Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.
Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.ORCID iD: 0000-0001-8940-456X
Show others and affiliations
2020 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, article id 2066Article in journal (Refereed) Published
Abstract [en]

The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline "AcetoScan" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

Place, publisher, year, edition, pages
2020. Vol. 11, article id 2066
Keywords [en]
AcetoBase, AcetoScan, FTHFS, acetogens, high-throughput sequencing
National Category
Microbiology
Identifiers
URN: urn:nbn:se:nrm:diva-4415DOI: 10.3389/fmicb.2020.02066PubMedID: 32983047OAI: oai:DiVA.org:nrm-4415DiVA, id: diva2:1617709
Funder
Swedish Energy Agency, 2014-000725Available from: 2021-12-07 Created: 2021-12-07 Last updated: 2024-01-17Bibliographically approved

Open Access in DiVA

fulltext(2378 kB)60 downloads
File information
File name FULLTEXT01.pdfFile size 2378 kBChecksum SHA-512
7e591000190a4c0333471d9731fa2bd160589d5bc2d67c4aa335153325a897d32bffa9bb0292973ce34fb849e76be5d12545faa7e174af482db987c3444a6f42
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Nylander, Johan A A
By organisation
Department of Bioinformatics and Genetics
In the same journal
Frontiers in Microbiology
Microbiology

Search outside of DiVA

GoogleGoogle Scholar
Total: 60 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 62 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf