More on this book
Community
Kindle Notes & Highlights
Shigella dysenteriae. The preferred treatment at first involved various forms of sulfa drugs, but Shigella strains soon showed resistance to those sulfas, so medical people turned to newer antibiotics, such as streptomycin and tetracycline. By 1953, strains of Shigella showed resistance also to both of those. Each bacterial strain, though, was resistant to only one drug. It could still be stopped by the others. Then in 1955 a Japanese woman returned from a stay in Hong Kong, sick with dysentery, and Shigella from her feces tested resistant to multiple antibiotics. From that point, resistance
...more
A whole set of resistance genes had evidently moved sideways, in the depths of the patients’ guts, from one kind of bacterium to another.
similar transfer between bacterial strains cultured together in flasks or dishes, and concluded that the capacity for multiple resistance was passed by conjugation. Yes, a sizable packet of genes, not just one bit of DNA, was moving across. And the exchange wasn’t limited to Shigella and Escherichia. Further research showed that the packet could cross boundaries between other species, even from genus to genus, among almost every group in the enteric bacteria, a large family of bugs that live within human bellies.
multiple resistance, to streptomycin and those three other antibiotics, was coded on an episome. They gave the episome a name: resistance transfer factor. It became known as R factor, for short, in parallel to Esther Lederberg’s F factor. This R factor could be transferred by conjugation. It could be transferred (at least in lab experiments) by transduction. It explained how harmless bacteria such as ordinary Escherichia coli could convey genes for multiple antibiotic resistance, across species boundaries, into dangerous bacteria such as Shigella dysenteriae,
episome had been replaced by a synonym, plasmid)
A plasmid, as known ever since, is a short stretch of DNA, sometimes circular like a bracelet, that exists and replicates in a cell independently of the cell chromosome. That independence facilitates its lateral passage to other cells
Shigellosis manifests as bowel inflammation and diarrhea, and the infectious dose for a human is low—only a trace needed to take hold and bloom in someone’s gut—meaning that it is highly transmissible through tainted water or food.
Private Cable’s Shigella was resistant to antibiotics that hadn’t yet been invented. More precisely, to antibiotic substances not yet discovered by humans. More precisely still, Cable’s strain was resistant in 1915 to penicillin and erythromycin, which went into use against human infections in 1942 and 1952, respectively.
resistance to antibiotics does exist in the wild because antibiotics exist in the wild. Some bacteria produce antibiotic substances as natural weapons, deterrents, for use in their competitive struggles against other bacteria.
Despite the absence of lab-produced drugs, a group of American researchers found bacteria, in a soil sample, that proved resistant to both tetracycline and streptomycin. How did antibiotic resistance arrive before manufactured antibiotics? Unknown, but again, the answer probably lay in the natural battles among bacteria.
vancomycin-resistant Staphylococcus aureus (a new demon to fear: VRSA), some
Maybe horizontal gene transfer also played a big role in the long history of microbial life.
“It may well be that gene exchange is so frequent,” they wrote, “that the evolutionary pattern in bacteria is much more reticulate than is commonly believed.” Weblike, not treelike.
frangibility
Koch’s lab assistant Julius Petri helped further by inventing the Petri dish, in which a pure strain grown on gelatin or agar could be protected from airborne contamination with a glass lid.
Maurice Panisset, published a book titled A New Bacteriology, making the case that all bacteria on Earth constitute a single interconnected entity, a single species—no, wait, maybe even a single individual creature—through which genes from all the variously named “species” flow relatively freely, by horizontal gene transfer, for use where needed. This freedom of transfer, this universal interchangeability of parts, gives the bacterial entity “a huge available gene pool,” Sonea
This is radically different, Sonea and Panisset claimed, from evolution as described by Darwin, who focused on animals and plants. Animal and plant species, as well as other eukaryotic species, arise mainly by genetic isolation. Bacteria are never so isolated. Instead of tortoises and mockingbirds marooned on islands, mutating and adapting, diverging slowly into distinct subspecies and eventually new species, finally reaching a point where they can’t or won’t mate with other populations—instead of that, you have relentless bacterial togetherness.
They called it a “superorganism,”
Sonea and Panisset’s superorganism was “just” the total global population of bacteria.
“reticulate evolution”
A 1982 essay in Science offered an overview, titled “Can Genes Jump Between Eukaryotic Species?,” with the implicit answer: probably. Some of these cases of distant transfer later turned out to be illusory—disproved when better data became available—but the basic premise was correct,
The bdelloids cope with such crises by hunkering into a dehydrated, dormant state, like instant coffee, in which they can survive for as long as nine years. When the water returns, they rehydrate and come alive. Another oddity of the bdelloids is that they reproduce without sex. Females give birth to females, no fertilization necessary. The fancy term for that is parthenogenesis. A male bdelloid has never been seen. Genetic evidence suggests that bdelloids have gone without sex for twenty-five million years—quite
Desiccation can be damaging to membranes and molecules, even when a creature survives the drought, and biologists suspect that such drying-and-rehydrating stresses cause bdelloid DNA to fracture and leave cell membranes leaky.
broken DNA, as a cell fixes it, using ambient materials, may include bits that weren’t part of the original. If that mended DNA happens to be in cells of the germ line, the changes will be heritable.
