Coffee is full of the good stuff, Shubrook, a nutritionist with the British Association for Nutrition and Lifestyle Medicine, told RNZ's Jim Mora.
Shubrook specialises in the role nutrition plays in mental health and eating disorders and is a regular contributor to BBCGoodFood.com.
Research has found that drinking coffee boosts certain bacteria strains like bacteroides in the gut, she said, which in turn reduce the risk of cardiovascular disease or type II diabetes.
Coffee has other powerful benefits too, she said, it is an anti-oxidant and an anti-inflammatory.
"We want lots of anti-oxidants because they help protect the body against disease. It's a natural anti-inflammatory. It has been shown to also help when we drink coffee to actually increase the enzymes of salivary secretions, so could potentially help with digestion.
"Anything that provides an anti-inflammatory benefit is the way forward we know inflammation is one of the biggest drivers for poor health, particularly over a long period of time and leads to chronic disease."
It is the polyphenols in coffee which have an anti-inflammatory effect, she said.
"One of the main compounds in coffee is called chlorogenic acid, and that is the main polyphenol that we find in coffee that has these anti-inflammatory benefits.
"And again, it's been shown to reduce the risk of things like type II diabetes, non-alcoholic fatty liver disease.
"So they're really important these polyphenols. And the other great thing with polyphenols is they actually act as a prebiotic."
While probiotics put bacteria into the gut, prebiotics feed them, she said.
"They love fibre and they love polyphenols. So, the other benefit of coffee is it's got these polyphenols that feeds that bacteria that's already in your gut - the good bacteria."
To get the ultimate benefit take the coffee black and do not add sugar, she said.
"The minute you start adding in sugars and creams and syrups, and those kinds of things, just you're robbing Peter to pay Paul, because sugar is inflammatory.
"So you're technically undoing the benefit of the anti-inflammatory-ness of the coffee. So, I do recommend to my clients that they drink it black."
Milk is fine but she recommends whole fat and plant-based milks may contain sugar, she said.
"They're not just almonds or oats or coconut or whatever it might be, they've normally got added extras in there … some have got added sugar, which again can be pro-inflammatory."
Lighter roasts of coffee beans have more antioxidants than the arabica blends, she said.
"A green banana has a higher prebiotic content than a ripe banana, like a really yellow banana. I think that's probably the same with coffee beans that the lighter roasted ones, you haven't over-ripened them in a way so actually, you're going get a higher polyphenol content in a lighter roast than a dark roast."
But dark roasts are beneficial, she said, even instant coffee.
"It's just less each time you're going down that route, so light is best and instant is the least polyphenol-rich."
The question of how many cups a day comes down to metabolism, she said.
"About 50 percent of us are fast metabolisers. 40 percent are medium and 10 percent are slow. So, if you are a slow metaboliser of coffee, you're more likely to be the person who has one cup and feels really quite jangly and anxious and a bit nauseous. I know I'm a fast metaboliser of coffee, so I can easily have two cups and I'm fine."
And coffee's effect on sleep is probably overstated, she said.
"Coffee actually contains an amino acid called tryptophan, which you can also find things like almonds and turkey and tryptophan is the precursor to serotonin, which is our happy hormone and serotonin then converts to melatonin, which is our sleep hormone.
"Now, I'm not promoting that we go out and drink loads of coffee to promote melatonin if you're a rubbish sleeper.
"But it just shows you how complex these things are. And I think coffee generally has had a pretty bad rap is in connection to sleep, I think for some they may find that either it doesn't affect them, or it might even be a little bit beneficial."
