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Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You
Suddenly, research findings require a paradigm shift in our view of the microbial world. The Human Microbiome Project at the National Institutes of Health is well under way, and unprecedented scientific technology now allows the censusing of trillions of microbes inside and on our bodies as well as in the places where we live, work, and play. This intriguing, up-to-the-minute book for scientists and nonscientists alike explains what researchers are discovering about the microbe world and what the implications are for modern science and medicine.
Rob DeSalle and Susan Perkins illuminate the long, intertwined evolution of humans and microbes. They discuss how novel DNA sequencing has shed entirely new light on the complexity of microbe-human interactions, and they examine the potential benefits to human health: amazing possibilities for pinpoint treatment of infections and other illnesses without upsetting the vital balance of an individual microbiome.
This book has been inspired by an exhibition, The Secret World Inside You: The Microbiome, at the American Museum of Natural History, which will open in New York in early November 2015 and run until August 2016. It will then travel to other museums in the United States and abroad.
Rob DeSalle and Susan Perkins illuminate the long, intertwined evolution of humans and microbes. They discuss how novel DNA sequencing has shed entirely new light on the complexity of microbe-human interactions, and they examine the potential benefits to human health: amazing possibilities for pinpoint treatment of infections and other illnesses without upsetting the vital balance of an individual microbiome.
This book has been inspired by an exhibition, The Secret World Inside You: The Microbiome, at the American Museum of Natural History, which will open in New York in early November 2015 and run until August 2016. It will then travel to other museums in the United States and abroad.
- GenresScienceNonfictionHealth
264 pages, Hardcover
First published November 24, 2015
12 people are currently reading
539 people want to read
About the author
Rob DeSalle
36 books17 followersRob DeSalle is curator of entomology in the Sackler Institute for Comparative Genomics at the American Museum of Natural History, New York City. He is author or coauthor of dozens of books, several based upon exhibitions at the AMNH, including The Brain: Big Bangs, Behaviors, and Beliefs and A Natural History of Wine, coauthored with Ian Tattersall and published by Yale University Press. He lives in New York City.
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Displaying 1 - 17 of 17 reviews
March 2, 2016
While not as entertaining as 10-percent Human, this book dives deeper into the science of the microbiome, covering the biology of the mouth, skin and digestive system. If you are serious about learning who rides along with us, this book will introduce you to our uninvited guests. The result is a better understanding of tooth decay - bacteria recolonize your teeth within seconds after brushing, but don't form plaques until they are fed - a better understanding of how the digestive system counters dangerous invaders - and a better understanding of the benefits of our personal microbiome. For readers with a scientific interest, this is well-researched and interesting.
September 28, 2022
The authors of this book couldn’t decide if they wanted it to be geared towards laymen or aspiring biologists. The book bounces wildly from complex scientific explanations of biological processes (like DNA sequencing or the role of DNA and RNA in protein synthesis) to more breezy explanations of the different types of bacteria you find on your keyboard or toilet. The book also takes a LOT of tangents on seemingly unrelated topics. It desperately needed better editing and organization.
That said, I did learn some things and there is a lot of good and interesting info buried in here. But I don’t know that I would recommend this book as your first introduction to learning about your microbiome. 2 Stars.
What follows are my notes on the book:
This book is about the recent paradigm shift in how we view the microbial world. Mankind only learned about the unseen world of microbes just over a 100 years ago. By the year 2000, only about 7K species of Bacteria and Archaea had been described and named. However, by this time it is recognized that there are probably tens of millions of bacterial species on the planet (and hundreds of millions of others that have gone extinct over the age of the earth).
The paradigm shift from focusing on single pathogenic organisms to understanding communities of organisms living in and on us was made possible by a revolution in human technology. There are thousands of species of bacteria living on our bodies, most of them in commensal or mutualistic relationships with us. These change depending on our age, sex, and myriad environmental factors. It is not always microbes that cause health problems, but disruption in the natural ecology of our bodies and the balance of our body’s cells with trillions of microbes contained within. Furthermore, while some microbes cause specific diseases, we are now aware of the possibility that different bacterial species in combination can cause illness.
