Bacteria maketh the man

This essay was written by Marc Veldhoen and was first published in the 2013 Mill Hill Essays.

When you are feeling unwell a visit to the GP often results in a prescription for antibiotics. You are, or should be, told to take the entire course of drugs in order to destroy all those disease-causing germs or bacteria. Other antibacterial and antimicrobial agents are used to prevent the spread of infection in hospitals, but they are also promoted to a much bigger market: everyday consumers. After all, prevention is better than cure. No wonder then that advertisements in the media frequently play up the fear of germs. Products such as soap, body-, mouth-, or face-wash, shampoo, eye drops, laundry detergents and other cleaning products that “kill 99.9% and give lasting protection from germs” are regularly promoted in the domestic battle against bacteria. However, increasingly louder voices have questioned the health benefits of such products, and started pointing towards the potential detrimental effects those bacteria-targeting strategies may have. Bacteria are one of the basic ingredients of life. We live with them all around us and, importantly, we are alive because of them. Many bacteria can be beneficial while some are capable of causing harm to human health. This essay aims to provide an insight into current scientific areas of microbial research and how the very old, complex and fascinating world of bacteria directly affects our daily lives and health.

It is difficult to comprehend a period of time spanning four billion years, the length of time that bacteria have been around on earth. For a good two billion years they ruled alone. They developed an enormous, almost unlimited, arsenal of chemical reactions which facilitate the generation of energy from a large variety of sources. Consequently, bacteria can be found in most places: on rocks, in water, at the bottom of oceans. They inhabit some of the most inhospitable spots on the planet such as acidic hot springs, under the icecaps, and deep inside the earth. They appear to be simple cells; singular, plain shaped, and protected from the outside world by a cell wall and a thin membrane with little apparent structure inside (Figure 1). However, first impressions are deceptive; these simple cells are actually biochemically so complex that we have much still to learn from them. One indication of their success is that there are approximately five nonillion (five million trillion trillion, or 5×1030) bacteria on earth, with a combined mass that exceeds that of all other life forms. This is even more impressive considering their tiny size. However, they have a colossal power of multiplication: one bacterium can become two in as little as 20 minutes when given the opportunity. Theoretically this would allow a bacterium to produce a colony that exceeds the mass of our planet within 48 hours. This of course does not happen, because multiplying bacteria find themselves swiftly starved of resources. They quickly consume all available nutrients whereupon their growth potential is severely limited or halted. Their biochemical power can be swiftly reactivated though. This biochemical capacity has been formed through evolution, the result of stringent selective pressures with limited resources. In the competitive world of bacteria the speed of cell division, and thus the most optimal use of resources, is vital. Those bacteria that proliferate fastest when resources are available will increase their presence in the population, out-competing those that are slower. Consecutive rounds of supply and starvation will quickly result in a population of bacteria that can replicate very fast indeed. Importantly, this is also how bacteria evolve to become resistant to antibiotics. Those surviving the biochemical warfare of antibacterial agents will quickly increase their proportional representation in the total population until they dominate.

Schematic representation of a bacterium and Eukaryote cell.
Figure 1. Schematic representation of a bacterium and Eukaryote cell.

Note the absence of defined structures within the bacterial cell, but the presence of many membrane structures, including mitochondria, in the eukaryote.

Although bacteria are relatively simple in their makeup, they have an ancient lineage and stand at the evolutionary crossroads where bacteria diverged from the other two known life forms: archaea and eukaryotes. The archaea are single-cell microorganisms distinct from bacteria especially biochemically (hence they are not sensitive to many antibiotics). Eukaryotic cells are much bigger than bacteria, often by around 100,000-fold in volume, and are characterised by a much greater level of complexity. Their cellular space contains several structures enclosed within membranes (Figure 1). Humans and all other multicellular organisms such as animals and plants and also fungi are made up of eukaryotic cells (unicellular eukaryotic organisms also exist). Importantly, all multicellular organisms are eukaryotes. No multicellular bacteria exist. This is surprising since bacteria have been around for a lot longer, are enormously varied, and are biochemically sophisticated. Yet, they have failed in building any multicellular system other than loosely organised colonies without complex cellular specialisation.

