diff --git a/src/nplinker/strain_collection.py b/src/nplinker/strain_collection.py
index a2f60d92..e471a563 100644
--- a/src/nplinker/strain_collection.py
+++ b/src/nplinker/strain_collection.py
@@ -15,8 +15,8 @@ class StrainCollection():
     def __init__(self):
         """A collection of Strain objects."""
         self._strains: list[Strain] = []
-        self._lookup: dict[str, Strain] = {}
-        self._lookup_indices: dict[int, Strain] = {}
+        self._strain_dict_id: dict[str, Strain] = {}
+        self._strain_dict_index: dict[int, Strain] = {}
 
     def __repr__(self) -> str:
         return str(self)
@@ -33,8 +33,8 @@ def __len__(self) -> int:
 
     def __eq__(self, other) -> bool:
         result = self._strains == other._strains
-        result &= self._lookup == other._lookup
-        result &= self._lookup_indices == other._lookup_indices
+        result &= self._strain_dict_id == other._strain_dict_id
+        result &= self._strain_dict_index == other._strain_dict_index
         return result
 
     def __contains__(self, strain: str | Strain) -> bool:
@@ -58,18 +58,18 @@ def add(self, strain: Strain) -> None:
             strain(Strain): The strain to add.
         """
         # if the strain exists, merge the aliases
-        if strain.id in self._lookup:
+        if strain.id in self._strain_dict_id:
             existing: Strain = self.lookup(strain.id)
             for alias in strain.aliases:
                 existing.add_alias(alias)
-                self._lookup[alias] = existing
+                self._strain_dict_id[alias] = existing
             return
 
-        self._lookup_indices[len(self)] = strain
+        self._strain_dict_index[len(self)] = strain
         self._strains.append(strain)
-        self._lookup[strain.id] = strain
+        self._strain_dict_id[strain.id] = strain
         for alias in strain.aliases:
-            self._lookup[alias] = strain
+            self._strain_dict_id[alias] = strain
 
     def remove(self, strain: Strain):
         """Remove a strain from the collection.
@@ -77,13 +77,17 @@ def remove(self, strain: Strain):
         Args:
             strain(Strain): The strain to remove.
         """
-        if strain.id not in self._lookup:
-            return
-
-        self._strains.remove(strain)
-        del self._lookup[strain.id]
-        for alias in strain.aliases:
-            del self._lookup[alias]
+        if strain.id in self._strain_dict_id:
+            self._strains.remove(strain)
+            # remove from dict id
+            del self._strain_dict_id[strain.id]
+            for alias in strain.aliases:
+                del self._strain_dict_id[alias]
+            # remove from dict index
+            for i in range(len(self)):
+                if self._strain_dict_index[i] == strain:
+                    del self._strain_dict_index[i]
+                    break
 
     def filter(self, strain_set: set[Strain]):
         """
@@ -102,7 +106,7 @@ def lookup_index(self, index: int) -> Strain:
         Returns:
             Strain: Strain identified by the given index.
         """
-        return self._lookup_indices[index]
+        return self._strain_dict_index[index]
 
     def lookup(self, strain_id: str) -> Strain:
         """Check whether the strain id is contained in the lookup table. If so, return the strain, otherwise return `default`.
@@ -116,11 +120,11 @@ def lookup(self, strain_id: str) -> Strain:
         Returns:
             Strain: Strain retrieved during lookup or object passed as default.
         """
-        if strain_id not in self._lookup:
+        if strain_id not in self._strain_dict_id:
             # logger.error('Strain lookup failed for "{}"'.format(strain_id))
             raise KeyError(f'Strain lookup failed for "{strain_id}"')
 
-        return self._lookup[strain_id]
+        return self._strain_dict_id[strain_id]
 
     def add_from_file(self, file: str | os.PathLike):
         """Read strains and aliases from file and store in self.