Here is a hack to convert dfs/matrices to biom format to take advantage of the write_biom function

convert_to_biom.R

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#' Convert dataframe objects to biom-format \code{biom-class} objects.
#'
#' Wrapper to convert dataframe objects to \code{biom-class} objects. Currently cannot
#' create sparse biom-format objects. The user can then export their previously
#' prepared files using \code{write_biom}.
#' \href{http://biom-format.org/documentation/biom_format.html}{the
#' biom-format definition}.
#'
#' #' The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the \href{http://www.earthmicrobiome.org/}{Earth Microbiome Project} and is a \href{http://gensc.org/}{Genomics Standards Consortium} candidate project. Please see \href{http://biom-format.org/}{the biom-format home page} for more details.
#'
#' @param data (Required) Dataframe or matrix of count data.
#' @param sample_metadata Dataframe of sample metadata.
#' @param observation_metadata Dataframe of feature metadata.
#' @param id Optional identifier for the project.
#' @return An object of \code{biom-class}.
#'
#' @references \url{http://biom-format.org/}
#'
#' @example
#'
#' # randomly create a count matrix
#' set.seed(101)
#' counts = matrix(sample(100,10*10),10,10)
#' rownames(counts) = paste("feature",1:10,sep="")
#' colnames(counts) = paste("sample",1:10,sep="")
#' # create a sample_metadata df
#' class = sample(0:1,10,replace=TRUE)
#' names(class) = colnames(counts)
#' class = as.data.frame(class)
#' # create a observation_metadata df
#' features = sample(c("bacteria_a","bacteria_b","bacteria_c"),10,replace = TRUE)
#' names(features) = rownames(counts)
#' features = as.data.frame(features)
#'
#' biom_obj = convert_to_biom(counts,sample_metadata=class,observation_metadata=feature_meta)
#' # write(biom_obj,output)
convert_to_biom <- function(data,sample_metadata=NULL,observation_metadata=NULL,id=NULL){
	id = id
	format = "Biological Observation Matrix 1.0.0-dev"
	format_url = "http://biom-format.org/documentation/format_versions/biom-1.0.html"
	type = "OTU table"
	generated_by = sprintf("biom %s",packageVersion("biom"))
	matrix_type = "dense"
	matrix_element_type = "int"
	date = as.character(Sys.time())
	shape = dim(data)

	if(!is.null(observation_metadata)){
		obs_names = colnames(observation_metadata)
		rows = lapply(1:nrow(data),function(i){ll = list(
				id=rownames(data)[i],
				metadata=lapply(1:ncol(observation_metadata),function(j){
						as.character(observation_metadata[i,j])}))
				names(ll$metadata) = obs_names
				ll
				})

	} else {
		rows = lapply(1:nrow(data),function(i){list(
				id=rownames(data)[i],
				metadata=NA)})
	}
	if(!is.null(sample_metadata)){
		sample_names = colnames(sample_metadata)
		columns  = lapply(1:ncol(data),function(i){ll = list(
				id=colnames(data)[i],
				metadata=lapply(1:ncol(sample_metadata),function(j){
					as.character(sample_metadata[i,j])}))
				names(ll$metadata) = sample_names
				ll
				})

	} else {
		columns  = lapply(1:ncol(data),function(i){list(
				id=colnames(data)[i],
				metadata=NA)})
	}
	data = as.list(as.data.frame(t(data)))
	names(data) <- NULL

	biomlist = list(id=id,format=format,format_url=format_url,type=type,generated_by=generated_by,
			date=date,matrix_type=matrix_type,matrix_element_type=matrix_element_type,shape=shape,
			rows=rows,columns=columns,data=data)
	biom(biomlist)
}