The relentless competition for resources and the need for speedy multiplication is likely to blame for this. The speed at which bacteria can replicate is directly related to the size of their genome, the slowest component to duplicate. This means that their genomes are under pressure to be small. Bigger bacterial genomes do exist in circumstances where additional genes are advantageous, for example to generate more energy or to generate energy from a different source, but there is still a selective pressure for small size in relation to other bacteria in the same environment. Part of this is geometry; it is the surface to volume ratio which determines the efficiency of energy production. As cells become larger, their surface area rises much slower than their volume. Bacteria rely on their surface membrane for energy generation and resource uptake, so bigger cells are less energy efficient. Possibly as a result of this relentless pressure, bacterial genomes are very dynamic. They are able to quickly add and shed genes. This is a high risk strategy, enabling swift adaptation to new circumstances with potential huge competitive advantages, like rapid gain of antibiotic resistance from other resistant bacteria, but with a potential loss of replication speed or cell viability. The tendency of bacteria to rapidly remove unrequired genes, even if these could be of use in the future, has prevented them from building up a genetic repertoire of energy governing genes beyond those that rely on extracellular sources.

How then were the eukaryotes liberated from the constraints of limited-size genomes, permitting the construction of complex yet biochemically similar cells, big genomes, cell specialisation and ultimately complex organisms? Clearly eukaryotes are much bigger, and size does matter. Bacteria do not have internal membranes; these can only be built with more genetic material which poses a proliferation disadvantage. In order to make energy, cells use a mechanism based on the generation of electricity across a membrane. This generates an electric field the power of which is harnessed to generate energy. A microscopic look at eukaryotic cells reveals large membranes, and suggests that they may have found a way to generate energy not solely depending on their surface membrane. Indeed, specific structures in eukaryotic cells are dedicated to the task of providing energy, called mitochondria in animals and chloroplasts in plants. They are of bacterial size and our cells typically contain several hundreds to thousands of them, depending on the cell’s metabolic needs. It is now recognised that these structures are independent entities that are in a mutually beneficial relationship with their host, the eukaryotic cell. In fact, they are adapted bacteria. Mitochondria are highly dynamic, they frequently divide and fuse partly independently of their host, change size and shape, have their own genome and can travel long distances throughout the cell. Their genes are of a bacterial nature, not wrapped in proteins, as those of Eukaryota and Archaea are. Their protein production and the machinery required for this are all distinctly bacterial and even sensitive to some antibiotics. They truly are the bacteria within us.

How this relationship exactly started is still hotly debated. The current hypothesis proposes that eukaryotic cells are the product of a mutually beneficial relationship between a metabolically versatile, hydrogen generating, bacterium (α-proteobacterium) and a hydrogen-liking methanogen, which gets its energy from methane. This liaison became stronger and more interdependent with time, with the methanogen engulfing the α-proteobacterium. Environmental conditions may have provided methanogens harbouring α-proteobacteria a competitive advantage. Most genes of the α-proteobacteria were lost or ended up incorporated in the methanogen’s genome, thereby removing unnecessary duplicate genes and streamlining gene expression. However, α-proteobacteria have retained several genes that largely related to local regulation of specific metabolic processes; the generation of energy, and their semi-independent regulation of duplication and movement. Gene loss and transfer ultimately created a chimeric cell with complete interdependence of the host and its mitochondria. The capacity to generate enormous amounts of energy, over intracellular membranes of hundreds to thousands of mitochondria, allowed changes in cell shape. It facilitated increases in size, building other cellular structures, multi-cellularity and cell specialisation, i.e. the evolution of complex organisms: animals and, with the help of additional cyanobacterial-like organisms, plants and algae. It also had far-reaching consequences, which are hugely influential in all our lives beyond the provision of energy. Mitochondria have an instrumental role in cell death, thereby influencing the physical shape of their host and preventing the development of cancer. They may even be the reason why there are two genders and one of the reasons behind why we age.

