The plagues of our modern society include diabetes, allergies, asthma, obesity, autism, and numerous digestive system disorders such as irritable bowel syndrome, colitis, Crohn’s disease, and celiac disease. The symptoms and difficulties inherent with each of these diseases is different. However, modern molecular biology research techniques have revealed a commonality. People with each of these ailments have a microbiome that is strikingly different from that of healthy people. Micro-bio-what?

This blog, Mostly Microbes, explores the interactions between microbes and us, their human hosts. In particular, I focus on the importance of the human microbiome for and during pregnancy, birth, infancy, and early childhood.

What is the microbiome?

The microbiome is all the microbial cells living in a particular location [1]. In the case of humans, the human microbiome includes over 100 trillion bacteria, viruses, and fungi that live in or on your body [2]. Perhaps as much as ten times more microbes make up your body than human cells [2] (though new estimates [3] put the number of human cells at 3.72 trillion instead of 10 trillion). You are their home. You may have immediately thought “ew- I want to wash my hands now!”, but hold on a minute. The vast majority of these microbes are helpful. We’ve been brought up to think of viruses and bacteria as “germs” that cause disease, but without your helpful microbes you wouldn’t be able to properly digest your food [4] and would lack certain vitamins [5-7]. In fact, it’s the loss of these helpful microbes that seems to correlate with several diseases [8-12]. These recent scientific breakthroughs are changing the way both basic science and medicine think about human health [13].

Why did we not know about these microbes before?

New techniques to identify microbes use the DNA sequence (the unique instruction codes of life) of the organisms instead of relying on the ability to culture these organisms in a petri dish. Historically, ~ 1% of bacteria, viruses, and fungi could be cultured. We knew this because significantly fewer cells were seen under a microscope than would grow on nutrient media in the lab of any microbial sample, whether from a tablespoon of soil to a scraping from a tooth’s surface (see Great Plate Count Anomaly [14] for more details; or this fantastic article in the Scientist). We did not know enough about the basic biology, such as nutritional and oxygen requirements, of these microbes to grow them, though now there are some new ideas about how to culture a wider diversity of bacteria [15, 16]. Molecular techniques developed several decades ago, such as Sanger sequencing of the 16S rRNA ribosomal gene, began the DNA based inventory of microbes. More recently, new “next generation” DNA sequencing techniques have allowed us to sequence hundreds of samples and generate millions of sequences in a few hours (though the data analysis takes a longer!). Additional techniques that provide more functional information, such as metagenomics, transcriptomics, and whole genome sequencing, have revealed the metabolic requirements of microbes and aided in culturing more species. Excellent tutorials several groups of scientists have developed on new molecular techniques can be found here: DNA extraction, PCR, or all steps to ID cultured and unculturable samples. Also see the link below to the MostlyMicrobes pinterest page for more such links. To summarize – we have new tools that let us do and learn more!

Why you are NEVER alone!

In 2007 the National Institutes of Health wisely invested 150 million of your tax dollars into a five year Human Microbiome Project (HMP). The findings of the HMP have changed the way we view the health and dysfunction of our bodies. No longer can we consider ourselves human. Instead, we should think of ourselves as walking, talking planets! Bacteria are so tiny that millions of them can fit on the antennae of an ant. The ratio of the size of E. coli compared to your body is a similar ratio to a human body compared to the Earth. Just like the Earth has different habitats – mountains, lakes, deserts, swamps – so does the human body. In each of the Earth and human habitats, specific organisms flourish in those particular conditions.

Habitats are simply places with a certain type of physical characteristics (temperature, pH, UV intensity, etc..) and characteristic organisms. These two facets of habitats are interlinked, with certain organisms being able to survive better in different physical habitats. For example, polar bears with their thick fur, layers of fat, and taste for seals and fish are well suited for colder, artic regions of the Earth, but would be out of place and couldn’t survive in hot, dry deserts with no seals. Similarly, some of the microbes in and on your body require specific nutrients, pH, or levels of oxygen to survive and are restricted to living in those habitats. These microbes also have a particular function in the ecosystem in which they live. Sometimes they are breaking down nutrients or toxins, sometimes they make vitamins, other times they simply take up a space and prevent a pathogen from living there.

