For my entire hospital career I have worked in oncology, where I have been part of teams taking care of people with cancer. Frequently patients have “neutropenic fevers,” a condition considered to be potentially harmful and almost always requiring admission to the hospital. Neutrophils are those brave little white blood cells that go out into our bodies and do battle with all the nasty things our bodies are exposed to every day. Neutropenia means the patient has none of those cells to speak of. We culture blood and urine, scan lungs, treat with antibiotics, and monitor for a few days to see if any microbes grow out in cultures. We teach people to fastidiously handwash, and avoid people who are sick. We make them wear masks in the hallways, in order to filter out airborne viruses. Their rooms have special filtration systems. We encourage them to make safe food choices, avoiding foods that can’t be washed or scrubbed clean, or might be undercooked. And you want to know the kicker? If these patients are infected, it’s usually because of microbes in their own body have run amok and caused infection.
You know what else is in the hospital? Microbes. Tons of antibiotic-resistant microbes, hanging out in patient bodies and everywhere else. Once someone is cultured positive for these microbes, they stay on “isolation” for the duration of the visit, sometimes for life in the case of microbes resistant to all antibiotics, in the (vain) hopes that staff, visitors and patients won’t go moving those resistant microbes around the hospital. A shift where I don’t where a yellow isolation gown to go into these rooms is pretty unusual.
Yong made my little grey cells stretch and reach, and now I have yet more ways to think about microbes, and I dearly wish he would re-write this book–maybe in magazine form–every couple years so I can keep up with all the interesting research. Like David Quammen, Yong doesn’t just stick to one branch of research science; he wanders around many fields as he explores the impact microbes have made on us. He’ll first have you thinking about their sheer evolutionary weight (literally and figuratively), reminding us that we evolved in context of a microbe landscape, not the other way round (and some thought apes were a stretch). Like living on a planet where most of the water is saltwater, it makes sense that microbes would impact the evolution of life.
Yong walks the reader through some of the science that show how animals evolved to use microbes (and perhaps vice versa?). Some are evolutionary, some genetic, some macro. There’s a lovely experiment where a glowing squid developed a sequestered area for those microbes–can’t set them free in the body, of course, so you have to create a special compartment.
In other words, I highly recommend this book. It’s quite well researched and documented, with extensive citations. There’s a bibliography and index, for those that want to delve further or pick and choose. As a further note, I’ll say that I always appreciate researchers/writers who express appreciation for those they interview and follow, without being fawning, and Yong does a nice job with that as well. There are parts I really liked, parts I liked less, but any book that keeps me thinking about it months later is a five star read.
I’m going to put my detailed book report below, with notes heavily on the medical and the ocean science. There’s also some interesting stuff about insects, for those who might lean that way, and trees.
Chapter 1: Living Islands:
One of my favorite, and most mind-blowing quotes: “Microbially, we are similar but different. When microbiologists first started cataloguing the human microbiome in its entirety they hoped to discover a “core” microbiome: a group of species that everyone shares. It’s now debatable if that core exists (citation). Some species are common, but none is everywhere. If there is a core, it exists at the level of functions, not organisms. There are certain jobs, like digesting a certain nutrient or carrying out a specific metabolic trick, that are always filled by some microbe–just not always the same one” (p. 17). He makes the analogy to macro-biology in apex predators, which might be a lion in parts of Africa, but be a wolf in parts of North America. He also makes the analogy work for temporal succession as well. As a human baby grows, its gut microbes change, just as an area of land subject to a forest fire will undergo succession. There’s mention of a scientist studying mole rats who is seeking to study the first idea, comparing microbiomes of animals that share extreme lifestyle traits and if the microbiome might have helped them ‘pre-adapt’ to their lifestyle.
There’s a fun tangent on what makes an individual. Anatomically, microbes share space with a being’s physical body. Developmentally, some animals use genes from them and microbes affect how they grow (ie. tube worms). Physiological ignores microbes that are needed for essential nutrients.
Chapter 2: The People Who Thought to Look:
Traces some of the pioneers and the development of the philosophy of microbes. Overall an interesting section that traces some of the influential thoughts and researchers, even if they were not recognized at the time. Leeuwenhoek with the first microscope, Pasteur in 1865 and a German doctor in 1876 did their bit showing how these small things could cause disease, as well as ferment liquor. Lister was the surgeon that made the big jump from bacteria to infection in human medicine. There were threads of ‘good bacteria’ starting to show up in the early 1900s. The first text, however, didn’t show up until 1962.