The bacterial influence on our lives is not just limited to a very distant past, solely providing us with energy from within our cells: animals and plants are surrounded by bacteria. A surprisingly large number of bacteria make their home on the surfaces of animals and plants. The surfaces consist of those areas where the body is exposed to the outside world, including the gut. From the legume family of plants to fish, fruit flies, cockroaches, mice and man, we all cohabit with bacteria. All these hosts offer a stable, nutrient-rich environment for microbes to live. Thus the health of the host is essential to the microbes. Hosts do not make themselves available to just any micro-organism. There are very many bacterial species – estimates are in the order of a billion species – but each host carries a very limited set of them. It is estimated that 1200 bacterial species have made a home on human surfaces, but with possibly as few as 200 species on each individual. Our interaction with them ranges from complete interdependence, mutual tolerance without known benefits, to harm. The bacterial species found in the gut, the most densely populated organ, are instrumental in maintaining many aspects of our health. Much of the food we consume arrives in the intestine only partially digested. We are simply not equipped with sufficient metabolic capacity to be able to get the maximum energy and absorb essential compounds such as vitamins out of our diet. Specialised bacterial communities have the required equipment, in the form of enzymes, to access and degrade the partially digested food particles. Their importance is highlighted when mice are housed under completely sterile conditions. In the absence of any microbes these mice have significantly less body weight than identical mice on the same diet kept under conditions where micro-organisms are present. This difference is surprising because germ-free mice consume nearly 30% more food. It is again the metabolic capacity of the bacteria, optimised to make best use of resources in their competitive world, which has a major impact on their host.

The relationship each host has with its associated micro-organisms, collectively called the microbiota or microflora, is the outcome of a lengthy and complex process. The microbial communities are highly interactive and form complex metabolic networks, with crossfeeding between different components of the community an important and widespread phenomenon. As such, some bacteria are only indirectly important for their hosts. Their purpose may lie in clearing metabolic products of beneficial bacteria whose waste products may be harmful for them. Different parts of the body differ strikingly from each other with respect to their physiology, such as the nature of available resources, acidity, moisture and oxygen levels. Accordingly, these different sites harbour different bacterial species. In addition, the composition of the microbiota changes throughout life, from the moment of birth, when we are first exposed to micro-organisms, until old age. The first bacteria are pioneers that create the conditions for subsequent colonisation. In the intestine, with the introduction of solid foods the gut microbial composition starts to resemble those present in the adult with increased diversity, with a decline in this diversity observed in old age. The underlying causes of these changes, such as the host’s defensive function, local environment and diet and how they influence health remain somewhat elusive, but are the subject of intense investigations.

The adult intestine contains approximately 100 trillion microbes. By comparison, the total number of our own cells that make up our entire body is 10 trillion. This effectively means that in terms of cell number we as a composite organism are less than 10% human. Importantly, it is the microbial chemical arsenal that is critical in maintaining our energy balance as an organism. This is achieved by the diverse sets of genes that encode enzymes these bacteria contribute. In the past decade we have been able to map all human genes. It was quite a surprise when we discovered that our genome contains far fewer genes than anticipated. The genetic contribution that micro-organisms make outnumbers our own genes by at least 150 to 1. Many perform essential functions that we cannot perform ourselves. After the completion of the human genome project much concerted effort has been made to map the bacterial communities in the human microbiome project. Thus far most analyses have largely been focused on identifying the bacterial families and their relative and numeric presence. As mentioned, bacteria are very good at losing and gaining genes, making the identification of their metabolic capacity especially difficult. Yet despite the gene sharing, in some cases specific metabolic products have been directly associated with one or few bacterial species. However, these seem to be the exception, with generally much more intricate mechanisms at play. At specific sites of the body different bacterial species are found to share very similar jobs. In addition, two different people can have different species of bacteria living at the same site which make use of the same metabolic genes. This suggests that useful metabolic genes were selected for, not bacterial species per se. These beneficial genes can be transferred between different species, which themselves are adapted to a certain environment.