Our body is not a single ecosystem but multiple dynamic ecosystems made up of very tiny, and very biologically diverse organisms. Besides Bacteria, there are two other domains of single-cell organisms: Archaea and Eukarya. The author presents different interpretations on which evolved first.
Bacteria are remarkably complex. For example the Bacillus subtilis has a single chromosome with 1.7 million pairs of DNA molecules (G, A C, T) and a genome with 1,914 genes. There is a brief exploration of viruses and whether they are considered life since they cannot replicate themselves without hijacking another cell’s biochemical machinery.
Bacteria and Archaea propagate by replicating their DNA and splitting into two cells. Both types of cells are promiscuous when it comes to exchanging DNA through Horizontal Gene Transfer (complicating theories on which evolved first). Scientists have artificially synthesized the 180 core genes into artificial chromosomes, placed those chromosomes into an otherwise empty bacterial cell and discovered these synthetic bacteria can function and reproduce.
Bacteria are incredibly varied and have found ways to successfully inhabit nearly every livable (and some unlivable) places on the planet. We have learned that perhaps as many as 90% of the cells in a typical human body are microbes, and that these make up to 3% of our body mass. Current estimates are that there are more than 10K species of microbes in and on our bodies.
Microbiologists have established several databases of bacterial DNA and Ribosomal sequences. Through the time consuming and labor intensive culturing process, scientists have characterized and named a little over 8K different species. However, not all species are conducive to being cultured.
The human body is collection of vastly different microbial ecosystems. In addition to different parts of the skin and internal organs, many areas can change over time (like dry to sweaty armpits after a workout, or a shower after being sweaty). Likewise, geographic location can have a substantial impact on the types of microbes in and on people (different weather, elevation, soils, diets, animals, urban vs rural, etc all contribute to a person’s microbiome).
On average there are 150 species of bacteria on human hands alone. Women tend to have much more microbial diversity on their hands than men do. The National Institute of Health started the $150M Human Microbiome Project to map out various microbiomes in humans. The environment on our skin is acidic, so only bacteria with a high pH tolerance tend to survive there. Also, the skin is cooler than our internal organs which effects the types of microbes that live there.
There are basically four general kinds of bacteria living on skin: Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, each of which taxonomists call a phylum. Phylotype is the technical name used for what we normally call a species when speaking of bacteria. Oily, moist, and dry areas of our skin all have different types of bacteria. Many skin disorders are caused by bacterial interlopers (acne, eczema, dermatitis for example). In damaged skin, such as burned flesh, other bacteria can thrive and multiply to cause other types of infections.
In one experiment, scientist collected samples before and after a roller derby with teams from San Francisco, Washington DC, and Eugene Oregon. Members of the three teams had distinctly different bacteria on their skin that were more common to their home geography. After the skin contact of these matches, many of the bacteria were exchanged on contact creating much more overlap in their skin microbiome.
Your belly button is an environment unto itself with nearly 2,400 phylotypes found in sixty different belly buttons sampled.
The microbiome of babies can be different depending on the type of birth. The amniotic sack is relatively sterile. When babies pass through the birth canal, their skin and nasal passages are exposed to many microbes in the mother that become the foundation for their skin and gut microbiome. Babies born by C-section (an operation conducted in a sterile room with sterile gloves and instruments) miss this microbial exposure, making them more susceptible to infections like staph.
In sampling subway surfaces, scientist discovered larger than usual frequency of Enterococcus on surfaces (this bacteria largely resides in feces). The bacterial composition on toilet seats is remarkably similar to that of pillow cases (another area exposed to large areas of skin). Places in kitchens that are cleaned regularly (sink) have less microbial diversity than areas that are not (like exhaust fans). Homes with dogs have different microbial environments than those without. There is evidence that being exposed in the home to the microbiome of a pet may help keep family members from developing allergies.
