Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

Detalhes bibliográficos
Autor(a) principal: Thorpe, Harry A
Data de Publicação: 2022
Outros Autores: Tourrette, Elise, Yahara, Koji, Vale, Filipa F., Liu, Siqi, Oleastro, Mónica, Alarcon, Teresa, Perets, Tsachi-Tsadok, Latifi-Navid, Saeid, Yamaoka, Yoshio, Martinez-Gonzalez, Beatriz, Karayiannis, Ioannis, Karamitros, Timokratis, Sgouras, Dionyssios N., Elamin, Wael, Pascoe, Ben, Sheppard, Samuel K., Ronkainen, Jukka, Aro, Pertti, Engstrand, Lars, Agreus, Lars, Suerbaum, Sebastian, Thorell, Kaisa, Falush, Daniel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10451/59116
Resumo: Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.
id RCAP_f2375c16d63c0a3dadd905d9cf4c69f7
oai_identifier_str oai:repositorio.ul.pt:10451/59116
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutationsHelicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.The authors thank Sabrina Woltemate for technical assistance. This work was supported by Sequencing Grants-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan (221S0002, 18KK0266, 19H03473, 21H00346 and 22H02871) to Y.Y. F.F.V. is financed by FCT through Assistant Researcher grant CEECIND/03023/2017 and a project grant PTDC/BTM-TEC/3238/2020. I.K. studentship was funded by the National Strategic Reference Framework Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020, project No. MIS5002486) and sequencing of strains was supported by the InfeNeutra Project (NSRF 2007-2013, project no. MIS450598) of the Ministry of Culture and Education, Greece. K.T. and the sequencing of KI isolates was supported by Erik Philip-Sörensen Foundation grant G2016-08, and Swedish Society for Medical research (SSMF). All primary bioinformatics and parts of the comparative genomics were performed on resources provided by Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under projects snic2018-8-24 and uppstore2017270, and those provided by the National Institute of Genetics and the Human Genome Center at the Institute of Medical Science (University of Tokyo). Work by S.S. was supported by the German Research Foundation (DFG, project number 158 989 968–SFB 900/A1) and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Network “New Strategies Against Multi-Resistant Pathogens by Means of Digital Networking—bayresq.net”. D.F. was supported by Shanghai Municipal Science and Technology Major Project No. 2019SHZDZX02.Springer NatureRepositório da Universidade de LisboaThorpe, Harry ATourrette, EliseYahara, KojiVale, Filipa F.Liu, SiqiOleastro, MónicaAlarcon, TeresaPerets, Tsachi-TsadokLatifi-Navid, SaeidYamaoka, YoshioMartinez-Gonzalez, BeatrizKarayiannis, IoannisKaramitros, TimokratisSgouras, Dionyssios N.Elamin, WaelPascoe, BenSheppard, Samuel K.Ronkainen, JukkaAro, PerttiEngstrand, LarsAgreus, LarsSuerbaum, SebastianThorell, KaisaFalush, Daniel2023-09-01T11:10:22Z2022-11-112023-03-07T14:42:48Z2022-11-11T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/59116engThorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun [Internet]. 11 de novembro de 2022;13(1):6842. Disponível em: https://www.nature.com/articles/s41467-022-34475-3cv-prod-315871510.1038/s41467-022-34475-3info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-08T17:04:15Zoai:repositorio.ul.pt:10451/59116Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:07:06.405113Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
title Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
spellingShingle Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
Thorpe, Harry A
title_short Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
title_full Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
title_fullStr Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
title_full_unstemmed Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
title_sort Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
author Thorpe, Harry A
author_facet Thorpe, Harry A
Tourrette, Elise
Yahara, Koji
Vale, Filipa F.
Liu, Siqi
Oleastro, Mónica
Alarcon, Teresa
Perets, Tsachi-Tsadok
Latifi-Navid, Saeid
Yamaoka, Yoshio
Martinez-Gonzalez, Beatriz
Karayiannis, Ioannis
Karamitros, Timokratis
Sgouras, Dionyssios N.
Elamin, Wael
Pascoe, Ben
Sheppard, Samuel K.
Ronkainen, Jukka
Aro, Pertti
Engstrand, Lars
Agreus, Lars
Suerbaum, Sebastian
Thorell, Kaisa
Falush, Daniel
author_role author
author2 Tourrette, Elise
Yahara, Koji
Vale, Filipa F.
Liu, Siqi
Oleastro, Mónica
Alarcon, Teresa
Perets, Tsachi-Tsadok
Latifi-Navid, Saeid
Yamaoka, Yoshio
Martinez-Gonzalez, Beatriz
Karayiannis, Ioannis
Karamitros, Timokratis
Sgouras, Dionyssios N.
Elamin, Wael
Pascoe, Ben
Sheppard, Samuel K.
Ronkainen, Jukka
Aro, Pertti
Engstrand, Lars
Agreus, Lars
Suerbaum, Sebastian
Thorell, Kaisa
Falush, Daniel
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Thorpe, Harry A
Tourrette, Elise
Yahara, Koji
Vale, Filipa F.
Liu, Siqi
Oleastro, Mónica
Alarcon, Teresa
Perets, Tsachi-Tsadok
Latifi-Navid, Saeid
Yamaoka, Yoshio
Martinez-Gonzalez, Beatriz
Karayiannis, Ioannis
Karamitros, Timokratis
Sgouras, Dionyssios N.
Elamin, Wael
Pascoe, Ben
Sheppard, Samuel K.
Ronkainen, Jukka
Aro, Pertti
Engstrand, Lars
Agreus, Lars
Suerbaum, Sebastian
Thorell, Kaisa
Falush, Daniel
description Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks by migration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.
publishDate 2022
dc.date.none.fl_str_mv 2022-11-11
2022-11-11T00:00:00Z
2023-09-01T11:10:22Z
2023-03-07T14:42:48Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/59116
url http://hdl.handle.net/10451/59116
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Thorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat Commun [Internet]. 11 de novembro de 2022;13(1):6842. Disponível em: https://www.nature.com/articles/s41467-022-34475-3
cv-prod-3158715
10.1038/s41467-022-34475-3
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799134624640663552