diff --git a/q2_types/per_sample_sequences/_methods.py b/q2_types/per_sample_sequences/_methods.py
index a5d37740..7ebd80d6 100644
--- a/q2_types/per_sample_sequences/_methods.py
+++ b/q2_types/per_sample_sequences/_methods.py
@@ -36,7 +36,9 @@ def partition_sample_data_mags(
     for i, samples in enumerate(arrays_of_mags, 1):
         result = MultiMAGSequencesDirFmt()
         all_samples = set(k for d in samples for k in d.keys())
-        manifest = pd.read_csv(mags.path / "MANIFEST", index_col=None)
+        manifest = pd.read_csv(
+            mags.path / "MANIFEST", index_col=None, dtype=str
+        )
         manifest = manifest[manifest["sample-id"].isin(all_samples)]
         manifest.to_csv(result.path / "MANIFEST", index=False)
 
diff --git a/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/24dee6fe-9b84-45bb-8145-de7b092533a1.fasta b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/24dee6fe-9b84-45bb-8145-de7b092533a1.fasta
new file mode 100644
index 00000000..c072c82b
--- /dev/null
+++ b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/24dee6fe-9b84-45bb-8145-de7b092533a1.fasta
@@ -0,0 +1,4 @@
+>NZ_00000000.1_contig1
+ATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATGTTTCCAGATGCAATGCGTGGGCACTGATG
+>NZ_00000000.1_contig2
+TTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGAAAACCATGCAGTGTTGACGTCAGTGA
diff --git a/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/fb0bc871-04f6-486b-a10e-8e0cb66f8de3.fasta b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/fb0bc871-04f6-486b-a10e-8e0cb66f8de3.fasta
new file mode 100644
index 00000000..e5910508
--- /dev/null
+++ b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/12345/fb0bc871-04f6-486b-a10e-8e0cb66f8de3.fasta
@@ -0,0 +1,4 @@
+>NZ_CP018863.1_contig1
+GCCTCCTCCCAGTTCGTCTCAGCGCTGCTGCTGGTCGGCGCCAAATTCCGTAACGGGCTGCACCTCGAACATTCCGGCCAGAGCGTCCCCAGCCTGGACCACGTTGCCATGACCGTGGCGGTACTGCGCAGCGTCGGGGTGGAGGTAGACGATTCCCGGCAGAACCACTGGTGGTCCGGCCCGGACCGGTCAAGGCCTTCGACGTCACCGTCGAACAGGACCTTTCCAATGCCGGCCCCTTCCTCGCGGCAGCCCTGGCCACGAAGGGAACGGTTCGGATCCCAGGCTGGCCGGAGAAAACCACGCAGGTAGGTGACAAATGGCGCAGCATCCTGGCGCAACTCGGCGCCACTGTCAGCTACGAGAACGGCACCCTCACCGTAACCGGCGGGGCAGAGATCACCGGGGCGCAGCTCGCCGACACCAGCGAACTTGCCCCCACCACGGCGGCGCTCTGTGCCCTGGCCGGCAGCGAATCCAGGCTCACCGGAATTGCCCACTTGCGGGGACACGAAACAGACCGGCTGGCGGCTCTGGTCGCGGAAATCAATGCCTTGGGTGGCGACGCCGAAGAAACCGAAGACGGGTTGATCATCCGTCCGAGGCCACTGCATGGCGGGGTCTTCCATTCATATGAGGACCACAGGATGGCCACCGCCGGAGCCATTATCGGGCTGGCAGTCGAGGGCGTGGAAGTCGAAGACATCGGCACCACGGCCAAGACCATGCCCGAGTTCCCGCGGCTATGGCAGGACCTGTTCGAGACTTCCGTCCGCCAGTCCGAGGCGGGAGCGCTCTAAGGTGGTGCGCGGCAACCGTACGTGGGACGAGTCCGATGTCCGCATCCGTCCCAACAAGCGCGGCTCGCGTCCGCGTACCAAGGAACGGCCTGCCCACGAAGACGCCGTCATCGGGCGGATCATCACCGTGGACCGCGGCCGCTACACCGCGGTCGTCGATGAAGACACTGCCCGGGAACGGGTGGTTGTCGCCGCCCGTG
