Greengenes 13_8 Download: A Comprehensive Guide for Microbial Ecology Research
Microbial ecology is the study of the interactions of microorganisms with their environment, each other, and plant and animal species. It includes the study of symbioses, biogeochemical cycles, microbial diversity, and evolution. Microbial ecology is a rapidly growing field that has many applications in environmental science, biotechnology, medicine, agriculture, and more.
One of the key challenges in microbial ecology research is to identify, characterize, and compare the microbial communities that inhabit different habitats and ecosystems. To do this, researchers often rely on marker gene sequencing, such as 16S rRNA gene sequencing, which is a widely used method to profile the taxonomic composition and phylogenetic relationships of bacterial and archaeal communities.
greengenes 13_8 download
However, marker gene sequencing requires a reliable reference database that contains curated sequences and taxonomies of known microorganisms. A reference database is essential for assigning taxonomic names to the sequences obtained from environmental samples, as well as for performing phylogenetic analysis and diversity estimation.
One of the most popular and comprehensive reference databases for microbial ecology research is greengenes, which is a full-length 16S rRNA gene database that provides a curated taxonomy based on de novo tree inference. Greengenes was first developed in 2006 by DeSantis et al. and has been updated several times since then. The latest version of greengenes is greengenes 13_8, which was released in August 2013 and contains 202,421 bacterial and archaeal sequences.
In this article, we will provide a detailed guide on how to download and use greengenes 13_8 database for microbial ecology research. We will also show you how to use QIIME, which is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed . QIIME is one of the most widely used tools for analyzing microbial communities using greengenes 13_8 data.
How to download and use greengenes 13_8 database
Before you can use greengenes 13_8 database for your microbial ecology analysis, you need to download it from one of the available sources and formats. You also need to have some prerequisites and requirements for downloading and using greengenes 13_8 database.
Prerequisites and requirements
To download and use greengenes 13_8 database, you need to have:
A computer with enough storage space (at least 10 GB) and memory (at least 4 GB)
A stable internet connection
A web browser that supports downloading large files (such as Chrome, Firefox, or Safari)
A software that can extract compressed files (such as 7-Zip, WinRAR, or Unzip)
A software that can read and edit text files (such as Notepad, WordPad, or TextEdit)
A software that can run QIIME scripts and commands (such as Python, Anaconda, or Miniconda)
If you do not have these prerequisites and requirements, you need to install them before proceeding to the next steps.
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How to download greengenes 13_8 database from different sources and formats
Greengenes 13_8 database is available for download from different sources and formats. Depending on your preference and needs, you can choose one of the following options:
Source
Format
Description
Size
URL
Greengenes website
FASTA
A plain text file that contains the nucleotide sequences of the 16S rRNA genes in greengenes 13_8 database. Each sequence has a unique identifier and a taxonomic annotation.
1.2 GB
(
Greengenes website
Newick
A plain text file that contains the phylogenetic tree of the 16S rRNA genes in greengenes 13_8 database. The tree is based on a multiple sequence alignment and a maximum likelihood inference.
1.1 GB
(
QIIME website
Greengenes formatted files
A set of files that are formatted for QIIME analysis. They include a FASTA file, a Newick file, a taxonomy file, and a representative set file. The taxonomy file contains the taxonomic annotations of the sequences in greengenes 13_8 database. The representative set file contains a subset of sequences that represent each operational taxonomic unit (OTU) in greengenes 13_8 database.
2.5 GB
(
Zenodo website
QIIME2 artifact
A binary file that contains the greengenes 13_8 database formatted for QIIME2 analysis. It includes a feature table, a feature data, and a phylogeny data. The feature table contains the counts of sequences per sample and per OTU in greengenes 13_8 database. The feature data contains the taxonomic annotations of the OTUs in greengenes 13_8 database. The phylogeny data contains the phylogenetic tree of the OTUs in greengenes 13_8 database.
1.9 GB
(
To download greengenes 13_8 database from any of these sources and formats, you need to follow these steps:
Click on the URL of your chosen source and format.
Save the file to your computer.
Extract the file using your preferred software.
Rename and move the file to your desired location.
Open and edit the file using your preferred software.
