Kissing between humans and Neanderthals? Could be oral – anal contact too. Or neither.

Umm – I really do not know what to say here. There is a new incredibly exciting paper out on Neanderthal oral microbiomes.

I saw some news stories about a new study on Neanderthal oral microbiomes. And one thing caught my eye – a claim about how the data provided evidence that Neanderthal’s and humans were kissing each other.
See for example the LA Times: Vegetarian Neanderthals? Extinct human relatives hid a mouthful of surprises – LA Times

The scientists also managed to sequence the oldest microbial genome yet — a bug called Methanobrevibacter oralis that has been linked to gum disease. By looking at the number of mutations in the genome, the scientists determined it was introduced to Neanderthals around 120,000 years ago — near the edge of the time period when humans and Neanderthals were interbreeding, Weyrich said 

There are a few ways to swap this microbe between species, she pointed out: by sharing food, through parental care, or through kissing. 

“We really think that this suggests that Neanderthals and humans may have had a much friendlier relationship than anyone imagined,” Weyrich said. “Certainly if they’re swapping oral microorganisms — or swapping spit — it’s not these brute, rash-type encounters that people were suspecting happened during interbreeding. It’s really kind of friendly interactions.”

And Redorbit: Neanderthals were vegetarian– and probably kissed early humans

Another surprise was the discovery of the near-complete genome for Methanobrevibacter oralis, a microbe known to live between the gums and teeth of modern humans, in the dental calculus of the Neanderthals. Weyrich said that this organism is the oldest of its kind to ever be sequenced, and that its existence in Neanderthals means that it had to have been spread to humans somehow – likely through kissing, which supports the growing notion that humans and Neanderthals were known to become intimate with one another on occasion.

And the Washington Post Neanderthal microbes reveal surprises about what they ate — and whom they kissed

And there is this doozy of a quote in the Post article

“In order to get microorganisms swapped between people you have to be kissing,” Weyrich said.

And many others.  Now – this seemed like it would be really hard to prove.  After all, it is really hard to prove from microbiome data that two people have been kissing even when we have high quality data from many samples and even when we have data from both the possible donor and recipient.  So how could one show that humans and Neanderthals were kissing with data from ancient samples and only from one of the partners in the putative exchange?  Well, as far as I can tell, you cannot.

Sadly the paper is not open access and I generally avoid writing about closed access papers here. But I am making an exception here because the media has run with what I believe to be an inaccurate representation of the science.

So I went to the paper.  Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.  I have access to it at UC Davis but if you do not have access to it, you could search for it in SciHub (for more about SciHub see Wikipedia).  I am not encouraging you to use SciHub – a site that makes papers available view what may be illegal means in some countries.  But if you want to see the paper, and you have determined that you are OK with using SciHub, well, that is an option. This is a link that might get you access in SciHub, if you wanted to do that.

Anyway – I read the paper.  And it really is quite fascinating.  It has all sorts of interesting information and really does represent an incredible tour de force of both lab and computational work. Kudos to all involved.  But alas, there is nothing in the paper about kissing. If you search in the paper for the word kiss – it is not found. The possible transfer of microbes between Neanderthal and humans is briefly discussed however.

From what I can tell, what they did here was the following:

  1. reconstructed a genome from their samples of Methanobrevibacter oralis subsp. neandertalensis.
  2. compared the genomes to other Methanobrevibacter genomes including just one other M. oralis (this one from humans)
  3. Inferred a possbile possible date range for the split between their M. oralis and that from humans 

It is cool and very interesting stuff.  See this figure for example.

And then based on this they write:

Date estimates using a strict molecular clock place the divergence between the M. oralis strains of Neanderthals and modern humans between 112–143 ka (95% highest posterior density interval; mean date of 126 ka) (Fig. 3b; see Supplementary Information). As this is long after the genomic divergence of Neanderthals and modern humans (450–750 ka)29, it appears that commensal microbial species were transferred between the two hosts during subsequent interactions, potentially in the Near East30.

So they are inferring transfer of commensal microbes based on molecular clock dating from one single M. oralis genome from Neanderthal and one from humans and a comparison of the inferred dating of their common ancestor versus the timing of supposed divergence between humans and Neanderthal. Personally it seems like a big big stretch to make that inference here. What if the dating from their analysis is off (such dating estimates are generally highly debated and unclear how accurate they are)?

