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Nutrition’s ‘dark matter’

AS ANY reader of this blog knows, the human body is a mash up of human and microbial cells – with the microbial cells outnumbering our own 10 to 1. When you also consider the fact the human genome (our first genome) contains only 22,000 genes, but that our gut microbiome (our second genome made up of the microbes and their genes) contains over 3 million, you really have to start wondering who’s controlling who.

If the avalanche of never-ending journal articles is any indication, the link between microbes and our health will soon flip modern medicine on its head. But don’t get too excited – yet – as researchers have only scratched the microbial surface and much work is needed to tease out what is correlation from what is causation. Nevertheless, the writing is on the wall and the way we treat and prevent disease today will look down right medieval in the very near future.

As microbial research throughout the world increases its page count in leading peer-review journals with each passing week, it’s hard to imagine a profession that will be more profoundly impacted by our micro understanding of health and disease than nutrition sciences. That is, the folks who help us try an understand what to eat based on the latest scientific research. As suggested before, the field of nutrition sciences may be a little slow on the uptake, given its myriad and tangled history of stakeholders and its entrenched notions of what constitutes a healthy diet.

If anything, the emergence of the microbiome as a ‘potential’ key player in obesity, heart disease, diabetes, IBD, mood disorders, some cancers, autoimmune disease, and more, will likely nudge nutrition researchers to start reframing these so-called western diseases into the more productive and accurate narrative as ecological diseases. We are in fact part of a larger biosphere and there are rules – that if tinkered with – have consequences.

Revisiting that notion of who is really in charge – us, or them – a study by researchers at Cornell University that followed the microbial journey of newborn for over two years offers some interesting hints. From their paper published in the Proceedings of the National Academy of Sciences, the researchers summarize the study as follows:

To investigate how life events impact the developing infant gut microbiome, we performed a case study to monitor the gut microbial composition of one infant over a period of 2.5 y. We analyzed a set of more than 60 fecal samples collected concurrently with detailed information regarding diet, health status, and activities. The infant was a full-term, vaginally delivered healthy male. He was placed in a daycare facility during weekdays starting at 3 mo and then removed from group care at 1 y. His diet regimen consisted of exclusive breast-feeding for the first 134 d of life, supplemented with formula until he was no longer breast-fed at 9 mo. The first solid food introduced to the diet was rice cereal at 4 mo, followed by table foods, and the replacement of formula with cow milk at 1 y. The child suffered from several ear infections for which he was treated with antibiotics, but was otherwise healthy, and he was immunized according to the US Centers for Disease Control and Prevention’s recommended schedule.

So here’s what they found. The figure to the right shows the 60 fecal samples taken over the 2.5 y – each represented by a black dot – plotted against the diversity of the bacteria in the sample as determined by 16S rRNA gene sequencing. The higher the number (1 thru 9) the greater the diversity of bacteria in that sample. The lowest diversity of bacteria was recorded on early on in the meconium sample (babies first tar-like poop) on the bottom left of the graph. Also note that a sample was taken from mom as well (top left just above 8), which showed an ‘adult-like’ diversity. As you can see, over the course of the 2.5 y our little baby boy’s gut bacteria became increasingly more diverse and more ‘adult-like’ (as expected).

You will also note numbers by some of the dots, which mark the day the sample was taken. Some samples, for example on Days 168 and 195, seem to show more diversity than expected if you followed the solid trend line cutting across the dots. On the flip side, some sample days (e.g., 413, 432, 441) showed a drop off in diversity in the samples for some reason. The next graph shows why.

In this graph a vertical bar indicates each day that a sample was taken and the bacterial phyla that were present (note that each phyla, for example Firmicutes, contains a great many species and strains of bacteria). As you can see, in the first 5 days the babies gut composition is dominated by Firmicutes, until day 6 when some Proteobacteria and Actinobacteria show up in the stool sample. And as the bar graph indicates – and as suggested by our first graph above – diversity increases over time but with some obvious fluctuations.

