How Many Bacterial Cells Can Fit Into An Animal Cell

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Proc Calif Acad Sci. Author manuscript; available in PMC 2011 Aug 24.

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Proc Calif Acad Sci. 2005 Jun three; 56(6 Suppl ane): 62–71.

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Species Numbers in Bacteria

Daniel Dykhuizen

Department of Environmental and Evolution, Stony Brook University, Life Sciences Edifice, Stony Brook, NY 11794-5245

Abstract

A modified biological species definition (BSD), i.e., that bacteria substitution genes within a species, but not usually betwixt species, is shown to apply to bacteria. The formal definition of bacterial species, which is more than conservative than the modified BSD, is framed in terms of Deoxyribonucleic acid hybridization. From this I estimate there are a million species of bacteria in xxx grams of rich forest topsoil and propose that there volition be at least a billion species worldwide.

Bacteria are a major component of the cellular life on Earth and are found everywhere from the top of mountains in Antarctica to the deep-sea vents. They are found in the deep subsoil, the open up ocean and all over every surface of you lot. The refrain for undergraduates is that only about 10 per centum of the cells moving with you are eukaryotic, the rest bacterial symbiotes. But because bacterial cells are so much smaller than eukaryotic cells, they make up just about ten percent of your weight. (Then, tomorrow, when you step on the scale yous tin can subtract x percent off the scale weight because it is not actually yours.)

Of the three cracking branches of cellular life, two are bacterial: the Eubacteria and the Archeae. The third branch is the Eukaryotes of which plants, animals, and fungi make up three kingdoms. The Eubacteria are divided into forty kingdoms and the Archeae are divided into two kingdoms. The question I will endeavor to answer in this paper is how many species of bacteria might there be. Earlier we can estimate the number of species of bacteria in that location may be in the world, we have to determine whether bacterial species are real entities and how they can exist defined.

Bacterial Species

Bacteria are different from eukaryotes in an essential characteristic of life history. Bacteria are haploid and always reproduce asexually by fission. They accept other mechanisms for sex, the transfer of genes betwixt lineages, such as transformation, transduction, and conjugation.

The effects of sex in leaner are different than in animals. In leaner only a small fraction of the genome is transferred, unlike animals, where 50% of the offspring genome is transferred from the male during sex. Sex in bacteria can be between clones of the aforementioned species, closely related species, or distantly related species, whereas in animals sex activity is virtually always express to members of the aforementioned species. During sexual activity in leaner, pieces of genes or whole genes are transferred and replace the alleles present past homologous recombination, rather than form heterozygotes of the female person and male alleles as in animals. Also, in bacteria, new genes tin can be added to the genome by non-homologous recombination.

The distinction between sexual and asexual as is made in plants and animals does not make sense for bacteria. The corporeality of sexual practice, or lateral factor transfer between lineages, in bacteria can vary from very little to a lot. Borrelia burgdorferi, the causative amanuensis of Lyme illness, is almost completely clonal, simply transferring small pieces of Deoxyribonucleic acid very rarely (Dykhuizen and Baranton 2001). In Heliobacter pylori (Suerbaum et al. 1998), the causative agent of stomach ulcers, and Neisseria gonorrhoeae (O'Rourke and Spratt 1994), the causative amanuensis of gonorrhea, there is and so much sex that alleles of different genes are in linkage equilibrium.

At that place is a certain flexibility in the bacterial genome as to what genes are present, even within a species. This part, which ranges from zero to nigh xx percent of the genome (Ochman et al. 2000; Daubin et al. 2003a), is represented by genes that are transferred into the cell past non-homologous recombination and are adequately readily lost again. Belonging to this class of genes are DNA parasites similar insertion sequences, transposons, lysogenic phage, small plasmids, and probably restriction modification systems. At that place are also genes that are involved in local adaptation to particular environments such as the genes in pathogenicity islands, antibody resistance genes in plasmids (mini chromosomes), genes for resistance to toxins and heavy metals, and genes and operons for various specialized functions. Generally, the genes in this puddle of transients are either DNA parasites or genes that are locally adapted (Eberhard 1990). The genes that are by and large useful to the organism beyond all the environments in which it lives are found in all strains and are normally associated with the major chromosome. Some of these genes are particular to a species or a small group of species, but almost are widely constitute throughout leaner. These genes, such equally those involved in poly peptide synthesis, Dna metabolism, free energy generation and usage, etc., are often called housekeeping genes.

