INTRODUCTION

Pick up an introductory biology textbook that describes bacteriophages. The presented phage life cycle, often using phage λ as an example, will typically be differentiated into two distinguishable types: the lytic cycle and the lysogenic cycle. This differentiation is real but overly simplistic. First, both the lytic cycle and the lysogenic cycle differ among different phages by numerous molecular details (Calendar and Abedon, 2006). Second, and as typically mentioned, not all phages display a lysogenic cycle (Chapter 5). Third, though atypically mentioned, not all phages display a lytic cycle (Russel and Model, 2006), at least in the sense of productive phage infection followed by a phage-induced bacterial lysis. In this chapter I provide an overview of the ecology of the virion-mediated population growth displayed by obligately lytic phages (sensu Chapter 1, Section 1.2.2.5). That is, I explore the ecology of phage adsorption and infection of susceptible bacteria, virion maturation within those bacteria, and then lytic release of phage progeny. I take an evolutionary ecological perspective, considering the impact of phage adaptations on phage population growth (as also does Chapter 2).

Productive phage infection

As described in greater detail in Chapter 1, phage infections may be differentiated into productive versus non-productive (the latter including lysogeny; Chapter 5), with production referring to the intracellular maturation and then release of phage virion particles.

INTRODUCTION

Bacteriophage therapy, the treatment of bacterial infections with bacteriophages, is a topic that has received increasing attention in recent years. While the primary practice of phage therapy has been conducted with an eye towards the treatment of bacterial infections in humans, the concept of eliminating undesirable bacterial populations using phages can be extended to agriculturally important animals, plants, and even finished foodstuffs. While the potential benefits of phage therapy have been well documented, the mechanisms of phage therapy are less well understood, except in general terms. There is little in the way of standard criteria for selecting dose size, timing, or frequency when treating bacterial infections with phages. One approach toward addressing such concerns attempts to gain a better understanding of the in vivo reality of phage therapy through the development of theoretical mathematical models. Most models have comprised a series of differential equations, with theoretical parameters selected to examine the impacts of various phage therapy constraints. In this chapter I give a basic overview of the mathematical modeling approaches which have been applied to simulate phage therapy regimens. Simulations will be provided, where appropriate, to illustrate the behavior of these models. Finally, I briefly explore the current limitations of modeling given our understanding of how phages and bacteria interact in vivo.

INTRODUCTION

A number of bacterial virus strains interact with eukaryotes, including with humans. The study of these interactions is still in an early discovery phase. To put this situation in perspective, it is estimated that there are about 1012 cells in a human, while the number of bacteria, and their viruses (most of which inhabit the large intestine) outnumber these human cells by a factor of at least 10 (Bäckhed et al., 2005). Study of the interactions of bacterial viruses, their genes, and their gene products on their animal “co-hosts” has only really begun. Early studies concentrated on their anatomical distribution in animals. These studies were followed by investigations of interactions with the immune system, particularly the adaptive immune system. More recently, studies have been initiated on the interactions of these viruses with the innate immune system and mammalian cells. Unfortunately, we currently do not have the technology to culture many of the bacterial strains associated with humans and other animals, which limits our ability to study the viruses associated with these organisms. However, the development of new molecular methods, particularly high-throughput genomic sequencing, are now providing tools to characterize the human “microbiome” in both normal and disease states (Relman, 2002). Despite the current dearth of knowledge concerning phage interactions with animals, there are already significant efforts to use the knowledge we have, to engineer the few phage strains that have been studied for antibacterial, vaccine, and gene therapy applications.

INTRODUCTION

Limitations on bacterial mobility may be described in terms of an environment's spatial structure: the degree to which diffusion, motility, and mixing are hindered or selectively enhanced. A large fraction of bacteria live within environments that possess spatial structure — within biofilms, within soil, or when growing in or on the tissues of plants and animals. This spatial structure also affects phage movement and therefore phage impact on bacterial populations. Gaining an understanding of phage growth within spatially structured environments consequently is pertinent to developing a comprehensive understanding of phage ecology. Here we employ a working assumption that phage population growth in the laboratory in semisolid media (as within phage plaques) represents one approximation of phage population growth within spatially structured environments in the wild. We thus present an introduction to phage plaque formation with the hope that at least some of our discussion may be relevant to future studies of in situ phage ecology, such as spatially fine-grained analyses of phage population expansion within biofilms.

See Chapter 16 for methods in modeling phage plaque formation, Abedon and Yin (in press) for a complementary review of phage plaque formation, Chapter 2 for phage growth given spatial structure as introduced in the guise of metapopulations, Chapter 3 for consideration of phage population growth as it occurs within non-spatially structured environments, and Chapter 11 for discussion of the phage ecology of soils.

