Bottled Bacteria, AquaBiomics. Just what's in your bottles

[Randy Holmes-Farley]

Aquabiomics detects individual strains and can categorize what is found to more specificity than the species level.

That is, they can separate one E Coli from another.

Your E Coli illustration actually works really well with Vibrio in reefs tanks.
Vibrio is likely in every reef tank. It's a common member of the coral holobiont. Some members of vibrio are bad actors, but many great tanks have lots of vibrio with no harmful effects.
Aquabiomics can tell vibrio fortis from another vibrio, and even one strain of vibrio fortis from another.
But the complication that is beyond their reach is that conditions act as triggers for otherwise harmless vibrio hanging out in the coral community to turn on lots of pathogenic traits and become virulent.
Salem has advocated for Eli to add this ability. (The techniques already exist) but understandably they aren't in a hurry to offer a product another level of complexity beyond what the customer base is currently trying to navigate.

Fortunately, there are a lot of cases where the good/bad identity isn't conditional. An enormous number of coral infections show up as one particular strain of Arcobacter, for instance.

Since you are the only one seemingly answering actual questions instead of just complaining about folks not reading the scientific literature to get answers, I'll ask you, taricha.

How confident is one that detecting a known pathogenic strain of some type of bacterium actually indicates a problem?

Since I need to prove I can actually look up stuff myself, I'll ask it this way:

Since it is established that finding pathogenic strains of bacteria in the GI tract of people says little about whether they are actually suffering any symptoms, why would one assume that this not frequently also the case in reef tanks? Do such tests just serve to scare people without apparent issues?

Why are so many enteric pathogen infections asymptomatic?

https://www.tandfonline.com/doi/full/10.1080/19490976.2023.2281010

A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea.


On the flip side, if the answer to actually having a bacterial coral problem is going to be to add some type of competitive bacteria product if a pathogenic species is found, why not just add that bacteria and see if it helps? That's a plan for dinos and cyano already.

The only reasons I can see to do the test are:

1. If the choice of competitive bacteria will depend on the pathogen found. Does it?
2. if the competitive bacteria are very expensive, making a pre dosing test a reasonable screen.
3 if the competitive bacteria might otherwise cause their own problem.

If none of 1-3 are true, what purpose is the identification of the species of bacteria present?

There may well be one and I just don't know what it is. I'm happy to be enlightened, and think it is unlikely that reading dozens more scientific papers will clarify those questions for me, but if one or more does, please point it out.

 

[A_Blind_Reefer]

 

[GlassMunky]

Since you are the only one seemingly answering actual questions instead of just complaining about folks not reading the scientific literature to get answers, I'll ask you, taricha.

How confident is one that detecting a known pathogenic strain of some type of bacterium actually indicates a problem?

Since I need to prove I can actually look up stuff myself, I'll ask it this way:

Since it is established that finding pathogenic strains of bacteria in the GI tract of people says little about whether they are actually suffering any symptoms, why would one assume that this not frequently also the case in reef tanks? Do such tests just serve to scare people without apparent issues?

Why are so many enteric pathogen infections asymptomatic?

https://www.tandfonline.com/doi/full/10.1080/19490976.2023.2281010

A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea.


On the flip side, if the answer to actually having a bacterial coral problem is going to be to add some type of competitive bacteria product if a pathogenic species is found, why not just add that bacteria and see if it helps? That's a plan for dinos and cyano already.

The only reasons I can see to do the test are:

1. If the choice of competitive bacteria will depend on the pathogen found. Does it?
2. if the competitive bacteria are very expensive, making a pre dosing test a reasonable screen.
3 if the competitive bacteria might otherwise cause their own problem.

If none of 1-3 are true, what purpose is the identification of the species of bacteria present?

There may well be one and I just don't know what it is. I'm happy to be enlightened, and think it is unlikely that reading dozens more scientific papers will clarify those questions for me, but if one or more does, please point it out.