Some individuals (eastward.g., Gogarten et al. 2002) accept been so enamored by this novel aspect of bacteria, the rapid and mayhap widespread transfer of DNA across species, that they have suggested bacterial cells are but holding vessels for the genetic variation available in the bacterial cistron pool. The part of this pool seen in whatsoever particular cluster (species?) is simply the genes that are selectively useful given the electric current surround. Thus, bacterial phylogeny would represent ecology more than history.

I do not recall this is true, but rather bacterial species can be defined in means that are very similar to the fashion animal species are defined. I proposed in 1991 that bacterial species could exist divers as a variant of the biological species definition (Dykhuizen and Greenish 1991). To restate and update that definition, I will define a species as a group of individuals where the observed lateral cistron transfer within the grouping is much greater than the transfer between groups such that phylogenetic history is preserved when genomes are compared. Beneath I volition illustrate what I hateful by this definition. Simply earlier this, I want to make two comments. The first is that I think the similarity between species in leaner and in animals occurs because species are real and acquired by the same basic biological science in both cases. Although information technology is still not clear what this basic biology is, just as it was not clear what basic biological science the Linnaean hierarchical organization of classification described before Darwin's theory of descent, I will present my thought of what this basic biology is later. The 2nd involves the idea of "observed transfer" in the definition. The rates of observed transfer will depend upon both the rate of transfer and the choice for or confronting the strains containing these transfers. More often than not, the rates of transfer will decrease with phylogenetic altitude (Majewski and Cohan 1998) and the selection against the transferred Deoxyribonucleic acid will increment with phylogenetic distance (Cohan et al. 1994), such that transfer is seen within species only not between species (see beneath). Of course, if the environment changes, as, for instance, humans using tremendous amounts of antibiotics for the health and growth of themselves and their animals, even rare transfers of DNA from phylogenetically distance sources will be strongly selected if they provide resistance. The ability to comprise Dna from outside the species is an advantage that more often than not distinguishes bacteria from animals. In animals and plants, incorporation of Dna from different taxa is unlikely, but can happen when associated with endosymbiosis.

The first example supporting a BSD involves Escherichia coli and Salmonella. It is well established that there is recombination betwixt strains of E. coli (Dykhuizen and Green 1991; Guttman and Dykhuizen 1994). However, there is too bear witness that at that place is little or no transfer between Eastward. coli and Salmonella and none from more distantly related bacterial species into either of these two closely related species. Because this is not more often than not realized, I will describe the show in item. Effigy ane shows the sequence distance between homologous genes of these two species plotted by a measure of codon bias (Abrupt 1991). Codon bias refers to preferential use of certain codons over others even though all the codons lawmaking for the same amino acrid. Highly used genes prove more than bias than less used genes. Highly used genes synthesize more protein, placing a larger demand upon the pools of charged tRNA. The preferred codons are the codons for tRNA types with the largest pools and the unpreferred codons are the ones with the smallest pools of tRNA. Thus, there is pick to use the preferred codons, which is stronger in highly used genes. Considering the codon preference in Due east. coli and Salmonella is the same, genes with high codon bias will diverge less chop-chop than ones with depression codon bias (Fig. 1).

Plot of codon bias past sequence divergence between genes plant in Due east. coli and Salmonella. CAI (Codon Adaptation Index) is a measure of codon bias. Ks is the number of substitutions per synonymous sites, where the distance is corrected for multiple hits using the Kimura ii-parameter model (Kimura 1980). This figure is modified from Figure 1 of Sharp 1991. Codon bias explains l% of the variation in synonymous site deviation. The open circles are the genes that might accept been laterally transferred after the species divide.

