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Horizontal gene transfer: Human gut microbes exchange genes more frequently in urban areas


Urban people have less diverse populations of microbes:

The researchers analyzed bacterial DNA to identify recent cases of horizontal gene transfer (HGT), a process that allows individual cells to mix up their genomes and acquire new functions from other bugs in the microbial community without having to reproduce. The team found that species in the gut frequently exchange genetic material, and that they do it more if they’re living inside people in industrialized or urban societies than if their hosts reside in rural or less developed environments.

“What’s novel and really impressive here” is the team’s use of whole-genome sequencing to study thousands of individual bacterial genomes, says Gladstone Institutes data scientist Katie Pollard, who was not involved in the study. While the results themselves aren’t unexpected given findings from previous work on HGT and industrialization in the context of the human microbiome, “this paper brings it all together and confirms it in a more rigorous way.”

Catherine Offord, “Gene Exchange Among Gut Bacteria Is Linked to Industrialization” at The Scientist

It’s not yet clear why there are fewer types of microbes in urban people’ guts or why they favor horizontal gene transfer more often.

But note: At one time, the researchers would be trying to explain it all in terms of Darwinism. That alone shows how much has changed without people really noticing.

The paper is open access.

See also: Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

Thanks, Jerry, You answered my question that at least for you the comment that I quoted from the article in the OP isn't really accurate, and that HGT is not something separate from Darwinism. That's what I thought, so I appreciate the feedback. Viola Lee
I personally consider HGT to be one of the engines of variation so if they happen to the gametes, it is a form of genetic change and subject to natural selection after getting passed on. So I do not see any real reason for not considering it part of Darwinism. Obviously any cell in the body can experience a change to its genome but only if it is in a gamete, will it affect future generations. There are way more than 47 but most are not common so do not get much attention unless you want to get published. As I said, I personally consider HGT a variation so is part of Darwinism or whatever the modern synthesis is today. I cannot see any reason why to exclude it. Reproduction then spreads the changes that occur. So your summary is essentially what I believe except where I have commented. But as I said Darwinism or its variations are not even the minor leagues of evolution. It is basically genetics and important in this regard. But as an explanation for major changes over time in life forms, it is a complete failure.
the discovery of HGT and neutral theory, the thinking has changed dramatically.
This has essentially changed nothing. jerry
Hi Viola Lee, I touched on this in the other thread but it is probably more appropriate here. Darwin drew heavily on selective breeding as the foundation of his theory. But instead of humans deciding what individuals bred with each other, based on favourable traits, he hypothesized that we could see a similar thing happening in nature by unfavourable traits being eliminated because individuals possessing them were less likely to reproduce. Or, that those with favourable traits would produce more offspring than those with less favourable traits. He knew that for his theory to be correct, traits had to be heritable, and there had to be a source of heritable traits. He didn’t rule out the inheritance of acquired characteristics. After the discovery of DNA and genes, it was believed that point mutations in the germline cells was the source of all heritable variation. But as we learned more about things like gene duplication, inversions, translocations, meiosis and HGT, we discovered that it was far more complicated than point mutation. If anything these discoveries further support Darwin’s theory as they provide more information on the source of heritable variation. Something that his theory needs. Steve Alten2
Thanks, Jerry. Layperson comments here: these are my understandings and may be wrong 1. HGT changes genes, but not really by mutation, because mutations are changes within the existing gene structure. It seems that maintaining this distinction is probably important. 2. You say that mutations are "usually changes that happen during the rise of new offsprings." If they are "usually" such changes, are there other situations that count as mutations? And can't I get mutations in my genes that are not in the gametes and thus don't get passed on? (And I'm too old to have offspring anyway, so can my genes still have mutations?) 3. I understand that there are a number of ways genes can mutate, although I have no idea how there could be 47. That's probably over my pay grade on this topic. 4. As I understand it, natural selection is separate from mutations themselves, or HGT. Natural selection is what happens to organisms after the mutations happens so that the mutations pass to a new generation. Is that accurate? 5. You write, "The key to Darwinism is mutations. Natural selection gets the biggest play in the popular literature since it’s easy to understand." I understand that, although I know (but not in much detail) that there are other aspects or mechanisms by which mutations or other genetic changes spread to more organism. I assume that those other mechanisms are also part of Darwinism? So there are two somewhat separate things here: first genes get changed so they can pass to a new organism (by mutation of various sorts or by HGT, although maybe HGT doesn't count as Darwinism according to the OP), and then those genes spread through more reproduction (sexual or asexual) by natural selection and other more technical means. Is that a reasonable summary? Viola Lee
I just found an old comment by Allen MacNeill. It’s engines of variation not mutations.
And the number 47 is already out of date. The list grows longer every day, as more research results are published. Also, most of the entries in the list are simply “headings”, encompassing dozens (and in some cases hundreds) of different, related mechanisms of phenotypic variation
Whether this list is 47 or in the thousands, none explain how a protein can arise. It can explain changes to a current protein but not a new one. People are often not very precise when they use various words snd terms. They often conflate meanings with other ideas that are similar. jerry
So HGT is not Darwinism for that reason?
Yes and no. Is HGT a mutation? If one considers this to be yes, then the new genome has to go through the natural selection process to survive. So it can be thought of as Darwinism. HGT is usually not considered a mutation. But is this a distinction without a difference? Mutations are usually changes that happen during the rise of new offsprings. Allen MacNeil who used to post here frequently referred to 47 engines of mutation. I’m not sure if HGT was one of them. Then he increased the number adding more ways the genome could change. HGT is a way the genome can change. The key to Darwinism is mutations. Natural selection gets the biggest play in the popular literature since it’s easy to understand. Humans are modifying genomes all the time and this is usually not referred to as mutations but the effect is the same. As I said on the other thread, no one has discovered how proteins could arise. jerry
Since these comments never showed up in the comments column, which now seems to be working, I'll repeat, "I just read the linked article “Darwin, It’s Not Your Evolution Anymore”, which was interesting, and it had this line, “Bacteria just do not play by Darwin’s rules.” I guess Darwinism is being used solely to refer to what happens to genes through reproduction. Is that true? So HGT is not Darwinism for that reason?" Viola Lee
Learning requires stability. Experimentation requires stability. When people of different types are pushed together and move in and out quickly, only the hardiest gut bacteria that can survive in all the guts remain in circulation. When a single type of people remain stable in one place, the bacteria have time and room to learn and vary, so they can handle different situations. It's the same with language. In places with lots of mobility and immigration, language becomes simple and rigid. In isolated small towns, language remains complex and poetic. And I'll bet that the hardy bacterium is the same type that leads to obesity and type 2 diabetes. polistra
I am not a biologist although I am quite interested in physiology and especially gut microbes, and I'm not clear how the word Darwinism is used here (it seems like maybe a synonym for materialism?), but I don't understand the remark "At one time, the researchers would be trying to explain it all in terms of Darwinism. That alone shows how much has changed without people really noticing." HGT has been known and studying for about 75 years. How is this being explained in some way different than "Darwinism"? Perhaps someone can explain? And note, I understand that in HGT genes are passed from organism to organism "horizontally", not "vertically" through reproduction. As I said, that's been known about for a long time and was a neat thing to discover. Edit: I just read the linked article "Darwin, It's Not Your Evolution Anymore", which was interesting, and it had this line, "Bacteria just do not play by Darwin’s rules." I guess Darwinism is being used solely to refer to what happens to genes through reproduction. Is that true? So HGT is not Darwinism for that reason? Viola Lee

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