The hologenome concept of evolution is based on four generalizations:
All natural animals and plants are holobionts containing abundant and diverse microbiota.
Holobionts can function as distinct biological entities, anatomically, metabolically, immunologically, during development and in evolution. Microbiomes participate in achieving fitness of the holobionts.
A significant fraction of the microbiome genome together with the host genome is transmitted from one generation to the next, and thus can propagate unique properties of the holobiont.
Genetic variation in holobionts can occur by changes in the host and/or microbiome genomes. Since the microbiome genome can adjust to environmental dynamics more rapidly and by more processes than the host genome, it can play a fundamental role in adaptation and evolution of holobionts.
Plants, Animals, and Humans are Holobionts
Development of non-culturing, DNA-based methods for analyzing bacterial communities has led to the determination of bacterial species diversity in a wide assortment of non-vertebrates, vertebrates, and plants. It is now clear that all natural animals and plants contain hundreds or thousands of different bacterial species as well as abundant viruses14
and often fungi15
; the two last-mentioned have not been studied extensively to date. For example, it has been reported that the human gut contains 5,700 bacterial species,16
and human skin contains 1,000 species.17
These are minimum numbers since rare species cannot be determined by current methods. Because of the large diversity of bacterial species, the gut microbiome contains ca. 9 million unique protein-coding genes or 400 times more bacterial genes than human genes.18
One of the unexpected findings of studies of gut microbiomes is the enormous variation between individual humans; the bacterial species composition within the human gut is unique to each person. Nevertheless, microbiomes of different individuals are closer to each other than to microbiomes of other primates,19 suggesting that there is something common (a core) to the human microbiome. Shapira20 has discussed the differences between conserved core microbiota and flexible, environmentally driven microbiota, with regard to their maintenance and contributions to host adaptation. It should be emphasized that “presence” or “absence” of a bacterial species depends on technical limits of detection. Methods developed to detect rare species may reveal that there are many more common (core) species than currently considered and that individual variation may be the result of quantitative rather than qualitative differences that are caused by a different diet or other environmental factors. Foods, such as red wine,21 tea, coffee,22 and chocolate,23 food additives, such as food emulsifiers24 and artificial sweeteners,25 and essentially any material that is put in the mouth affect the gut microbiome at all ages. Also, microbiomes are affected by physical activity26 and illnesses, e.g. cancer27 and diabetes.28 Clearly, the complexity and dynamics of microbiomes are only beginning to be appreciated.
Microbiomes change also with age. Newborns are dominated by facultative anaerobes such as the Proteobacteria, after which the diversity of strict anaerobes within the Firmicutes and Bacteroidetes phyla increases towards a more adult-like profile by approximately one year.29,30 The microbiome in young children is shaped by mode of delivery,31 diet,32 exposure to environmental factors, such as furry pets,33 and, of course, antibiotic treatment.34 During most of adult life, the microbiome appears to be more or less stable.35 In older people (>65 years), however, the gut microbiome is extremely variable between individuals and differs from the microbiome of younger adults.36
Microbiomes Affect the Fitness of Holobionts
A large number of studies have demonstrated the beneficial interactions between microbiomes and their hosts, leading to a better-adapted holobiont. Table 1
summarizes major contributions of the microbiome to holobionts.
Examples of Microbial Participation in the Fitness of Holobionts.
A large number of studies have shown that resident microbes protect holobionts from pathogens. For example, following oral infection, the numbers of Listeria monocytogenes were 10,000-fold higher in the small intestine of germfree (GF) mice compared to conventional (CV) mice.37 Also Staphylococcus aureus infection is prevented by resident Corynebacterium species.38 Blocking binding sites and production of antibiotics are two common mechanisms by which resident bacteria protect the holobiont against pathogens.39,40 A strong argument for the role of bacteria in combatting infectious disease is the successful treatment of patients, suffering from severe diarrhea caused by Clostridium difficile infection, with fecal transplants from healthy donors (see further on).41
There are many examples of microbiomes contributing to their hosts by carrying out metabolic processes that the animal or plant is unable to carry out by itself. In humans, gut bacteria have been shown to perform many beneficial biochemical reactions, amongst them: (1) production of metabolites from dietary components, such as the conversion of dietary fiber to the short-chain fatty acids (SCFAs), acetate, propionate, and butyrate42 important for colonocyte health and regulatory activity of the body; (2) modification of metabolites that are produced by the host, such as converting primary bile acids to secondary bile acids, thus assisting in bile acid recycling43; (3) de novo synthesis of compounds, e.g. the important microbial immune modulator polysaccharide A, produced by the common gut bacterium Bacteroides fragilis44; and (4) synthesis of vitamin K as well as most of the water-soluble B vitamins.45
The human microbiotas play a role in energy metabolism and obesity, as will be discussed later in the review, and, although gut bacteria contributing to obesity are generally considered harmful, under certain conditions they are also beneficial. During the third trimester of pregnancy, these so-called “obese bacteria” become abundant46 and induce metabolic changes that promote energy storage in fat tissue that in turn encourages growth of the fetus and milk production in the mother. Also, during our evolution, food insecurity was a frequent occurrence, and the ability to store energy in the form of fat was probably advantageous for survival (“thrifty genotype hypothesis”47).