Like the dog that did not bark, Figure 1 is very articulate in what it does not show. In that location are no points in the upper right and lower left sections (except the four open circles). If a cistron had been transferred into either species from a more than distantly related species, the distance between E. coli and the Salmonella copies would be much greater than expected for amount of codon bias seen. If there had been a recent transfer between E. coli and Salmonella, the gene copy that had been evolving in i species since the separation of the two species would exist replaced by one from the other species and the distance would be likewise small-scale given the codon bias. The circles in the effigy are noted by the author as having as well pocket-sized a altitude given the bias and are possible cases of lateral gene transfer between the species. However, he suggests that for the three open circles on the left, the mutation rate is lower because these genes are contiguous and near the origin, giving a smaller than expected distance, rather than these genes having transferred betwixt the species well after the species split. This supposition has been strongly supported (Ochman 2003). The open up circumvolve on the right represents the tufA and tufB genes. These are very highly synthesized genes, expected to have strong codon bias. The position and phylogeny of the duplications make it very unlikely that the small altitude was caused by recent lateral transfer rather than stiff selective constraint (Precipitous 1991). In conclusion, although there is strong bear witness that in that location is recombination between lineages for housekeeping genes within E. coli, there is no prove of gene transfer between E. coli and Salmonella. Thus, we tin consider these as two distinct species by my definition of species. Using whole genome sequences, Daubin and collaborators (2003b) have shown recombination inside Escherichia coli and Chlamydophila pneumoniae, but lack of recombination between at least seven species. Thus, it seems that my definition of species volition be robust.

Salmonella enterica has been thought to have very limited recombinational exchange (Feil et al. 2001, Maynard Smith 1995). This conclusion was based upon studying two examples of each of eight subspecies. To show recombination within a taxon, one needs at least three individuals. Thus, this test could not decide recombination inside the subspecies. Brown et al. (2003) recently have shown that in that location is extensive recombination within 1 of the subspecies. Thus, the decision is that Salmonella enterica is likely to be eight dissever species.

We suggested that if there is no genetic exchange between species, and so all the gene trees should exist congruent (Dykhuizen and Green 1991). Lawrence et al. (1991) showed gene tree congruence for three genes beyond a number of species in enterobacteria. More recently this work has been extended using whole genomes (Lerat et al. 2003). They found concordance for 203 out of 205 gene trees across 11 species. The two exceptions were inconsistent considering of a unmarried lateral gene transfer (LGT) outcome. The determination of Lerat et al. (2003) very strongly supports our definition of bacterial species: "Our assay indicates that single-re-create orthologous genes are resistant to horizontal transfer, even in bacterial groups subject field to loftier rates of LGT" (p. 101).

The Neisseria are a group of species that are primarily commensals of the mucous membranes of mammals. In that location are a group of seven species that are ordinarily institute associated with humans, six of which are found in the back of the mouth and the seventh, N. gonorrhoeae, in the urogenital tract. These bacteria are naturally competent for transformation throughout their entire life cycle and have high rate of LGT (Spratt et al. 1995). N. meningitidis and N. gonorrhoeae are closely related, with the DNA of coding genes >98% sequence identity. Although there is extensive genetic commutation inside each species (Maynard Smith et al. 1993), there is little substitution betwixt them (Vazquez et al. 1993), befitting to the Biological Species definition. This is presumably because they are physically isolated, living in different parts of the body. The vi species living in the throat practise exchange Dna even though they are more distantly related with sequence similarity among species ranging from 91% to 77%. Because of potent selection, pieces of the factor for the penicillin bounden protein from two of the naturally penicillin resistant species have been incorporated into N. meningitidis, rendering it resistant to penicillin, even though the departure is 14% for one species and 23% for the other (Spratt et al. 1995). Conspicuously, strong selection can incorporate genetic textile from other species into the genome. However, what happens when there is no strong pick? When housekeeping genes are sequenced from these species, fragments from other species are nowadays in many of the genes. These fragments are recent transfers that have non yet been purged by selection, because when the fragments are removed, the cistron trees generally friction match (Maynard Smith 1995). If fragments had been incorporated in the past, the gene trees would not match. Thus, the fragments must have been selected against.

This is proven by an exception. The adk gene is scrambled (Feil et al. 1995). Why exercise nosotros see all-encompassing recombination in this cistron and not in others? I think the answer is that adk has simply one polymorphic amino acid across the genus whereas the other genes have many. Thus, I conclude that in that location is option against fragments from other species considering of amino-acrid differences, i.e., the genome is co-adjusted. This maintains species boundaries. Because of this general property of cellular life, the co-adapted gene complex, species definitions tin exist very similar for leaner, animals and plants.

