Hi everyone, i performed a 16s rRNA analysis for studying the intestinal microbiome of mice and assess the effect of chronic and metabolic stress in mices. Also i’ taking in consideration the sex.

I have 17 samples:

- Control Group: 3 males(CM) and 3 females (CH)

*Group expossed to chronic stress: 3 males (EM) and 3 females (EH)

*Group for Metabolic stress: 3 males (DM) and 2 females (DH)

And, for assessing effect of the treatments, a teacher suggest me for an ANOVA analysis.

I followed the MiSeq SOP. So i got my distance matrix from the follow code :

mothur > dist.shared(shared=final.opti_mcc.shared)

My design file are in the format .tsv.

It was correct to use this files?

this is what i obtained comparing treatments (control x Stress x Metabolic stress) :

Ctl-Dta-Est Among Within Total

SS 0.892772 5.3959 6.28867

df 2 14 16

MS 0.446386 0.385421

Fs: 1.15818

p-value: 0.003*

Ctl-Dta Among Within Total

SS 0.463626 3.49937 3.96299

df 1 9 10

MS 0.463626 0.388819

Fs: 1.1924

p-value: 0.022

Ctl-Est Among Within Total

SS 0.460655 3.87668 4.33733

df 1 10 11

MS 0.460655 0.387668

Fs: 1.18827

p-value: 0.025

Dta-Est Among Within Total

SS 0.413579 3.41576 3.82934

df 1 9 10

MS 0.413579 0.379528

Fs: 1.08972

p-value: 0.096

What does that abbreviations means… SS, df , MS and Fs ? These results are enough to prove a hypothesis?

I’ve seen from another methods (for example, Rstudio) that i need a Fstat file, or a genind file with my samples information. It is posible to obtain these files from Mothur?

Thanks!