Package 'etec16s'

Dataset of 16S samples from 12 subjects challenged with enterotoxigenic Escherichia coli.

Description

Data used in 'Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment'. Measurements are number of reads clustered into OTUs (operatonal taxanomic units) by DNAClust.

Author(s)

Joseph N. Paulson

References

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

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Curated dataset of many healthy and moderate-to-severe diarretic gut 16s samples on the 454 FLEX platform.

Description

Data used in 'Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment'.

DNA was amplified using 'universal' primers targeting the V1-V2 region of the 16S rRNA gene (small subunit of the ribosome) in bacteria - 338R (5'- CATGCTGCCTCCCGTAGGAGT -3') and 27F (5'- AGAGTTTGATCCTGGCTCAG -3'). Both forward and reverse primers had a 5' portion specific for use with 454 GS-FLX Titanium sequencing technology and the forward primers contained a barcode between the Titanium and gene specific region, so that samples could be pooled to a multiplex level of 132 samples per instrument run.

16S rRNA gene sequencing was performed for all available stool samples. After sequencing, 124 samples passed quality controls, corresponding to data from 5 volunteers with the most unambiguous cases of diarrhea during the study (54 samples) and 7 volunteers without diarrheal symptoms who had the most stool samples (78 samples). The raw data have been submitted to NCBI under project ID: PRJNA298336.

Briefly, the sequenced reads were filtered for quality and were clustered with DNAclust36 to 99 percent identity clusters that were further annotated with Ribosomal Database (RDP) (rdp.cme.msu.edu, release 10.4). Sequences without a nearly identical match to RDP (> 100 bp perfect match and > 97 percent identity, as defined by BLAST) were marked as having "no genus match" and assigned an operational taxonomic unit (OTU) identifier. Chimera checking was done with Perseus/UCHIME.

Selected OTUs (e.g., OTUs belonging to the pre-infection biomarker) were aligned with Mega BLAST against the NCBI nt database. Manual inspection of the results based on percent identity and query sequence coverage was used to refine the automatically determined taxonomic classification. If the best BLAST hit differed by more than 3 percent from the query sequence, or covered less than 95 percent of the query sequence, classification was done at the genus level only based on the taxonomy labels of the top hits.

format

Data is stored as an MRexperiment-class object. Using MRcounts one can obtain the 16S count matrix produced using using DNAclust (http://dnaclust.sourceforge.net/). The pData function accesses a data frame with the following columns:

SubjectID:

Subject ID

Dose:

Quantity of ETEC given

Day:

Relative Day

AnyDayDiarrhea:

Did the subject ever get diarrhea during the study

Diarrhea:

Did subject have diarrhea on day of student

AntiGiven:

Was antibiotic given on specific day

AntibPrev:

Was antibiotic given previously

The fData function accesses a data frame with the following columns:

OTU.ID:

OTU cluster id

Center:

Sequencing read center ID

Phylum:

phylum

Class:

class

Order:

order

Family:

family

Genus:

genus

Strain:

Strain

clusterCenter:

The OTU cluster's representative sequence

Author(s)

Joseph N. Paulson

References

'Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment'

See Also

MRexperiment-class for the class definition, cumNorm to normalize the counts.

Examples

data(etec16s)
head(pData(etec16s))
head(fData(etec16s))

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