The habitats inside our body are also diverse with many niches for different microbes. The mouth has at least 250 species. 80M bacteria can be exchanged in a 10 second French kiss. There is a very wide range of environmental conditions in the digestive track (acidity varies greatly as you move through the stomach and colon). There are 10B microbial cells per milliliter in the lower gut compared to 10K in the stomach. 1,200 species have been categorized so far in the oral microbiome, half of them considered prevalent. It is likely that only 24% of the microbes in the oral microbiome are sufficiently well know with no developed taxonomy for the remaining 3/4s.
The large intestine is a pretty benign place allowing bacteria to proliferate. Many of these perform useful functions that our intestines cannot perform on their own (like absorb amino acids and B vitamins). Many of these bacteria also help regulate the efficiency of the intestinal wall and some metabolic functions. Sex organs have their own unique microbiomes. Circumcised penises have different bacteria than uncircumcised ones. Vaginas largely fall into five common types of bacterial communities. When the normal balance gets disturbed it can lead to yeast infections and other conditions. The temperature in the lungs can vary between 26C and 32C (78.8-89.6F) leading to great variation in lung microbes.
Just like pollution can lead to algae blooms in contaminated water, the body can experience microbial blooms where certain types of bacteria not normally present or present in limited numbers suddenly grows leading to illness. These blooms could be a result of genetic disposition or changes in the environment (like diet).
In “bubble mice” (mice born and raised in sterile environment for testing purposes), scientists are able to test their bodies’ reaction to the introduction or withholding of specific bacteria or combinations of bacteria. In one study they showed how the gut microbiome differed between normal and obese mice. High fat diets disturb the mucous membranes of the intestines. By introducing A. muciniphila microbes into the guts of obese mice, this helped repair the damaged intestinal tissues from a high fat diet. Sterile mice without significant gut bacteria were fed a Western diet high in sugar did not gain excess weight, demonstrating that the gut microbiome plays a role in developing obesity. This growing awareness of the microbiomes impact on diseases is helping to reshape approaches to disease management.
That said, I did learn some things and there is a lot of good and interesting info buried in here. But I don’t know that I would recommend this book as your first introduction to learning about your microbiome. 2 Stars.
What follows are my notes on the book:
This book is about the recent paradigm shift in how we view the microbial world. Mankind only learned about the unseen world of microbes just over a 100 years ago. By the year 2000, only about 7K species of Bacteria and Archaea had been described and named. However, by this time it is recognized that there are probably tens of millions of bacterial species on the planet (and hundreds of millions of others that have gone extinct over the age of the earth).
The paradigm shift from focusing on single pathogenic organisms to understanding communities of organisms living in and on us was made possible by a revolution in human technology. There are thousands of species of bacteria living on our bodies, most of them in commensal or mutualistic relationships with us. These change depending on our age, sex, and myriad environmental factors. It is not always microbes that cause health problems, but disruption in the natural ecology of our bodies and the balance of our body’s cells with trillions of microbes contained within. Furthermore, while some microbes cause specific diseases, we are now aware of the possibility that different bacterial species in combination can cause illness.
Our body is not a single ecosystem but multiple dynamic ecosystems made up of very tiny, and very biologically diverse organisms. Besides Bacteria, there are two other domains of single-cell organisms: Archaea and Eukarya. The author presents different interpretations on which evolved first.
Bacteria are remarkably complex. For example the Bacillus subtilis has a single chromosome with 1.7 million pairs of DNA molecules (G, A C, T) and a genome with 1,914 genes. There is a brief exploration of viruses and whether they are considered life since they cannot replicate themselves without hijacking another cell’s biochemical machinery.
Bacteria and Archaea propagate by replicating their DNA and splitting into two cells. Both types of cells are promiscuous when it comes to exchanging DNA through Horizontal Gene Transfer (complicating theories on which evolved first). Scientists have artificially synthesized the 180 core genes into artificial chromosomes, placed those chromosomes into an otherwise empty bacterial cell and discovered these synthetic bacteria can function and reproduce.
Bacteria are incredibly varied and have found ways to successfully inhabit nearly every livable (and some unlivable) places on the planet. We have learned that perhaps as many as 90% of the cells in a typical human body are microbes, and that these make up to 3% of our body mass. Current estimates are that there are more than 10K species of microbes in and on our bodies.