How to use greengenes 13_8 database with QIIME
QIIME is a powerful and versatile tool for analyzing microbial communities using greengenes 13_8 data. QIIME can perform various tasks such as quality control, OTU picking, taxonomic assignment, phylogenetic inference, diversity analysis, statistical testing, and visualization.
To use greengenes 13_8 database with QIIME, you need to follow these steps:
Install QIIME on your computer using one of the available methods . You can use either QIIME1 or QIIME2 depending on your preference the greengenes 13_8 database as your reference database using the parameter -t gg_13_8_otus/trees/99_otus.tree if you want to use phylogenetic metrics. This script will generate a text file that contains the alpha diversity values for each sample.
beta_diversity.py: This script calculates various beta diversity metrics for each pair of samples in your dataset using different methods, such as Bray-Curtis, Jaccard, UniFrac, etc. You can specify the greengenes 13_8 database as your reference database using the parameter -t gg_13_8_otus/trees/99_otus.tree if you want to use phylogenetic metrics. This script will generate a distance matrix file that contains the beta diversity values for each pair of samples.
How to generate interactive and informative visualizations using greengenes 13_8 data
Visualizations are useful for exploring, summarizing, and communicating your greengenes 13_8 data and results. Visualizations can help you to identify patterns, trends, outliers, and relationships in your data and results. Visualizations can also help you to present and share your findings with others in an attractive and understandable way.
To generate interactive and informative visualizations using greengenes 13_8 data, you can use the following QIIME scripts or commands:
make_emperor.py: This script creates an interactive 3D plot of your samples based on their beta diversity values. You can choose different axes, colors, shapes, and sizes to represent different variables in your data. You can also rotate, zoom, and pan the plot to explore different perspectives. This script will generate an HTML file that contains the interactive 3D plot.
make_otu_heatmap.py: This script creates a heatmap of your samples based on their OTU table values. You can choose different colors, scales, and clustering methods to represent different aspects of your data. You can also hover over the cells to see the OTU IDs and counts. This script will generate an HTML file that contains the heatmap.
summarize_taxa_through_plots.py: This script creates a series of bar plots of your samples based on their taxonomic composition at different levels. You can choose different colors, labels, and sorting methods to represent different features of your data. You can also click on the bars to see the taxonomic names and percentages. This script will generate an HTML file that contains the bar plots.
make_phylogeny.py: This script creates a phylogenetic tree of your OTUs based on their greengenes 13_8 database sequences. You can choose different colors, labels, and branch lengths to represent different attributes of your data. You can also click on the nodes to see the OTU IDs and taxonomic annotations. This script will generate an HTML file that contains the phylogenetic tree.
Conclusion
In this article, we have provided a comprehensive guide on how to download and use greengenes 13_8 database for microbial ecology research. We have also shown you how to use QIIME, which is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
We have covered the following topics:
What is greengenes 13_8 download and why is it useful for microbial ecology research?
What are the main features and advantages of greengenes 13_8 download?
How to download and use greengenes 13_8 database from different sources and formats?
How to use greengenes 13_8 database with QIIME?
How to interpret and visualize greengenes 13_8 data?
We hope that this article has helped you to understand and appreciate the value of greengenes 13_8 download and QIIME for microbial ecology research. We also hope that this article has inspired you to explore and analyze your own microbial communities using these tools.
If you want to learn more about greengenes 13_8 download and QIIME, here are some tips and resources for further learning and exploration:
Visit the official websites of greengenes and QIIME for more information, documentation, tutorials, and support.
Read the original publications of greengenes and QIIME for more details, methods, and results.
Join the online communities of greengenes and QIIME for more discussions, questions, and answers.
Explore the online repositories of greengenes and QIIME for more data, code, and examples.
Follow the latest news and updates of greengenes and QIIME on social media, such as Twitter, Facebook, and YouTube.
FAQs
Here are some frequently asked questions about greengenes 13_8 download and QIIME:
What are some alternative databases to greengenes 13_8 for microbial ecology research?
Some alternative databases to greengenes 13_8 for microbial ecology research are:
SILVA: A comprehensive database of quality checked and aligned ribosomal RNA (rRNA) sequences from the Bacteria, Archaea and Eukarya domains .
