Taxonomical composition
1 How did the taxonomical composition evolve over time?
2 Were there local differences in taxonomical composition?
3 How does rarity based abundance change over time?
We pick up again the concept of rarity previously exposed in Amplicon Sequence Variants.
4 How does taxonomic composition change based on rarity?
4.1 How did rarity based taxonomical composition change over time?
5 Did we find bacteria of human origin (BHO)?
Yes! Bacterial species first isolated from the human gastrointestinal track or other bodily fluids are considered of human origin. The most well-known of which is Escherichia coli, although there are many more species of bacteria living inside our bodies.
| Species | Reference |
|---|---|
| Alistipes indistinctus | Nagai et al. (2010) |
| Alistipes onderdonkii | Sakamoto et al. (2020) |
| Alistipes timonensis | Lagier et al. (2012) |
| Bacteroides dorei | Bakir et al. (2006) |
| Bacteroides vulgatus | Eggerth and Gagnon (1933) |
| Bacteroides thetaiotaomicron | Cato and Johnson (1976) |
| Bacteroides stercoris | Johnson, Moore, and Moore (1986) |
| Bacteroides plebeius | Kitahara et al. (2005) |
| Bacteroides coprocola | Kitahara et al. (2005) |
| Bacteroides eggerthii | Holdeman and Moore (1974) |
| Butyricicoccus faecihominis | Takada et al. (2016) |
| Coprobacter fastidiosus | Shkoporov et al. (2013) |
| Escherichia-Shigella coli | Devanga Ragupathi et al. (2018) |
| Intestinimonas timonensis | Durand et al. (2017) |
| Intestinimonas butyriciproducens | Kläring et al. (2013) |
| Parabacteroides merdae | Sakamoto and Benno (2006) |
| Porphyromonas asaccharolytica | Shan and Collins (1988) |
| Prevotella bivia | Shan and Collins (1990) |
| Prevotella disiens | Shan and Collins (1990) |
| Prevotella buccalis | Shan and Collins (1990) |
| Prevotella amnii | Lawson, Moore, and Falsen (2008) |
5.1 Where were BHO detected? When?
5.2 Are there compositional differences between samples based on the presence of BHO?
References
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