Monday, September 26, 2016

“Let Them Eat Dirt” Book Review

I recently finished a book that just came out, called Let Them Eat Dirt: Saving Your Child from an Oversanitized World, by microbiology researchers Drs. B. Brett Finlay and Marie-Claire Arrieta. The publisher was kind enough to share an advance copy with me, and also put me in contact with Dr. Finlay to discuss the book. The book focuses on the gut microbe community, especially as it relates to pregnancy and childhood, so it fits right into the scope of BacterioFiles.

Summary
In many ways, Let Them Eat Dirt is similar to a book I read a couple years ago, Missing Microbes by Martin Blaser, and Dr. Finlay confirmed that that book was an inspiration behind this one, which was intended to be less academic and more accessible to non-biologists (and I would say it accomplished that goal).

This book is split into three main sections. The first discusses how important microbes can be and how it is practically impossible to avoid coming in contact with them, but that’s okay because the vast majority are harmless or even beneficial to health. It also gives some history of microbiology and of the science of human-microbe symbiosis.

The second section presents various ways that microbes affect babies, and vice versa. I learned some things in this section, and it was quite interesting. Starting with pregnancy, it discusses how the microbial community in the mother’s gut changes over the course of pregnancy, and actually comes to resemble microbe communities associated with obesity. Various things can affect the community composition even more, or disrupt it in harmful ways, including unhealthy diet, stress, antibiotics, and infection. This disruption can be harmful to the mother, but can also affect the baby before birth, and even throughout life after birth, since the mother’s microbes are the seed for the baby’s gut community. So it’s important for expecting mothers to take care of their microbes, and the authors offer suggestions for doing this, like getting a flu shot.

Then the book discusses the transfer of microbes from mother to infant during and after birth, another very interesting topic. This transfer can be disrupted in various ways, including by antibiotics or caesarian section birth, but is important, and the authors discuss the issues well and give advice on how to make good decisions. The next few chapters focus on how the gut community develops after birth: the importance of breastfeeding and the amazing properties of breastmilk, but also the difficulties that many encounter trying to breastfeed; the transition from milk to solid food and how best to introduce new foods to support a varied diet and avoid food allergies; and other related topics like when to use or avoid antibiotics, the effects of pets on microbes, and how to keep children clean but not too clean. I was pretty on board for most of this section.

The third section discusses the associations that scientists have been finding between microbes and various chronic diseases/conditions. There are chapters here discussing the connections between gut microbes and obesity, diabetes (types 1 and 2), intestinal diseases such as Crohn’s and irritable bowel syndrome, allergies and asthma, and even neurological conditions such as depression, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). As you might expect, the book links each of these conditions to microbes in the body, and discusses the research that has been done with each, then makes suggestions for how to approach and think about each of these conditions, especially as it relates to microbes.

The last two chapters are a little different: the penultimate is a strong message in favor of vaccines for preventable diseases, emphasizing their importance as a public health strategy and coming against the discredited link between vaccines and autism. This chapter also discusses recent research into how gut microbes can modify the effectiveness of certain vaccines, such as the flu shot; mice without gut microbes have much less response to it (as I’ve discussed on BacterioFiles in episode 196).

The final chapter wraps things up with speculation about how microbial communities could be an important consideration in healthcare of various kinds, from doctors prescribing specific diets to patients for the sake of their microbes, or modifying microbial communities directly with probiotics or antimicrobials (in even more targeted and effective ways than is done today), or developing more effective vaccines by taking microbes into account. It emphasizes that many aspects of research into the microbiota are in very early stages, so it’s premature to put too much faith in things like probiotics and fecal transplants to cure any and all diseases (and definitely don’t try fecal transplants at home!). But there’s a lot of promise for the future.

My Impressions
This book was entertaining and enjoyable to read, especially for a microbiologist. It seemed to explain microbiological concepts well, in a way that is accessible to scientists and non-scientists. And in addition to all the science in each chapter, there are anecdotes to give some personal touches, and at the end of each chapter is a section with advice for how to apply the concepts from the chapter.

For example, at the end of chapter 9, there’s a story about how one of the authors told her 3-year-old daughter about the “little bugs in her tummy” that were happy and friendly and colorful, and how they helped keep her healthy as long as she made sure to feed them with tasty foods like vegetables. What a great way to get children interested in taking care of their microbes!

I also really appreciated the way the authors repudiated various different forms of pseudoscience, like the Paleo Diet (the idea that we can know, and also follow the diet that our prehistoric ancestors ate, and this will result in optimal health for modern humans). They also mention the idea, most often encountered among anti-vaccine advocates, that infectious disease helps develop the immune system (and therefore should not be prevented by vaccines). In fact, while exposure to microbes is important in this respect, infection is often more harmful than helpful even beyond the short-term symptoms of the disease. And then there’s the whole chapter about vaccines that was right on target.

Broadly speaking, the book seemed to cover the science accurately and support it well, convincingly showing that our microbes are important for many aspects and that modern lifestyles in developed countries avoid microbes too much in many ways.

