e20774","DOI":"10.1371\/journal.pone.0020774","article-title":"Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene","volume":"6","author":"Malik","year":"2011","journal-title":"PLoS One"},{"key":"2025111306113658100_msaf276-B62","doi-asserted-by":"publisher","first-page":"e00918","DOI":"10.1128\/mbio.00918-22","article-title":"Two different species of Mycoplasma endosymbionts can influence Trichomonas vaginalis pathophysiology","volume":"13","author":"Margarita","year":"2022","journal-title":"mBio"},{"key":"2025111306113658100_msaf276-B63","doi-asserted-by":"publisher","first-page":"179","DOI":"10.3389\/fcimb.2020.00179","article-title":"Impact of symbiosis between Trichomonas vaginalis and Mycoplasma hominis on vaginal dysbiosis: a mini review","volume":"10","author":"Margarita","year":"2020","journal-title":"Front Cell Infect Microbiol."},{"key":"2025111306113658100_msaf276-B64","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1016\/j.pt.2014.05.005","article-title":"What is the importance of zoonotic trichomonads for human health?","volume":"30","author":"Maritz","year":"2014","journal-title":"Trends Parasitol"},{"key":"2025111306113658100_msaf276-B65","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"2025111306113658100_msaf276-B66","doi-asserted-by":"publisher","first-page":"4666","DOI":"10.1128\/AEM.00092-08","article-title":"Specific interaction of the unmodified bacteriocin lactococcin 972 with the cell wall precursor lipid II","volume":"74","author":"Mart\u00ednez","year":"2008","journal-title":"Appl Environ Microbiol."},{"key":"2025111306113658100_msaf276-B67","doi-asserted-by":"publisher","first-page":"2393","DOI":"10.1099\/00221287-142-9-2393","article-title":"Lactococcin 972: a homodimeric lactococcal bacteriocin whose primary target is not the plasma membrane","volume":"142","author":"Mart\u00ednez","year":"1996","journal-title":"Microbiology"},{"key":"2025111306113658100_msaf276-B68","doi-asserted-by":"publisher","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2025111306113658100_msaf276-B69","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1186\/1471-2105-7-339","article-title":"Tools for integrated sequence-structure analysis with UCSF chimera","volume":"7","author":"Meng","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2025111306113658100_msaf276-B70","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.pt.2018.05.006","article-title":"Trichomonas vaginalis: pathogenesis, symbiont interactions, and host cell immune responses","volume":"34","author":"Mercer","year":"2018","journal-title":"Trends Parasitol."},{"key":"2025111306113658100_msaf276-B71","doi-asserted-by":"publisher","first-page":"e04266","DOI":"10.7554\/eLife.04266","article-title":"Antibacterial gene transfer across the tree of life","volume":"3","author":"Metcalf","year":"2014","journal-title":"Elife"},{"key":"2025111306113658100_msaf276-B72","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat Methods."},{"key":"2025111306113658100_msaf276-B73","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.1017\/S0950268813002902","article-title":"Distribution and risk factors of Trichomonas vaginalis infection in England: an epidemiological study using electronic health records from sexually transmitted infection clinics, 2009\u20132011","volume":"142","author":"Mitchell","year":"2014","journal-title":"Epidemiol Infect."},{"key":"2025111306113658100_msaf276-B74","doi-asserted-by":"publisher","first-page":"5965","DOI":"10.1038\/s41598-019-42435-z","article-title":"Structural bases of peptidoglycan recognition by lysostaphin SH3b domain","volume":"9","author":"Mitkowski","year":"2019","journal-title":"Sci Rep."},{"key":"2025111306113658100_msaf276-B75","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/1471-2105-7-123","article-title":"Detecting outliers when fitting data with nonlinear regression\u2014a new method based on robust nonlinear regression and the false discovery rate","volume":"7","author":"Motulsky","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2025111306113658100_msaf276-B76","doi-asserted-by":"publisher","first-page":"1437572","DOI":"10.3389\/fmicb.2024.1437572","article-title":"Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors","volume":"15","author":"Mpeyako","year":"2024","journal-title":"Front Microbiol."},{"key":"2025111306113658100_msaf276-B77","doi-asserted-by":"publisher","first-page":"1417","DOI":"10.1091\/mbc.01-11-0531","article-title":"Kinesin-II is required for flagellar sensory transduction during fertilization in Chlamydomonas","volume":"13","author":"Pan","year":"2002","journal-title":"Mol Biol Cell"},{"key":"2025111306113658100_msaf276-B78","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1042\/BC20060084","article-title":"Phagocytosis by Trichomonas vaginalis: new insights","volume":"99","author":"Pereira-Neves","year":"2007","journal-title":"Biol Cell."