Number of Species in 30 Grams of Soil

Whereas in that location are many species definitions (e.chiliad., Cohan 2002), I wish to use the formal definition of species in bacteria because it is both useful and conservative. Information technology states, "The phylogenetic definition of species mostly would include strains with approximately lxx% or greater Deoxyribonucleic acid-Deoxyribonucleic acid relatedness and with 5°C or less Δt_yard. Both units must exist considered" (Wayne et al. 1987:463). Thus two strains are different species if less than 70% of the DNA will re-acquaintance after having been melted to single strands. This benchmark is required considering up to about 30% of the DNA of a bacterial cell tin exist transient. Also, mismatches will subtract melting temperature of the re-associated DNA. For two strains to be dissimilar species, this subtract must be more than 5°C. This translates to 7–viii% deviation in Deoxyribonucleic acid sequence (Caccone et al. 1988). Thus, by this conservative definition, N. gonorrhoeae and N. meningitidis would exist considered the same species.

We can utilize this definition to approximate the number of bacterial species in a customs. The rate of re-association of single stranded DNA with its homologue depends upon the concentration of the homologue. Every bit the number of unlike fragments of Deoxyribonucleic acid increases, the time becomes longer. Effigy ii shows the re-association of Due east. coli Deoxyribonucleic acid and dogie thymus Dna. The genome of a calf is larger than the genome of Eastward. coli, consequently information technology takes much longer for the calf thymus DNA to re-acquaintance than the Due east. coli. Re-association kinetics are measured in terms of the concentration of DNA in moles per liter (C₀) times the time in seconds (t). This is the Cot value. If the concentration of Deoxyribonucleic acid is held constant, so the number of molecules of each unique sequence decreases as the genome size increases. For example, if the concentration of DNA is 12pg, a solution volition contain 4000 copies of a genome of 0.003pg merely only 4 copies of a genome of 3pg. In this example it will accept on average 1000 times longer for the Deoxyribonucleic acid in the large genome to discover its homologue. The Cot value, when half the Deoxyribonucleic acid is re-associated, gives an estimate of genome size. If we recollect of the bacteria from a natural community equally a unmarried species of bacteria, how large would its "genome" be? The number of species in the community tin be estimated by dividing this "genome" past the average size of a bacterial genome.

Deoxyribonucleic acid rehybridization kinetics. This figure is a modification of Figure 3 of Torsvek, et al. (1990a). The E. coli genome is about 4.v megabases and the unique Deoxyribonucleic acid in cows is almost 1,000 times larger as is human. Thus the initial hybridization of the soil bacterial Dna at same signal that the calf thymus starts to re-hybridize suggests that the near common species in the soil is about ane tenth of 1 per centum of the total number. The line at the far right is the re-association kinetics for a homogenous sample like the calf thymus DNA, shifted so it has the same Cot as the soil bacteria at 50% re-association. This shows that the unlike species of Dna from the soil have very dissimilar frequencies.

Torsvik, Goksøyr and Dane (1990a) isolated thirty grams of top-soil from a beech forest north of Bergen, Kingdom of norway. The soil contained 1.5 × 10^x leaner per gram past microscopic observation. Less than 1% of these could exist cultivated. After the eukaryotes and viruses were eliminated, Deoxyribonucleic acid was extracted from the bacteria. The DNA was sheared, melted, and allowed to re-associate at a temperature that was 25°C less than the melt temperature. Equally seen in Figure 2, the re-association started at about the same time as the calf thymus DNA, which implies that the most common species is less than ane% of the population. The re-association at 50 per centum is ten times more complex than the dogie thymus DNA. This gives an estimated complexity of ii.seven × ten^ten bp. If you accept the average genome size of soil leaner at vi.viii × 10^vi bp (Torsvik et al. 1990b), which is a little larger than E. coli, yous stop up with an guess of almost 4000 common species. The rare species accept withal non re-hybridized. Actually the 4000 is an underestimate, because the re-association is 25 degrees below the melt temperature. If this re-associated DNA is melted, just x percent of the re-associated DNA fits within the definition of species (a Δt_m of less than 5°C). This suggests that we take underestimated the number of species by ten fold. Using strains isolated from the soil, Torvick et al. (1990b) showed that the Deoxyribonucleic acid hybridization gave a number of species ten-fold also low. So we finish up with 40,000 common species.

