If the number of individuals within a species is fairly constant throughout the community it has a high evenness. Evenness is the proportion of species or functional groups present on a site. The bacteria population can be quite different from one site to another when you compare gut content and gut wall. I know that working with molecular biology is expensive, but if possible, I suggest you try using repetitions to confirm whether or not it was a noise.First thigh you should do is to check, using rarefaction curves, how much your microbiota has been represented in your 16S dataset.
Many of these points are touched on in the this thread. USDA-ARS, Grassland, … A steep gradient indicates low evenness as the high-ranking species have much higher abundances than the low-ranking species. I am not sure if FISH is feasible for you samples. We show on metagenomics benchmarks that it outperforms the state-of-the-art methods...Join ResearchGate to find the people and research you need to help your work.© 2008-2020 ResearchGate GmbH.
Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. In some papers, the term “species richness” is used in the title and in the text it is assumed to mean the number of species, but this may not be made clear.
Given the Shannon index, diversity is a plain number which accounts for both the total number of species within your sample and their abundance.
Btw: This is a good example how singletons can influence your community metrics.One important caveat to keep in mind when dealing with 16S data is that it can be severely skewed by 16S gene copy number in the genomes. Therefore I thought there is actually no need for individuals to be even on a community.
As an example, in two theoretical communities A and B, both with the same species richness (Despite a difference in proportion of all three species Nevertheless, from the species richness point of view, both communities appear perfectly alike; there should definitely be supportive statements coming from calculations of advanced diversity indices.As a real example of applying species richness indices in environmental monitoring, Olawusi-Peters and Ajibare studied shellfish (Crustacea) communities in Nigeria to evaluate the degree of human-induced impact on marine ecosystems. Species abundance is the number of individuals per species, and relative abundance refers to the evenness of distribution of individuals among species in a community.
But the actual index is dependent on the distribution. qPCR and 16S rDNA pyrosequencing are two different techniques.
In that observed OTUs are more in control individuals but Shannon index is significantly higher in diseased persons. And the primers for qPCR may generate more bias, especially when we facing environmental samples.
The dominance of one OTU may be true but we also need to consider the possibility of primer bias. Do you intend to verify bacteria attached to gut mucosae? k Another issue is DNA extraction bias.
At the same time, Phylogenetic diversity (PD_whole_tree) calculated in qiime is higher in control individuals.
You can envision this in an ecological context as well. That means that 16S data often agrees very poorly with more reliable estimates of species abundance based on shotgun metagenomics, or even FISH analysis.I came across this discrepancy in my own work on compost derived enrichment cultures, and showed that correcting for expected 16S gene copy number can correct for this bias (see Kembel SW, Wu M, Eisen JA, Green JL. Search for more papers by this author. We show on metagenomics benchmarks that it outperforms state-of-the-art methods in t...We propose a new model for fast classification of DNA sequences output by next-generation sequencing machines. You may also look at the microdiversity within this OTU and see whether the differences occur in the hypervariable regions only and if so, whether these are common to operons (something which Patrik suggested above).We have used this approach to look at OTUs that get selected in certain soil types and not others.
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