},{"key":"2025111306113658100_msaf276-B79","doi-asserted-by":"publisher","first-page":"106674","DOI":"10.1016\/j.ympev.2019.106674","article-title":"Diverse trichomonas lineages in Australasian pigeons and doves support a columbid origin for the genus Trichomonas","volume":"143","author":"Peters","year":"2020","journal-title":"Mol Phylogenet Evol."},{"key":"2025111306113658100_msaf276-B80","doi-asserted-by":"publisher","first-page":"e01784","DOI":"10.1128\/mBio.01784-18","article-title":"The protozoan Trichomonas vaginalis targets bacteria with laterally acquired NlpC\/P60 peptidoglycan hydrolases","volume":"9","author":"Pinheiro","year":"2018","journal-title":"mBio"},{"key":"2025111306113658100_msaf276-B81","doi-asserted-by":"publisher","first-page":"333","DOI":"10.3347\/kjp.2017.55.3.333","article-title":"PCR identification and phylogenetic analysis of Trichomonas gallinae from domestic pigeons in Guangzhou, China","volume":"55","author":"Qiu","year":"2017","journal-title":"Korean J Parasitol"},{"key":"2025111306113658100_msaf276-B84","author":"R Core Team","year":"2021"},{"key":"2025111306113658100_msaf276-B82","doi-asserted-by":"publisher","first-page":"31994","DOI":"10.1074\/jbc.M102591200","article-title":"A new lysozyme fold. Crystal structure of the muramidase from Streptomyces coelicolor at 1.65 \u212b resolution","volume":"276","author":"Rau","year":"2001","journal-title":"J Biol Chem"},{"key":"2025111306113658100_msaf276-B83","doi-asserted-by":"publisher","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"Ravel","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025111306113658100_msaf276-B85","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1006\/expr.1998.4297","article-title":"Trichomonas vaginalis: in vitro phagocytosis of lactobacilli, vaginal epithelial cells, leukocytes, and erythrocytes","volume":"89","author":"Rend\u00f3n-Maldonado","year":"1998","journal-title":"Exp Parasitol."},{"key":"2025111306113658100_msaf276-B86","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.protis.2015.02.002","article-title":"Is Trichomonas tenax a parasite or a commensal?","volume":"166","author":"Ribeiro","year":"2015","journal-title":"Protist"},{"key":"2025111306113658100_msaf276-B87","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1007\/978-3-030-80682-8_12","volume-title":"Lifecycles of pathogenic protists in humans","author":"Riestra","year":"2022"},{"key":"2025111306113658100_msaf276-B88","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"Edger: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2025111306113658100_msaf276-B89","doi-asserted-by":"publisher","first-page":"3793","DOI":"10.1007\/s00203-021-02414-3","article-title":"Vaginal microbiome: normalcy vs dysbiosis","volume":"203","author":"Saraf","year":"2021","journal-title":"Arch Microbiol."},{"key":"2025111306113658100_msaf276-B90","doi-asserted-by":"publisher","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the National Center for Biotechnology Information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025111306113658100_msaf276-B91","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1002\/mrd.22489","article-title":"The ImageJ ecosystem: an open platform for biomedical image analysis","volume":"82","author":"Schindelin","year":"2015","journal-title":"Mol Reprod Dev."},{"key":"2025111306113658100_msaf276-B92","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/0006-3002(52)90045-0","article-title":"The measurement of lysozyme activity and the ultra-violet inactivation of lysozyme","volume":"8","author":"Shugar","year":"1952","journal-title":"Biochim Biophys Acta."},{"key":"2025111306113658100_msaf276-B93","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1016\/j.pt.2020.07.014","article-title":"Lateral gene transfer mechanisms and pan-genomes in eukaryotes","volume":"36","author":"Sibbald","year":"2020","journal-title":"Trends Parasitol"},{"key":"2025111306113658100_msaf276-B94","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal Omega for making accurate alignments of many protein sequences","volume":"27","author":"Sievers","year":"2018","journal-title":"Protein Sci"},{"key":"2025111306113658100_msaf276-B95","doi-asserted-by":"publisher","first-page":"e3003235","DOI":"10.1371\/journal.pbio.3003235","article-title":"Archaea produce peptidoglycan hydrolases that kill bacteria","volume":"23","author":"Strock","year":"2025","journal-title":"PLoS Biol"},{"key":"2025111306113658100_msaf276-B96","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1128\/aac.32.9.1323","article-title":"Effects of antimicrobial agents on growth and chemotaxis of Trichomonas vaginalis","volume":"32","author":"Sugarman","year":"1988","journal-title":"Antimicrob Agents Chemother"},{"key":"2025111306113658100_msaf276-B97","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1093\/glycob\/cwq212","article-title":"Cloning and characterization of a small family 19 chitinase from moss (Bryum coronatum)","volume":"21","author":"Taira","year":"2011","journal-title":"Glycobiology"},{"key":"2025111306113658100_msaf276-B98","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1186\/s12879-021-06432-w","article-title":"Prevalence and factors associated with Trichomonas vaginalis infection among female sex workers in Togo, 2017","volume":"21","author":"Tchankoni","year":"2021","journal-title":"BMC Infect Dis."