The "Junk" in our gut questions Common Design


A new study published in the journal Nature Microbiology found that humans have lost half of the gut bacteria (microbiota) that were present in our primate ancestors. The study, conducted by researchers at Cornell University, compared the gut microbiomes of chimpanzees and bonobos, our closest living relatives, with those of humans. The researchers found that humans were missing a significant number of bacterial groups that are present in chimpanzees and bonobos.

The researchers believe that this loss of gut bacteria may be due to changes in human diet and lifestyle over the past few million years. Humans have evolved to eat a more diverse diet than our primate ancestors, which may have led to the loss of some bacterial groups that were specialized for digesting certain foods. Additionally, changes in human social behavior, such as the development of agriculture and cities, may have led to changes in the environment that our gut bacteria live in.

The loss of gut bacteria may have a number of implications for human health. The gut microbiome plays an important role in digestion, immune function, and overall health. Studies have shown that people with certain diseases, such as obesity, inflammatory bowel disease, and cancer, often have different gut microbiomes than healthy people. The researchers who conducted the new study believe that restoring the lost gut bacteria in humans may be beneficial for health.

The study is the first to show that humans have lost a significant number of gut bacteria since our primate ancestors. The findings suggest that changes in human diet and lifestyle over the past few million years may have had a major impact on the composition of our gut microbiome. This loss of gut bacteria may have implications for human health, and further research is needed to understand the full impact of this loss.

Horizontal gene transfer (HGT) is the process by which genetic material is transferred between organisms that are not directly related often through their microbiota. This can happen through a variety of mechanisms, such as transformation, transduction, and conjugation. HGT can occur between microbiota bacteria, archaea, and eukaryotes.

Transferred elements (TEs) are genetic elements that can move from one genome to another. TEs can be genes, transposons, or other types of genetic material. TEs can be transferred between organisms through HGT.

When TEs are transferred between organisms, it can give the false impression of Neodarwinian common ancestry. This is because the genes or other genetic material that are transferred may be shared by two or more organisms, even if the organisms are not closely related. This can make it difficult to determine the true evolutionary history of organisms.

For example, if two bacteria share a gene that is known to have been transferred horizontally, this does not mean that the two bacteria are closely related. It simply means that the gene has been transferred between the two bacteria at some point in the past.

HGT can make it difficult to determine the true evolutionary history of organisms. However, HGT is also a natural process that has played a role in the Lamarckian evolution of life on Earth. By understanding how HGT works, we can better understand the evolutionary history of organisms and how life has changed over time.

Here are some additional details about HGT and TEs:

  • HGT is thought to be a relatively common event in the microbial world. Studies have shown that up to 50% of the genes in some bacteria may have been acquired through HGT.

  • TEs are a very diverse group of genetic elements. They can be short or long, and they can code for proteins or non-coding RNA.

  • TEs can be very mobile. They can move within a genome, or they can be transferred between genomes.

  • TEs can have a significant impact on the evolution of organisms. They can introduce new genes into a genome, or they can change the expression of existing genes.

HGT and TEs are important processes that have played a role in the evolution of life on Earth. By understanding these processes, we can better understand the diversity of life and how life has changed over time.

Non-Darwinian epigenetics controls are epigenetic mechanisms that can influence the expression of genes without changing the DNA sequence. NeoDarwinism changes these sequences These mechanisms can be inherited from one generation to the next, and they can have a significant impact on the phenotype of an organism.

Transposable elements (TEs) are a type of non-coding DNA (Neo Darwinism must code for natural selection)  that can move around within the genome. TEs can be inserted into genes, disrupting their expression. They can also silence genes by binding to regulatory regions.

The expression of TEs can be controlled by epigenetic mechanisms such as DNA methylation and histone modification. DNA methylation is the addition of methyl groups to DNA, which can silence genes. Histone modification is the addition or removal of chemical groups to histone proteins, which can also affect gene expression.

Non-Darwinian epigenetic controls can play a role in a variety of biological processes, including development, aging, and disease. For example, epigenetic changes have been linked to cancer, Alzheimer's disease, and other conditions.

One of the most well-studied examples of non-Darwinian epigenetic control is the case of the agouti mouse. Agouti mice have a gene that produces a protein called agouti, which promotes the production of black fur. However, if the agouti gene is silenced by epigenetic mechanisms, the mouse will have yellow fur.

The agouti mouse experiment shows that epigenetic changes can have a dramatic impact on the phenotype of an organism. This suggests that non-Darwinian epigenetic controls may play an important role in evolution.

However, it is important to note that non-Darwinian epigenetic controls are not always passed on from parent to offspring. In some cases, epigenetic changes can be reversed, or they can be passed on only to a subset of the offspring.

Overall, non-Darwinian epigenetic controls are a complex and fascinating area of research. They have the potential to shed light on a wide range of biological processes, from development to disease.

Article snippets

A new study finds that hundreds of bacterial groups have evolved in the guts of primate species over millions of years, but humans have lost close to half of these symbiotic bacteria

In the study, researchers compared populations of gut bacteria found in chimpanzees and bonobos, our closest relatives, with those of humans—which in total amount to some 10,000 different lineages of bacteria.

The scientists analyzed the evolutionary relationships of these bacteria in primates and identified groups of bacteria that were present in distant ancestors of humans and primates.

Strikingly, the results showed that these ancestral symbionts are being lost rapidly from the human lineage.

the study's authors suspect changing diets probably caused the divergence.

The working idea is that the losses we see spanning all human populations, regardless of lifestyle, were likely driven by dietary shifts that happened early in human evolution

In particular, human diets shifted away from complex plant polysaccharides found in leaves and fruits towards more animal fat and protein, Moeller said.

Jon Sanders, a former postdoctoral researcher in Moeller's lab, is first author of the study, "Widespread Extinctions of Co-diversified Primate Gut Bacterial Symbionts From Humans," published May 11 in Nature Microbiology

In the study, the researchers analyzed metagenomes, which are assembled by piecing together short base pair sequences from a whole community of genomes; the metagenomes revealed which microorganisms were present in a sample and their relative abundances.

Analyses of 9,640 human and non-human primate metagenomes, including newly generated ones from chimpanzees and bonobos, revealed significant evidence that gut bacteria groups shared an evolutionary history with their hosts, according to the paper.

The results showed that 44% of clades—a group that has evolved from a common ancestor—that have a shared evolutionary history with African apes were absent from the human metagenomic data and 54% were absent from industrialized human populations. At the same time, only 3% of bacterial clades in African apes that did not share an evolutionary history with these hosts were absent in humans.

This is the first microbiome-wide study showing that there are a great number of ancestral co-diversifying [shared evolution] bacteria that have been co-living within primates and humans for millions of years," Moeller said.

Ancestral bacteria may be passed from one generation to another from mothers to babies, and by social transmission with other members of the same species

The discrepancy in extinct bacteria between the general human population and those from industrialized countries may point to differences related to modern diets and medicines, such as antibiotics that are known to alter microbiomes.

Some researchers have speculated that the disruption of ancestral flora could be playing a role in modern diseases, such as autoimmune disorders and metabolic syndrome

A second related paper, "Home-site Advantage for Host Species-specific Gut Microbiota," also led by Moeller and Sprockett, which published May 12 in Science Advances, showed that gut bacteria locally adapt to the hosts they live in, providing a possible mechanism for the long-term stability of these symbioses.

https://phys.org/news/2023-05-humans-lost-primate-ancestors-gut.html




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