I think, the spam-column (and the user_id) should be an indexed column. Can you add this index to your database and run the analysis again?

ALTER TABLE `mlf2_entries` ADD INDEX(`spam`);
ALTER TABLE `mlf2_entries` ADD INDEX(`user_id`);

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That was a huge improvement of two of the queries!

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includes/main.inc.php, line 344:

SELECT COUNT(*) FROM mlf2_entries WHERE spam = 1

This query went from 500 millisecond to 0,5 milliseconds!

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includes/main.inc.php, line 336:

SELECT COUNT(*) FROM mlf2_entries WHERE pid = 0 AND spam = 0

This query went from 600 milliseconds to 150 milliseconds!

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Before the improvement, the top five queries took about 3,2 seconds in total. After the improvement, the top five queries took about 2,2 seconds in total.

Best regards,
Daniel