Microbiologists have established several databases of bacterial DNA and Ribosomal sequences. Through the time consuming and labor intensive culturing process, scientists have characterized and named a little over 8K different species. However, not all species are conducive to being cultured.
The human body is collection of vastly different microbial ecosystems. In addition to different parts of the skin and internal organs, many areas can change over time (like dry to sweaty armpits after a workout, or a shower after being sweaty). Likewise, geographic location can have a substantial impact on the types of microbes in and on people (different weather, elevation, soils, diets, animals, urban vs rural, etc all contribute to a person’s microbiome).
On average there are 150 species of bacteria on human hands alone. Women tend to have much more microbial diversity on their hands than men do. The National Institute of Health started the $150M Human Microbiome Project to map out various microbiomes in humans. The environment on our skin is acidic, so only bacteria with a high pH tolerance tend to survive there. Also, the skin is cooler than our internal organs which effects the types of microbes that live there.
There are basically four general kinds of bacteria living on skin: Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, each of which taxonomists call a phylum. Phylotype is the technical name used for what we normally call a species when speaking of bacteria. Oily, moist, and dry areas of our skin all have different types of bacteria. Many skin disorders are caused by bacterial interlopers (acne, eczema, dermatitis for example). In damaged skin, such as burned flesh, other bacteria can thrive and multiply to cause other types of infections.
In one experiment, scientist collected samples before and after a roller derby with teams from San Francisco, Washington DC, and Eugene Oregon. Members of the three teams had distinctly different bacteria on their skin that were more common to their home geography. After the skin contact of these matches, many of the bacteria were exchanged on contact creating much more overlap in their skin microbiome.
Your belly button is an environment unto itself with nearly 2,400 phylotypes found in sixty different belly buttons sampled.
The microbiome of babies can be different depending on the type of birth. The amniotic sack is relatively sterile. When babies pass through the birth canal, their skin and nasal passages are exposed to many microbes in the mother that become the foundation for their skin and gut microbiome. Babies born by C-section (an operation conducted in a sterile room with sterile gloves and instruments) miss this microbial exposure, making them more susceptible to infections like staph.
In sampling subway surfaces, scientist discovered larger than usual frequency of Enterococcus on surfaces (this bacteria largely resides in feces). The bacterial composition on toilet seats is remarkably similar to that of pillow cases (another area exposed to large areas of skin). Places in kitchens that are cleaned regularly (sink) have less microbial diversity than areas that are not (like exhaust fans). Homes with dogs have different microbial environments than those without. There is evidence that being exposed in the home to the microbiome of a pet may help keep family members from developing allergies.
The habitats inside our body are also diverse with many niches for different microbes. The mouth has at least 250 species. 80M bacteria can be exchanged in a 10 second French kiss. There is a very wide range of environmental conditions in the digestive track (acidity varies greatly as you move through the stomach and colon). There are 10B microbial cells per milliliter in the lower gut compared to 10K in the stomach. 1,200 species have been categorized so far in the oral microbiome, half of them considered prevalent. It is likely that only 24% of the microbes in the oral microbiome are sufficiently well know with no developed taxonomy for the remaining 3/4s.
The large intestine is a pretty benign place allowing bacteria to proliferate. Many of these perform useful functions that our intestines cannot perform on their own (like absorb amino acids and B vitamins). Many of these bacteria also help regulate the efficiency of the intestinal wall and some metabolic functions. Sex organs have their own unique microbiomes. Circumcised penises have different bacteria than uncircumcised ones. Vaginas largely fall into five common types of bacterial communities. When the normal balance gets disturbed it can lead to yeast infections and other conditions. The temperature in the lungs can vary between 26C and 32C (78.8-89.6F) leading to great variation in lung microbes.
Just like pollution can lead to algae blooms in contaminated water, the body can experience microbial blooms where certain types of bacteria not normally present or present in limited numbers suddenly grows leading to illness. These blooms could be a result of genetic disposition or changes in the environment (like diet).
