create shared with just core microbiome

I have a dataset where I want to only keep the OTUs that are found between pairs of samples (I thought this was what get.coremicrobiome did cause I didn’t read the wiki carefully). Is there a way in mother to select only the OTUs that are shared between groups?

decided this was more an R task

otu <- read.table(file="", header=T, stringsAsFactors = FALSE)

expdata <- read.table(file="crossoverSDIplusaddldata.csv", fill=T, header=T, stringsAsFactors = FALSE, sep=",")
group.pair <- select(expdata, group, Milk.stool.pair)

otu <-  right_join(group.pair, otu, by=c("group"="Group"))

df.otu <- otu %>%
    gather(variable, value, -Milk.stool.pair) %>%  # gather the columns into 'long' format
    group_by(variable, Milk.stool.pair) %>% # group by column name and group
    summarize(keep = all(value != 0)) %>% # variables and groups where all values are non-zero
    ungroup %>% group_by(variable) %>%  # reset grouping
    summarize(keep = any(keep)) %>%  # variables where at least 1 group met the aforementioned criterion
    dplyr::filter(keep) # final list

otu.common <- otu[df.otu$variable]