Symbiotic bacteria play a role in the development of animals and plants. For example, Rhizobia strains cooperate with legume plants to produce root nodules that perform nitrogen fixation,48 and Vibrio fischeri triggers the formation of the light organ in squid, where luminescence occurs helping the squid avoid predation. In humans and other vertebrates, the gut microbiome promotes the development of the immune system and body organs. Exposure to microorganisms educates the immune system, induces innate and adaptive immunity,49 and initiates memory B and T cells that are essential to combat various pathogens. In addition, the gut microbiome encourages the development of bone mass50 and blood vessels in the intestinal wall.51
Gut microbiotas modulate brain development and behavior, including anxiety and mood disorders,52,53 as will be discussed later in the review. Microbial gut–brain signaling is bidirectional. The circuitry of neurons, hormones, and chemical neurotransmitters enables messages to be transmitted between the brain and the gut. The gut microbiota influences the body’s level of the potent neurotransmitter serotonin, which promotes feelings of happiness and peacefulness.54 Conversely, the rate at which food is being moved and how much mucus is lining the gut—both of which can be controlled by the brain—have a direct impact on gut microbiota.
The mechanism for transmission of host DNA to offspring is well understood and need not be discussed here. Transmission of the microbiome from parent to offspring also occurs, but with a variety of mechanisms: (1) vegetative reproduction in plants and many animals, such as worms and corals (vertical transmission); (2) via oocytes in sponges, herbs, and many insects (vertical transmission); (3) coprophagy (eating the feces of parents) in many animal species (both vertical and horizontal transmission); (4) physical contact starting at birth in most animals, including humans (both vertical and horizontal); and (5) mother’s milk in mammals (vertical).
In humans, transmission to the offspring occurs initially via inoculation with maternal vaginal and fecal microbes when the baby transits the birth channel (vertical transmission). Kissing and hugging provides additional microbiota to the offspring. Breastfeeding is an additional route of maternal vertical microbial transmission.55 Human milk contains ca. 105 bacteria per mL, composed of hundreds of species.56 Analyses of the DNA of several bacterial strains isolated from mother’s milk demonstrated that they were identical to those found in the offspring,57 providing support for vertical transmission. Mother’s milk is also a continuous source of modified oligosaccharides that support the growth of these bacteria but are not digestible by the infant.58 In essence, these oligosaccharides function as natural prebiotics. The Bifidobacterium species contain unique genetic loci responsible for vigorous growth on these oligosaccharides,59 suggesting a remarkable co-evolution between the symbiotic bacteria and their human host, benefiting both.
Long-term transmission of microbiota in great apes, including humans, was studied using both 16S ribosomal gene sequences60 and rapidly evolving gyrB gene sequences.61 The host species phylogenies based on the composition of these microbial communities were completely congruent with the known evolutionary relationships of the hosts. The authors concluded that over evolutionary timescales the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.
Genetic Variation and Evolution of Holobionts
Genetic variation occurs more rapidly in genomes of microorganisms than in host genomes, thereby offering a potential for manipulating the microbiome to prevent and treat certain diseases of holobionts. Genetic variation in holobionts can occur, in addition to mutation and DNA rearrangement, also by three other mechanisms: (1) amplification or reduction of specific microbes, (2) acquisition of novel microbes from the environment, and (3) horizontal gene transfer from microbes to microbe or from microbe to host.
Amplification/reduction refers to the increase/ decrease of one group of symbionts relative to others. This can occur rapidly when conditions change. An increase in the number of a particular microbe is equivalent to amplification of a whole set of genes. Considering the large amount of genetic information encoded in the diverse microbial population of holobionts, microbial amplification/reduction can be a powerful mechanism for contributing to adaptation, development, and evolution of holobionts. Since genetic variation by amplification is driven by the environment, it has a Lamarckian aspect to it.62 Amplification is also a crucial step in genetic variation by acquisition of novel microbes because pioneer microbes need to amplify in order to become established in its host.