In “bubble mice” (mice born and raised in sterile environment for testing purposes), scientists are able to test their bodies’ reaction to the introduction or withholding of specific bacteria or combinations of bacteria. In one study they showed how the gut microbiome differed between normal and obese mice. High fat diets disturb the mucous membranes of the intestines. By introducing A. muciniphila microbes into the guts of obese mice, this helped repair the damaged intestinal tissues from a high fat diet. Sterile mice without significant gut bacteria were fed a Western diet high in sugar did not gain excess weight, demonstrating that the gut microbiome plays a role in developing obesity. This growing awareness of the microbiomes impact on diseases is helping to reshape approaches to disease management.
August 31, 2016
This book probably deserves more than the three starts I give to it, but I stick to my verdict. I bought this book because it promised me an introduction to the microbiom (to scientists and non-scientists alike), and in some way I got that. But in another way I got a very high-level introduction to biology, DNA sequencing, protein-forming amino acids etc.
These things are all very interesting, but they are way above my level - and besides what I really wanted to know more about.
Granted, it may be necessary to have these subjects covered - from a scientific perspective. But for someone who, like me, is interested in the millions of microbes living on us this article is somewhat a detour.
If you want to know the characteristics of our bacteria (their shapes, history and classification) this is your book. If not, I would suggest you look elsewhere.
These things are all very interesting, but they are way above my level - and besides what I really wanted to know more about.
Granted, it may be necessary to have these subjects covered - from a scientific perspective. But for someone who, like me, is interested in the millions of microbes living on us this article is somewhat a detour.
If you want to know the characteristics of our bacteria (their shapes, history and classification) this is your book. If not, I would suggest you look elsewhere.
August 17, 2016
Fascinating book that really brought the latest info to the reader. I only gave it two stars because it was badly in need of better writers or a great editor. Poorly organized and skipped from way too much info on a subject to too little. Sometimes it was way over my head using terms that were not clearly explained and sometimes it explained way too much. I'll be looking for another book on this subject. Someone mentioned 10% Human so will look for that.
May 11, 2016
Bottom line, respect your microbes! Good or bad they play a very important roll in life. Lots of little interesting facts about our bodies, evolution and the microbiome. I was sad it was such a short book, and rationed out pages to read so that it lasted longer. It really sounds like we are at the very beginning stages of learning what role microbes play in our bodies and how they impact our moods, digestion, and illness. Can't wait to learn more as new research comes along!
March 1, 2017
The author went into further detail about genes and microbes than I had read before. A lot of information was presented in a clear and digestible way.
November 11, 2015
Welcome to the Microbiome by Rob DeSalle and Susan Perkins. Published by Yale University Press
If you thought bacteria were tiny blobs that cause disease, then think again, because there’s far more to them than that. Welcome to the Microbiome is a book that offers the possibility of thinking about our inner world in a very different way. Humans like to think they are the superior race, but it may be no exaggeration to say that without the bugs that have evolved with us we would not be where we are today.
The gut is only one area of the body Rob DeSalle and Susan Perkins describe in their guided tour of the many habitats where the microbes live side by side with us. The types of colonies that reside within the digestive tract have far reaching effects on the general health of all our organs. But the study of how microbes interact and largely coexist with us is a rapidly developing area in science and one that many hope will revolutionise our approach to medicine.
The authors take the reader though the whole process of evolution and relevant physiology and biochemistry using straightforward narrative and description to explain how bugs interact with us. They also describe how new technology for studying microbes has revealed our bodies ‘are swamped with bacterial genes – genes that are busy transcribing and translating their own proteins in tandem with our own DNA replication processes.’ This seems to turn on its head the concern we have for whether there is life somewhere out in space. It is a description that takes the phrase ‘we are not alone’ to a whole new level. The invasion occurred a long time ago and is more up close and personal than we could have ever imagined. There is a constant shuffle for dominance being waged amongst these colonies of tiny organisms because some of them are very much on our side. So the question is what will our scientists do next to harness the remarkable properties of these intriguing residents?