RDP: A curated database of aligned 16S rRNA gene sequences and associated taxonomic information from Bacteria and Archaea .
EZBioCloud: A web-based platform that provides integrated access to various microbiological resources, such as 16S rRNA gene sequences, genomes, metagenomes, and taxonomies .
How to update greengenes 13_8 database with new sequences and taxonomies?
To update greengenes 13_8 database with new sequences and taxonomies, you need to follow these steps:
Download the latest version of greengenes 13_8 database from the greengenes website .
Download the new sequences and taxonomies that you want to add to the greengenes 13_8 database from other sources, such as NCBI , GenBank , or EMBL .
Format the new sequences and taxonomies according to the greengenes 13_8 database specifications .
Merge the new sequences and taxonomies with the existing greengenes 13_8 database using a software such as MOTHUR , VSEARCH , or USEARCH .
Rebuild the phylogenetic tree of the updated greengenes 13_8 database using a software such as FastTree , RAxML , or ClustalW .
How to deal with intragenomic variation and chimeras in greengenes 13_8 data?
Intragenomic variation refers to the presence of multiple copies of the same gene within a single genome that differ in their nucleotide sequences. Chimeras refer to the artificial sequences that result from the erroneous joining of two or more different sequences during PCR amplification or sequencing. Both intragenomic variation and chimeras can introduce noise and bias in greengenes 13_8 data and affect the accuracy and reliability of microbial ecology analysis.
To deal with intragenomic variation and chimeras in greengenes 13_8 data, you need to follow these steps:
Detect and remove chimeric sequences from your samples using a software such as UCHIME , VSEARCH , or USEARCH .
Detect and remove intragenomic variants from your samples using a software such as DADA2 , Deblur , or UNOISE .
Pick OTUs from your samples using a software such as UCLUST , VSEARCH , or USEARCH .
Assign taxonomy to your OTUs using a software such as BLAST , RDP , or SortMeRNA .
Perform phylogenetic analysis and diversity estimation using your OTUs using a software such as QIIME , MOTHUR , or Phyloseq .
How to compare greengenes 13_8 data with other sources of microbial data, such as metagenomics or metatranscriptomics?
Metagenomics is the study of the collective genomes of microorganisms in an environmental sample. Metatranscriptomics is the study of the collective transcripts of microorganisms in an environmental sample. Both metagenomics and metatranscriptomics can provide complementary information to greengenes 13_8 data, such as functional genes, metabolic pathways, gene expression, etc.
To compare greengenes 13_8 data with other sources of microbial data, such as metagenomics or metatranscriptomics, you need to follow these steps:
Download or generate metagenomic or metatranscriptomic data from your samples using a software such as MG-RAST , MetaPhlAn , or KEGG .
Process and annotate your metagenomic or metatranscriptomic data using a software such as HUMAnN , MetaCyc , or eggNOG .
Integrate and compare your greengenes 13_8 data with your metagenomic or metatranscriptomic data using a software such as QIIME2 , STAMP , or LEfSe .
How to cite greengenes 13_8 database and QIIME in academic publications?
If you use greengenes 13_8 database and QIIME in your academic publications, you need to cite them properly and acknowledge their authors and contributors. Here are some examples of how to cite greengenes 13_8 database and QIIME in different citation styles:
APA style: DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., ... & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and environmental microbiology, 72(7), 5069-5072. Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., ... & Huttley, G. A. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature methods, 7(5), 335-336.
MLA style: DeSantis, Todd Z., et al. "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB." Applied and environmental microbiology 72.7 (2006): 5069-5072. Caporaso, J. Gregory, et al. "QIIME allows analysis of high-throughput community sequencing data." Nature methods 7.5 (2010): 335-336.
Chicago style: DeSantis, Todd Z., Philip Hugenholtz, Noriko Larsen, Mireya Rojas, Eliza L. Brodie, Kristine Keller, Torben Nielsen et al. "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB." Applied and environmental microbiology 72, no. 7 (2006): 5069-5072. Caporaso, J. Gregory, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D. Bushman, Elizabeth K. Costello et al. "QIIME allows analysis of high-throughput community sequencing data." Nature methods 7, no. 5 (2010): 335-336.
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