A friend who rode cross country swore by his Brooks leather saddle. Said it helped reduce or even avoid "swamp butt." Plastic saddles offer NOTHING in this regard, so the difference in ventilation could be considerable.

However, for me, it doesn't matter, as I sweat profusely on hot rides. A little more airflow for me makes almost zero difference. Hygiene, saddle & bike fit, use of quality cycling shorts and chamois creme is usually the key to these issues. But as you say, skin microbiome is important too. I'd avoid antibacterial soaps, perfumes and oil-based lotions. Our skin has been evolving for hundreds of thousands of years before these consumer products came along. Sure, some modern products may help, but I'm doubtful. Good diet also affects overall health, so consider this aspect. And don't forget proper hydration (water and electrolytes) either!