I would like to estimate DE between a gene in a case and control, however, there are two underlying teams (A and B) (the experiment was run in two batches) so I would like to consider them as well. 

the data format is sth like below and I have made sure, "condition" and "team" are factor

but in reality there are 12 controls and 12 cases, which each are also split into half team A and team B

diagdds = phyloseq_to_deseq2(mydata, ~ condition + team)
diagdds = DESeq(diagdds, test="Wald", fitType="parametric")
res = results(diagdds, cooksCutoff = FALSE, contrast = c("condition", "A", "B"))
sigtab.deseq = res[which(res$padj < 0.05), ]

I wonder if the design should be sth like design = ~ condition + team 

I am not sure, if it is right, since I can see a clear distinction in my PCA between these case/control so I expected to see some significant taxa - but by adding "+ condition", there is nothing significant.

I appreciate your comments,

Hi akp, 

Please make sure both the Treatment as well as Condition variables are factor variables (using as.factor)

dds$Treatment <- as.factor(dds$Treatment)

dds$Condition <- as.factor(dds$Condition)

That makes a difference with the results! Also make sure you are calling results correctrly:

deseq2res_comparison = results(DESeq2result, contrast = c("Condition", "case", "control"))

Besides that as Ryan said, reproducible code and proper titles will help. 

Best,

Manasi