Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms.
Genotyping-by-sequencing
Housefly
Isolation by distance
Microbiome
Musca domestica
Pathogens
Population structure
SNPs
Vector
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
21 Jan 2020
21 Jan 2020
Historique:
received:
03
06
2019
accepted:
31
12
2019
entrez:
23
1
2020
pubmed:
23
1
2020
medline:
29
9
2020
Statut:
epublish
Résumé
Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms. Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time. We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.
Sections du résumé
BACKGROUND
BACKGROUND
Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms.
RESULTS
RESULTS
Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time.
CONCLUSION
CONCLUSIONS
We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.
Identifiants
pubmed: 31964338
doi: 10.1186/s12864-020-6445-z
pii: 10.1186/s12864-020-6445-z
pmc: PMC6975039
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
66Subventions
Organisme : Teknologi og Produktion, Det Frie Forskningsråd
ID : 11-116256
Références
Vet Med Sci. 2019 Sep 27;:null
pubmed: 31560174
Insect Mol Biol. 2003 Apr;12(2):99-106
pubmed: 12653931
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nat Methods. 2013 Oct;10(10):996-8
pubmed: 23955772
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Bioinformatics. 2011 Nov 1;27(21):2957-63
pubmed: 21903629
J Hosp Infect. 1992 Mar;20(3):209-15
pubmed: 1348776
Cancer Res. 1967 Feb;27(2):209-20
pubmed: 6018555
Am Nat. 2009 Feb;173(2):212-24
pubmed: 20374141
Genome Biol. 2016 May 06;17(1):95
pubmed: 27154554
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Med Vet Entomol. 2005 Mar;19(1):53-9
pubmed: 15752177
Poult Sci. 2008 Jul;87(7):1428-34
pubmed: 18577626
Heredity (Edinb). 2011 Jul;107(1):1-15
pubmed: 21139633
Bioinformatics. 2012 Oct 1;28(19):2537-9
pubmed: 22820204
Am J Trop Med Hyg. 1999 Oct;61(4):625-9
pubmed: 10548298
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
J Anim Sci. 2015 Aug;93(8):3773-82
pubmed: 26440156
Environ Entomol. 2013 Dec;42(6):1322-8
pubmed: 24246478
Genetics. 1943 Mar;28(2):114-38
pubmed: 17247074
Med Vet Entomol. 2004 Sep;18(3):241-6
pubmed: 15347391
Microbiome. 2019 Nov 8;7(1):147
pubmed: 31699144
Mol Ecol Resour. 2008 Jan;8(1):103-6
pubmed: 21585727
PLoS One. 2011 May 04;6(5):e19379
pubmed: 21573248
Sci Rep. 2017 Nov 24;7(1):16324
pubmed: 29176730
Appl Environ Microbiol. 2007 Oct;73(19):6030-5
pubmed: 17675422
Emerg Infect Dis. 2013 Mar;19(3):425-30
pubmed: 23628089
Appl Environ Microbiol. 2007 Aug;73(16):5261-7
pubmed: 17586664
J Med Entomol. 2009 Sep;46(5):1164-6
pubmed: 19769050
Med Vet Entomol. 2003 Dec;17(4):429-35
pubmed: 14651658
PLoS One. 2012;7(6):e39315
pubmed: 22720093
Mol Ecol. 2012 Jun;21(12):2839-46
pubmed: 22574758
PLoS One. 2014 Feb 28;9(2):e90346
pubmed: 24587335
PLoS One. 2017 Jan 12;12(1):e0169753
pubmed: 28081167
J Med Entomol. 2001 Mar;38(2):218-22
pubmed: 11296826
Nat Rev Genet. 2011 Jun 17;12(7):499-510
pubmed: 21681211
Genome Biol. 2014;15(10):466
pubmed: 25315136
Transbound Emerg Dis. 2018 Oct;65(5):1152-1157
pubmed: 29877056
Emerg Infect Dis. 2004 Aug;10(8):1490-2
pubmed: 15496257
Parasitol Res. 2007 Jun;101(1):243-6
pubmed: 17370089
J Hered. 2002 Jul-Aug;93(4):254-9
pubmed: 12407211
Trop Biomed. 2005 Jun;22(1):53-61
pubmed: 16880754
J Hered. 2005 Sep-Oct;96(5):502-12
pubmed: 16135710
Genome Biol. 2015 Nov 19;16:250
pubmed: 26581564
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Lancet. 1991 Apr 27;337(8748):993-7
pubmed: 1673210
Mol Ecol. 2015 Mar;24(6):1164-71
pubmed: 25678037
Nat Methods. 2010 May;7(5):335-6
pubmed: 20383131