What habitats are in and on me?

Habitats can be characterized first by their physical (abiotic) aspects. These abiotic aspects include: temperature range, nutrient type and amount, oxygen amount, pH range, and amount of moisture. The HMP has begun constructing maps of where different bacteria live in and on our bodies. Over 18 body habitats of 113 healthy females and 15 body sites of 129 healthy males were sampled for a total of 4,788 samples. These body sites included five major body areas, including nine from the mouth, 4 skin sites, a stool sample to represent the digestive system, and genital sites. Some subjects were sampled at different times to look at microbiome stability over time [2]. DNA was extracted, bacterial 16S rRNA amplified and sequenced from those DNA extractions, then the bacterial 16S rRNA sequences compared. The study sought to determine if 1) different body sites have specific bacterial communities, 2) how bacterial diversity compares across body sites of the same person, and 3) if these bacterial communities at each body site are similar across individual humans.

Do different body sites have specific bacterial communities?

Indeed, there are specific bacterial communities at different body sites. This is probably most easily seen in the graph from the HMP2012 Nature paper (Figure 3) where the differences between samples taken from several individuals at different body sites are plotted. Each dot represents the different types and numbers of a type of bacteria present in that particular sample. Those samples that are most similar to each other cluster together. This analysis suggests that the most different sites are oral, gastrointestinal (GI), and urogenital, while skin and nasal sites are more similar to each other.

Researchers also compared the abundance of bacterial species across body sites. They found changes in the abundance of specific bacteria for each body site (Figure 4a and b). Indeed, researchers have found that our bodies contain several habitats with distinct physical conditions and biological organisms. Some bacteria survive best in habitats like your mouth where there is a lot of moisture, fluctuating temperature, and the amounts of nutrients vary depending on if and what you are eating. In contrast, the bacteria that live on the skin of your arms are adapted to living in a hot, dry, low nutrient, and UV intensive region.

The HMP made a neat interactive program called SitePainter where you can specify which bacterial taxa you are interested in and it maps where the bacterium is found on the body. An example I did using the RDP phylum level analysis for Chloroflexi and Proteobacteria are seen in Figures 5 and 6. Notice how the Chloroflexi are only found in one location in the mouth, whereas Proteobacteria are found in many different locations. The phylum level is the second highest level taxonomic categories. Within a given phylum are many classes and even more species. Since the first image is at the phylum level, we see the broadest level of organization that encompasses many subgroups (classes) of organisms with more restrictive patterns of colonization.

Figure 4 shows a SitePainter screenshot at the class level of Betaproteobacteria. Within the class of Betaprotobacteria, there are a variety of families (an unknown, Figure 7, and Oxalobacteraceae, Figure 8, in this example). It’s at the family level where the different colonization patterns become obvious and where the diversity of bacteria really starts to be revealed. So what is diversity and why does it matter?

What is diversity?

Diversity is simply how many distinct types of organisms are present. For example, a city street may have three different types of birds (pigeons, starlings, and sparrows), whereas a rural street may have ten different types of birds (starlings, sparrows, blue jays, American bluebirds, cardinals, towhees, crows, nuthatches, wrens, and chickadees). In this case the city street would be less diverse than the rural street.

In this initial survey of the healthy human microbiome, within each person sampled, the most diverse body sites were the GI and oral sites, while vaginal sites were the least diverse.  Interestingly, although both oral and GI sites both had high diversity, in the mouth the same species were seen in different people. This would be like finding the same three bird species (pigeons, starlings, and sparrows) on a city street of Alabama and a city street in California. In contrast, the types of bacterial species was different when different people’s GI system was compared. No matter the level of diversity, the unique microbiome of a person was stable over time.

Why does diversity matter?

Ecosystems depend on a diversity of organisms to maintain a healthy and sustainable environment. Each group of organisms – plants, animals, fungi, bacteria – all do jobs essential for proper ecosystem function and create a network of interactions and sometimes also interdependence. Without plants and microbes to provide oxygen, animals wouldn’t survive very long. Likewise, the animal waste product carbon dioxide is essential for plant photosynthesis. Of course, within those larger groups of plants and animals are subsets of organisms that have specific jobs essential for ecosystem function. Some insects and birds serve as plant pollinators. Other insects, birds, and mammals feed on different plants. Those insects, birds, and mammals then serve as food for other animals. Then there are the detritivores – the recyclers of the ecosystem. They feed on animal and plant waste and carcasses to return those nutrients to the environment. Microbes also have specific jobs that other species are dependent on for proper ecosystem functioning.

