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Feb 27, 2023Liked by Joomi Kim

As someone infected in early March 2020 who went on to develop Long Covid (mostly resolved at 27 months) that included severe gastrointestinal involvement, I find this research interesting. I would be curious of any research into how this might may have played out in patients — specifically in the disease course, short and long term, for people infected with SARS-CoV2.

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Feb 27, 2023·edited Feb 27, 2023Liked by Joomi Kim

So the researchers finally discovered something that my gut directly informed me about long ago, when I noticed that during a viral infection things often went awry in my gut.

Seriously, though, this is interesting and clarifying. I like clarifications. Thank you!

[Substack is acting like it is under some kind of attack. Sorry if this posts more than once in my attempts to get it to post at all. -- Done!]

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Joomi - in case you are not aware, Steve Kirsch had a doc on his VSRF webinar a couple of months ago. She talked extensively about the gut microbiome.

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Just a long shot but I had problems as well, severe reflux, acid, etc. I did some reading. I found out pineapple juice does great things for the digestive system.

So I came across organic pineapple juice at Costco. I helped me tremendously. Heartburn gone.

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Thank you Bentley. Who knew such a simple thing could treat heartburn! So very many things we've been lied to about.

A question from my sister who suffers from heartburn. When do you drink and how much of it do you drink?

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I drank it daily at breakfast. One tall tumbler full. I was surprised because I thought pineapple is acidic. It’s going to make my stomach burn but actually it does just the opposite. It puts good gut bacteria back into your system. It only drank it about a month, and I noticed the difference. Before I couldn’t even drink a glass of red wine, it burned so bad. I was even on prescription medication for it until I read the side effects. I hope it works for her. Best of luck.

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God bless you Bentley. So appreciate your response.

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🎯👏👏 thanks for drawing attention to these papers, I wouldn't have found them otherwise, as you said bit obscure journals compared to the usual publishing suspects.

I'd really like to see someone check the microbiome patterns of those vaccinated vs unvaccinated, plus BEFORE 2020 and AFTER 2020.

Could be more mutant drift than suggested.

Given our symbiotic relationship with the microbial world, I would hazard a guess that the bacteria etc, are intervening between SarsCov2 virae and ourselves from a benign perspective. Ie they maybe taking the damage for us, in an effort to minimise their hosts long term damage. Much like what they do with all the toxic substances in our food and environment. But let's hope so at least. The other alternative is far less appealing.

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Feb 28, 2023Liked by Joomi Kim

Joomi, of all the people writing complicated scientific analyses on Substack, your writing is the clearest. I’m going to become a paid subscriber.

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Feb 28, 2023Liked by Joomi Kim

even more important, if this is true, then the gut might be acting as a reservoir for ongoing infection esp in LC patients. and perhaps it would explain the role of Antibiotics like azithromycin and doxy in treatment of acute covid?

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Dr. Robert Clancy's bio includes this statement:

"...the best way to create immunity against infection in the respiratory tract was to stimulate the gut immune system, whereby these activated cells migrate to the lung and make antibodies against organisms responsible for the infection."

See https://centrefordigestivediseases.com/team/professor-robert-llewellyn-clancy/

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Does this support the possibility of fecal-oral transmission?

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Or could explain the headlines about drug resistant GI bug going around.

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Sabine Hazan, MD, is a gastroenterologist who studies this and has been shouting from the rooftops for almost 3 years that it’s all in the gut. I haven’t seen as much of her “shit” lately as I’m permanently banned from Twitter , but shes completed and has more studies in the works

Ethical Skeptic also noted the coincidence of the Midwest sludge spreading on the fields immediately preceded their massive spike in cases in fall 2020. The farms are assured that sludge (human poop) from waste water treatment plants are organic material for fertilizer and they spray it over the fields after the last crop harvests. In New England where I live, farmers use cow manure and spread it in the early spring as the snow melts. We don’t have the farms of that scale here! Happy for that.

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I know that. Her point was that all the focus was on the lungs when the gut is also a significant gateway.

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Hi Joomi,

Thank you for sharing. I have posted about this last year, here

https://gettr.com/post/p17ugbg97cd

https://gettr.com/post/p1846qg710c

and here

https://gettr.com/post/p18eoyq548a

I do not find their evidence very convincing and extraordinary claims require extraordinary evidence.

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author

How do you interpret the plaque assays in the pure bacterial strains (which they said they purchased) from the second study?

I agree that some of the evidence from the first study alone would not be very convincing but IMO the results from the second one would be hard to explain without some kind of direct interaction between the virus and gut bacteria.

At any rate, as I wrote at the end of the article, we can be agnostic about how we interpret the results... but at the very least they deserve more attention (other independent groups should work on it)

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Hi Joomi,

Ok, let's take a look to that paper:

*1st analysis with electron microscopy:

"we observed virus like structure of around 25–100 nm size interacting with the outside of the wall of bacterial cells and found inside bacteria. The immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirms the presence of SARS-CoV-2 both outside and inside bacteria."

