Advertisement

  • Loading metrics

Open Access

Review

Review articles synthesize the best available evidence on a topic relevant to the pathogens community.

See all article types »

Host microbiota can facilitate pathogen infection

Abstract

Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host’s life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.

Citation: Stevens EJ, Bates KA, King KC (2021) Host microbiota can facilitate pathogen infection. PLoS Pathog 17(5): e1009514. https://doi.org/10.1371/journal.ppat.1009514

Editor: James B. Bliska, Geisel School of Medicine at Dartmouth, UNITED STATES

Published: May 13, 2021

Copyright: © 2021 Stevens et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was funded by a E.P. Abraham Junior Research Fellowship (St. Hilda’s College) to K.B. and a European Research Council Starting Grant (COEVOPRO 802242) to K.C.K. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Introduction

An infection by pathogens (and parasites) can vary from relatively benign to lethal. The degree of harm caused during infection can be driven by aspects of pathogen biology, such as transmissibility [1], infective dose [2], or whether they are facultative/obligate [3], as well as by host biology, and the surrounding biotic or abiotic environment [4]. While hosts can be genetically predisposed to susceptibility [5], disease outcomes can be made worse if hosts have a comorbidity [6] or an impaired or over-reactive immune response [7]. When invading a host, pathogens will also interact with other microbial species [8]. The outcome of infection is thus held in the balance by the complex interactions between a host, its microbiota, and both the biotic and abiotic environment [4].

Microbiota are vital to the functioning of their multicellular host organisms. This realisation has fuelled great interest in the effects of microbes on plant [9] and animal host health [10]. Microbe-mediated protection against infection is a widespread phenomenon across host species [11], with components of the microbiota and their interactions with a host and the wider microbial community mediating susceptibility to invading pathogens and internal pathobionts [12,13]. There are several ways to categorise and define pathogens based on their biology [3]. Here, we use the term “pathobiont” to mean normally harmless components of the microbiota which have pathogenic potential in some contexts [14–16]. We distinguish these from “invading pathogens,” by which we mean pathogens (including parasites) acquired from a source external to the host (i.e., from a different host or from the environment).

It is well established that host microbiota generally play a beneficial role in preventing or fighting infection [17–20]. Microbe-mediated protection can be mediated via resource competition [21,22], interference competition [23], or the host immune response [24,25]. However, the relative magnitude of these benefits might decrease when microbiota components, in some cases, directly or indirectly facilitate the onset of disease caused by invading pathogens or pathobionts (Table 1). Although some invading pathogens can exploit cues or changes in the resource/immunological environment shaped by the microbiota itself, the context of host health is also an important determinant of infection. Diminished host health can remove the beneficial services the microbiota normally provides. Changes in host health can correlate with dysbiosis of host microbiota [26–28], and opportunistic microbiota components can transition to become harmful among the perturbation [26,29–31]. This perturbation and transition of commensals towards pathogenicity can sometimes even be caused by invading pathogens [32,33]. Moreover, protective microbes can become relatively costly to their host in the absence of the invading pathogens they would otherwise suppress [31,34,35] (i.e., the same microbial species is protective in one context, but costly in another; see “Costly protective symbionts”).

thumbnail
Download:
Table 1. Summary of the drivers and mechanisms by which the microbiota facilitate harmful infection.

https://doi.org/10.1371/journal.ppat.1009514.t001

To understand the multifaceted contributors to infectious disease, the potentially harmful aspects of the microbiota and its components warrant consideration. Microbe-based therapies for disease are being investigated as alternatives to antimicrobials for a wide range of animal hosts, from endangered amphibians to humans [36–38]. A thorough evaluation of the potential for host microbiota to contribute to infectious disease is necessary to establish their utility in disease management as anti-infective prophylactics, probiotics, and prebiotics. In this review, we will discuss the conditions under which microbiota can promote or worsen infection outcomes, with evolutionary consequences. We will then discuss the implications of this potential to facilitate pathogen invasion and infection from within for microbiota manipulation.

Promotion of pathogen invaders

Microbiota components modify the within-host environment

Metabolic environment.

Microbiota metabolites are beneficial to hosts in myriad ways. They help to prime the immune system, act as antimicrobials to combat infection, and aid host metabolism [24,80–82]. However, microbiota metabolites can also provide a convenient and easily attainable source of food for invading pathogens to exploit. Metabolic cross-feeding, in which a product of metabolism from one strain is used by another strain, generates novel niches that may benefit pathogens [83]. This assimilation of resources can enhance energy production within the pathogen, enabling increased virulence and rapid growth, and thus more severe disease. For example, the human gut commensal Bacteroides thetaiotaomicron (Bt) can exacerbate infection caused by enterohaemorrhagic Escherichia coli (EHEC) via metabolic cross-feeding [84]. Bt modifies the metabolic environment at the site of EHEC infection, increasing metabolites involved in gluconeogenesis which are then sensed by the virulence-regulating transcription factor Cra. Virulence is up-regulated as a result and, concurrent with invasion of the gut epithelial barrier (also facilitated by Bt), EHEC induces a greater degree of host pathology and higher risk of mortality.

