The use of the 16S rDNA sequence has been a valuable tool for evaluating the microbiome of a great many environments.
Use of pyrosequencing in microbiome studies.
www.MRDNAlab.com Where you can get 16S pyrosequencing, metagenome, fungal diversity, protozoan diversity.
MICROBIOME all kinds of fun
Check out all the national and international sites:
Such as the Canadian Microbiome Initiative
The International Human Microbiome Consortium
The goal of the IMHC is to work under a common set of principles and policies to study and understand the role of the human microbiome in the maintenance of health and causation of disease and to use that knowledge to improve the ability to prevent and treat disease. The Consortium’s efforts are focused on generating a shared comprehensive data resource that will enable investigators to characterize the relationship between the composition of the human microbiome (or of parts of the human microbiome) and human health and disease.
The IHMC is open, at any time, to the funders and PIs of human microbiome research programs that have the capacity to mount a comprehensive analysis of the human microbiome in health and/or disease, and that agree to carry out their efforts according to a set of commonly agreed-upon IHMC policies (see Principles in the Membership section).
The principles, structure and operating modes of the IHMC were defined progressively through several meetings organised since November 2005 (see Historical perspective and previous meetings). The IHMC was officially launched at its meeting held in Heidelberg on October 15-16 2008.
Human Microbiome Project
The HMP roadmap initiative calls for the development of new tools & technologies, informatics capabilities and resources needed for the advancement of the field of metagenomics. The data sets produced by metagenomic sequencing and related components will be very large and complex, requiring novel analytical tools for distilling useful information from vast amounts of sequence data, functional genomic data and subject metadata.
As well, whole genome sequencing technologies are currently limited to the relatively small class of microbes that can be cultured. In order to maximize the number of sequences available in the reference set, new techniques must be developed to culture or otherwise isolate for analysis currently unculturable organisms. In the long-term, methods for sequencing individual microbes or otherwise analyzing all of the members of complex populations will substantively advance this field.
Resources for generating your own microbiome data
Pyrosequencing 454 service provider, illumina, and ion torrent
MR DNA LAB http://www.mrdnalab.com is a great low cost pyrosequencing provider. As a Research laboratory they understand that fellow scientists needs are important. Dr. Scot E Dowd is fun to work with and as crazy busy as he is manages to help out students, scientists, and anyone. It is great to have a personal touch when obtaining pyrosequencing for microbial diversity studies.
Tools for analysis
DNAclust is a fast clustering algorithm specifically designed for high-stringency clustering of DNA sequences, e.g. for 16S rRNA analyses or removal of duplicates/near duplicates in high-throughput shotgun datasets.
A GUI software package designed for non-statisticians to perform multivariate analysis
A toolkit for rapid development of custom software packages for visualization and analysis of large datasets
Metastats is a statistical package for comparing metagenomicdata-sets. Metastats was specifically designed for comparing clinical data comprising two treatment populations (e.g. sick vs. healthy) each comprising multiple samples, however thesoftware will also work for small number of samples. Metastats identifies features of the samples that "explain" the difference between the treatment populations. The features can be OTUs (e.g. inferred from 16S data), taxonomic groups, or other groupings (genes, functional groups, etc.) for which count data are available. Metastats primarily relies on a non-parametric t-test and reverts to Fisher's exact test for sparse features. Additional tests (presence/absence, odds ratios, etc.) are currently being implemented. Metastats is available as a web service, as standalone R and C code, as well as part of the Mothur package.
|MicrobiomeUtilities A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology|
A platform-independent software package for describing and comparing microbial communities. Mothur incorporates the functionality of a number of computational tools, calculators & visualization tools into a single program
'Quantitative Insight Into Microbial Ecology'. Qiime allows a range of community analyses suitable for microbiome data using traditional and high-throughput sequencing methods
A rapid and sensitive general-purpose k-mer search tool
A package for speciation of 16S sequences
A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample
Provides a suite of tools for the comparison of microbial communities using phylogenetic information
A 16S rRNA gene database and workbench compatible with ARB
Provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial and Archaeal small-subunit 16S rRNA sequences
SitePainter allows users to visualize the different HMP body sites based on gradients of colors to represent available datasets
|Manual of Procedures (MOP) A reference document for current National Institutes of Health (NIH) policies and procedures as they apply to the Human Microbiome Project (HMP) Core Microbiome Sampling study|
|Core Microbiome Sampling Protocol|
|16S Data Flow for HMP Sequencing Centers Guidelines for the HMP sequencing Centers for submitting 16S rRNA gene data and metadata to the HMP DACC|
|Provisional 16S 454 Protocol|
|Primer name||Sequence (5'-3')|
|B27F||AGA GTT TGA TCC TGG CTC AG|
|U1492R||GGT TAC CTT GTT ACG ACT T|
|928F||TAA AAC TYA AAK GAA TTG ACG GG|
|336R||ACT GCT GCS YCC CGT AGG AGT CT|
|1100F||YAA CGA GCG CAA CCC|
|1100R||GGG TTG CGC TCG TTG|
|337F||GAC TCC TAC GGG AGG CWG CAG|
|907R||CCG TCA ATT CCT TTR AGT TT|
|785F||GGA TTA GAT ACC CTG GTA|
|805R||GAC TAC CAG GGT ATC TAA TC|
|533F||GTG CCA GCM GCC GCG GTA A|
|518R||GTA TTA CCG CGG CTG CTG G|
RTL also offers free and fee for service bioinformatics services including biostatistics