Although metabolic assistance may well have been the basis of the mutualistic relationship between hosts and their particular microbiota, it has not remained that way. Early microbial colonisation of the body’s surfaces has been shown to directly influence the maturation of the immune system. Here there is an apparent contradiction. The immune system is a collection of cells and their products, found throughout the body, which is classically thought to protect us from the threat of microorganisms. Yet its maturation and function depends on them. At the body’s surfaces, where this threat is most acute, there exists the largest collection of immune cells and micro-organisms in an intricate balancing act. A crucial challenge faced by the immune system is to distinguish between beneficial and pathogenic microbes. The microbiota make fundamental contributions to the development and function of the host immune system, making it better equipped and more diverse in cells and weapons to combat harmful microbes. One contribution of the microbiota is to form a barrier against harmful bacteria. This is achieved with help of the cells of our body’s surfaces, the skin, lungs and intestine, which actively provide substrates to attract particular groups of bacteria or to allow them to hold on tightly in favour of other species. In addition, antimicrobial products are secreted, by the host and the microbiota, which are selectively more harmful for undesired species. In the intestine, clumps of immune cells can be found which before colonisation with micro-organisms are very small. Upon first contact these expand in size harbouring many white blood cells (Figure 2). One kind of white blood cell, the B cells, produce antibodies, which are small proteins that can recognise specific structures. Antibodies have a protective role in keeping many undesirable bacteria away from the intestinal surfaces. The bacteria, in return, directly influence the physiology of the barriers they live on. They make major contributions to the architecture and function of the tissues they have made their home, and play an important role in the balance between health and disease. In the intestine and on the skin they contribute to processes of inflammation against unwanted bacteria and enhance wound healing. Thus we and our microbiota fight on the same side against infectious agents. Scientific reports have highlighted how reductions in microbiota diminish our immunity against so called hospital infections (Clostridium difficile and Campylobacter jejuni), and how pathogens such as Salmonella are directly attacking the microbiota, their fellow bacteria, to secure a safer environment.

Immune structures found in the intestine depend on the presence of bacteria.
Figure 2. Immune structures found in the intestine depend on the presence of bacteria.

Left microscopy picture shows a mouse intestine, stained with green to identify B cells and grey to identify the intestinal wall, such as found without the absence of bacteria.The right picture shows the fully matured structure after bacterial colonisation of mouse intestine.

We are a composite organism, with partly independent bacteria-derived structures within our cells and carrying with us microbes occupying our every surface. Clearly these are not just germs that need eliminating but constitute a fundamental part of what makes us human. Like our genes, microbial genes have the ability to influence our health and disease-risk. For many decades, we have been aware that diseases often arise as a combination of our genetic make-up and factors in the environment. For example, the presence of the same disorder in both members of a pair of identical twins is only 20 to 40% on average. Our genome is inherited according to predictable rules, part maternal part paternal. Different rules apply for the mitochondria, which are nearly exclusively inherited via the maternal line. In contrast, the microbiota and their genes are acquired from the environment. Although initially largely derived from both parents, it is subject to change throughout life depending on age, diet and chance encounters such as with other microorganisms. In addition, gene loss and gain continues to play a role between the species present. Undesirable immune responses, such as autoimmunity (the immune system takes action against our own bodies) and allergies (the immune system acts against something innocent such as pollen or cat hair), have now been correlated with changes in the microbial composition. In summary, although it is important to maintain a particular type of bacterial species containing a useful trait, it might be more important to conserve a group of different species adapted to different living conditions but sharing this same trait. This allows individual species to be selected from a varied pool according to changes in circumstances such as diet and disease. Having only a limited pool of species would increase the chance of things going awry in the highly interactive bacterial communities, contributing or even causing disease. The often unnecessary use of diverse antimicrobial agents may, with time, limit the available diversity of beneficial microbes. The agents may target specific bacteria, but other species that are indirectly beneficial are affected and may affect others in a complex cascade. It has been suggested that each human generation born could be starting life with a smaller pool of microbes than the previous one. The long-term consequence of reducing the bacterial diversity surrounding us, even some of those which have known harmful effects, has received limited attention from researchers as yet. But the reduction in diversity may harm our adaptation to change, and could be aiding the dramatic increase in conditions such as inflammatory bowel disease, obesity, diabetes, multiple sclerosis, rheumatoid arthritis, allergies and asthma. As such, bacteria probably deserve a lot more respect than they are generally given, and killing 99.9% of them in our immediate domestic surroundings without acute danger to ourselves may ultimately harm us in many ways.

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