diff --git a/R/data_curation.R b/R/data_curation.R
index b58cf3c..f056c37 100644
--- a/R/data_curation.R
+++ b/R/data_curation.R
@@ -900,6 +900,11 @@
 #'   - metadata (join on genome IDs returned by BV-BRC)
 #'
 #' @param user_bacs Character vector. Mixed taxon IDs and/or species strings (used for naming).
+#' @param genome_id_file Character or NULL. Optional path to a file listing genome
+#'   IDs (one per line). If provided, genome IDs are read from this file instead of
+#'   being resolved from `user_bacs`; blank lines and surrounding whitespace are
+#'   ignored. `user_bacs` is still required for naming the per-selection DuckDB.
+#'   Default NULL.
 #' @param filter_type Character. "AMR" or "microTraits". Default "AMR".
 #' @param base_dir Character. Project root. Default "results/" in legacy scripts; now default ".".
 #' @param abx Character or vector. Antibiotic filter. "All" for all antibiotics, else names.
@@ -912,6 +917,7 @@
 #'   - table_name: "metadata"
 #' @export
 retrieveMetadata <- function(user_bacs,
+                             genome_id_file = NULL,
                              filter_type = "AMR",
                              base_dir = ".",
                              abx = "All",
@@ -920,11 +926,34 @@ retrieveMetadata <- function(user_bacs,
                              verbose = TRUE) {
   base_dir <- normalizePath(base_dir, mustWork = FALSE)
 
-  if (isTRUE(verbose)) message("Resolving genome IDs for user inputs.")
-  genome_ids <- .retrieveQueryIDs(
-    base_dir = base_dir, user_bacs = user_bacs,
-    overwrite = overwrite, verbose = verbose
-  )
+  # -------------------------------
+  # GENOME ID RESOLUTION (UPDATED)
+  # -------------------------------
+  if (!is.null(genome_id_file)) {
+    if (!file.exists(genome_id_file)) {
+      stop("Provided genome_id_file does not exist.")
+    }
+
+    if (isTRUE(verbose)) {
+      message("Using genome IDs from file: ", genome_id_file)
+    }
+
+    genome_ids <- readLines(genome_id_file, warn = FALSE)
+    genome_ids <- trimws(genome_ids)
+    genome_ids <- genome_ids[genome_ids != ""]
+  } else {
+    if (isTRUE(verbose)) message("Resolving genome IDs for user inputs.")
+
+    genome_ids <- .retrieveQueryIDs(
+      base_dir = base_dir,
+      user_bacs = user_bacs,
+      overwrite = overwrite,
+      verbose = verbose
+    )
+  }
+
+  genome_ids <- unique(as.character(genome_ids))
+
   if (length(genome_ids) == 0) {
     message("No genome IDs available for the specified inputs.")
     return(NULL)
@@ -1735,6 +1764,10 @@ genomeList <- function(base_dir = ".",
 #'
 #' @param user_bacs Character vector. Species and/or taxon IDs (e.g.
 #'   `c("Shigella flexneri", "623")`).
+#' @param genome_id_file Character or NULL. Optional path to a file listing genome
+#'   IDs (one per line), passed through to `retrieveMetadata()`. If provided, the
+#'   metadata step is restricted to these genome IDs instead of resolving them from
+#'   `user_bacs`. Default NULL.
 #' @param base_dir Character. Project root directory. Default `"."`.
 #' @param method Character. Download method passed to `retrieveGenomes()`.
 #'   `"ftp"` (default) or `"cli"`.
@@ -1751,6 +1784,7 @@ genomeList <- function(base_dir = ".",
 #'
 #' @export
 prepareGenomes <- function(user_bacs,
+                           genome_id_file = NULL,
                            base_dir = ".",
                            method = c("ftp", "cli"),
                            overwrite = FALSE,
@@ -1765,6 +1799,7 @@ prepareGenomes <- function(user_bacs,
   if (isTRUE(verbose)) message("Step 0: Building AMR metadata (retrieveMetadata)")
   invisible(retrieveMetadata(
     user_bacs = user_bacs,
+    genome_id_file = genome_id_file,
     filter_type = "AMR",
     base_dir = base_dir,
     abx = "All",
diff --git a/man/prepareGenomes.Rd b/man/prepareGenomes.Rd
index a764058..29edd07 100644
--- a/man/prepareGenomes.Rd
+++ b/man/prepareGenomes.Rd
@@ -6,6 +6,7 @@
 \usage{
 prepareGenomes(
   user_bacs,
+  genome_id_file = NULL,
   base_dir = ".",
   method = c("ftp", "cli"),
   overwrite = FALSE,
@@ -17,6 +18,11 @@ prepareGenomes(
 \item{user_bacs}{Character vector. Species and/or taxon IDs (e.g.
 \code{c("Shigella flexneri", "623")}).}
 
