diff --git a/src/silo/preprocessing/metadata_info.cpp b/src/silo/preprocessing/metadata_info.cpp
index d2e980404..46e6b35a8 100644
--- a/src/silo/preprocessing/metadata_info.cpp
+++ b/src/silo/preprocessing/metadata_info.cpp
@@ -24,8 +24,8 @@ std::unordered_map<std::string, std::string> validateFieldsAgainstConfig(
 
    std::unordered_map<std::string, std::string> validated_metadata_fields;
    for (const auto& [field_name, access_path] : found_metadata_fields) {
-      if (std::find(config_metadata_fields.begin(), config_metadata_fields.end(), field_name)
-       != config_metadata_fields.end()) {
+      if (std::find(config_metadata_fields.begin(), config_metadata_fields.end(), field_name) !=
+          config_metadata_fields.end()) {
          validated_metadata_fields.emplace(field_name, access_path);
       } else {
          SPDLOG_WARN(
@@ -77,7 +77,7 @@ void detectInsertionLists(
          }
          if (contained_insertions->ColumnCount() == 1) {
             metadata_fields_to_validate[top_level_entry] = fmt::format(
-               "list_string_agg({}.{})", top_level_entry, contained_insertions->ColumnName(0)
+               "list_string_agg({}.\"{}\")", top_level_entry, contained_insertions->ColumnName(0)
             );
          }
 
@@ -85,7 +85,7 @@ void detectInsertionLists(
          for (size_t idx2 = 0; idx2 < contained_insertions->ColumnCount(); idx2++) {
             const std::string& sequence_name = contained_insertions->ColumnName(idx2);
             list_transforms.push_back(fmt::format(
-               "list_transform({0}.{1}, x ->'{1}:' || x)", top_level_entry, sequence_name
+               "list_transform({0}.\"{1}\", x ->'{1}:' || x)", top_level_entry, sequence_name
             ));
          }
          metadata_fields_to_validate[top_level_entry] =
diff --git a/src/silo/preprocessing/preprocessor.cpp b/src/silo/preprocessing/preprocessor.cpp
index be102a3ed..bc960b574 100644
--- a/src/silo/preprocessing/preprocessor.cpp
+++ b/src/silo/preprocessing/preprocessor.cpp
@@ -302,7 +302,7 @@ void Preprocessor::createAlignedPartitionedSequenceViews(
 
    (void)preprocessing_db.query(fmt::format(
       "CREATE OR REPLACE TABLE sequence_table AS\n"
-      "SELECT metadata.{} AS key, {},"
+      "SELECT metadata.\"{}\" AS key, {},"
       "{}"
       "{} \n"
       "FROM '{}', partition_key_to_partition "
@@ -397,7 +397,7 @@ void Preprocessor::createPartitionedSequenceTablesFromSequenceFiles() {
             "SELECT unaligned_tmp.key AS key, unaligned_tmp.sequence AS unaligned_nuc_{}, "
             "partitioned_metadata.partition_id AS partition_id "
             "FROM unaligned_tmp RIGHT JOIN partitioned_metadata "
-            "ON unaligned_tmp.key = partitioned_metadata.{} ",
+            "ON unaligned_tmp.key = partitioned_metadata.\"{}\" ",
             sequence_name,
             database_config.schema.primary_key
          )
@@ -441,7 +441,7 @@ void Preprocessor::createPartitionedTableForSequence(
          partitioned_metadata.partition_id AS partition_id
          {}
          FROM {} AS raw RIGHT JOIN partitioned_metadata
-         ON raw.key = partitioned_metadata.{};
+         ON raw.key = partitioned_metadata."{}";
       )-",
       table_name,
       order_by_select,
diff --git a/src/silo/preprocessing/sequence_info.cpp b/src/silo/preprocessing/sequence_info.cpp
index 0843dfc58..0e62d7f02 100644
--- a/src/silo/preprocessing/sequence_info.cpp
+++ b/src/silo/preprocessing/sequence_info.cpp
@@ -36,7 +36,8 @@ std::string SequenceInfo::getNucleotideSequenceSelect(
    std::string_view seq_name,
    const PreprocessingDatabase& preprocessing_db
 ) {
-   const std::string column_name_in_data = fmt::format("alignedNucleotideSequences.{}", seq_name);
+   const std::string column_name_in_data =
+      fmt::format("alignedNucleotideSequences.\"{}\"", seq_name);
 
    return fmt::format(
       "{0} AS nuc_{1}",
@@ -51,7 +52,8 @@ std::string SequenceInfo::getUnalignedSequenceSelect(
    std::string_view seq_name,
    const PreprocessingDatabase& preprocessing_db
 ) {
-   const std::string column_name_in_data = fmt::format("unalignedNucleotideSequences.{}", seq_name);
+   const std::string column_name_in_data =
+      fmt::format("unalignedNucleotideSequences.\"{}\"", seq_name);
    return fmt::format(
       "{0} AS unaligned_nuc_{1}",
       preprocessing_db.compress_nucleotide_functions.at(seq_name)->generateSqlStatement(
@@ -65,7 +67,8 @@ std::string SequenceInfo::getAminoAcidSequenceSelect(
    std::string_view seq_name,
    const PreprocessingDatabase& preprocessing_db
 ) {
-   const std::string column_name_in_data = fmt::format("alignedAminoAcidSequences.{}", seq_name);
+   const std::string column_name_in_data =
+      fmt::format("alignedAminoAcidSequences.\"{}\"", seq_name);
 
    return fmt::format(
       "{0} AS gene_{1}",
@@ -107,7 +110,9 @@ void SequenceInfo::validate(
    auto aa_sequence_names_to_validate = extractStringListValue(*result, 0, 1);
 
    for (const std::string& name : nuc_sequence_names_to_validate) {
-      if (std::find(nuc_sequence_names.begin(), nuc_sequence_names.end(), name) == nuc_sequence_names.end()) {
+      if (std::find(
+             nuc_sequence_names_to_validate.begin(), nuc_sequence_names_to_validate.end(), name
+          ) == nuc_sequence_names_to_validate.end()) {
          throw silo::preprocessing::PreprocessingException(fmt::format(
             "The aligned nucleotide sequence {} which is contained in the input file {} is "
             "not contained in the reference sequences.",
@@ -117,8 +122,9 @@ void SequenceInfo::validate(
       }
    }
    for (const std::string& name : nuc_sequence_names) {
-      if (std::find(nuc_sequence_names_to_validate.begin(), nuc_sequence_names_to_validate.end(), name)
-          == nuc_sequence_names_to_validate.end()) {
+      if (std::find(
+             nuc_sequence_names_to_validate.begin(), nuc_sequence_names_to_validate.end(), name
+          ) == nuc_sequence_names_to_validate.end()) {
          // TODO(#220) handle the cases when segments are left out appropriately
          throw silo::preprocessing::PreprocessingException(fmt::format(
             "The aligned nucleotide sequence {} which is contained in the reference "
@@ -139,8 +145,9 @@ void SequenceInfo::validate(
       }
    }
    for (const std::string& name : aa_sequence_names) {
-      if (std::find(aa_sequence_names_to_validate.begin(), aa_sequence_names_to_validate.end(), name)
-          == aa_sequence_names_to_validate.end()) {
+      if (std::find(
+             aa_sequence_names_to_validate.begin(), aa_sequence_names_to_validate.end(), name
+          ) == aa_sequence_names_to_validate.end()) {
          throw silo::preprocessing::PreprocessingException(fmt::format(
             "The aligned amino acid sequence {} which is contained in the reference "
             "sequences is not contained in the input file {}.",