+>NZ_CP018863.1_contig2
+CCCGGGAGCTTCGTCGCAGTCCGGTGGTGGCCGGCGACTTCGTAGCGCTCGTCGGTGACATTACCGGTGAGCCGGATACGTTGGCCCGGCTGGTCCGGATTGAGGAACGCCGGACGCTGTTGCGCCGCAGCGCCGACGATACAGATCCCGTGGAGCGGGTAGTCGTCGCCAATGCAGACCAGCTGGTCATCGTCGTGGCCGCCGCAAACCCCGAGCCGCGCACCGGTTTCATCGACCGCGCCTTGGTAGCGGCGTACGACGCCGGTATCAGCCCGCTGCTGTGCGTCACCAAAGCGGACGTCAAGGATCCCGAAGAACTGCTCTCCAACTACCGGCACCTGGACCTGCCCGTGATCGTCAGCCGGACGGCCGGCACGGAGGGCTCCGGGGTGGATGCACGGTCCGCCGACGGGCTGTCTGCCCGTCTCGACCGTGACGCCGTAGCGGCGCTCCGTGGCTATCTGGATGGGATGGTCAGCGTCATGCTCGGCCATTCGGGCGTGGGCAAGTCCACCATGGTCAATGCCCTCACGGGGGCGGAGCGCGCCACGGGGGGAGTCAACGCGGTGACCGGGCGGGGCCGGCATACCTCCTCCTCGGCGCTGGCCCTGAAGCTGGCCGACGCTCCGGCTGGCAGCTGGATCATCGACACGCCCGGCATCCGTTCTTTTGGACTGGCCCACGTGGACCCGGACCGGATCATTTCCGCTTTTCCCGATTTGGAGCCCGGGACGGCGGACTGCGAGCGGGGCTGCAAGCACGACGACCATGCCGTCAACTGCGGCGTGGACGCCTGGGTGGCCTCCGGGCAGGCCGGCGAATCCGGCCCGGCACGGCTGGCCTCGCTGCGCCGTTTGCTGGGAACGGAAGAACGCGCCCAGGCGAAGGAACTCGGGTTCCAGTAGCACCGCCGTCGTCGGTCAGGGACTTCACATCCCGCATCCGGCCGCCAAATAAGGATAAGTTGAAGCCTATGACCCGTGACGTTCAAAGCTATAAC
diff --git a/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/67890/d65a71fa-4279-4588-b937-0747ed5d604d.fasta b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/67890/d65a71fa-4279-4588-b937-0747ed5d604d.fasta
new file mode 100644
index 00000000..b2330298
--- /dev/null
+++ b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/67890/d65a71fa-4279-4588-b937-0747ed5d604d.fasta
@@ -0,0 +1,6 @@
+>NZ_CP018863.1_contig1
+GCCTCCTCCCAGTTCGTCTCAGCGCTGCTGCTGGTCGGCGCCAAATTCCGTAACGGGCTGCACCTCGAACATTCCGGCCAGAGCGTCCCCAGCCTGGACCACGTTGCCATGACCGTGGCGGTACTGCGCAGCGTCGGGGTGGAGGTAGACGATTCCCGGCAGAACCACTGGTGGTCCGGCCCGGACCGGTCAAGGCCTTCGACGTCACCGTCGAACAGGACCTTTCCAATGCCGGCCCCTTCCTCGCGGCAGCCCTGGCCACGAAGGGAACGGTTCGGATCCCAGGCTGGCCGGAGAAAACCACGCAGGTAGGTGACAAATGGCGCAGCATCCTGGCGCAACTCGGCGCCACTGTCAGCTACGAGAACGGCACCCTCACCGTAACCGGCGGGGCAGAGATCACCGGGGCGCAGCTCGCCGACACCAGCGAACTTGCCCCCACCACGGCGGCGCTCTGTGCCCTGGCCGGCAGCGAATCCAGGCTCACCGGAATTGCCCACTTGCGGGGACACGAAACAGACCGGCTGGCGGCTCTGGTCGCGGAAATCAATGCCTTGGGTGGCGACGCCGAAGAAACCGAAGACGGGTTGATCATCCGTCCGAGGCCACTGCATGGCGGGGTCTTCCATTCATATGAGGACCACAGGATGGCCACCGCCGGAGCCATTATCGGGCTGGCAGTCGAGGGCGTGGAAGTCGAAGACATCGGCACCACGGCCAAGACCATGCCCGAGTTCCCGCGGCTATGGCAGGACCTGTTCGAGACTTCCGTCCGCCAGTCCGAGGCGGGAGCGCTCTAAGGTGGTGCGCGGCAACCGTACGTGGGACGAGTCCGATGTCCGCATCCGTCCCAACAAGCGCGGCTCGCGTCCGCGTACCAAGGAACGGCCTGCCCACGAAGACGCCGTCATCGGGCGGATCATCACCGTGGACCGCGGCCGCTACACCGCGGTCGTCGATGAAGACACTGCCCGGGAACGGGTGGTTGTCGCCGCCCGTG