But let’s just say that this is in fact good evidence for some sort of more recent common ancestry of the M. oralis found in their sample and the M. oralis found in a human than one would expect based on knowledge of Neanderthal and human common ancestry. Does that mean swapping of the microbes between humans and Neanderthal? Not at all. Maybe the M. oralis comes from food. And if it is living in some sort of food source (could be animal, or plant or something else) and it comes into both humans and Neanderthal separately, then one could easily have a way for the one found in their Neanderthal sample to have a more recent common ancestry with the one found from humans than the common ancestry of the “hosts” here.

Interestingly, the genome they used to compare to Methanobrevibacter oralis JMR01 actually came from a fecal sample and not an oral sample – see Draft Genome Sequencing of Methanobrevibacter oralis Strain JMR01, Isolated from the Human Intestinal Microbiota. So this microbe is not solely found in the mouth and it apparently can survive transit between the mouth and another orifice, and may even be a gut resident (i.e., not just transiting).

So anyway – it seems woefully premature to conclude that the data they have here provides evidence for exchange between humans and Neanderthals of M. oralis. Could have occurred. But also could be separate colonization from similarly environmental sources.

And finally, even if we assume that the M. oralis was exchanged, which again there seems to be no good evidence for, what is to suggest that this was do due to kissing? Nothing as far as I can tell. How about sharing utensils? How about contact with fecal contaminated water (since M. oralis seems to do OK in feces)? Or I guess would could go extreme and say this could be evidence for oral anal contact between Neanderthal and humans, if we wanted to sensationalize this even more. After all, we do know many cases of microbes getting exchanged by oral – anal contact. But we don’t do we? How about we stick to what we have good evidence for and then carefully discuss possibilities, of which kissing is one, but it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best.

This There is really amazing science in this work. But the kissing claims are premature as far as I can tell (I honestly hope I am wrong and that there is more data than presented in the paper, but if there is it should be presented somewhere – or maybe I have misinterpreted the paper – but I don’t think so). If the claims are as premature as they seem to be, this is damaging in my mind to the field of microbiome science.

UPDATE 3/10/17

Thanks to Ed Yong for updating his Atlantic article on this story to add a reference to my concerns.

He wrote

But after the paper was published, and several publications noted Weyrich’s suggestion about kissing in their headlines, Jonathan Eisen from the University of California, Davis, expressed skepticism about the claim. “Maybe the M. oralis comes from food,” he wrote in a blog post. It could have been picked up independently from the environment, or from water contaminated with feces, or from other kinds of sexual contact. A kissing route “it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best,” Eisen said.

UPDATE 2 – Made a Storify of some responses

Overselling the microbiome award: CBC Fresh Air & JA Tetro on kissing microbiomes

Well, so there I was, enjoying a relatively peaceful and quiet Valnetine’s day.  When I noticed a Tweet directed to me from one of my favorite scientist’s out there

So I decided to check it out.  I clicked on the link and got to a CBC Fresh Air news story on Soundcloud:

▶ Kissing and romance and bacteria with Jason Tetro Feb 14/15 by CBC Fresh Air

I plugged in my headphones (was not sure if my kids should hear it) and listened away.  And what I heard was excrutiatingly painful.  The CBC Fresh Air reporter was discussing kissing and the microbiome with JA Tetro.  And Tetro made some of the most misleading, ridiculous overstatements about the microbiome I have heard in many years:

  • He basically implied or specifically said that, in humans, attraction to partners and relationship success was determined by finding a partner with similar microbiomes to oneself.  
  • Furthermore he discussed how maintaining similar microbiomes (e.g., via consuming the same probiotics or fermented foods) would help maintain attraction and how things like travel away from a partner might lead to repulsion.  
  • He said things like tha our immune systems determine if a partner is right for you from kiss-based comparison of a partner’s microbiome to one’s own.  
  • And that if the microbiome in a kissing partner is a match this leads to bliss and addiction and that salive is the first line of defense when it comes to relationships.  
  • He even went so far as to say that this is all about “trying to find your mother because our microbiomes come from our mother.”  

