Metagenomic Evaluation of Bacteria from Voles
Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from...
Published in: | Vector-Borne and Zoonotic Diseases |
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Mary Ann Liebert
2018
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/233229 2024-02-04T10:05:03+01:00 Metagenomic Evaluation of Bacteria from Voles Koskela, Katja A Kalin-Mänttäri, Laura Hemmilä, Heidi Smura, Teemu Kinnunen, Paula M Niemimaa, Jukka Henttonen, Heikki Nikkari, Simo Departments of Faculty of Veterinary Medicine Doctoral Programme in Microbiology and Biotechnology Department of Virology HUSLAB 2018-03-06T22:12:01Z 11 application/pdf http://hdl.handle.net/10138/233229 eng eng Mary Ann Liebert 10.1089/vbz.2016.1969 The authors thank Heidi Rossow for sample preparation. The authors wish to acknowledge CSC - IT Center for Science, Finland, for computational resources. This work is part of the European Biodefence project EDA B-1325-ESM4-GP and has been partially funded by EU grant FP7-261504 EDE-Next and cataloged as EDENext 442 (www.edenext.eu). Koskela , K A , Kalin-Mänttäri , L , Hemmilä , H , Smura , T , Kinnunen , P M , Niemimaa , J , Henttonen , H & Nikkari , S 2017 , ' Metagenomic Evaluation of Bacteria from Voles ' , Vector Borne and Zoonotic Diseases , vol. 17 , no. 2 , pp. 123-133 . https://doi.org/10.1089/vbz.2016.1969 , https://doi.org/10.1089/vbz.2016.1969 85010792546 5d3ce6cd-00f5-4229-877f-22f7404689d6 http://hdl.handle.net/10138/233229 000392883100005 openAccess info:eu-repo/semantics/openAccess diagnostics rodents PCR zoonotic POLYMERASE-CHAIN-REACTION RIBOSOMAL-RNA SEQUENCES RATS RATTUS-NORVEGICUS ANAPLASMA-PHAGOCYTOPHILUM GASTROINTESTINAL-TRACT RESPIRATORY-TRACT MICROBIAL ECOLOGY DNA BARTONELLA PATHOGENS 3142 Public health care science environmental and occupational health Article publishedVersion 2018 ftunivhelsihelda 2024-01-11T00:01:14Z Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus). With the more conventional 16S rDNA PCR analysis, 90 (33%) of the recovered 269 sequence types could be identified to genus level, including Bartonella, Francisella, Mycoplasma, Anaplasma, and Acinetobacter in 31, 15, 9, 9, and 9 sequences, respectively. Seventy-five (28%) matched best with sequences of uncultured bacteria, of which 40/75 could be classified to the order Clostridiales and, more specifically, to families Lachnospiraceae and Ruminococcaceae. Pyrosequencing from 23 samples revealed comparable and similar results: clinically relevant bacterial families such as Mycoplasmataceae, Bartonellaceae, Anaplasmataceae, and Francisellaceae were recognized. These analyses revealed significant bacterial diversity in vole livers, consisting of distinct and constant sequence patterns reflecting bacteria found in the intestinal gut, but including some known zoonotic pathogens as well. The molecular bacterial sequence types determined with the two different techniques shared major similarities and verified remarkable congruency between the methods. Peer reviewed Article in Journal/Newspaper Tundra HELDA – University of Helsinki Open Repository Vector-Borne and Zoonotic Diseases 17 2 123 133 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
diagnostics rodents PCR zoonotic POLYMERASE-CHAIN-REACTION RIBOSOMAL-RNA SEQUENCES RATS RATTUS-NORVEGICUS ANAPLASMA-PHAGOCYTOPHILUM GASTROINTESTINAL-TRACT RESPIRATORY-TRACT MICROBIAL ECOLOGY DNA BARTONELLA PATHOGENS 3142 Public health care science environmental and occupational health |
spellingShingle |
diagnostics rodents PCR zoonotic POLYMERASE-CHAIN-REACTION RIBOSOMAL-RNA SEQUENCES RATS RATTUS-NORVEGICUS ANAPLASMA-PHAGOCYTOPHILUM GASTROINTESTINAL-TRACT RESPIRATORY-TRACT MICROBIAL ECOLOGY DNA BARTONELLA PATHOGENS 3142 Public health care science environmental and occupational health Koskela, Katja A Kalin-Mänttäri, Laura Hemmilä, Heidi Smura, Teemu Kinnunen, Paula M Niemimaa, Jukka Henttonen, Heikki Nikkari, Simo Metagenomic Evaluation of Bacteria from Voles |