That conclusion is not correct, the staining of nucleocapsid protein does not imply the presence of whole SARS-CoV-2 virions, and immuno-labelling of nucleocapsid protein is not specific to SARS-CoV-2 nucleocapsid. So from their first results we observe that those bacteria are displaying some kind of metabolic behaviour in which vesicles (virus-like particles) with the presence of nucleocapsid type proteins, are involved. I do not know enough about bacteria and their life cycles under different circumstances to make any further conclusion.

*2nd analysis with Surface-Activated Chemical Ionization/Electrospray Ionization mass spectrometry (SACI/ESI-MS) technology:

"Bacterial growth in presence of 15N detected de novo synthesis of spike protein"

"15 N-labelled spike protein was detected only in presence of 15 N as additional source of nitrogen and not in control sample (where only 14 N-labelled spike was identified). Such a synthesis went in parallel to an increase of the viral RNA load, in line with what already observed previously in. 1 These results provide evidence that SARS-CoV-2 RNA is both replicated and translated in the bacterial cultures of faecal origin."

First we have to understand that this method characterizes peptides as we can see in figure 6 in the paper. How specific the peptides detected are for the SARS-CoV-2 spike protein would require further analysis in my estimation. But at least we can conclude that some peptides related to coronavirus spike like proteins were detected with the presence of 15N and therefore synthesized, most probably, by the bacteria in the culture (assuming no contamination).

The authors then try to summarize that result with their previous result of increase RNA load and they make the following conclusion, "These results provide evidence that SARS-CoV-2 RNA is both replicated and translated in the bacterial cultures of faecal origin." No, that conclusion is not correct. Those results would indicate some plausibility of that but not a prove.

The only thing we are seeing so far is a bacteria culture in which some proteins, that may be related to coronaviruses in general and SARS-CoV-2 in particular, i.e. nucleocapsid and S1/S2 type peptides, are involved in metabolic processes of those bacteria under the presence of RNA that can be characterized under the constellation of SARS-CoV-2 type genomes, in particular, and coronavirus type genomes, in general. I don't see any viable virion yet in the whole process. So there is no prove of bacteriophage behaviour or direct interaction between whole, replication competent, virions and the bacteria.

*3rd analysis with plaque assays:

"Finally, by performing plaque assays with aliquots of supernatants from cultures of faecal microbiota derived from SARS-CoV-2 infected individuals on pure cultures of two faecal bacteria (F. prausnitzii and D. formicigenerans) reported to be strongly reduced in COVID-19 patients, we observed the formation of plaques characteristic for the presence of phages."

"RNA was extracted and NGS sequenced from aliquots individually collected from the plaques. The reads obtained from F. prausnitzii and D. formicigenerans viral plaques mapped a span of 62% and 48% of the SARS-CoV-2 genomic reference sequence respectively (NCBI Reference Sequence: NC_045512)."

In this section we can clearly see that "Obtained reads from F. prausnitzii and D. formicigenerans phage plaques map and cover [ONLY] 62% and 48% of the SARS-CoV-2 genomic reference sequence". This result do not indicate the presence of viable replication competent SARS-CoV-2 virions, as most of the genome is not present. In other words, they do not find the genome of SARS-CoV-2 in their sample. Which completely contradicts their conclusions.

Regarding their statement on "plaques characteristic for the presence of phages", again, I do not know enough on Bacteria and their life cycles to estimate why the plaque is formed, or if it is indeed characteristic for the presence of phages, but I don't see any prove of this in this paper.

CONCLUSION: Of course I agree with you that further analysis are required given the odd nature of these findings, however I don't see any reason why these results will not show with other coronaviruses if we repeat the same process. What I would also like to see, as I indicated in my GETTR, here https://gettr.com/post/p1846qg710c), is the following: "Inoculation of a cell culture with the supernatant of sample A and sample B(A+) [using the terminology of their first study] in order to see if there is viable SARS-CoV-2 viruses in the bacteria culture after the 30 day period when you observed the maximum viral RNA load. The bacteria may be replicating some portion of the genetic material via other mechanism, and they may even be synthesizing some of the proteins."

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"the staining of nucleocapsid protein does not imply the presence of whole SARS-CoV-2 virions": I don't disagree with you there.

"immuno-labelling of nucleocapsid protein is not specific to SARS-CoV-2 nucleocapsid": that depends on the specific antibody used. Not all antibodies are the same. Some are more specific than others.

"I don't see any reason why these results will not show with other coronaviruses": yes I agree with you. If we see it with SC2 it might be the case with other coronas and even other types of viruses. SC2 might not be special in that regard. No one is saying they are.

You criticize this statement from the authors:

"These results provide evidence that SARS-CoV-2 RNA is both replicated and translated in the bacterial cultures of faecal origin."