I could do on and on.  It was the worst, most misleading, innacurate material I have probably ever heard about microbiomes.  Tetro and CBC Fresh Air should be ashamed.

Sadly, I found some other misleading, inaccurate material from Tetro about the same topic in an article about kissing microbiomes from a few months ago: Swapping spit and testing chemistry: How kissing, germs help you pick your partner where Tetro is quoted

Tetro says that when you kiss your date, his or her germs make their way into your mouth’s ecosystem. And if it’s a match, you’ll want to keep smooching. 

“This study does one amazing thing, it shows you that kissing is the best way to find a mate for the long term. It might sound really gross but if the bacteria from the other person harmonizes with your bacteria, your immune system is all good. You feel a sense of calm and happiness, maybe even addiction,” he explained. 

“But if the bacteria don’t align with your microbes, you actually feel disgust and revolt. Your immune system is rejecting that person as a possible mate.”


“This study proves that when it comes to finding the right mate, the old game of spin the bottle actually has a base in science,” he said. 

More completely inaccurate, made up material with no basis in science.  As far as I can tell, this is basically made up.  Sure there may be a theory behind this.  But to present it as established facts about the microbiome is ridiculous.

This is all a shame really since the paper which the CBC Fresh Air story is referring to is actually a perfectly fine paper and the authors of the paper do not seem to be pushing these over the top ridiculous ideas.  And for this terrible story I am giving CBC Fresh Air and JA Tetro an “Overselling the microbiome award“.

I note before I finished writing this up I looked around and the discussion on Twitter about the article and saw that Bik and others had tried to get Tetro to tone down his claims but he refused. See for example Tweets below:










// and many more — but the gist was — Tetro presented not a single reference to back up his claims and did not seem to understand that what he did was misleading – to present personal ideas as though they were supported by research. So I felt the need to write a post providing some counter to his claims.

As an aside, the ridiculousness about kissing and microbomes did spawn one good thing: someone sent me this satire post amid the Twitter discussion: Love Transplants

BREAKING NEWS: Global chocolate distributor, Venus Inc., released a statement earlier today detailing their newest product line focused on manipulating the natural human microbiome to increase and sustain romantic relationships.

UPDATE 1: More from Tetro on kissing and the microbiome

Uggh. Was pointed to some more bad material from Tetro on kissing and the microbiome.  This time in Shape Magazine.

Question from Shape: 

Is it true that if the microbes aren’t in sync, kissing can make someone feel ill? Why is this? 

Answer from Tetro:

It’s due to the immune response, which is involved in everything from prevention of infection to allergies. For example, studies have shown a kiss from someone who has recently eaten peanuts can induce an allergic reaction for peanut allergy sufferers. This is due to the rapid nature of the immune system. When we kiss deeply, some 80 million bacteria are transferred. With that much, the immune system will react. If the bacteria are recognized and liked, then the response is one of happiness, joy and even addiction. But if they are not aligned, then like an allergic response, the person will feel uneasy and even defensive. When that happens, it’s best to move on.

Again.  This stuff about if the bacteria are recognized then the response is one of joy, happiness and addiction appears to be completely made up.

Another question from Shape:

Can people be a match, but over time fall out of interest with each other because microbes change?

Answer from Tetro:

Absolutely. Depending on the way people live, eat, exercise and perform hygiene, the microbiota can change over time. If this happens in one and not another, this could lead to a problem and possibly an eventual demise. To prevent this, the best way to help is to keep the microbiomes aligned using bacteria common to both. The best way to do this is though the use of probiotics.

So – is Tetro trying to sell probiotics?  WTF?  This also appears to be completely made up.

UPDATE 2: Oh wait, more awful material from Tetro – this time in Glamour.

We’ve found that microbes actually drive the majority of our how our bodies work, from general health to mental health to romantic health,” says Jason Tetro, microbiologist, probiotic company Bio-K+ advisory board member, and author of The Germ Code.

Microbes “drive the majority of how our bodies work”.  Really?  So our genes don’t matter?  Or our history?  Oh FFS.  This is just more off the deep end. And some other doozies like

“If you like the bacteria on someone’s body, you’ll like how he smells. If you experience that quasi-allergic reaction to his scent, it’s a sign your bacteria aren’t harmonizing,” says Tetro. Barely any of it has to do with how his actual body smells; it’s mostly chalked up to the scent his bacteria is giving off.