+>NZ_CP018863.1_contig2
+CCCGGGAGCTTCGTCGCAGTCCGGTGGTGGCCGGCGACTTCGTAGCGCTCGTCGGTGACATTACCGGTGAGCCGGATACGTTGGCCCGGCTGGTCCGGATTGAGGAACGCCGGACGCTGTTGCGCCGCAGCGCCGACGATACAGATCCCGTGGAGCGGGTAGTCGTCGCCAATGCAGACCAGCTGGTCATCGTCGTGGCCGCCGCAAACCCCGAGCCGCGCACCGGTTTCATCGACCGCGCCTTGGTAGCGGCGTACGACGCCGGTATCAGCCCGCTGCTGTGCGTCACCAAAGCGGACGTCAAGGATCCCGAAGAACTGCTCTCCAACTACCGGCACCTGGACCTGCCCGTGATCGTCAGCCGGACGGCCGGCACGGAGGGCTCCGGGGTGGATGCACGGTCCGCCGACGGGCTGTCTGCCCGTCTCGACCGTGACGCCGTAGCGGCGCTCCGTGGCTATCTGGATGGGATGGTCAGCGTCATGCTCGGCCATTCGGGCGTGGGCAAGTCCACCATGGTCAATGCCCTCACGGGGGCGGAGCGCGCCACGGGGGGAGTCAACGCGGTGACCGGGCGGGGCCGGCATACCTCCTCCTCGGCGCTGGCCCTGAAGCTGGCCGACGCTCCGGCTGGCAGCTGGATCATCGACACGCCCGGCATCCGTTCTTTTGGACTGGCCCACGTGGACCCGGACCGGATCATTTCCGCTTTTCCCGATTTGGAGCCCGGGACGGCGGACTGCGAGCGGGGCTGCAAGCACGACGACCATGCCGTCAACTGCGGCGTGGACGCCTGGGTGGCCTCCGGGCAGGCCGGCGAATCCGGCCCGGCACGGCTGGCCTCGCTGCGCCGTTTGCTGGGAACGGAAGAACGCGCCCAGGCGAAGGAACTCGGGTTCCAGTAGCACCGCCGTCGTCGGTCAGGGACTTCACATCCCGCATCCGGCCGCCAAATAAGGATAAGTTGAAGCCTATGACCCGTGACGTTCAAAGCTATAAC
+>NZ_CP018863.1_contig3
+GACGATCTGCGCCTGGCCCATGTGATGGCCGATTCCGTGGATTCGCAGACCATGGCCCGCTTCAAGGCGCTGGACCTGAAAATCGAGACCAAGCCGGATCTCACCCCTGTCACGGATGCGGACCGCGCCGCTGAAGAGGCCATCCGCGGCCAACTCTCCCGGGCCCGGCCGCGCGACGCGGTCCTCGGCGAGGAATACGGCAGCAGCGGCCACGGCTCCCGCCGCTGGATCATCGATCCCATCGACGGCACGAAGAACTTCGTCCGCGGGGTGCCGGTCTGGGCCACCTTGATCGCGCTGGTAGACGAAGACCGTCCCGTGGTCGGCCTGGTCAGCGCGCCGGCTCTGGGCAAGCGCTGGTGGGCCGCGACCGGAACCGGTGCCTACATGGGACGTTCGCTGTCCGCGGCCACCCGGCTCCGGGTATCCGATGTCAACCGGCTCGAGGACGCGTCCCTCTCCTATTCCAGCCTCACCGGCTGGCAGGAACGCGGCAACTTCCCGGAGTTCCTCGGCCTCACCGAATCCGTCTGGCGCACCCGTGCCTACGGGGACTTCTGGTCCTACTGCATGGTGGCCGAGGGCGCCGTCGACATTGCCTGCGAACCCGAACTCAACCTCTATGACATGGCGGCCCTCGTGCCGATCGTGACCGAGGCCGGCGGACGGTTCAGTTCGCTCGAGGGCGAGGACGGACCCTTCGGCGGCAACGCGTTGGCCACGAACGGCACGCTGCACGACGAGGTCCTCTACCGGCTCAATCCGCAGTTGCGCGGCCAGCGTCCGGCCGCACACCCGGAGGACGGGTCCCTGCCGGAAACCGCTCCGGAGGCCTCCATGGAGGCGGACGGCCTGCGCTGACGCTGTCTTTTGTGACGAATTACGACGGCGGCCGTCCCCATTCCGGGGATGGCCGCCTTTTCGTTCCCGTAACAAAGATGCGGCCCCTCCGGCCGGACAATAATCTCGATGGCAGGTCACGAGTGCCAGCGCTAAACCC
diff --git a/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/MANIFEST b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/MANIFEST
new file mode 100644
index 00000000..8f46c041
--- /dev/null
+++ b/q2_types/per_sample_sequences/tests/data/collated_mags_numeric/MANIFEST