You say, "No, that conclusion is not correct. Those results would indicate some plausibility of that but not a prove."

Their exact words were "these results provide evidence" which to me has a very similar meaning as what you said: "Those results would indicate some plausibility..." It seems like you are taking a very uncharitable reading of what the authors said.

More to the point: even if what we are seeing is incomplete virions or virus-like particles, and it's not unique to SC2 (it happens with other viruses as well), it's STILL a significant finding.

I don't think anyone has claimed that the work proved that we are seeing viable virus; if the authors of the study claimed that, I would disagree with them.

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Hi Joomi,

I agree with most of what you say, however the framing of words, "These results provide evidence", is a much stronger statement than "Those results would indicate some plausibility".

In relation to the uncharitable reading, yes that is probably true after reading so so many fraud papers in SARS-CoV-2 related research.

After reading something like: "The immuno-labelling with Anti-SARS-CoV-2 nucleocapsid protein antibody confirms the presence of SARS-CoV-2 both outside and inside bacteria" I got a bit discourage I guess.

Note: The nucleocapsid protein is a very conserved protein and I truly don't think that you can find antibodies that are exclusively specific for SARS-CoV-2 in that particular proteome. specially given the fact that SARS-CoV-2 is not even particular to itself. We must always remember that we are talking about genome constellations, protein constellations and epitope constellations that cannot be mapped to each other in a bijective way (a one-to-one correspondence). And any proxy method must always be confirmed via secondary analysis. If we did that instead of being so convinced about our "evidence", we would find that those constellations have been extremely underestimated and the variability of that which we are trying to measure is considerably high and intertwined in a very very complex manner, requiring for new methodologies that would not be so fast to ascertain our certainty, but our lack of it.

In any case, any antibody assay specificity refers to a constellation of epitopes and it is never and never will be specific to one epitope. Furthermore, you cannot characterize in a one to one correspondence a constellation of proteins to a constellation of epitopes. And unless you completely make sure that you can accurately measure the background signal for any given assay, your measurement will have a lot less accuracy than the established specificity and sensitivity from the manufacturer. Actually, the problem is even worst due to the fact that different methods of producing antibody assays will target different epitope constellations that, again, cannot be mapped via a bijective function to the protein constellations we are trying to identify. Some regions will not be mapped correctly. But... anyway, the manufacturers will always talk about 99% values of specificity and sensitivity, regardless of the reality of what we are actually measuring.

So the burden of prove should be quite high in my estimation, given that most of our conclusions are probably wrong and require further, consistent and predictive, reproducible evidence, that are not restrain to any given methodology, proxy measurement, or protocol.

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And isn’t it interesting that there are studies showing the positive impact of drinking probiotic rich Kefir (fermented milk) - Kefir: A protective dietary supplementation against viral infection

Reham Samir Hamida et al. Biomed Pharmacother. 2021 Jan. https://pubmed.ncbi.nlm.nih.gov/33186795/ To me, it is advisable to eat/drink natural probiotics to keep your gut biome in top shape so as to successfully fight against Covid & other pathogens. https://pubmed.ncbi.nlm.nih.gov/35789583/

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Also why ivermectin, derived from the bacteria avermectin, would have a positive effect against SARS-CoV2. Bacteria and viruses are always in little balancing wars against each other.

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Thanks! I saw this article awhile back- it's an interesting finding. I'm not sure what the connection is with this post though...

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Virology does not meet the basic criteria for science such as proper control experiments. When control experiments have been performed the results show evidence of a 'virus' (CPE / genome assembly) can be obtained without adding any sample containing a purported 'virus. For example Dr Stefan Lanka has 'found' the SARS CoV2 genome from a sample of pure yeast, using the exact same protocols and genomic assembly software that virologists use (Dr Lanka was himself a virologist until he realised viruses are just cellular debris).

Even kidney specialists have published articles warning virologists that the breakdown of kidney cells produces particles that are indistinguishable from 'coronaviruses'.

When you look at the history of viruses you find it was never scientific to begin with. It was a desperate attempt to prop up the already failing germ theory by inventing tiny pathogens that nobody could see. After the EM was invented these particles could still not be found in samples taken from sick people. That's when they invented the 'witchcraft' of cell cultures which require the use of monkey KIDNEY cells - which are known to breakdown to 'viruses'. Then genomics came along and added more hocus pocus with 'genomes' being assembled out of nothing and called 'viruses'.

If virology is not proper science (and it isn't) then everything downstream from virology is automatically invalidated also. The fundamental flaw of virology is the circular reasoning fallacy. They assume their samples contain viruses, and proceed from there.

Virologists have been offered an opportunity to prove their methods with a set of blinded experiments. This has really got their knickers in a twist.

https://drsambailey.com/resources/settling-the-virus-debate/

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Couple that with a new study out about -dishwasher rinse aids -breaking down the gut epithelial layer https://www.jacionline.org/article/S0091-6749(22)01477-4/fulltext

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