Individual species of the microbiota cannot always be pinpointed for their role in facilitating infection. While Bt was specifically identified in the previous example as a contributor to EHEC infection [84], microbial metabolites from multiple components of the microbiota can also collectively enhance EHEC virulence [85]. A comparison between human and mouse microbiota metabolites illustrated that the increased severity of EHEC infection in humans, compared to that in mice, is driven by distinct human gut microbiota metabolites [29]. These metabolites specifically induce increased expression of flagellin in the pathogen, increasing its ability to invade host tissues. Distinct microbial communities can thus shape different infection outcomes via metabolite production.

The metabolic environment within a host is a crucial contributor to the pathogenesis of invading organisms. It can be extensively modified by components of the microbiota to both the detriment and the benefit of the host. Changes in host health can likewise alter the within-host metabolic environment, contributing to disease onset from resident commensals [62]. Given the diversity of species housed by the animal gut, there are complex interactions to pick apart. Research is moving towards characterising the functionality of the microbiome by holistically sampling its taxonomic and genomic repertoire in addition to the chemical phenotype. Progress has been made in uncovering pathogen-induced disease phenotypes that are enhanced by the microbiota through application of multi-omics strategies [86,87] (see Table 2). Nonetheless, data integration and interpreting meaningful biological signatures of infection (e.g., biomarkers of infection) remain a challenge [88].

thumbnail
Download:
Table 2. Representative examples of omics approaches used to deduce the role of microbiota components in facilitating infection and worsening infection outcomes.

https://doi.org/10.1371/journal.ppat.1009514.t002

Immunological environment.

Microbiota can prime the host immune response, altering their susceptibility to invading pathogens. Pathogen infectivity can be indirectly reduced by host microbiota this way [89–93]. Conversely, launching the immune response can inadvertently boost infection by some infectious agents [49]. Reynolds and colleagues [49] found that Lactobacillaceae species abundance in the mouse duodenum positively correlated with susceptibility to the nematode parasite Heligmosomoides polygyrus and heightened immunosuppressive regulatory T-cell and Th17 responses. Subsequent treatment of mice with Lactobacillus taiwanensis—a rodent commensal dominant in infected mice—elevated regulatory T-cell frequencies and promoted the establishment of H. polygyrus. The fact that microbiota composition changed after H. polygyrus exposure towards more “helpful” bacterial species suggests that parasites could actively modify the microbiota to improve their survival. This manipulation could occur directly via antimicrobials [94] or by pathogen-induced host inflammation [95]. Physical disruption of the host site might also cause changes in resource availability, shifting microbiota composition [96].

Invading pathogens might evolve in response to host microbiota

Microbes can evolve quickly [100] because of their large population sizes and rapid generation times. Microbiota components can evolve within their host’s lifetime with consequences for host health [101]. For example, a mildly pathogenic strain of the gut microbiota component Enterococcus faecalis has been shown in nematode hosts to evolve to become more protective due to competitive interactions with a virulent pathogen [23]. Likewise, the pathogen Candida albicans was shown to evolve towards protective mutualism when introduced to a new host in a mouse model [102].

Invading pathogens, in turn, may evolve to overcome or exploit the host microbiota. They can readily overcome barriers to their establishment, including from host resistance [103], antibiotic treatments [104], and vaccines [105]. Theory has shown that pathogens can evolve virulence factors to overcome commensals in the host microbiota, either directly killing their competitors [106] or inducing host inflammation as a form of “proactive invasion” [95]. Experimental evolution approaches in animal model systems have produced mixed evidence on the ability of evolving pathogens to escape suppression by protective microbes. Martinez and colleagues [107] found that niche blocking by Wolbachia in Drosophila melanogaster effectively suppressed the pathogen Drosophila C virus (DCV), which did not evolve to overcome the protective symbiont. In contrast, Rouchet and Vorburger [108] found the parasitoid wasp, Lysiphlebus fabarum, readily counteradapted to the protection given by sympatric Hamiltonella defensa in aphids. A variety of pathogens may have evolved to exploit host microbiota for replication and transmission. Poliovirus and Trichuris muris, for example, have been empirically found to depend on interactions with mouse intestinal microbiota to trigger replication and hatching, respectively, at key host sites [47,48]. Poliovirus was able to better associate with host cells, and its replication was enhanced by up to 500% after binding lipopolysaccharide on enterobacterial surfaces [48]. Similarly, fimbriae on the surface of gut colonisers E. coli and Salmonella typhimurium were found to bind to proteins at the poles of eggs of the parasitic nematode, T. muris. This interaction with enterobacteria provides an essential cue, triggering the emergence of infective larvae [47].