Also in this section is a confusing bit about how the an obscure research categorizing microbes by rRNA in the 1970s ended up revolutionizing how microbe populations and genetics were described. This, I fear, was a bit less accessible, but the end result was the it made identification/classification possible without being able to grow the microbes in the lab or even find them under the microscope (a benefit in hot springs).
Chapter 3: Body Builders:
A complex chapter that examines the interplay of microbes and ‘host’ organisms, beginning with the Hawaiian bobtail squid which has light organs due to luminous bacteria. The absolutely fascinating thing is that squid are born sterile with the light organ covered in cilia and mucus. They draw in bacteria, and once they reach a magic size of five V fischeri cells touching the layer, genes turn on that start making the environment inhospitable to other microbes, as well as breaking down the mucus to make room for more V.fischeri. Once the microbes move into the light organ, the squid continues to ‘remodel,’ absorbing the cilia and constricting the ducts, transforming into the final organ (p.51)
Indirectly, one of the fascinating examples listed here is of a type of tube worm known for covering ship hulls in warm waters, beginning in Hawaii but now world-wide. In the larvae stage, they are microscopic and abundant, and travel until they reach a nice biofilm that has P.-luteo, and without it, the larvae wouldn’t settle down into the sedentary tube worm form. I found this particularly intriguing as biofilms are such a huge issue in medicine when it comes to implanted/non-organic devices inside human bodies, but I supposed water systems engineers and the like deal with it as well.
He digresses into a discussion of the immune system and it’s general conception of an antagonistic model, with the immune system ‘fighting’ microbes. However a study of Bacteroides fragilis, a common gut bacteria, carries a polysaccharide that helps boost or restore helper T cells. Unfortunately, after mentioning this highly tempting 2002 study, he then switches to a study of hyenas and that traces of different microbe types can be seen in scent-markings, and that these represent different species of hyenas, different groups and fitness levels, etc. It’s breaking down where scent markers come from.
He then jumps back to a neurobio study done by Patterson in 2001 where triggering an immune response in pregnant mice lead to mice pups that were anxious, startled easily and not social, kind of like autism. Patterson got together with the gut researcher mentioned above, Mazmanian, and they noted definite improvements in the mice’s behavior in terms of decreased startle and improved communication (but not sociability). Mazmanian is continuing the research, looking for evidence that the effect is reproducible in people. The acting theory is that the virus created an ‘excessively permeable’ gut, along with unusual microbes, that allowed a toxin known to cause anxiety to travel to the mouse brain. The B.fragilis improved the gut environment, preventing leaky gut and perhaps improving immune function.
The last section begins with an anecdotal ‘study’ about a man who was shot in the gut in 1822, allowing the doctor who ‘saved’ him to monitor and catalog his stomach contents. The doctor noted connection between mood and gut digestion, which we should all know by now, right? Apparently, biologists call it the ‘gut-brain axis’ (note to self for future research). He reviews a handful of mouse studies that looked at feeding a gut bacteria to germ-free mice. The one to make note of is the one where they found that L.rhamnosus helped timid mice overcome anxiety, were more able to be in exposed parts of a maze/open field, tried to paddle to get out of water (instead of just floating). The bacteria affected the vagus nerve, and then how different parts of the brain responded to GABA (severing the vagus nerve removed any beneficial effects).
Chapter 4: Terms and Conditions Apply
Chapter 5: In Sickness and in Health
Chapter 6: The Long Waltz:
Exploring the mutual evolutionary connection between microbes and some of the species they live with. This is largely on an insect level, beginning with an unusual bacteria found in a man’s wound that was able to be grown in a lab, a microbe that normally requires an insect to survive due to genetic loss. This is the starting point for examining the genetic connections that we observe at this point in time, in perhaps their more final forms. It continues with a beewolf wasp that passes on Streptomyces bacteria to its larvae so that they overwinter safely.
A quick discussion on routes of transmission of such bacteria, which every medical person knows all too well is followed by a more general discussion/assertation that animals ‘sculpt’ their microbiome. In 1991, Lynn Margulis called this the ‘holobiont,’ an equivalent to an ‘ecosystem’ in some ways, although more connected. Coral reefs are an example of this. Interestingly, this is a revolutionary idea (and quite non-Western??) in the sense that a community lives or survives together, rather on the basis of an individual’s genes.
Chapter 7: Mutually Assured Success
Chapter 8: Allegro in E Major
Chapter 9: Microbes a la Carte
Chapter 10: Tomorrow the World