HMP, Human Microbiome Project, Update & What It Means to Your Health

The Human Microbiome Project (HMP) is an initiative of the US National Institutes of Health investigating the microbiomes of diverse body sites over multiple points in time. I wrote about many of the highlights from the project and the implications of them for everyday living in my book, “Probiotics: How to Use Them to Your Advantage”.

In the latest wave of HMP data collection and analysis published in a study in  late 2016, 265 healthy individuals, aged 18-40, provided 1631 new samples one month and one year apart for each body part. This article summarizes the findings from the published study and highlights what those mean to your health.

One of the surprising results from the study was that the genomes from many prevalent and abundant species in the body-wide microbiome could not be closely matched to the closest available reference genomes. This means that we really don’t know details about those species. There is an urgent need for isolating such genomes to better understand them.

Strain identification in the published HMP study showed that there are clusters of subspecies specific to certain body sites, such as different subspecies of Haemophilus parainfluenzae in the mouth areas. Although there were 18 different body sites sampled in HMP initiative, the new data primarily sampled 6 body sites: inside of nose, cheek, plaque above the gum line, tongue, stool and vagina. The majority of studies on the human microbiome, however, continue to focus on the gut.

Microbial strains in the study were basically stable over time in each person, with differences greater between people than in a single individual over time. This shows that each person really is unique, and although we may share common microbes in some instances, and certain microbes may be beneficial to most or all of us, the mishmash of our own personal microbiotas makes us function in some of the particular ways we do. This fact is one reason why more studies on specific strains of probiotics for specific conditions is so critical and why, if you are expecting certain results, it is best to take a probiotic proven in research than to take one without clinical backing.

What Did the HMP Study Show You Need to Be Healthy?

Unlike us consumers who just want to know which-microbes-we-should-have-where, HMP researchers realized that there probably was not one microbiome associated with health for everyone for our entire bodies as whole bodies, nor for everyone for specific body parts. Instead, the overall metabolic functions, such as carbohydrate utilization and vitamin production, of each body-site microbiome were important keys to health.

To that end, researchers in this study focused primarily on the metabolic functions of the microbes present while taking note of microbes that were most responsible for these functions. Analysis of the data showed that the functional capabilities of the microbes found could be divided into universal, human-enriched, and body site-enriched categories. This means that there are some things microbes can do regardless of where they are able to live, some things that they can do because they live in/on us, and some things that they can do specifically because they live in/on a specific human body part.

The importance of this finding is that it shows that some microbes perform the same functions regardless of their place in/on the human body whereas others perform different functions in different places. Therefore, trying to establish a microbe and have it perform a certain way in an environment in which it is not well-suited to perform that way is not going to work very well unless the microbe adapts, and that does not happen instantaneously. For instance, the dominant normal residents of a healthy mouth are usually not the same dominant normal residents in a healthy colon so taking a probiotic shown to benefit oral health and expecting it to solve your IBS problems may or may not work.

It also shows that our bodies, with their numerous areas and parts, need a variety of microbes to be healthy. There is not one microbe, or even a handful of microbes, that can keep all of our body parts healthy. Disrupting the various colonies of microbes in/on our bodies with antibiotics and antibacterials can have negative consequences that cannot necessarily be reversed simply by taking a low-dose probiotic supplement with a low variety of microbes. You have to at least provide support for those microbes.

In addition to the universal, human-enriched, and body site-enriched categories, HMP researchers also wanted to know which metabolic functions or pathways were core to the microorganisms in specific body niches. A pathway was core to a specific body niche if it was detected in more than 75% of individuals at a relatively abundant level and made sense for the types of microbes associated with human microbiome samples. They investigated whether these functions were core to at least one body site (result A), to sites from multiple body areas (result B) or to all 6 targeted body sites (result C). There were more metabolic pathways associated with result A than for result B, and more for result B than for result C. This makes sense because each site’s microbes will have more individualized needs and expressions based on their environment yet still share some common needs and expressions with microbes from other sites.

Thus, microbial essential functions are core to many body sites, and coreness to one or several human body areas may be a functional adaptation of microbes to humans as hosts.  At least that is the continuing hypothesis. A rough analogy can be made to humans. During the winter, sedentary people in colder climates need warmer clothing, will typically actively perspire less, and if eating seasonally and locally, will eat less summer produce (functional adaptations) than sedentary people in warmer climates, yet people in both locations have essential functions such as breathing air and drinking water.

As expected, changes in microbial functions in the gut tracked during the study were relatively slow, probably due to the routine dietary intakes of the participants, while functional dynamics in the mouth area were rapid due to the need to quickly extract nutrients from a variety of food and drink sources.

More Results on the Microbes, Including Probiotics

Analysis of the data from the HMP study also showed that in the gut microbiome, Bacteriodetes phylum bacteria, such as the Bacteroides genus, showed variations primarily between individuals rather than in a single individual over time, whereas the Firmicutes phylum showed changes over time within each individual. What this means is that although much research (and hype) has been dedicated to understanding the Bacteriodetes/Firmicutes balance in health conditions such as obesity, it may be that the Bacteroidetes aspect is relatively stable and the Firmicutes aspect is the one which shows the most change. Supporting the Bacteroidetes and influencing the Firmicutes with a healthy diet loaded with fibrous vegetables, cultured or fermented foods and drinks, and certain probiotics, then, seems sensible.

Oral and skin microbiomes, on the other hand, were less stable, which makes sense since we eat different foods and come into contact with different environments over short periods of time.

Some notable results from the study concerning probiotic microbes were that:

  • Bifidobacterium bifidum was one of the abundant bacteria in stool
  • Lactobacillus crispatus was abundant in the vagina near the cervix, and as expected, it was more abundant with lower pH.

Although the HMP objectives and results generally may seem too broad to be applicable to your circumstances, there are gems of information in them. My goal is to show you what the HMP may mean for your health.

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