Biodiversity Exploratories Information System

general

id 22247
versionID 1.1.10
title 16S rRNA gene (V3 region) DNA-based analysis of bacterial community composition (Species level) on nine pig carcasses, 9 forest plots, SCH, 2014
owners
owner1 Jörg Overmann
owner2 Johannes Sikorski
owner3 Javier Pascual
projectName ProFunD
datasetManager
datasetManagerName Jörg Overmann
institute Ludwig-Maximilians-University Munich
email joerg.overmann@dsmz.de

researchObjects

approxNumberOfPlots
noOfGP 9
noOfEP 9
noOfMIP 9
noOfVIP 9
habitats
grassland no
forest yes
experimentalManipulation yes
relativePositionToGround
aboveGround yes
belowGround no
repeatedMeasurement
timeBasedRepetition
numberOfRepetitions 3
plotBasedRepetition
numberOfSubPlots 0
taxa
taxon1 Microbes
processesAndServices
processOrService1 Decomposition
environmentalDescriptors
environmentalDescriptor1 Other
bioticDataTypes
bioticDataType1 Abundances

methodology

introduction Sequence read counts of bacterial taxa at species level, as determined by high-throughput sequencing of the 16S rRNA gene V3 region. Data are based on DNA extracted from carcass sample.
In brief, nine piglet cadavers from a local farmer in Gögglingen (Baden-Württemberg, Germany) were obtained directly after still birth and kept frozen at -20 ºC until 24 hours before the start of incubation experiments. Piglets were exposed on nine different experimental plots (EPs). Piglet cadavers were placed in black wire cages in order to exclude large vertebrate scavengers while allowing smaller scavengers like arthropods and other small animals to access the carrion. The carcasses were monitored at times 0 h, 48 h and 96 h, since microbial activity is highest during the first days after death. Stages of decomposition were defined based on established visual criteria. From each piglet and at each sampling event, a piece of tissue (≈ 125 mm3) from the snout was cut out with a sterile scalpel, inserted into a sterile tube filled with 3 ml of Allprotect Tissue Reagent preservation solution, transported to the laboratory at 4ºC and then preserved at -20ºC until analysis. The piglet cadavers remained on the plot and were monitored for further non-microbial parameter until complete decomposition. For further details, see Pascual et al (2017).
measurements
theory The sum of all read counts per sample are set to 100%. This allows to determine the relative abundance per OTU per sample.
type High-throughput sequencing
equipment
instruments HiSeq2500
calibration -
procedures Forward and reverse reads from V3 Illumina Amplicon sequencing longer than 100 bp were trimmed and dimers filtered out based on detection methods implemented in FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). FASTQ-files were synchronized for those rare cases where only one of both reads has been filtered out. Reads were joined using fastq-join (Aronesty, 2013) allowing 20 percent mismatch and a minimum overlap of 6.
Potential chimeric sequences were detected using Uchime (Edgar et al., 2011) and removed from the datasets. Sequences were clustered into OTUs using a cutoff of 97% sequence identity with QIIME V1.9.1 (Caporaso et al., 2010b) following an open reference OTU picking strategy with UCLUST (Edgar, 2010). Taxonomy was determined using hierarchical classification based on the SILVA Database (v.123) (Yilmaz et al., 2014) and employing UCLUST (Edgar, 2010).
For further details see Pascual et al 2017.

Aronesty E (2013). Comparison of Sequencing Utility Programs. The Open Bioinformatics Journal 7: 1-8
Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 15:2194-2200.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., et al. (2010b) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335–336.
Yilmaz, P., Parfrey, L.W., Yarza, P., Gerken, J., Pruesse, E., Quast, C., et al. (2014) The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic Acids Res 42: D643–D648.
Pascual, J., von Hoermann, C., Rottler-Hoermann, A.-M., Nevo, O., Geppert, A., Sikorski, J. et al. (2017) Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition. Environmental Microbiology 19: 3310-3322.

description

acronyms
acronymPair1
acronym1
meaning1
keywords
keyword1 bacterial community on pig carcass

time

when
format dd.MM.yyyy
startDate 04.08.2014
endDate 08.08.2014
dateEntry 2017-11-22
dateLastModified 2018-08-08

data

fileType structuredData
manipulations
errors
qualityLevel raw
dataStatus complete
dataStructure
dataFormat
missingValues
NA
matrix
columnName
rowName
contentType
matrixUnit
variables
name typeOfVariable units description block
1 Plot_ID string Name of plot 0
2 Species string Taxonomy and Name of Species Taxon 0
3 OTU string OTU designation 0
4 Piglet string Name of pig 0
5 Time_point string hours Time point of Sample 0
6 Sample_name string Name of Sample 0
7 Read_count integerNumber Number of Illumina Read Counts 0

references

database
papers
paper1 Pascual, J., von Hoermann, C., Rottler-Hoermann, A.-M., Nevo, O., Geppert, A., Sikorski, J. et al. (2017) Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition. Environmental Microbiology 19: 3310-3322.
relatedDatasets
dataset1 22267
citation Overmann, Jörg; Johannes Sikorski; Javier Pascual (2018): 16S rRNA gene (V3 region) DNA-based analysis of bacterial community composition (Species level) on nine pig carcasses, 9 forest plots, SCH, 2014. v1.1.10. Biodiversity Exploratories Information System. Dataset. https://www.bexis.uni-jena.de/PublicData/PublicData.aspx?DatasetId=22247

comment

comment The raw sequence reads are available in the Sequence Read Archive (SRA) under https://www.ncbi.nlm.nih.gov/sra/?term=SRR4212934