Insights into archaeological human sample microbiome using 16S rRNA gene sequencing

Alisa Kazarina, Ilva Pole, Viktorija Leonova, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka, Guntis Gerhards, Elina Petersone-Gordina

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Human body is inhabited by a vast number of microorganisms, collectively known as human microbiome, and there is a tremendous interest in evolutionary changes of human microbial ecology, diversity and function. The field of paleomicrobiology - study of ancient human microbiome - is powered by modern techniques of Next Generation Sequencing (NGS), which allows extracting microbial genomic data directly from archaeological sample of interest. One of the major techniques is 16S rRNA gene sequencing, by which certain 16S rRNA gene hypervariable regions are being amplified and sequenced. However, some limitations of this method exist including taxonomic precision and efficacy of different regions used. The aim of this study was to evaluate the phylogenetic sensitivity of different 16S rRNA gene hypervariable regions for microbiome studies in the archaeological samples. Towards this aim, archaeological bone samples and corresponding soil samples from each burial environment were collected in Medieval cemeteries in Latvia. The Ion 16S™ Metagenomics Kit targeting different 16S rRNA gene hypervariable regions was used for library construction (Ion Torrent technologies). Sequenced data were analysed by using appropriate bioinformatic techniques; alignment and taxonomic representation was done using Mothur program. Sequences of most abundant genus were further aligned to E. coli 16S rRNA gene reference sequence using MEGA7 in order to identify hypervariable region of the segment of interest. Our results showed that different hypervariable regions had different discriminatory power depending on the groups of microbes, as well as the nature of samples. On the basis of our results we suggest that wider range of primers can provide more accurate recapitulation of microbial communities in archaeological samples.

Original languageEnglish
Title of host publicationIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Subtitle of host publicationProceedings
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2264-2266
Number of pages3
ISBN (Electronic)9781509030491
DOIs
Publication statusPublished - 15 Dec 2017
Externally publishedYes
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: 13 Nov 201716 Nov 2017

Publication series

NameIEEE International Conference on Bioinformatics and Biomedicine-BIBM
ISSN (Print)2156-1125
ISSN (Electronic)2156-1133

Conference

Conference2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/TerritoryUnited States
CityKansas City
Period13/11/1716/11/17

Keywords*

  • 16S rRNA gene
  • ancient human microbiome
  • archaeology
  • bioinformatics
  • genomics
  • microbiome
  • molecular biology
  • Next-Generation Sequencing

Field of Science*

  • 1.6 Biological sciences
  • 3.1 Basic medicine

Publication Type*

  • 3.1. Articles or chapters in proceedings/scientific books indexed in Web of Science and/or Scopus database

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