1 Eli MEtchnikoff

microbome祖师爷.

2 Phylogenetics of organisms

核糖体RNA (rRNA)功能非常重要,可以将RNA变为蛋白质.序列非常保守.在所有生物种很相似.所以可以用来比较其序列来确定进化的依据.

rRNA tree based.

16S ribosomal RNA structure. (细菌)

二级结构是预测出来的.

RNA不稳定,所以一般都是测DNA.

The collective genomes of soil microflora. metagenome.

3 The human Microbiome Project

300 healthy participants.

Utilize next generation sequencing

what is normal microbome?

https://www.hmpdacc.org/ihmp/

16S and sequencing.

Targeted sequening 16S rna

16S只能知道是什么菌.但是whole genome知道所有的基因的功能.

Taxa.

97 % similiary is one OTU (Operate Taxonomy Unit)

Operational Taxonomic Unit (OPT)

MetaHIT

929 reference genomes.

k-mers

Challenge:

Metagenomics classification

跟已知的数据库进行对比.

HUMAnN 2.0 pipeline