},{"key":"2025111306113658100_msaf276-B99","doi-asserted-by":"publisher","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2025111306113658100_msaf276-B100","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.molstruc.2012.09.076","article-title":"Structure and properties of the metastable bacteriocin Lcn972 from Lactococcus lactis","volume":"1031","author":"Turner","year":"2013","journal-title":"J Mol Struct."},{"key":"2025111306113658100_msaf276-B101","doi-asserted-by":"publisher","first-page":"e1003482","DOI":"10.1371\/journal.ppat.1003482","article-title":"Trichomonas vaginalis exosomes deliver cargo to host cells and mediate host\u2236parasite interactions","volume":"9","author":"Twu","year":"2013","journal-title":"PLoS Pathog"},{"key":"2025111306113658100_msaf276-B102","doi-asserted-by":"publisher","first-page":"376","DOI":"10.3389\/fimmu.2018.00376","article-title":"Role of lactobacilli and lactoferrin in the mucosal cervicovaginal defense","volume":"9","author":"Valenti","year":"2018","journal-title":"Front Immunol"},{"key":"2025111306113658100_msaf276-B103","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/s41587-023-01773-0","article-title":"Fast and accurate protein structure search with foldseek","volume":"42","author":"van Kempen","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2025111306113658100_msaf276-B104","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1111\/j.1574-6976.2007.00099.x","article-title":"Bacterial peptidoglycan (murein) hydrolases","volume":"32","author":"Vollmer","year":"2008","journal-title":"FEMS Microbiol Rev."},{"key":"2025111306113658100_msaf276-B105","doi-asserted-by":"publisher","first-page":"39032","DOI":"10.1074\/jbc.M004797200","article-title":"Characterization of a \u03b2-N-acetylglucosaminidase of Escherichia coli and elucidation of its role in muropeptide recycling and \u03b2-lactamase induction","volume":"275","author":"V\u00f6tsch","year":"2000","journal-title":"J Biol Chem"},{"key":"2025111306113658100_msaf276-B106","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1002\/pro.3714","article-title":"Collection of antimicrobial peptides database and its derivatives: applications and beyond","volume":"29","author":"Waghu","year":"2020","journal-title":"Protein Sci."},{"key":"2025111306113658100_msaf276-B107","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Wang","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2025111306113658100_msaf276-B108","doi-asserted-by":"publisher","first-page":"e15388","DOI":"10.1371\/journal.pone.0015388","article-title":"Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs","volume":"5","author":"Wohlk\u00f6nig","year":"2010","journal-title":"PLoS One"},{"key":"2025111306113658100_msaf276-B109","doi-asserted-by":"publisher","first-page":"e00024","DOI":"10.1097\/in9.0000000000000024","article-title":"Peptidoglycan-induced modulation of metabolic and inflammatory responses","volume":"5","author":"Wolf","year":"2023","journal-title":"Immunometabolism (Cobham)"},{"key":"2025111306113658100_msaf276-B110","author":"World Health Organisation","year":"2024"},{"key":"2025111306113658100_msaf276-B111","doi-asserted-by":"publisher","first-page":"114985","DOI":"10.1016\/j.biopha.2023.114985","article-title":"Immunological mechanisms of inflammatory diseases caused by gut microbiota dysbiosis: a review","volume":"164","author":"Zhao","year":"2023","journal-title":"Biomed Pharmacother."},{"key":"2025111306113658100_msaf276-B112","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1007\/s00436-022-07726-x","article-title":"The prevalence and risk factors of Trichomonas vaginalis in Wuhan and the Tibetan area, China: a two-center study","volume":"122","author":"Zhu","year":"2023","journal-title":"Parasitol Res."}],"container-title":["Molecular Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/mbe\/advance-article-pdf\/doi\/10.1093\/molbev\/msaf276\/65043491\/msaf276.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/11\/msaf276\/65043491\/msaf276.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/mbe\/article-pdf\/42\/11\/msaf276\/65043491\/msaf276.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T11:11:46Z","timestamp":1763032306000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/mbe\/article\/doi\/10.1093\/molbev\/msaf276\/8306986"}},"subtitle":[],"editor":[{"given":"Ana Carolina","family":"Junqueira","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,10,29]]},"references-count":112,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2025,10,29]]}},"URL":"https:\/\/doi.org\/10.1093\/molbev\/msaf276","relation":{},"ISSN":["0737-4038","1537-1719"],"issn-type":[{"value":"0737-4038","type":"print"},{"value":"1537-1719","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,11]]},"published":{"date-parts":[[2025,10,29]]},"article-number":"msaf276"}}