Animals, including humans, and plants come into contact with billions of microorganisms during their lifetime, via air, water, and interaction with organic and inorganic surfaces. Occasionally some of these microbes will find a niche and under appropriate conditions will amplify in the host and become part of the microbiome. Acquisition of a microbe introduces hundreds of new genes into the holobiont. Rather than trying to create genes that have already evolved in microbes, animals and plants acquired pre-evolved genetic information in the form of microbes. Microbes were on this planet for 2.1 billion years before there were any animals or plants. During this time, they developed into organisms encompassing enormous biochemical diversity. The first eukaryote was probably formed by the acquisition of bacteria to eventually form mitochondria63 and chloroplasts.64 Uptake of microbes into multicellular organisms continued to provide genetic variation for holobionts throughout evolution.
An example of a major evolutionary event that was driven by the acquisition of bacteria is the ability of many animals, including humans, to use plant fibers as nutrients.65 However, animal genomes do not contain the information for synthesizing enzymes that degrade the complex polysaccharides in plant material. Instead, they rely on microorganisms that are present in their digestive tract. These microbes anaerobically convert polysaccharides to fatty acids that are a source of carbon and energy for their host animal. It is likely that these bacteria were acquired by a gradual process of internalizing them from the soil. Instead of plant fiber being broken down in the soil prior to ingestion, it “rots” in the gut after consumption.
Another important mode of genetic variation in holobionts, referred to as horizontal gene transfer (HGT), involves the transfer of groups of genes between bacteria of different taxa and from microbiomes to their host. Intimate contact between microbes and between microbes and host in holobionts would promote HGT. It has been suggested that nutritional adaptation is one of the key selective pressures on the microbiome in the mammalian gut, and that HGT processes contribute to that adaptation.66 Until 2010, only a few examples of HGT events were recognized in which genes from microbes were transferred sometime in the past to animals. These included transfer of: Wolbachia genes to the chromosomes of their insect hosts,67 bacterial and fungal genes into the telomere region of rotifers,68 fungal genes to aphids,69 and cellulose genes from bacteria to nematodes.70 However, an examination of a large number of high-quality genomes, that became available recently, has led to the conclusion that HGT in animals and plants was a general phenomenon that resulted in the incorporation of tens or even hundreds of active foreign genes into the eukaryotic genome.71
In humans, 145 genes (not present in other primates) were attributed to HGT.72 These genes are distributed throughout the genome and play a variety of roles, such as amino-acid metabolism (2 genes), macromolecule modifications (15 genes), lipid metabolism (13 genes), antioxidant activities (5 genes), and innate immune response (7 genes). Most of the 145 genes identified in the study came from bacteria, but some originated from viruses and yeasts. Analysis of a moss identified 128 genes found in land plants but absent from algae.73 These genes were acquired by HGT from prokaryotes, fungi, or viruses. Many of these genes are involved in some essential plant-specific activities, such as xylem formation, plant defense, nitrogen recycling, and the biosynthesis of starch, polyamines, hormones, and glutathione.
A key event in the evolution of placental mammals was the acquisition by HGT, from a retrovirus, of the gene coding for the protein syncytin.74 Initially, the function of syncytin was to allow retroviruses to fuse host cells so that viruses could move from one cell to another. Now, syncytin is necessary for the development of the placental syncytium, an essential part of the mother–fetus barrier. In addition, retroviral-derived DNA appears to have played a crucial function in the generation of the progesterone-sensitive uterine decidual cell, allowing nutrient provision to the developing embryo.75 These data indicate that the integration of viral DNA into host genomes by HGT played a primary role in major evolutionary events.
Horizontal gene transfer (HGT) from microbe to microbe can also affect human metabolism and evolution. An example is the ability of Japanese to break down agar (an abundant ingredient in their diet) since they have a bacterium in their gut that contains genes that code for the porphyranases that degrade the polysaccharide agarose of agar. Westerners lack this bacterium in their gut and therefore cannot digest agar. The group of genes coding for agarose digestion was driven into a resident gut bacterium by HGT from a marine bacterium that was present on raw seaweed.76 Bacteria with the transferred genes spread throughout the Japanese population by vertical and horizontal transmission.
In summary, the evidence brought forth up to now in this review supports the concept that holobionts with their hologenomes can be considered levels of selection in evolution. Furthermore, genetic variation and the evolution of holobionts involve, in addition to classical genetic variations in the host, also acquisition of novel microbes and HGT of microbial genes into host chromosomes. In the following section, we will be discussing the relationship between the hologenome concept and some human diseases, thereby reinforcing the holobiont as a unified biological entity.