Food and the Human Microbiota 

As human beings, we have always had a perception of ourselves as individual, living beings existing within the context of our environment. Modern science, however, is radically changing this picture. Most people know that micro-organisms live on our body but with an explosion in microbiological research, it is becoming increasingly clear that these large populations of micron-sized bacteria and other organisms inhabiting the human body play a vital role in our health. The medical community’s paradigm shift in its views of human health paints a picture of dynamics of ecological communities instead of a single living being. This new field, called microbial ecology involves multi-disciplinary teams of biologist, medical researchers and ecologists working together to study the microbiota found in the human body and is revealing new insights into age old problems.

The bacterial organisms found on or in our body outnumber humans cells by a ratio of 10 to 1.While it may creep us out that there are an estimated 100 trillion microbial organisms on or in the human body at any one time, this is the stark reality of the human body. We are a host, an entire planetary system with diverse communities of other living beings depending on us for their survival. Their lives are measured in spans of 20 minutes and our 60 to 100 year life span must seem like an eternity to them.

No amount of washing will eliminate these microorganisms, and you wouldn’t want to – they are all necessary for our survival. This new perspective that sees ourselves as hosts, as ecosystems to large communities of friendly micro-organisms is sure to break down the artificial, dualistic view of ourselves and to establish a deeper bond with our own larger planetary ecology.

Humorous introduction to Microbial Ecology, Part 1
Humorous introduction to Microbial Ecology, Part 2
Introduction to the microbiome
Earth Microbiome Project : Rick Stevens at TEDxNaperville
How the microbioime affects brain and behavior
The assembly of an infant gut microbiome framed against healthy human

The Health Link

This humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked. Disorders in our internal ecosystem — a loss of diversity, say, or a proliferation of the “wrong” kind of microbes — may predispose us to obesity and a whole range of chronic diseases, as well as some infections. (NY Times, May 15, 2013)

There are deep connections between the larger ecosystem found in the global environment that surrounds us and which we are all familiar with and the new frontier of the microbiota of the human body. A growing number of researchers hold that human health should now be redefined as a collective property of the human-associated microbiota. From this new perspective, scientists are now framing our industrialized societies unintended side effects as destructive agents which are damaging the human-associated ecology. Toxins, pesticides, chemicals, antibiotics all affect the biodiversity of friendly bacteria. In particular,our highly processed food sources are now significantly deprived of the kinds of nutrients that are important the the sustainability of these friendly bacteria populations. Commonly found processed food ingredients such as the emulsifier Xanthan Gum have always been thought to be benign from the old perspective. In light of this ecological model, however, researchers are discovering that it damages the lining of the gut, causing harmful effects to microbiota populations there. Food safety labs do not yet operate from this paradigm so do not test for potential harm to microbiota populations. Researchers talk of impoverished “Westernized microbiome” and suggest that the time has come to embark on a project of “restoration ecology” — not in a coral reef or rain forest, but in the human body itself.  Some researchers are now investigating the alarming increase in autoimmune diseases in the West to see if these can be explained as pathologies in host / microbiota community relations.

Figure 1:Human diseases related to microbial ecology pathologies (Source: Gutflora)

Figure 2: Microbiota impacts on human health and disease (Source: Science Magazine)

How microbiota causes autoimmune diseases
The Human Microbiome: Energy Balance and Obesity
How the microbioime affects brain and behavior


Figure 3: Grass analogy to human microbiota pathologies and treatment (Source: Nature)

NIH Human Microbiome Project

The Human Microbiome Project (HMP) is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome” of microbes carried in and on the human body. Microbial ecologists, realizing that >99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ, primarily by sequencing the 16S ribosomal RNA gene (16S) as a phylogenetic and taxonomic marker to identify members of microbial communities. The need to develop corresponding new methods for culture-independent studies in turn precipitated a sea change in the study of microbes and human health, inspiring the new term “metagenomics” both to describe a technological approach—sequencing and analysis of the genes from whole communities rather than from individual genomes—and to emphasize that microbes function within communities rather than as individual species. This shift from a focus on individual organisms to microbial interactions culminated in a National Academy of Science report, which outlined challenges and promises for metagenomics as a way of understanding the foundational role of microbial communities both in the environment and in human health.

Pioneering medical microbiologists applied these approaches, finding far more microbial diversity than expected even in well-studied body site habitats. Technological advances further enabled sequencing of communities across the human body, and immunologists began exploring the fundamental role of microorganisms in the maturation of the innate and adaptive immune systems. Initial metagenomic studies of human-associated microbial communities were performed using the traditional Sanger platform. Upon introduction of pyrosequencing, the number of 16S-based data sets increased dramatically. The time was right to invest in a concerted study of the microbial communities associated with the human body and the metabolic capabilities they provide—the human microbiome  (NIH HMP on PLOS)


Figure 4: Timeline of microbial community studies using high-throughput sequencing (Source: NIH HMP on PLOS)

Each circle represents a high-throughput sequence-based 16S or shotgun metagenomic bioproject in NCBI (May 2012), indicating the amount of sequence data produced for each project (circle area and y-coordinate) at the time of publication/registration (x-coordinate). Projects are grouped by:

  1. human-associated (red),
  2. other animal (black), or
  3. environmental (green) communities
  4. shotgun metagenomic projects are marked with a grey band

Selected representative projects are labeled