topic_facet |
diagnostics rodents PCR zoonotic POLYMERASE-CHAIN-REACTION RIBOSOMAL-RNA SEQUENCES RATS RATTUS-NORVEGICUS ANAPLASMA-PHAGOCYTOPHILUM GASTROINTESTINAL-TRACT RESPIRATORY-TRACT MICROBIAL ECOLOGY DNA BARTONELLA PATHOGENS 3142 Public health care science environmental and occupational health |
description |
Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus). With the more conventional 16S rDNA PCR analysis, 90 (33%) of the recovered 269 sequence types could be identified to genus level, including Bartonella, Francisella, Mycoplasma, Anaplasma, and Acinetobacter in 31, 15, 9, 9, and 9 sequences, respectively. Seventy-five (28%) matched best with sequences of uncultured bacteria, of which 40/75 could be classified to the order Clostridiales and, more specifically, to families Lachnospiraceae and Ruminococcaceae. Pyrosequencing from 23 samples revealed comparable and similar results: clinically relevant bacterial families such as Mycoplasmataceae, Bartonellaceae, Anaplasmataceae, and Francisellaceae were recognized. These analyses revealed significant bacterial diversity in vole livers, consisting of distinct and constant sequence patterns reflecting bacteria found in the intestinal gut, but including some known zoonotic pathogens as well. The molecular bacterial sequence types determined with the two different techniques shared major similarities and verified remarkable congruency between the methods. Peer reviewed |
author2 |
Departments of Faculty of Veterinary Medicine Doctoral Programme in Microbiology and Biotechnology Department of Virology HUSLAB |
format |
Article in Journal/Newspaper |
author |
Koskela, Katja A Kalin-Mänttäri, Laura Hemmilä, Heidi Smura, Teemu Kinnunen, Paula M Niemimaa, Jukka Henttonen, Heikki Nikkari, Simo |
author_facet |
Koskela, Katja A Kalin-Mänttäri, Laura Hemmilä, Heidi Smura, Teemu Kinnunen, Paula M Niemimaa, Jukka Henttonen, Heikki Nikkari, Simo |
author_sort |
Koskela, Katja A |
title |
Metagenomic Evaluation of Bacteria from Voles |
title_short |
Metagenomic Evaluation of Bacteria from Voles |
title_full |
Metagenomic Evaluation of Bacteria from Voles |
title_fullStr |
Metagenomic Evaluation of Bacteria from Voles |
title_full_unstemmed |
Metagenomic Evaluation of Bacteria from Voles |
title_sort |
metagenomic evaluation of bacteria from voles |
publisher |
Mary Ann Liebert |
publishDate |
2018 |
url |
http://hdl.handle.net/10138/233229 |
genre |
Tundra |
genre_facet |
Tundra |
op_relation |
10.1089/vbz.2016.1969 The authors thank Heidi Rossow for sample preparation. The authors wish to acknowledge CSC - IT Center for Science, Finland, for computational resources. This work is part of the European Biodefence project EDA B-1325-ESM4-GP and has been partially funded by EU grant FP7-261504 EDE-Next and cataloged as EDENext 442 (www.edenext.eu). Koskela , K A , Kalin-Mänttäri , L , Hemmilä , H , Smura , T , Kinnunen , P M , Niemimaa , J , Henttonen , H & Nikkari , S 2017 , ' Metagenomic Evaluation of Bacteria from Voles ' , Vector Borne and Zoonotic Diseases , vol. 17 , no. 2 , pp. 123-133 . https://doi.org/10.1089/vbz.2016.1969 , https://doi.org/10.1089/vbz.2016.1969 85010792546 5d3ce6cd-00f5-4229-877f-22f7404689d6 http://hdl.handle.net/10138/233229 000392883100005 |
op_rights |
openAccess info:eu-repo/semantics/openAccess |
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Vector-Borne and Zoonotic Diseases |
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17 |
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2 |
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123 |
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133 |
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1789973957050368000 |