Copy courtesy of Yale University Press via NetGalley
If you thought bacteria were tiny blobs that cause disease, then think again, because there’s far more to them than that. Welcome to the Microbiome is a book that offers the possibility of thinking about our inner world in a very different way. Humans like to think they are the superior race, but it may be no exaggeration to say that without the bugs that have evolved with us we would not be where we are today.
The gut is only one area of the body Rob DeSalle and Susan Perkins describe in their guided tour of the many habitats where the microbes live side by side with us. The types of colonies that reside within the digestive tract have far reaching effects on the general health of all our organs. But the study of how microbes interact and largely coexist with us is a rapidly developing area in science and one that many hope will revolutionise our approach to medicine.
The authors take the reader though the whole process of evolution and relevant physiology and biochemistry using straightforward narrative and description to explain how bugs interact with us. They also describe how new technology for studying microbes has revealed our bodies ‘are swamped with bacterial genes – genes that are busy transcribing and translating their own proteins in tandem with our own DNA replication processes.’ This seems to turn on its head the concern we have for whether there is life somewhere out in space. It is a description that takes the phrase ‘we are not alone’ to a whole new level. The invasion occurred a long time ago and is more up close and personal than we could have ever imagined. There is a constant shuffle for dominance being waged amongst these colonies of tiny organisms because some of them are very much on our side. So the question is what will our scientists do next to harness the remarkable properties of these intriguing residents?
Copy courtesy of Yale University Press via NetGalley
May 26, 2019
Excellent, plain-language look at the microbiome
I loved this book. Authors Rob DeSalle and Susan Perkins wrote an enjoyable, well-thought-out book about on the microbes that live in us, on us and around us (our microbiome). The authors use plain language to successfully explain our relationship with the microbial world. I initially thought that the book would be about how a happy microbiome would be the panacea for all medical ills, but I was wrong. The book is very well balanced and leaves a lot of unanswered questions because we just don’t have the answers yet. Patricia Wynne provided beautiful illustrations that help explain certain points. I strongly recommend this book for anyone interested in science.
Disclosure: I received a complimentary copy of this book via Netgalley for review purposes.
March 3, 2023
I really wanted to like this book, but after finding two factual errors in the first chapter, I skimmed it and put it down. Other reviews call out good key learnings. I ended I using those to revisit specific passages in the book. This is the only reason I gave it three stars.
+ Lots of good information. Use other reviews to locate it.
- Very little actionable information for anyone seeking to optimize their microbiome.
- Poorly edited, with visible, glaring mistakes.
+ Lots of good information. Use other reviews to locate it.
- Very little actionable information for anyone seeking to optimize their microbiome.
- Poorly edited, with visible, glaring mistakes.
August 4, 2018
This is a good book. It is very accessible and gives the reader a fairly thorough introduction to how microbes effect human health. I think this kind of book is probably a challenge to write because you don't want to come off as condescending and you also don't want to overload the reader with too much complex terminology but DeSalle pulled that tightrope walk off splendidly.
April 20, 2020
This book is more an overview of biology, immunology, and microbial diversity in general. Where it is superficial in some areas it is too dense in others. No offence to the author, but there are certainly better microbiome books out there.
November 9, 2024
It’s okay, I took it more as a textbook that went into depth about DNA/RNA sequencing and more on the factual side. Although it does touch base with microbes and stuff I felt like it wasn’t what I was expecting it to be. It’s alright though and a good read if you are into science.
July 12, 2018
An interesting book, but need to be re-titled !
This entire review has been hidden because of spoilers.
January 18, 2017
Simple overview of what microbes are & why they are important for beginners. It is helpful to know the basics of DNA - they do an overview of how DNA functions, but it is hard to follow (& very boring) if you have no background to reference. Reading the wikipedia entry on how DNA is translated to RNA and then amino acids was a big help to me.
November 28, 2015
I found this book to be very interesting especially the parts about the mouth and the gut. You learn how bacteria works with or against us and how this can alter our health.
I got this for free in a Goodreads Giveaway.
I got this for free in a Goodreads Giveaway.
October 14, 2015
You couldn't ask for a better introduction to the current science in this exploding field.
April 24, 2017
Much more academic than actionable
Displaying 1 - 17 of 17 reviews