Omit sex, and you streamline reproduction but sacrifice adaptability. Parthenogenetic populations can thrive in the short term, but in the long term, they tend to go extinct. All this is relevant. Maybe bdelloid rotifers, reproducing asexually for millions of years—with no remixing of gene combinations, only mutations to supply incremental change—have gotten much of their freshening innovation from HGT.
Weismann barrier, named for August Weismann, the German biologist of the nineteenth century who defined the concept.
Bacteria cannot cross that barrier, Weismann’s barrier—so said the skeptical view—to insert bits of their own DNA into animal genomes. Impossible. And again it turned out to be possible.
computational biology, meaning the analysis of huge amounts of biological data using computer and mathematical skills. It’s essentially the same as what I’ve earlier mentioned as bioinformatics.
These transferred genes came from bacteria in the genus Wolbachia, a group of aggressive intracellular parasites that infect at least 20 percent of all insect species on Earth. Wolbachia bacteria target the germline cells of the animals they enter, especially ovaries and testes, and, once established, a Wolbachia infection is passed from mother to offspring within her infected eggs. It does not usually pass within infected sperm. Wolbachia work around that constraint, the absence of sperm-to-offspring transmission, and proliferate themselves by manipulating the reproductive outcomes of their
...more
Since they invade not just any cells but primarily the germline cells, that puts Wolbachia close to the very molecules of DNA that will be duplicated in the production of egg cells and passed to offspring. Such proximity seems to offer special opportunity for getting Wolbachia DNA spliced into the insect’s DNA.
four insects and four nematode worms had taken aboard Wolbachia genes by horizontal transfer. The most dramatic case was one species of fruit fly, which had accepted almost the entire genome of Wolbachia (more than a million letters of code) into its own nuclear genome.
Researchers at the time were so reluctant to believe that bacterial genes could be transferred into animal genomes that, before publishing a new genome sequence, they routinely edited out the bacterial stretches.
Her group had recently discovered evidence, for instance, of bacterial DNA transferred horizontally into the genomes of human tumors.
there’s at least some chance that such insertions might play a role in causing cancer.
Hotopp’s team did find bacterial DNA lurking within some normal human genomes, an interesting result. More peculiar and disquieting, though, was that they found it 210 times more common in tumor cells than in healthy cells.
bits of naked bacterial DNA, possibly from broken-open bacterial cells, may often get integrated into cells (not necessarily germline cells) of a person’s body. Into cells of the stomach lining, for instance. Or blood cells. By “integrated,” what I mean is, not just absorbed or injected into the human cell but patched into its DNA.
The bad news is that it might trigger cancer.
How? By disrupting the cell genome in a way that allows runaway cell replication.
The alternate hypothesis offered by Hotopp’s team, supported by genome data and now crying for further investigation, is that horizontal transfer of bacterial DNA may discombobulate one human cell, in the stomach, in the blood, wherever, and turn it cancerous.
An artifact, in scientific parlance, is an illusion produced by a methodological mistake.
it seemed almost as though the Weismann barrier had become a theological dogma.
inosculation.
“Each gene has its own history.” If each gene has its own history, Woese was wrong to draw such grand conclusions from a single molecule, however fundamental, and sketching the course of evolution as a single neat image was impossible. Pennisi saw that. Her piece ran in May 1998 under the headline “Genome Data Shake Tree of Life.”
the phylogeny of species didn’t look like a tree anymore. Not during the early phase of life on Earth, anyway. It looked more like a net. Evolution was “reticulate” as well as branching.
What might the tree look like? Again he drew a sketch, and, to his surprise, the editors of Science printed it. He called this one “a reticulated tree.” It was a tangle of rising and crossing and diverging and converging limbs. It had its antecedent (as Doolittle acknowledged) in a somewhat similar figure offered by Martin in his “Mosaic” paper. Martin’s tree resembled a sea fan, one of those delicate structures built by a colony of coral-like animals on the ocean floor. Its long limbs and branches rose wavily, diverging from a simple base.
Its impacts could be understood in four ways. First, new genes received by sideways transfer, from a different lineage or species, may allow a population of microbes (the recipient bug and its offspring) to colonize an entirely new ecological niche. Second, it may allow organisms to acquire a new sort of adaptation abruptly, without passing through the dangerous stage of being only half adapted to one situation or another. Third, this transformation happens fast compared with incremental mutation, which proceeds slowly. Fourth, HGT is a “font of innovation,” bringing drastically new genetic
...more
horizontal gene transfer might be the “principal explanatory force” in prokaryote evolution.
He noted that only 1 percent of the genes in an average bacterial or archaeal genome—and maybe far less than 1 percent in the genome of a eukaryote—are so deeply and complexly essential to the organism that they couldn’t be swapped by HGT.
A recent estimate suggests that each human body contains about thirty-seven trillion human cells. It also contains about a hundred trillion bacterial cells, for almost a three-to-one ratio of bacterial to human. (Another study proposes a lower ratio, roughly one-to-one, but that still means thirty-seven trillion bacterial cells in your body.) And this doesn’t even count all the nonbacterial microbes—the virus particles, fungal cells, archaea, and other teeny passengers—that routinely reside in our guts, our mouths, our nostrils, our follicles, on our skin, and elsewhere around our bodies.
...more
a whole new branch of biology: metagenomics, the study of living creatures and communities that can be known only from their genetic material.