INTRODUCTION

The modeling of bacteriophage growth is complicated by spatial structure. Spatial structure, for phages, consists of impediments to environmental mixing, impediments to phage diffusion, and impediments to bacterial motility. A spatially structured environment, however, is perhaps best described by what it is not: a well-mixed, fluid culture. Spatial structure as observed within the laboratory can consist simply of unstirred (or unshaken or not bubbled) broth cultures (Buckling and Rainey, 2002). More commonly, so far as phage growth is concerned, we find bacteriophages growing as plaques within bacterial lawns. Within agar, phages generally are free to diffuse, though not as readily as in broth cultures, while bacteria typically are somewhat immobilized. This spatial structure, in broad terms, replicates the spatial association seen within such naturally occurring microenvironments as biofilms, soil, and sediments as well as the various surfaces associated with plants, animals, and other multicellular organisms. Here we consider the mathematical modeling of phage growth within relatively homogeneous spatially structured environments as approximated by phage plaque formation within a soft agar overlay. We first consider a variety of models that are limited to describing the enlargement of plaques and then additional models that consider other aspects of phage plaque growth. Mathematically, the modeling results we discuss come from reaction—diffusion (RD) differential equations and stochastic cellular automata (CA).

INTRODUCTION

Evolutionary biology and microbiology, with the ushering in of the molecular revolution, developed a tenuous relationship (Woese, 1994). Further isolating these disciplines, once unified university biology departments split in two, with organismal versus molecular emphases. Because phage biologists were pioneers in molecular biology, they were placed on the molecular side of the divide along with the rest of microbiology, whereas evolutionary biologists, with their less reductionist approaches to biology, were grouped with researchers in zoology, botany, paleontology, and ecology (Rouch, 1997). Consequently, microbiologists were physically isolated from model organism researchers such as Drosophila evolutionary geneticists, and intellectually removed from discoveries such as rapid ecological radiations of wild populations and theories explaining biodiversity and speciation. Evolutionary biologists, in turn, were isolated from microbial experiments that bore on evolution, even though some historically significant discoveries in evolutionary biology used microbes, especially bacteriophages. Despite these past rifts, there exists a newfound appreciation for the power of using microbes to explore evolution and ecology: as molecular researchers had long realized, there are profound advantages to employing small, relatively simple, and rapidly replicating organisms as models for deciphering universal biological truths. Microbiologists, too, in this age of genomics, are increasingly aware of the crucial importance of ecology and evolution in their research.

INTRODUCTION

A virus depends intimately upon its host in order to reproduce, which makes the host organism a crucial part of the virus's environment. This basic facet of viral existence means that ecology, the scientific field focusing on how organisms interact with each other and their environment, is particularly relevant to the study of viruses. In this chapter we explore some of the ways in which the principles of ecology apply to viruses that infect bacteria — the bacteriophages (or “phages” for short). In turn, we also discuss how the study of phages and their bacterial hosts has contributed to different subfields of ecology.

Due to their ease of manipulation, large population sizes, short generation times, and wealth of physiological and genetic characterization, laboratory communities of microbial organisms have been popular experimental tools for testing ecological theory (Drake et al., 1996; Jessup et al., 2004). Building upon this foundation of knowledge, the ecological experimentalist can explore whether mechanistic understanding at the organismal level informs an understanding of patterns at the community level (Bohannan and Lenski, 2000a). Further, the initial composition of microbial consortia can be controlled, and thus researchers are able to probe the effects of different community structures on ecological phenomena, such as stability, diversity, and resilience to invasion.

INTRODUCTION

Found in Clostridium botulinum, Corynebacterium diphtheriae, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae, etc., prophage-encoded bacterial virulence factors (øVFs) provide an additional level of interaction between phages, bacteria, and environments (Langley et al., 2003; Brüssow et al., 2004;øVF, which stands for phage-encoded virulence factor, we pronounce “phee-vee-eff.”). In some cases multiple prophages are present in the same cell and each may encode a separate virulence factor (VF). For example, some strains of enteropathogenic E. coli encode several variants of the VF, Shiga toxin, and in a number of Salmonella strains about 5% of the genome consists of prophages, most of which contain VF genes. Despite their unambiguous genomic association with prophages, a question still under debate is whether these VF genes should be considered phage genes or bacterial genes. Supporting the concept that they are simply unusually located bacterial genes, in some bacterial strains the prophage is clearly defective and no progeny phage will ever be produced. On the other hand, there are some VFs that cannot be released from the bacterial cell except following prophage induction, implying a great deal of phage involvement in VF expression. In this chapter we consider the evolutionary ecology and ecological impact — on phages, bacteria, and animals — of phage encoding of bacterial VF genes, especially prophage-encoded exotoxins.

