Cities Have Unique Microbial 'Fingerprints' – Study | Hacker News Reader

Cities Have Unique Microbial 'Fingerprints' – Study

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62 pointsjourney_1616230 comments

This is fascinating to me. An anecdote as a frequent traveler: I often notice that when I travel to different cities around the world, it takes my gut a few weeks to fully adjust. When people don't travel often, they tend to blame "travelers diarrhea", etc on unsanitary conditions in the place they are visiting. But from my perspective, it seems that it has very little to do with how sanitary a place is, and much more to do with how different the local microbiome is from what you're used to.

I'd also be curious to have my own microbiome sequenced and analyzed, since I've been very nomadic for a decade, and my usual approach (apart from covid) is to dive right in and expose myself to local microbiomes by drinking tap water, eating street food, etc.

I suspect that humanity has a lot left to learn about how microbes interact with human life.

I tend to notice the scent of a new a place. In fact, when I recall previous travels, the scent is associated with the memory. I wonder if this is related to microbiome.

For that reason, some urban legend says eating onions could help.

Sorry I don't follow the logic, how do onions relate to that?

I have so much to say on this topic. I've spent the last 6 years traveling around the world. I have been sick with some kind of stomach issue many times on many different continents.

I have sooo many stomach issues after this. I'm convinced exposing myself to so many nasty bugs has altered my gut and done some damage.

I have tried to get to the bottom of it with a doctor and all they did was tell me it's stress.

For people interested in the consequences of this diversity, look into lambic/geuze and other spontaneously Fermented beer using coolshipping as part of their inoculation. There is still ongoing and healthy skepticism on the actual source of yeast for these beers, yet they still rely on some sort of expression of the local microflora for their flavors and that is awesome in the literal sense.

Lambic itself is an amazing culture of fermentation and companionship via blending from your own and other brewers stock, I recommend Belgium and the senne Valley to anyone that is adventurous when it comes to beer/wine/cheese

https://www.goodbeerhunting.com/blog/2019/2/15/a-recipe-for-...

https://newschoolbeer.com/home/2020/11/de-garde-brewing-cool...

https://www.goodbeerhunting.com/blog/2017/10/18/dont-call-it...

Yeast etc. does float about in the air and is even found in siberian ice cores though, so it'd make sense that some ends up in the wort during cooling.

I understand that the lambic breweries re-use the same oak barrels though, but that yeast/bacteria has to come from somewhere first? I would have thought there would be a combination of yeast/bacteria from the coolship cooling combined with that existing in the barrel.

It'd be interesting if a number of breweries across the world made wort to the same recipe, with the same malt etc. and then let cool with their own coolship.

Also http://www.milkthefunk.com/wiki/Lambic and their wiki in general has some great information on sour beers.

http://www.milkthefunk.com/wiki/Spontaneous_Fermentation#Sou... talks a bit about where they may come from.

>I would have thought there would be a combination of yeast/bacteria from the coolship cooling combined with that existing in the barrel.

Yes that is exactly it, they do steam their barrels, but Brett can survive very deep in wood and inoculation rate does not matter at those scales. The mythos of lambic is, that its purely spontaneous from the air, the more nuanced take is, its a mix of the the air, the building and the barrels.

>It'd be interesting if a number of breweries across the world made wort to the same recipe, with the same malt etc. and then let cool with their own coolship.

There are a ton of breweries making beer the way lambic brewers mdo and the beers have huge variance, though they always come back to the same template

I second milk the funk, I am a very active user on the forum and there are very few wikis that I know of that are as well researched and nuanced as milk the funk. Dan does an amazing job!

Ah that's very interesting re. brett surviving very deep into the wood.

You mean lots of breweries outside of Belgium do a turbid mash and use aged hops too? I'd not realised that. I started reading 'American Sour Beers: Innovative Techniques for Mixed Fermentations' but need to get round to finishing that to understand more about how sour beer is made elsewhere too.

ASB is very thorough but had age a bit by now. 100% Brett and LAB fermentation is impossible for the latter and was a contamination, and not very viable for the former but made viable by bad qc at some of the big yeast labs.

This is more of a "there's literally dozens of us" kind of situation, but the US has a few producers that pay a lot of respect for lambic/geuze they sell their beer under the label of Methode traditionelle. Black project, jester King, American solera, de garde, beachwood blender, allagash, and that's really just off the top of my head. The UK has Mills, kemker Kultuuuuur of Germany has done it a few times. Antidoot Belgium also as far as I know. A recent issue of craft beer and brewing had a recent issue on Spons that was very exhaustive.

Cheers, will look out for those breweries.

Maybe a dumb question, but does this mean the whole thing about SF having the best sourdough because of its water is/could be true?

maybe water. The sourdough culture itself likely shifts, changes, and evolve continued re-use.

The water would probably more affect the flavor due to hardness and mineral composition favoring certain microbes over others and the expression of acids etc

I captured, isolated, and built up wild saccharomyces yeast from my suburban backyard last Sept and have been brewing with it regularly since. Currently have batch 4 and 5 on tap. If lambic producers can coolship in the middle of a major European city, you've likely got the fun stuff in your backyard as well.