Problems
I did have a couple of complaints about the content though. For one, a lot of the research findings presented here are somewhat preliminary, much of it discovered in the past 5 or 10 years. Similarly, much of the research has been done in animals and not humans yet, so whether or not the results can be extrapolated to humans remains to be seen. Of the rest, much is observational and therefore shows only correlation, not causation—that is, it’s not known whether microbe changes cause health conditions, or health conditions cause changes in microbe communities, or a third issue causes both.

So I expect a lot of the findings are likely to be discredited as new studies are done in the next decade. So it’s important to be cautious with this research field and not put too much weight on a given study or finding. To the authors’ credit, though, Dr. Finlay mentioned that it was their intent that each claim they made should be supported by at least one published study, so the book is currently a good summary of the science on the issue, however much may become obsolete in the future. And the book does advise readers to stay abreast of the research, rather than assuming it is all settled.

Otherwise, the biggest problem I had with the book was the chapter on how microbes might affect neurological conditions such as ASD and ADHD, especially the section on ASD. It mentions some small studies and anecdotes of autism symptoms improving with treatments of antibiotics, fecal transplants, probiotics, and modified diets. It did try to make clear that the evidence for these treatments is not very good, and that it is not clear where causation lies regarding microbial changes and developmental changes, but overall it struck me as far too close to a vast number of pseudomedical treatments for autism, collectively known as “autism biomed.”

This term refers to treatment of children on the autistic spectrum using “supplements, pharmaceuticals, all-natural remedies, homeopathy, chelation, HBOT and special diets,” as one website describes it; overall, treatments with very little evidence of benefit and some with much potential for harm, to which parents, often desperate for any solution, subject their children. As you can tell, it sounds uncomfortably similar to what is mentioned in the book. My impression from speaking with the author is that this similarity was not intentional, and that the authors weren’t really aware of autism biomed or how this section of the book could be taken as supporting pseudomedical treatments. However, the similarity is there.

So I’d like to mention here some things that perhaps were not adequately emphasized in the book. There is no “cure” for autism; if you have children on the spectrum, accept them for who they are, rather than trying all sorts of unproven treatments to try to make them be “normal.” Taking care of their microbes is a good idea, the same as you would for any child, and if their behavior suddenly changes, consider the possibility that gut problems may be causing them discomfort and reducing their ability to cope with life.

But be aware that there are many unscrupulous healthcare providers that will claim to have all sorts of revolutionary treatments for autism outside the mainstream, so be skeptical of such claims and check whether they have good evidence to support them. Also, don’t go see a naturopath; their treatments are often not supported by evidence, aren’t helpful, and are potentially harmful. Check out Naturopathic Diaries, run by a former naturopath, or Science-Based Medicine for more info.

Conclusion
So in sum, this book was well written, and for the most part a good presentation of the science of gut microbes and health. It gives plenty of good advice to consider, including the suggestion to keep up to date with research in the field, and offers a lot of hope for advances to be made in the future. So if it is a subject that interests you, and especially if you’re planning to have children (or even already have some), read it and consider the advice, but also consider that the science and the recommendations that follow from it may change significantly in the future.

BacterioFiles 269 - Magnetic Microbes Maim MRSA

This episode: Killing pathogens by attaching magnetotactic bacteria to them and then raising the heat with magnetic fields!
Download Episode (10.6 MB, 11.6 minutes)

Show notes:
News item

Journal Paper:
Chen C, Chen L, Yi Y, Chen C, Wu L-F, Song T. 2016. Killing of Staphylococcus aureus via Magnetic Hyperthermia Mediated by Magnetotactic Bacteria. Appl Environ Microbiol 82:2219–2226.

Other interesting stories:
  • Plant root symbiont that degrades plastic pollutants (paper)
  • Phages can kill pathogens in gut without affecting other microbes (paper)
  • Mouth bacteria could inhibit other cavity-forming microbes (paper)
  • Plant accepts help from fungus only when necessary
  • Bacteria seem involved in forming deposits of platinum metals

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, support the show at Patreon, or check out the show at Twitter, or Facebook

    Monday, September 19, 2016

    BacterioFiles 268 - Sophisticated Cyanobacterium Sight

    Synechocystis cells
    under electron microscope
    Credit: Conrad Mullineaux
    This episode: Spherical cyanobacterium Synechocystis acts like a tiny eyeball in sensing light, allowing cells to move closer to light sources!
    Download Episode (9.7 MB, 10.6 minutes)

    Show notes:
    News item

    Video 1: Synechocystis cells moving toward light sources
    Video 2: Synechocystis cells avoiding point of bright light on surface

    Journal Paper:
    Schuergers N, Lenn T, Kampmann R, Meissner MV, Esteves T, Temerinac-Ott M, Korvink JG, Lowe AR, Mullineaux CW, Wilde A. 2016. Cyanobacteria use micro-optics to sense light direction. eLife 5:e12620.