INTRODUCTION

How do bacteriophages exist in the hostile environments that their bacterial hosts inhabit? In most environments, from the desert to the mammalian gut, bacteria live for most of their existence in a starved state (Koch, 1971; Morita, 1997) where energy, carbon, and other resources are in scarce supply. Under such conditions we know that the latency period for phage infection lengthens, that the burst size is greatly reduced (Kokjohn et al., 1991), and that the half-life of virion infectivity (rate of decay) is short (Miller, 2006); yet total counts of virus-like particles present in environmental samples are high. Clearly bacteriophages have evolved strategies for surviving under these unfavorable conditions. As survival-enhancement strategies, many biological entities, from bears to bacteria, have evolved dormant states. During phage infection we recognize analogous dormant states as lysogeny and as pseudolysogeny. In this chapter we explore several aspects of the ecological consequences of these “reductive” infections.

In addition to the material presented here, we direct the reader to additional reviews considering lysogeny, pseudolysogeny, and phage infection of starved bacteria: Barksdale and Arden (1974), Ackermann and DuBow (1987), Schrader et al. (1997a), Robb and Hill (2000), and Miller and Ripp (2002). Related issues, especially of phage contribution to bacterial genotype and phenotype, are also considered in Chapters 11 and 14.

In order to place western diseases in an evolutionary context it is necessary to consider the experience of human disease throughout human evolutionary history. To achieve this I adopt a framework drawn from the work of Boyden (1987) and Cohen (1989), illustrated in Table 2.1. This approach emphasises the need to understand the way of life, ecology and health experience of hunter–gatherer people, because such an understanding informs us about the context in which members of our species lived for so much of its evolutionary history. An examination of the enormous impact of agriculture and then of urban living on human health illustrates how changes in ways of life have had profound effects on disease experience in the past. As will become clear in later chapters, it is also increasingly apparent that an understanding of the evolutionary history of human exposure to infectious disease and nutritional pressures, which was profoundly affected by these innovations, is relevant to our understanding of western diseases. Finally, I consider the decline of infectious diseases and rise of non-communicable disease in the west, the so-called epidemiologic transition, and trends in the prevalence of western diseases over the nineteenth and twentieth centuries.

Human ecology and health in the Palaeolithic

Anthropologists have used various kinds of evidence to try to find out more about the ways of life of humans during this period, and to characterise their experiences of health and disease.

In this chapter I focus on three aspects of female reproductive life that have been adversely affected by affluent western life: the relatively unrecognised problem of a high rate of impaired reproductive function and infertility in women; the consequences of a lack of breastfeeding for mothers and children; and the menopause. The focus on women is not exclusive and I also discuss briefly how men's reproductive function has been affected by life in the affluent west and consider the debate about whether an analogy can be drawn between menopause in women and the less extreme age-related decline in reproductive function experienced by men.

Impaired reproductive function

My main purpose here is to examine the effects of the high levels of obesity, insulin resistance and insulin seen in western populations (see Chapter 3) on reproductive function. I also consider some other features of the western lifestyle that may affect reproductive function.

Obesity, hyperinsulinaemia and impaired reproductive function

Women living in western societies generally experience higher levels of the ovarian steroid hormones progesterone and oestradiol over a lifetime than do those living in less affluent countries and in the affluent east (see Chapter 5). In fact, ovarian hormone levels in western women are considered to represent the extreme of global variation in ovarian function. As we have seen, this is likely to be a result of mechanisms that evolved to link the availability of energy with fecundity in hunter–gatherer populations.

Breast cancer is one of the biggest causes of mortality in western societies. Other reproductive cancers are less well known but also common, including endometrial and ovarian cancers in women and prostate cancer in men. They are often cited as examples of ‘western’ cancers, since levels are much higher in affluent western populations than elsewhere. As with most other cancers, and non-communicable diseases in general (see Chapter 2), increased lifespan is one obvious explanation of high rates of these diseases in affluent western populations, but increased lifespan cannot explain all of the association between westernisation and reproductive cancers. So, why does an affluent western lifestyle bring an increased risk of reproductive cancers?

In this chapter I draw on the work of biological anthropologists and epidemiologists to answer this question. After summarising geographical and temporal trends in the incidence of reproductive cancers, I describe the main known risk factors for these diseases. I then go on to show that the affluent western lifestyle has increased exposure to all of these risk factors, focusing in particular on the evidence linking western life to increased exposure to endogenous gonadal hormones: oestrogen and progesterone secreted by the ovaries in women, and androgens secreted by the testes in men. Here I draw particularly on the pioneering work of Ellison (Ellison 1999).

What are reproductive cancers?

Cancerous tumours, including those of the reproductive system, result from the unregulated division of undifferentiated cells.