There are ever fewer common species than rare ones. If the species are ranked past number of individuals and so that the nigh common species is first and the rarest species is last, then nosotros can separate the species into two classes, each containing one-half the individuals in the sample. The ratio of the number of rare species to the number of common species gives u.s. an judge of the full number of species when we can only estimate the number of common species. Consider an instance with 52 species. The two nigh common species brand up half the number of individuals. And then the ratio of rare species to common species is 25 to 1. This is about average ratio found in the literature for animals and plants (Dykhuizen 1998). The ratio estimated from the data of Ruth Patrick (1968) on natural communities of diatoms is 25 if we use only the information from a single experimental box, simply 35 if we combine the data from all 8 boxes. Thus, as a first approximation, we will use a ratio of 25 to estimate the number of species in 30 grams of soil. This is 25 times 40,000 or a million species. In that location are caveats to this estimation. For example, a lot of the rarity might exist in rare genes that are laterally transferring dorsum and forth rather than in rare species. Thus, we need another way of estimating the number of species in this 30 grams of soil. This is provided by the work of Curtis and collaborators (2002).

Curtis et al. (2002) proposed using log normal species abundance curves to narrate bacterial communities. If the total number of bacteria and the number of the most common species are known and if it is causeless that the rarest species is present as a unmarried private, and so the full number of species can be estimated. There are 5 × 10^eleven bacteria in 30 grams of soil and the almost common species is between i% and 0.ane% of this number. Reading off Figure four of Curtis et al. (2002), the possible values for the numbers of the most common species give an gauge that bridge the value of a million species in this 30 grams of soil.

The Number of Bacterial Species in the Globe

We know very trivial about how many communities of leaner there are and what the diverseness may be within them. Although there may be a one thousand thousand bacterial species in 30 grams of rich soil in Norway, this might be one of the more than diverse communities because it is in a nutritionally rich, structured and stable environment. I would expect similar soils (where I do not know what I mean by "similar") to have the same species, such that the number of species present in this type of soil worldwide would be well-nigh ten meg in 3000 kilograms of soil (Curtis et al. 2002). The bacterial communities in sandy loam, sandy clay loam, loamy sand, and clay loam in England were tested by DNA-Deoxyribonucleic acid hybridization and found to exist different (Griffiths et al. 1996). There is some cross-hybridization between certain soil types. When in that location is some cross-hybridization, is this because the communities contain the same species in very different densities or is information technology because some of the species are shared between the communities, but almost are dissimilar? Some other fashion of asking this question is: "Are the rare species in one surround, mutual in another or are rare species rare and common species common?" The data of Patrick (1968) for a number of communities of protists in very similar experimental environments suggests the latter is true. Finley et al. (2002) suggests it is true for fresh-water protists. This might non be true of diatoms because the environs in the ocean is not structured as in soil and frewshwater lakes. Notwithstanding, I will assume it is also true for leaner, i.e., rare species are rare and common, common, even in different soil types. Thus, the different soil types are probable to stand for different communities of bacteria. How many soil types are there in the world that support different communities of bacteria? Practice different plants on the same soil type requite dissimilar communities? We will need more than information to answer these questions to be able to estimate how many species of soil bacteria at that place are in the world.

Curtis et al. (2002) suggested at that place are about two million species in the body of water. This is derived from estimating there are 163 species in a ml of seawater from the Sargasso Sea so extrapolating this to two million in the sea. Nevertheless, the Sargasso Ocean has very different bacterial customs than Long Island Sound (Lee and Fuhrman 1990). Fifty-fifty within the Sargasso Sea, the communities at the surface and at 500 meters are different (Lee and Fuhrman 1990). Whereas at that place is no cross-hybridization between the Sargasso Sea and Long Island audio, there was some for the different communities at the surface and at 500 meters. Once more, is in that location cross-hybridization because the aforementioned species are nowadays at the ii depths, but in different ratios, or is there some species overlap, giving some cantankerous-hybridization, but with nearly of the species different? If nosotros presume the latter, then the estimate of Curtis et al. (2002) is probably a considerable underestimate.