    Other interesting stories:
  • Discovering how to get more biofuels out of algae
  • Bacteria could help prevent cavities
  • Probiotic carrying virus in its genome fights pathogens better than without virus (paper)
  • Giving probiotic to pregnant mice influences immune system of babies (paper)
  • Combined phage and probiotics could treat E. coli infections (paper)

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, check out the show at Twitter, or Facebook

    Monday, September 12, 2016

    BacterioFiles 267 - Crust Color Cooks Communities

    Used with permission
    Biocrusts in Moab, Utah
    Credit: Estelle Couradeau
    This episode: Cyanobacteria in biocrusts produce pigments that heat their surroundings up to 10 degrees hotter!
    Download Episode (7 MB, 7.6 minutes)

    Show notes:
    News item

    Journal Paper:
    Couradeau E, Karaoz U, Lim HC, Nunes da Rocha U, Northen T, Brodie E, Garcia-Pichel F. 2016. Bacteria increase arid-land soil surface temperature through the production of sunscreens. Nat Commun 7:10373.

    Other interesting stories:
  • Engineering better bioplastic production from bacteria
  • Groups of bacteria can show a kind of memory
  • Bacteria in gut are competing and killing each other a lot
  • Exercise helps mice gut health, regardless of weight (paper)
  • Bacteria help insects tolerate cabbage toxin

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, check out the show at Twitter, or Facebook

    Monday, September 5, 2016

    BacterioFiles 266 - Solar Cyborg Cells Capture Carbon

    From: Jiang, B., Henstra, A.M., Paulo, P.L., Balk, M., Van Doesburg, W., and Stams, A.J.M. (2009) Atypical one-carbon metabolism of an acetogenic and hydrogenogenic Moorella thermoacetica strain. Archives of Microbiology 191: 123-131.
    Cells of Moorella thermoacetica
    forming spores in culture
    This episode: Adding exotic elements to convert spore-forming bacteria into light-capturing cyborgs that convert carbon dioxide into useful chemicals!
    Download Episode (9.7 MB, 10.5 minutes)

    Show notes:
    News item 1/News item 2

    Journal Paper:
    Sakimoto KK, Wong AB, Yang P. 2016. Self-photosensitization of nonphotosynthetic bacteria for solar-to-chemical production. Science 351:74–77.

    Other interesting stories:
  • Unusual archaeal virus sorta looks like Ebola (paper)
  • Understanding how probiotics could prevent cancer in mice (paper)
  • Giant viruses have immune system against virophages
  • Using evolution to help yeast produce more ethanol from biomass (paper)
  • Remnants of viruses in our DNA helps us fight off infections

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, check out the show at Twitter, or Facebook

    Monday, August 29, 2016

    BacterioFiles 265 - Predator Protein Protects Predator

    By flickr user AJC1 - CC BY-NC-SA 2.0, https://www.flickr.com/photos/ajc1/4187842186
    Bdellovibrio bacteriovorus
    attacking prey bacterium
    This episode: Predatory bacteria have a particular protein that protects them from their own prey-damaging enzymes!
    Download Episode (7.3 MB, 7.9 minutes)

    Show notes:
    News item

    Journal Paper:
    Lambert C, Cadby IT, Till R, Bui NK, Lerner TR, Hughes WS, Lee DJ, Alderwick LJ, Vollmer W, Sockett RE, Lovering AL. 2015. Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus. Nat Commun 6:8884.

    Other interesting stories:
  • Bacterial proteins could be used to break open cells upon command
  • Animal gut fungi could break down plant material for biofuels
  • Fungal partners help determine which trees can grow in a forest
  • Parasitic fungi contribute to ocean algae turnover (paper)
  • Fungus in tree inhibits other fungi and plants (paper)

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, check out the show at Twitter, or Facebook

    Monday, August 22, 2016

    BacterioFiles 264 - Small Cells Stimulate Satiety

    This episode: Proteins from gut bacteria seems to affect hunger and satiety in their (rodent) hosts!
    Download Episode (7.7 MB, 8.3 minutes)

    Show notes:
    News item 1/News item 2

    Journal Paper:
    Breton J, Tennoune N, Lucas N, Francois M, Legrand R, Jacquemot J, Goichon A, Guérin C, Peltier J, Pestel-Caron M, Chan P, Vaudry D, do Rego J-C, Liénard F, Pénicaud L, Fioramonti X, Ebenezer IS, Hökfelt T, Déchelotte P, Fetissov SO. 2016. Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth. Cell Metab 23:324–334.

    Other interesting stories:
  • Now even bacteria could make opiates
  • Soil bacteria slime could help make wound dressings
  • CRISPRs targeting phage RNA instead of DNA can have some benefits for cells
  • Engineering biotech pathways for better processes
  • Bacteria can produce antimicrobial silver nanoparticles (paper)

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

    Subscribe at iTunes or Google Play, check out the show at Twitter, or Facebook