There is really short and briliant script for create backup of indexes queries. This code iterate over all collections and create backup of createIndex() queries.

print(`// Backup indexes of : ${db.getName()} : database`);
print(`use ${db.getName()};`);

db.getCollectionNames().forEach(function (collection) {
    indexes = db.getCollection(collection).getIndexes().forEach(function (index) {
        if (index.name === '_id_') return; // skip defalut _id indexes
        const keys = tojsononeline(index.key);
        delete index.id; delete index.key; delete index.v; delete index.ns;
        print(`db.${collection}.createIndex(${keys}, ${tojsononeline(index)});`);
    });
});

You can save this backup code to file and run int directly with mongoshell command:

mongo --quiet mongodb://localhost:27017/mydb ./backup.indexes.js > myindexes.js

Example output:

db.users.createIndex({"settings" : 1}, {"name" : "settingsIndex", "background" : true});
db.users.createIndex({"name" : 1}, {"name" : "nameIndex", "background" : true});
db.users.createIndex({"email" : 1}, {"name" : "emailIndex", "background" : true});