In this symposium, Nancy Knowlton mentioned the big variety of bacteria on corals and presented evidence for species specificity (Rohwer et al. 2002). We also know at that place is a community of bacteria in the deep sub-soils. Even at 500 k, the U.S. Department of Energy continues to find bacteria in their deep wells. Antarctic rocks contain bacteria that just metabolize three or four hours a year when the sun is directly on them; otherwise they are frozen. At that place are bacteria everywhere. Thus there must be many communities and consequently very many species.

From all this, my guess is at that place are a billion species and the more than I get used to this number, the more than I feel it is a gross underestimate. But for now, it is as far as my mind will become, given so footling data. Thus, there are but as well many species of leaner to count. Returning to Paul Ehrlich's statement, we need other measures of biodiversity, especially for bacterial communities, than sampling and counting every species. Perchance we can apply Dna re-clan measures or some method involving PCR to get estimates of the variety. These measures can be used over time to look at community stability and ecosystem health. In an aside, information technology seems that PCR distension direct from bacterial communities, sequencing these PCR products and estimating species number using rarification statistics from these sequences underestimates species variety by well-nigh tenfold.

Questions and Answers

How Many Named Species of Bacteria are There?

There are almost 30,000 formally named species that are in pure culture and for which the physiology has been investigated. Species now are being defined by PCR amplifying ribosomal genes and sequencing. The benchmark for defining species is that the ribosomal genes are at least 3% unlike. This method is probably is even more bourgeois than Deoxyribonucleic acid/DNA re-association methods for defining species. We're probably defining species by ribosomal sequence at the level of genera or family.

What is Known Nearly the Distribution of Bacterial Species Around the World?

Almost nothing. We know something well-nigh the biogeography of infectious diseases. Many of them are worldwide with very piddling population differentiation, like E. coli. Some of them are very specific to particular regions. And so for case, the spirochete that causes Lyme disease is generally found on the coastal plane of the east declension of the United states from the islands off Maine downward to Maryland, and in the region of central Wisconsin, southern Minnesota and into the upper peninsula of Michigan. There is also a region in the central valley of California. At that place are low densities of this spirochete in other areas, simply information technology seems that the biotic cycle in these regions prevents high densities of both ticks and Lyme disease. Particularly along the northeast coast of the United States, information technology seems that the high density of Lyme disease matches the region of the last major glaciation. This correlation is probably because of the lower biodiversity (specially of reptiles) afterward the glaciation. I must add one thing. The bacterial ecologists have a motto, which I don't think is completely right, but does accept some bearing. The motto is that is that everything gets everywhere, information technology'due south the environment that counts. So you find the same species in Yellowstone as you do in the hot springs in Iceland.

What will Happen as Biodiversity Decreases?

I'm speculating right now, but I retrieve nosotros're going to get more epidemics as biodiversity declines. What will happen is that the other species that are left will go upward in numbers, and the organisms that infect them of course will go upwardly in numbers. This means that there is a larger chance for them to jump to humans, which are a vast and untapped resource. We brand the oil fields of Iraq await like a pocket-size player every bit far as energy resources for leaner get.

How Many Species of Bacteria are Found on Humans?

When I beginning my classes, I say that the bacteria on you are 90 percent of the cells that y'all walk around with. Merely ten percent of the cells that you lot walk around with are y'all. But they're much smaller. They are only x pct of the biomass. And then yous would only lose x percent of your weight if y'all got rid of all your bacteria. I don't call back nosotros actually know how many species are establish on humans. We're talking about 400–500 in your rima oris, around the plaque. It seems that most 100 in your abdominal tract requite you normal intestinal functioning. Germ-free mice don't function well. And then that's not a very happy answer, but at least nosotros're talking in the hundreds. Many of them are probably unique to humans.

Is Anybody Doing Like Work Amidst Single Cell Eukaryotic Organisms?

Of this kind of measure within a organisation I don't recollect and so. Single prison cell eukaryotic organisms are already much larger than bacteria. At that place's an attempt to do that picking out private ones and looking at what species they would fall into. There's a lot of work trying to do the taxonomy of unmarried jail cell eukaryotes. That'south very exciting.

Acknowledgments

I give thanks the California Academy of Sciences for giving me the opportunity to present this textile and to Nina Jablonski for patience. I thank Michael Feldgarden for proofreading and give-and-take. I was supported by NIH grant #GM60731. This newspaper is contribution #1136 from the graduate programme in Environmental and Evolution at Stony Brook University.

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Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160642/

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