In some cases, a little diversity can be lost without much disruption of the ecosystem processes. For example, losing a single species of bee that pollinates several different kinds of plants might not be too much of a problem if another species of insect can do the same job as efficiently and effectively. However, if only one bee species can pollinate a particular plant and insect pollination is essential for the plant’s survival, losing the single bee species has a greater consequence. It’s similar with the human microbiome. In the digestive system, especially the intestines, diversity seems to be extremely important. The more microbial diversity, the wider variety of jobs that can be done. In this case, the jobs are digesting an assortment of foods. Particular microbes have distinct sets of genes that allow them to break down specific nutrients or synthesize vitamins and other nutrients missing from the host’s diet. A wider diversity of microbes leads to processing a broader array of foods.

From head to toes, inside and out, you are mostly microbes. As the ecosystems of planet Earth has a series of habitats with specific organisms that are essential for proper ecosystem functioning, so does the human body. Without the many microbes that call you home, your ecosystem can malfunction. Though microbes are invisible to the naked eye, their importance is becoming increasingly apparent. It is my hope that this blog will serve to connect you to this invisible and essential part of yourself.

REFERENCES

1. Lederberg, J., and A. McCray. 2001. Ome sweet ‘omics: — A genealogical treasury of words, p. 8. The Scientist, vol. 15.
2. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
3. Bianconi, E., A. Piovesan, F. Facchin, A. Beraudi, R. Casadei, F. Frabetti, L. Vitale, M. C. Pelleri, S. Tassani, F. Piva, et al. 2013. An estimation of the number of cells in the human body. Annals of Human Biology 40:463-471.
4. Cantarel, B. L., V. Lombard, and B. Henrissat. 2012. Complex carbohydrate utilization by the healthy human microbiome. PLoS ONE 7:e28742.
5. LeBlanc, J. G., C. Milani, G. S. de Giori, F. Sesma, D. van Sinderen, and M. Ventura. 2013. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Current Opinion in Biotechnology 24:160-168.
6. Hausmann, K. 1955. The significance of intestinal bacteria for vitamin B12 and folic acid supply in humans and animals. Klin Wochenschr 33:354-9.
7. Albert, M. J., V. I. Mathan, and S. J. Baker. 1980. Vitamin B12 synthesis by human small intestinal bacteria. Nature 283:781-2.
8. Cho, I., and M. J. Blaser. 2012. The human microbiome: at the interface of health and disease. Nature Reviews Genetics 13:260-270.
9. Hofer, U. 2014. Microbiome: Bacterial imbalance in Crohn’s disease. Nature Reviews  Microbiology 12:312-313.
10. Turnbaugh, P., M. Hamady, T. Yatsunenko, B. Cantarel, A. Duncan, R. Ley, M. Sogin, W. Jones, B. Roe, J. Affourtit, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457:480 – 484.
11. Ley, R., P. Turnbaugh, S. Klein, and J. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022 – 1023.
12. Qin, J., Y. Li, Z. Cai, S. Li, J. Zhu, F. Zhang, S. Liang, W. Zhang, Y. Guan, D. Shen, et al. 2012. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490:55-60.
13. Khanna, S., and P. K. Tosh. 2014. A clinician’s primer on the role of the microbiome in human health and disease. Mayo Clinic Proceedings 89:107-114.
14. Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annual Review of Microbiology 39:321-346.
15. Keller, M., and K. Zengler. 2004. Tapping into microbial diversity. Nature Reviews Microbiology 2:141-150.
16. Tanaka, T., K. Kawasaki, S. Daimon, W. Kitagawa, K. Yamamoto, H. Tamaki, M. Tanaka, C. H. Nakatsu, and Y. Kamagata. 2014. A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Applied and Environmental Microbiology 80:7659-7666.

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