Also indicated on the graph are major life events, such as breast milk start, a fever at Day 92, and antibiotics at Day 240 and so on. If you will look back at our first graph for that drop in diversity at Day 85, you will note that it precedes a fever at Day 92. So, diversity drops and a few days later a pathogen takes advantage and an infection ensues.

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On Day 161 the baby receives first formula and some table foods (peas), which is then followed by an increase in the diversity in bacteria (see Days 168 and 195 in first graph). Interestingly, following the infant’s first treatment with the antibiotic cefdinir (a broad-spectrum cephalosporin), a significant drop in diversity is noted in samples taken on Days 413, 432, and 441 (see first graph). You can also clearly see a drop in species belonging to the Bacteroidetes group. The friendly fire impact of broad-spectrum antibiotics is clearly noted in this infant and countless other studies. Clearly life events have an impact on the infants gut composition.

But perhaps the most astonishing finding was recorded when the researchers looked at the functional gene dynamics (via shotgun metagenomics) present in a handful of samples. In the graph with the vertical bars you will note an asterisk for Days 1, 6, 85, 92 and so on. In the first analysis – 16S rRNA gene analysis – the researchers were able to get a list of the various bacteria present and group them by phyla (e.g., Protobacteria). While this tells us which bacteria are present, it does not tell us what they are doing – that is, their function. An analogy to how shotgun metagenomics works would go something like this: Imagine you pick 100 random people off the street and give each of them a colored t-shirt that corresponds to the colors assigned for each of our phyla above; orange for Actinobacteria, blue for Firmicutes and so on. Assume also that we have handed out the colored t-shirts in even numbers of 25 – that is, we have four groups (phyla) of twenty-five and have sequestered this mob in a room (assume this room represents your gut – stay with me). Since we picked the people randomly we have no idea what their various skill sets are or what they do for a living – all we know is they are separated by t-shirt color (phyla). In the room we might have a plumber, 3 phone technicians, 7 lawyers, 4 electricians, 7 hair stylist and so on. But we would never know this from t-shirt color alone (phyla) – but shotgun metagenomcs can tell us what their skills (functions) are – regardless of their t-short color. In the case of our room, our 7 hair stylist are represented in 3 out 4 of our t-shirt colors. In other words, t-shirt color (phyla) tells us very little about what a person (bacteria) does (functions).

When the researchers looked at gene function in the meconium sample (Day 3), they found that genes involved in carbohydrate metabolizing of lactose/galactose and sucrose from mother’s milk were enriched, in addition to genes associated with virulence and antibiotics resistance. As the baby was born vaginally and therefore received its first seeding of bacteria from mom as he passed through the birth canal, it can be assumed the baby received these genes through vertical transition from passing of bacteria from mother to infant (see Kids are Mammals).

On Day 6, “genes associated with vitamin biosynthesis showed up” and the sample on Day 85 produced carbohydrate-using genes for amylose, arabinose, and maltose showed up. And so it went – our baby boy’s gut microbiome was becoming more adult-like month after month. But the most astonishing finding was in the genes enriched in Days 98, 100 and 118.

If you remember from our second graph above, rice cereal was added to the diet on Day 134 and peas on Day 161. However, weeks before “genes facilitating the breakdown of plant-derived polysaccharides” were present before these foods were introduced to the diet. That is, while the baby will still on a exclusive breast-milk diet, its gut microbiome began metabolically priming for the plant-derived diet to come. This priming or preprogramming if you will indicates that they may be in charge more than we previously thought. This is truly humbling with regards to our dominant anthrocentric view of the world.

This simple and elegant study reveals that large shifts in the abundance of major bacterial groups occur with life events like illness, antibiotic treatment, and diet. Though our adult microbiome is more diverse and presumably more resilient, shifts in composition (taxonomically and functionally) will likely reflect similar life events which will dial up or down our susceptibility to disease.