+\item{genome_id_file}{Character or NULL. Optional path to a file listing genome
+IDs (one per line), passed through to \code{retrieveMetadata()}. If provided, the
+metadata step is restricted to these genome IDs instead of resolving them from
+\code{user_bacs}. Default NULL.}
+
 \item{base_dir}{Character. Project root directory. Default \code{"."}.}
 
 \item{method}{Character. Download method passed to \code{retrieveGenomes()}.
diff --git a/man/retrieveMetadata.Rd b/man/retrieveMetadata.Rd
index 6c92a36..bed8547 100644
--- a/man/retrieveMetadata.Rd
+++ b/man/retrieveMetadata.Rd
@@ -6,6 +6,7 @@
 \usage{
 retrieveMetadata(
   user_bacs,
+  genome_id_file = NULL,
   filter_type = "AMR",
   base_dir = ".",
   abx = "All",
@@ -17,6 +18,12 @@ retrieveMetadata(
 \arguments{
 \item{user_bacs}{Character vector. Mixed taxon IDs and/or species strings (used for naming).}
 
+\item{genome_id_file}{Character or NULL. Optional path to a file listing genome
+IDs (one per line). If provided, genome IDs are read from this file instead of
+being resolved from \code{user_bacs}; blank lines and surrounding whitespace are
+ignored. \code{user_bacs} is still required for naming the per-selection DuckDB.
+Default NULL.}
+
 \item{filter_type}{Character. "AMR" or "microTraits". Default "AMR".}
 
 \item{base_dir}{Character. Project root. Default "results/" in legacy scripts; now default ".".}
diff --git a/tests/testthat/test-prepareGenomes.R b/tests/testthat/test-prepareGenomes.R
new file mode 100644
index 0000000..a230d49
--- /dev/null
+++ b/tests/testthat/test-prepareGenomes.R
@@ -0,0 +1,62 @@
+# Regression tests for genome_id_file handling.
+#
+# PR #29: prepareGenomes() accepted a genome_id_file argument but hardcoded
+# genome_id_file = NULL in its internal retrieveMetadata() call, so a
+# user-supplied genome list was silently ignored via the wrapper (it worked
+# only when calling retrieveMetadata() directly).
+
+test_that("prepareGenomes() forwards genome_id_file to retrieveMetadata()", {
+  captured <- new.env()
+  gfile <- tempfile(fileext = ".txt")
+  writeLines(c("511145.12", "83333.111"), gfile)
+  on.exit(unlink(gfile), add = TRUE)
+
+  # Stub everything prepareGenomes() touches so we isolate the pass-through.
+  # retrieveMetadata() records the genome_id_file it receives; .filterGenomes()
+  # returns NULL so prepareGenomes() exits cleanly right after.
+  local_mocked_bindings(
+    .ensure_bvbrc_cache = function(...) invisible(NULL),
+    retrieveMetadata = function(..., genome_id_file = NULL) {
+      captured$gid <- genome_id_file
+      invisible(NULL)
+    },
+    .filterGenomes = function(...) NULL,
+    .package = "amRdata"
+  )
+
+  res <- prepareGenomes(
+    user_bacs = "Shigella flexneri",
+    genome_id_file = gfile,
+    verbose = FALSE
+  )
+
+  expect_null(res)
+  # Before the fix this was NULL (the bug); now it is the file path.
+  expect_identical(captured$gid, gfile)
+})
+
+test_that("retrieveMetadata() errors on a missing genome_id_file", {
+  missing <- file.path(tempdir(), "definitely_not_here_9f8a.txt")
+  expect_error(
+    retrieveMetadata(
+      user_bacs = "x",
+      genome_id_file = missing,
+      verbose = FALSE
+    ),
+    "does not exist"
+  )
+})
+
+test_that("genome_id_file parsing trims whitespace and drops blank lines", {
+  # Mirrors the readLines/trimws/drop-empty/unique logic in retrieveMetadata().
+  gfile <- tempfile(fileext = ".txt")
+  writeLines(c("511145.12", "  83333.111  ", "", "   ", "511145.12"), gfile)
+  on.exit(unlink(gfile), add = TRUE)
+
+  ids <- readLines(gfile, warn = FALSE)
+  ids <- trimws(ids)
+  ids <- ids[ids != ""]
+  ids <- unique(as.character(ids))
+
+  expect_identical(ids, c("511145.12", "83333.111"))
+})