The cognitive dissonance sure is strong today

 

[Dan_P]

I'm sorry man for dragging you into it

Truly

I didn't know

I suspect the trauma will not be long lasting. You both seem like social media ninjas. I suspect this isn’t your first scrap

 

[Randy Holmes-Farley]

If you have such a disdain for it/us why still be here? Just so you can seem smart and know everything despite not even owning a reef tank for many years?

Not sure what you mean by "here", but I consider my role at Reef2Reef to be two fold:

1. To learn things myself.
2. To shed light on scientific issues that may be very hard for nonscientific folks to understand, or even to know what questions to ask about products and services.

There are a great many products and services sold to reefers that are beyond their understanding, and when these are promoted as being beneficial, folks often buy them unaware of potential complications. Some are purely bogus (say, Vibrant), some are simply misleading (IMO) such as maintaining rubidium concentrations, some are very hard to evaluate (secret concoctions), and some may be great products or ideas that are just very hard to know when or how they are best to implement and best not.

Often times, an unbiased and scientifically focused discussion of these complexities can help folks know what is worth their acquiring as a tool, and what may be best left alone. Many people appreciate such discussions, whether I personally provide critical scientific input or just know some useful questions to ask, and make others feel more free to express expert, unbiased opinions or show their own results that may be counter to the current prevailing reefing trend..

 

[Randy Holmes-Farley]

The cognitive dissonance sure is strong today

Sorry, i don't follow the intent of that. The google AI tells me that:

"Some examples of cognitive dissonance include: Smoking, Eating meat, and Supporting fast fashion."

I don't smoke, I do eat meat, and I'm not even sure what fast fashion is. Maybe I do have it.

 

[Solo McReefer]

I suspect the trauma will not be long lasting. You both seem like social media ninjas. I suspect this isn’t your first scrap

 

[Dan_P]

If you have such a disdain for it/us why still be here? Just so you can seem smart and know everything despite not even owning a reef tank for many years?

What triggered this response? I read all the posts, did I miss something?

 

[GlassMunky]

Sorry, i don't follow the intent of that. The google AI tells me that:

"Some examples of cognitive dissonance include: Smoking, Eating meat, and Supporting fast fashion."

I don't smoke, I do eat meat, and I'm not even sure what fast fashion is. Maybe I do have it.

Further proving my point of being willfully ignorant to things very simple to see.

 

[GlassMunky]

What triggered this response? I read all the posts, did I miss something?

Glad you find it interesting. Maybe after you answer the same questions 56,321 times trying to help people, and don't have time to look up everything you might want to know, you wont' find it so unexpected.

His attitude here and other places makes it very clear he doesn’t like answering the same questions us stupid people ask all the time and the only ones worthy of his time are others with a PHD

 

[GlassMunky]

What triggered this response? I read all the posts, did I miss something?

He has many times in many threads been given the source to information pertinent to the conversation at hand but won’t look at it because it’s not the format he thinks is credible enough

 

[telegraham]

Glad you find it interesting. Maybe after you answer the same questions 56,321 times trying to help people, and don't have time to look up everything you might want to know, you wont' find it so unexpected.

Doesn't the apostrophe go between the n and the t? Is that a new question?

 

[Dan_P]

I find it so interesting that you have time to share here, yet no time to seek answers where answers can be found. Smells like words for the sake of words.

Because I'm handy with copy/paste, I've shared your thoughts with those who can actually help.

Ouch, what triggered this?

 

[telegraham]

I suspect the trauma will not be long lasting. You both seem like social media ninjas. I suspect this isn’t your first scrap

It was interesting but then took a turn. Now it's entertainment, much like a monkey exploring the extrinsic value of a football.

 

[AquaBiomics]

You are right. I'm caught. I've been paid thousands of dollars by a new competitor of yours to plant suggestive questions to make folks ask questions and think deeper about what is a "favorable strain" of bacteria, as well as asking to be educated myself since your web site fails to do that. That is literally the term used above, with no clarification what that means. I strongly think you and I may have qute different definitions of what that means.

