data-esophagus: (Data) Small example dataset from a human esophageal...
In phyloseq: Handling and analysis of high-throughput microbiome census data
Description
Details
Author(s)
References
Examples
Description
Includes just 3 samples, 1 each from 3 subjects. Although the research article mentions 4 subjects,
only 3 are included in this dataset.
Details
abstract from research article (quoted):
The esophagus, like other luminal organs of the digestive system, provides a potential environment for bacterial colonization, but little is known about the presence of a bacterial biota or its nature. By using broad-range 16S rDNA PCR, biopsies were examined from the normal esophagus of four human adults. The 900 PCR products cloned represented 833 unique sequences belonging to 41 genera, or 95 species-level operational taxonomic units (SLOTU); 59 SLOTU were homologous with culture-defined bacterial species, 34 with 16S rDNA clones, and two were not homologous with any known bacterial 16S rDNA. Members of six phyla, Firmicutes, Bacteroides, Actinobacteria, Proteobacteria, Fusobacteria, and TM7, were represented. A large majority of clones belong to 13 of the 41 genera (783/900, 87%), or 14 SLOTU (574/900, 64%) that were shared by all four persons. Streptococcus (39%), Prevotella (17%), and Veilonella (14%) were most prevalent. The present study identified 56-79% of SLOTU in this bacterial ecosystem. Most SLOTU of esophageal biota are similar or identical to residents of the upstream oral biota, but the major distinction is that a large majority (82%) of the esophageal bacteria are known and cultivable. These findings provide evidence for a complex but conserved bacterial population in the normal distal esophagus.
(end quote)
A description of the 16S rRNA sequence processing can be found on the mothur-wiki
at the link below. A cutoff of 0.10 was used for OTU clustering in that example,
and it is taken here as well to create example data, esophagus, which was
easily imported with the import_mothur() function.
Author(s)
Pei et al. zhiheng.pei@med.nyu.edu
References
Pei, Z., Bini, E. J., Yang, L., Zhou, M., Francois, F., & Blaser, M. J. (2004).
Bacterial biota in the human distal esophagus.
Proceedings of the National Academy of Sciences of the United States of America, 101(12), 4250-4255.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384727
mothur-processed files and the sequence data can be downloaded from a zip-file,
along with additional description, from the following URL:
http://www.mothur.org/wiki/Esophageal_community_analysis
Examples
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data(esophagus)
UniFrac(esophagus, weighted=TRUE)
# How to re-create the esophagus dataset using import_mothur function
mothlist <- system.file("extdata", "esophagus.fn.list.gz", package="phyloseq")
mothgroup <- system.file("extdata", "esophagus.good.groups.gz", package="phyloseq")
mothtree <- system.file("extdata", "esophagus.tree.gz", package="phyloseq")
show_mothur_cutoffs(mothlist)
cutoff <- "0.10"
esophman <- import_mothur(mothlist, mothgroup, mothtree, cutoff)
Example output
phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.
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Description Details Author(s) References Examples
Description
Includes just 3 samples, 1 each from 3 subjects. Although the research article mentions 4 subjects, only 3 are included in this dataset.
Details
abstract from research article (quoted):
The esophagus, like other luminal organs of the digestive system, provides a potential environment for bacterial colonization, but little is known about the presence of a bacterial biota or its nature. By using broad-range 16S rDNA PCR, biopsies were examined from the normal esophagus of four human adults. The 900 PCR products cloned represented 833 unique sequences belonging to 41 genera, or 95 species-level operational taxonomic units (SLOTU); 59 SLOTU were homologous with culture-defined bacterial species, 34 with 16S rDNA clones, and two were not homologous with any known bacterial 16S rDNA. Members of six phyla, Firmicutes, Bacteroides, Actinobacteria, Proteobacteria, Fusobacteria, and TM7, were represented. A large majority of clones belong to 13 of the 41 genera (783/900, 87%), or 14 SLOTU (574/900, 64%) that were shared by all four persons. Streptococcus (39%), Prevotella (17%), and Veilonella (14%) were most prevalent. The present study identified 56-79% of SLOTU in this bacterial ecosystem. Most SLOTU of esophageal biota are similar or identical to residents of the upstream oral biota, but the major distinction is that a large majority (82%) of the esophageal bacteria are known and cultivable. These findings provide evidence for a complex but conserved bacterial population in the normal distal esophagus.
(end quote)
A description of the 16S rRNA sequence processing can be found on the mothur-wiki
at the link below. A cutoff of 0.10 was used for OTU clustering in that example,
and it is taken here as well to create example data, esophagus, which was
easily imported with the import_mothur() function.
Author(s)
Pei et al. zhiheng.pei@med.nyu.edu
References
Pei, Z., Bini, E. J., Yang, L., Zhou, M., Francois, F., & Blaser, M. J. (2004). Bacterial biota in the human distal esophagus. Proceedings of the National Academy of Sciences of the United States of America, 101(12), 4250-4255. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384727
mothur-processed files and the sequence data can be downloaded from a zip-file, along with additional description, from the following URL: http://www.mothur.org/wiki/Esophageal_community_analysis
Examples
1 2 3 4 5 6 7 8 9 | data(esophagus)
UniFrac(esophagus, weighted=TRUE)
# How to re-create the esophagus dataset using import_mothur function
mothlist <- system.file("extdata", "esophagus.fn.list.gz", package="phyloseq")
mothgroup <- system.file("extdata", "esophagus.good.groups.gz", package="phyloseq")
mothtree <- system.file("extdata", "esophagus.tree.gz", package="phyloseq")
show_mothur_cutoffs(mothlist)
cutoff <- "0.10"
esophman <- import_mothur(mothlist, mothgroup, mothtree, cutoff)
|
Example output
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