@@ -0,0 +1,4 @@
+sample-id,mag-id,filename
+12345,24dee6fe-9b84-45bb-8145-de7b092533a1,12345/24dee6fe-9b84-45bb-8145-de7b092533a1.fasta
+12345,fb0bc871-04f6-486b-a10e-8e0cb66f8de3,12345/fb0bc871-04f6-486b-a10e-8e0cb66f8de3.fasta
+67890,d65a71fa-4279-4588-b937-0747ed5d604d,67890/d65a71fa-4279-4588-b937-0747ed5d604d.fasta
diff --git a/q2_types/per_sample_sequences/tests/test_methods.py b/q2_types/per_sample_sequences/tests/test_methods.py
index e65ee757..0e6b635d 100644
--- a/q2_types/per_sample_sequences/tests/test_methods.py
+++ b/q2_types/per_sample_sequences/tests/test_methods.py
@@ -9,6 +9,7 @@
 import os
 from unittest.mock import patch
 
+import pandas as pd
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt, \
@@ -27,7 +28,7 @@ def test_partition_sample_data_mags(
         mock_validate_mag_ids
     ):
         # Partition mags
-        p = self.get_data_path("collated_mags")
+        p = self.get_data_path("collated_mags_numeric")
         mags = MultiMAGSequencesDirFmt(path=p, mode="r")
         mock_validate_num_partitions.return_value = 2
         partitioned_mags = partition_sample_data_mags(mags, 2)
@@ -43,15 +44,15 @@ def test_partition_sample_data_mags(
 
         # Compare dirs
         exp_partitions = [
-            ("sample1", mag_ids_sample_1), ("sample2", mag_ids_sample_2)
+            ("12345", mag_ids_sample_1), ("67890", mag_ids_sample_2)
         ]
-        for _id, mag_ids in exp_partitions:
+        for _id, mag_fns in exp_partitions:
             dircmp = filecmp.dircmp(
                 partitioned_mags[_id].path,
                 mags.path
             )
             self.assertListEqual(
-                ["MANIFEST", _id], dircmp.common
+                sorted(["MANIFEST", _id]), sorted(dircmp.common)
             )
             dircmp = filecmp.dircmp(
                 f"{partitioned_mags[_id].path}/{_id}",
@@ -59,10 +60,17 @@ def test_partition_sample_data_mags(
             )
             self.assertListEqual(
                 [
-                    *mag_ids,
+                    *mag_fns,
                 ],
                 dircmp.common
             )
+            obs_manifest = pd.read_csv(
+                f"{partitioned_mags[_id].path}/MANIFEST", index_col=None
+            )
+            self.assertListEqual(
+                obs_manifest["mag-id"].to_list(),
+                [os.path.splitext(x)[0] for x in mag_fns]
+            )
 
     def test_collate_sample_data_mags(self):
         p1 = self.get_data_path("partitioned_mags/mag1")