And much of the rest of the article is not quoting Tetro but the ideas clearly come from him.  I am intrigued about the part at the beginning saying he is on the Bio-K+ advisory board.  This appears to be the Bio-K+ probiotics company.  I wonder if this has anything to do with Tetro saying things like this, about probiotics:

And if you make it past a kinda queasy kiss and end up having sex with the guy, you can expect more of the same physical reaction (perhaps unless he’s been taking probiotics in between when you first kissed and had sex. Science suggests they can potentially change someone’s microbes to match yours, says Tetro). 

Perhaps all this ridiculousness is just marketing for Bio-K+?  I wonder if they provide relationship probiotics?  Uggh.  This just gets worse and worse the more I dig.

UPDATE 3: Even more from Tetro this time from the Globa and Mail: Why women’s germs are important to the health and happiness of us all

While ancient cultures never used kissing as a means to find a mate – it was simply an act of food sharing – modern society views this touching of lips and sharing of saliva as a part of the ritual of selecting a spouse. When the microbes of the mouth meet the immune system of a potential partner, a reaction happens. If the microbes are seen as friendly – similar to the rearing women – then there will be a sense of harmony and happiness

If, however, the germs are foreign to the system, inflammation will incur as well a sense of unease, ruining any chance for a long-term relationship. As a result, those with the most closely resembled microbiomes will find themselves making the best mates.

And then

Further research into the links between the female microbiome and society will no doubt unveil even more fruitful facts. For now, as we prepare to honour women the world over on March 8, we can all take a moment to be thankful for women for their beneficial microbes, for making the human species happy and healthy.

Again, there is no scientific basis for these claims.  There is no literature out there showing microbes exchanged via kissing lead to any of these responses.  There certainly is no literature showing that somehow the immune system examines the microbes and if there is a match (to one’s mother) then this leads to harmony and happiness.  And there is no literature on the opposite occurring when there is not a match.  This is just completely made up.  Presented as though it is established in the scientific literature.

UPDATE 4: Some papers on kissing and microbiomes and related topics

Just thought I would add some links to papers on kissing and microbiota and related topics.  I have scoured the literature on this in the past and again now and find nothing – absolutely nothing – that supports the outlandish claims of Tetro.

Key paper: Shaping the oral microbiota through intimate kissing.  The most recent and most detailed paper on the topic.  Open access from the journal Microbiome.  This is a pretty good paper by Kort et al.  It has some background references worth looking at too. Here are their conclusions:

This study indicates that a shared salivary microbiota requires a frequent and recent bacterial exchange and is most pronounced in couples with relatively high intimate kiss frequencies of at least nine intimate kisses per day or in couples sampled no longer than 1.5 h after the latest kiss. The microbiota on the dorsal surface of the tongue is more similar among partners than unrelated individuals, but its similarity does not clearly correlate to kissing behavior. Our findings suggest that the shared microbiota among partners is able to proliferate in the oral cavity, but the collective bacteria in the saliva are only transiently present and eventually washed out, while those on the tongue’s surface found a true niche, allowing long-term colonization.

Other papers of possible interest – and there are pretty few – most of which are on kissing and pathogens

UPDATE 5: Some reasonable stories about the kissing / oral microbiota paper:

UPDATE 6: Some other ridiculous stories about kissing and microbiomes – with completely different – but equally bogus claims – compared to the ones described above. For example, some discuss the idea that a match for oral microbiomes would be ones that are most different from one’s own – the exact opposite of Tetro’s claims.  Though this at least has some logical basis, there is no evidence for it.  None.

UPDTAE 7: Sadly the ridiculous ideas from Tetro spread to other places

How Bacteria Affects Your Love Life –

UPDATE 8: April 29 2015. More ridiculous microbe claims from Tetro

Here is a painful quote from a new article by Tetro: “Almost all bacteria love milk and use the various components for nutrition and growth”.  Where does this come from?  So – anaerobic thermophiles from Yellowstone love milk?  Intracellular symbionts of aphids love milk? Photoautotrophs love milk? WTF.