Best we honor thy gut bugs. Peace out.

10 Comments

  1. This is awesomely fascinating! Thanks so much for analyzing this study and explaining it so clearly. I for one welcome our ancient, yet under-appreciated microbial overlords.

  2. So cool, thank you for reporting on this. As a momma with an 11 month old, I am so interested in what’s going on with her microbiome! We can’t wait to participate in your poop project!

  3. Please explain to me the Strep B bacteria in pregnant women and do they really need to take antibiotics?
    Thanks

    • sorry, going to need to ask your doctor about that one.

  4. An adjunct study could be charting Mom’s macronutritional status and microbiome variability at the same time. It’s especially fascinating that the “genes facilitating the breakdown of plant-derived polysaccharides” were present before these foods were introduced to the diet.” This flies in the face of a recent recommendation– or does it?– from the health powers-that-be in Canada, that first foods should be animal protein. The rationale, I believe, was that the digestive system was not yet ramped up for cereals.
    http://www.thehealthyhomeeconomist.com/new-health-canada-guidelines-advise-meat-as-baby-first-food/

  5. Thanks Jeff, interesting article. Questions though – not sure what you mean by “this priming or preprogramming if you will indicates that they may be in charge more than we previously thought.”

    Are you suggesting that the microbiome caused the baby to eat the plant-derived diet by “metabolically priming” to process the rice and peas he was eventually fed? By “in charge” do you mean leadership, supervision, or some sort of responsibility?

    Or do you mean that the microbiome instinctively knew it was about time the kid started eating solid food so it got prepared to handle it?

    • Thanks for the question(s). It would be the last one: it seems the gut microbiome “instinctively” knew to enrich for plant polysaccharides ahead of their actual arrival. I think the additional interesting question would be were there genes associated with meat consumption present as well? That is, genes associated with animal protein degradation. I know two of the authors of the paper – one of which is involved in our upcoming American Gut project – and asked this question. Turns out, they did not look for this in the current study – nor has anyone else in other studies of infants. So, we are going to look at this in the upcoming American Gut project – as well as mine the data of some previous projects. Will be interesting. I also extended to the question to some folks working with Chimpanzees – as all chimps eat meat. We will likely look at this in 2013 as part of a chimp project we are starting. Thanks again for the good questions. :)

      • I can’t wait to see those results since I’m a believer in the Primal/Paleo Diet….

  6. ‘However, weeks before “genes facilitating the breakdown of plant-derived polysaccharides” were present before these foods were introduced to the diet. That is, while the baby will still on a exclusive breast-milk diet, its gut microbiome began metabolically priming for the plant-derived diet to come.’

    That the mother was eating these starchy foods might also be a factor in whether or not her offspring developed these polysaccharide-digesting genes. What about babies whose breastmilk comes from mamas who don’t eat much starch or sugar or grains (or if these carbohydrate-rich foods are fermented first)? I wonder if the “seeding” of the growing infant’s gut flora happens similarly to the ways in which breastmilk provides protection (antibodies, etc.) from viruses when the mother is exposed.

    This is FASCINATING–thanks!

  7. I think the reason the microbes changed before the foods were presented must be because of changes in the mothers’ breast-milk. We know that the very first milk (colostrum) directly after birth is of a different composition than later on . A mothers’ milk will certainly change over time, regulated by hormones, to provide the growing baby exactly what it needs and in what quantities when it needs it. I am sure the results will be quite different in baby that drank only formula from birth. The micro organisms can only ‘react’ to their environment, not the other way around. They grow or die according to what is happening in the gut because of outside influences. (In my opinion..)

    Thanks for the research, it is obvious that present mainstream dietitians and nutritionist do not know it all and a lot of what they are taught in their studies are completely wrong.

    I hope your research helps in providing some real answers. Just try and always keep an open mind, remember that your assumptions today might be proven completely wrong tomorrow.

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