I think we could use a little more info here, but I'm going to try to answer your question. Not sure what recipe you're using, but if the sprouts you're talking about are bean sprouts like those used in the garnish for many Vietnamese soups, add them at the end to maintain their crisp and crunchy texture. And Fresno chiles will work as a sub for jalapeños in certain contexts but their heat is slightly different; jalapeños have an up-front spicy bite to them that drops off after a minute or so, while Fresno chiles tend to slowly build heat in your mouth (the green Fresno chiles are milder than the more mature red chiles). If you're also using the chiles in the soup, I would seek out the kind of chiles that will give you the kind of heat/intensity you desire. I have often seen and used red bird's eye chiles in Asian noodle soups.
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