Families and households, too. If your home includes pets, they stretch the overlap out into the surroundings a bit more, kids mingle with other families pools of life, etc.

There's another layer of mites, molds, and so on that's multicellular and participates in our health but isn't counted here. The things that we don't see or think about, the things that fleas count as annoying little bugs.

Vicious jungles, full of life, red in tooth and claw, all the way down.

I've always believed that when you go to a new place, you meet what I call 'foreign germs'. And when people from other places come to visit you, they bring their 'foreign germs' with them.

That's why you always seem to pick up some form of infection when you travel, or when people travel to see you.

This happens at scale too. European colonists brought their diseases to the Americas, resulting in deadly epidemics amongst the locals. The Europeans had built up their own immunity after centuries of exposure.

Complete isolation (e.g. closing borders) feels like an unsustainable strategy, as the local population would fall behind in the human-germ immuno-arms race, risking total wipeout when the borders inevitably become porous. So, ironically, while a high degree of global population mixing may be responsible for pandemics like Covid, it's probably healthy for the species in the long run.

What I've read is that Europeans lived in bigger and dirtier cities that the Native Americans, which is why they were carrying far deadlier germs, and when the "biomes" met, the Americans ended up with a 80-95% death rate, while the Europeans only got syphilis in the exchange. Bad enough, but an annoyance rather than a civilization ender.

Reversely, Europeans were always militarily superior to Africans, but they could not survive the malaria and other African diseases until the late 1800s. Which is why Africa was colonized much later.

One speculation is that since humans are native to Africa, that is where nature has evolved our worst enemies. But I may on thin scientific ice here.

>> Europeans were always militarily superior to Africans,

So this covers a big time span - say 1520s to 1920s - and at other points in human civilisation it was the reverse. Pretty much the whole Ethiopian Empire thing for example.

But one big reason the Sahel regions were militarily inferior by say 1880 was that in the 1500s Europeans started taking slaves from the Sahel regions because Africans had that immunity against the diseases in the Americas - we shipped so many at such a profit that Africa was losing populations at such a rate they could not develop - constant war feeding a population shifting off continent.

It's an interesting open question what would have happened if Slavery had been banned in the 1500s say.

Sure, "always" is overly broad.

You touch on a fascinating and little known thing:

The transatlantic slave trade arose in part because both European and enslaved native plantation workers tended to die off from Malaria after a few years.

Many Africans has some immunity to Malaria - which as I understand it was also brought to the new world by Europeans - so importing them turned out to be a more sustainable solution.

And yeah, the dynamics of living on a continent where one of the main industries for centuries is hunting your neighbors to sell to foreigners arriving on ships is very hard for me to imagine.

Sorry I started a reply but it tried to steer between massively simplified and book-length and I gave up.

This is a fascinating history with huge ramifications - and that malaria connection is the certainly under-researched that I know of.

It's not unusual for health regions or big hospitals to publish their own charts of antibiotic resistances to bacteria, because what's circulating around can vary from city to city. And that impacts choice of therapy (usually you want to start before your resistance results come back).

Here's a Canadian lab providers': https://www.lifelabs.com/healthcare-providers/reports/antibi...

I'm amazed at how much uniqueness they found. It makes sense there were region-specific microbes, given how alcohol and cheeses taste different depending on where they were made. But I thought, with global travel, "universal" microbes would make up more much more than 0.2% (31 of the 16,000+, if I understood the article). Either I underestimated how fragile microbes are in new environments, or how quickly they mutate.

I find your response interesting b/c my instinct was in the opposite direction. Are cities the best way to understand variation or are there hyperlocal differences based on how much runoff, foot traffic, grass-watering etc happens in a place? Are residential neighborhoods where people mostly drive in temperate coastal climates more similar to each other than to their closer urban centers with lots of foot traffic?

I've been making "Half Moon Bay" sourdough bread for a couple years. Unfortunately it's not as sour as I would like, or expect from "San Francisco" sour dough which isn't too far away. My assumption is it's due to the microbes in my kitchen, but maybe professional bakers use additives that I don't know about?

The sourness is often just a factor of cold proof time. The bacteria pick up in activity as the yeasts slow down.

That's true, but in my experience it's relatively minor. I can maximize the sourness of my bread with various process tweaks, but it still remains relatively subtle.

I wish I knew the source to this, but an acquaintance owns a yeast lab and he's said that there's a study looking into the biodiversity and source of sourdough. They found that over time the origin of the feeding material is a much greater contribution than the original culture. Ie, over time the flour you use will cause a drift in your culture and be the factor of the quality of your sourdough.

For sourdough I've had good results with active starters that I retarded overnight. You can probably also cause biases in the fermenting dough by creating a dough that's higher in simple sugars (LAB/LAY is much more fast acting and prefers glucose), maybe an autolyse does that for you.

Interesting. Maybe I'll try mixing in a few grams of sugar in the loaf I plan on making today.

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