If an expert scientist comes away from your web site not knowing if the service is useful or how it would be used, and especially if folks reading comments like "planning to evaluate the effects of husbandry techniques on "favorable strains"" cannot know what that even means, I do not think it is my fault that you have communicated it poorly to potential users. You say I, as a reefer, need to read the scientific literature more than I already do to understand what you mean? Seriously? Maybe my answer to the last 3,000 questions asking about how to raise pH should just say,

"one wonders why you cannot read the literature and figure that out for yourself".

Yep, that 's the ticket.

Your post and other posts here seem to suggest that there's no possibility of folks having different opinions on what beneficial and detrimental bacteria are, how they were identified, or validated, in what scenarios they may be favorable or unfavorable for the same bacteria, etc..

Best that folks just accept your assertions.

The service we provide is exactly the opposite of what you're claiming. Which anyone who had spent even a moment looking into it will see.

"Just accept my assertions?" What assertions? Do you have some different opinion on the identities of the bacteria we find in client samples? Do you have some different opinion on their functions? Its hard to tell what you even object to.

Most scientists I've worked with talk about the challenge of translating scientific data into a form thats easily digestible by the general public. So if your big gotcha is calling me out on not doing that perfectly - OK, you got me. Its a non-stop effort, a work in progress.

Many other hobbyists including active posters here on R2R are contributing to that effort through their experiments.

You choose instead to just rant any time the topic of bacteria or DNA comes up. Very productive and very professional. A great service to the hobby.

 

[Dan_P]

He has many times in many threads been given the source to information pertinent to the conversation at hand but won’t look at it because it’s not the format he thinks is credible enough

Thanks for quick reply.

OK, I get it.

There is a method scientists use to evaluate information quality based on years of training, but I don’t think explaining how this works is going to make you feel any better after the apparent slight.

 

[Randy Holmes-Farley]

The service we provide is exactly the opposite of what you're claiming. Which anyone who had spent even a moment looking into it will see.

"Just accept my assertions?" What assertions? Do you have some different opinion on the identities of the bacteria we find in client samples? Do you have some different opinion on their functions? Its hard to tell what you even object to.

Most scientists I've worked with talk about the challenge of translating scientific data into a form thats easily digestible by the general public. So if your big gotcha is calling me out on not doing that perfectly - OK, you got me. Its a non-stop effort, a work in progress.

Many other hobbyists including active posters here on R2R are contributing to that effort through their experiments.

You choose instead to just rant any time the topic of bacteria or DNA comes up. Very productive and very professional. A great service to the hobby.

Rant? Or asking uncomfortable questions?

I only entered this thread when it was stated by someone that:

"I do like the idea Salem is going in, in that we may be able to shift the more favorable strains by what we carbon dose."

THAT and that alone is what started this whole discussion. You felt it more useful to attack me than to address my questions.

So I'll ask a more specific question in the hope that you can focus on it:

How are those "favorable" strains chosen?
What is the evidence they are favorable to have increased, and in what scenarios?

 

[Dan_P]

Doesn't the apostrophe go between the n and the t? Is that a new question?

Geez, raise the critiques up a notch, no?

 

[Randy Holmes-Farley]

You choose instead to just rant any time the topic of bacteria or DNA comes up. Very productive and very professional. A great service to the hobby.

I'm also still waiting for the specific answers to the exact literal question I asked, and if they are easy to provide, doing so seems way better than attacking the person asking. if you do not have the answer, then say so.

I'm not really seeing why my questions cause such a defensive overreaction.

1. Again, this may be showing my unfamiliarity with with Aquabiomics can actually do, but the difference between harmful and desirable bacteria may be so minor that I am not convinced they can actually tell important but fine differences.

Can you?

 

[Randy Holmes-Farley]

His attitude here and other places makes it very clear he doesn’t like answering the same questions us stupid people ask all the time and the only ones worthy of his time are others with a PHD

That's of course ridiculous to say. You have no idea how many thousands of hours I have happily answered questions for people in hundreds of thousands of posts over several decades.