Microbiome-mediated protection can drive the evolution of increased [109] and decreased [110] pathogen virulence. McNally and colleagues [109] found that manipulating the microbiota generated increased competition between commensal competitors and increased the intensity of bacterial warfare. Using theory, they found that stronger competition selected for increased expression of pathogen weapons (virulence factors). Enhanced production of virulence factors by many pathogenic bacteria can inadvertently harm the host. For example, release of Shiga toxin-encoding phage by shigatoxinagenic E. coli [111], and similarly TcdA released by Clostridioides difficile, can clear commensals both directly and via provocation of host inflammation [112,113].

Host microbiota has the potential to influence the evolutionary trajectory of invading pathogens. Manipulating host microbiota offers a promising route to treat or prevent infection, but such approaches should be scrutinised in light of the evolutionary potential of target pathogens.

Harmful infection from within

Transitions of commensal microbes to pathogens.

Commensals in the microbiota can transition along the parasite–mutualist continuum [66,76,114]. Transitions towards pathogenicity can be influenced by changes to the within-host environment—onset of illness or compromised immunity [7], diet [26], antibiotic treatment [115], or stress [28,116]—as well as changes in the external environment [28]. Infection by invading pathogens can also induce otherwise commensal bacteria to become pathogenic [33,117].

A well-studied example of a transition to pathogenicity is that of C. difficile, the causative agent of colitis. C. difficile can be at very low abundance in the human gastrointestinal tract. A healthy gut microbiota usually provides colonisation resistance against C. difficile expansion [52]. However, following a period of antibiotic treatment which diminishes the protective power of the microbiota, this bacterium can proliferate extensively to dominate the intestinal niche [71]. In this context, it is a highly problematic pathogen which can cause recurrent disease. Faecal microbiota transplants have proven useful in such cases, whereby the dysbiotic gut microbiota of a C. difficile patient is replaced with that of a healthy donor to eliminate the infection [118].

How can these transitions to pathogenicity occur among pathobionts? Metabolic changes in components of the microbiota can underpin the transition. Recent work on the Drosophila gut microbiome demonstrates that catabolism of host gut luminal uridine by pathobionts drives the generation of uracil and ribose. These metabolites respectively trigger an inflammatory host immune response and increased expression of virulence genes in pathobionts. Quorum sensing regulates both processes and is therefore necessary for a transition to virulence. Deletion of genes involved in nucleotide metabolism in strains of enteric Drosophila pathobionts blocked quorum sensing and thus the commensal-to-pathogen transition. Metabolites such as uracil and ribose may therefore act as pathogen-specific indicators, used by metazoan hosts to distinguish good from bad within the gut. Recognition of these indicators equips hosts to modulate immunity and gut-microbe homeostasis in response to changes within the microbiota [58].

In polymicrobial infections, metabolic cross-feeding can be an essential source of nutrients, enhancing the ability of commensal microbes to establish infection. The pathobiont Aggregatibacter actinomycetemcomitans, for example, requires L-lactate produced by the commensal bacterium Streptococcus gordonii to establish polymicrobial periodontal infection in a murine abscess model [119]. A. actinomycetemcomitans also exhibits enhanced respiratory metabolism in the presence of S. gordonii [120], as the latter increases the bioavailability of oxygen to the opportunist by providing electron acceptors. A. actinomycetemcomitans uses these electron acceptors to increase energy yield in the form of ATP production, which promotes increased virulence. With more energy available, the pathobiont can invest in the production of toxins, adhesins, and immunomodulatory proteins, among many other virulence factors [120].

Pathobionts have an array of tools available to adapt to environmental change within their niche [69,121–123]. Factors which contribute to the commensal bacterial lifestyle can be repurposed upon immune compromisation in the host or upon nutrient limitation or community disruption of the microbiota. Such changes within the host environment can lead to pathobionts proliferating beyond their niche to invade host tissues [69,123]. Adhesive proteins, for example, are required for asymptomatic colonisation of a new host, yet are also important in attaching to host cells to initiate invasion [123,124]. They can additionally contribute to the development of bacterial biofilms [69,70] to facilitate persistence of an infection under adverse conditions (e.g., antibiotic treatment). Likewise, toxins play a significant destructive role in the onset of disease. Toxins induce host cell lysis and stimulate inflammation, and they are recognised as major drivers of the symptoms of bacterial infection [125]. Recent research has also highlighted the contribution of toxins to pathobiont colonisation or persistence in different niches within the host during asymptomatic carriage, thus they aid both the commensal and pathogenic lifestyles of pathobionts [126]. Gene expression changes underpin transitions to pathogenicity and are driven by the need to adapt to changing conditions [121,122]. Infection can therefore be instigated by pathobionts within the host microbiota, following a transition from commensalism to a pathogenic state.

Costly protective symbionts.

In wild animal systems, beneficial microbiota components otherwise known as defensive/protective symbionts have been shown to prevent pathogen establishment and reproduction [127]. They are so effective at defending that the evolution of host resistance is slowed in the face of pathogen infection [128]. Many of these symbionts can, however, impose a physiological burden upon their host that is measured in the absence of an invading threat. [127]. For example, while the endosymbiont Wolbachia in numerous arthropod hosts defends against parasitic viruses [129], bacteria [130], and nematodes [131], Wolbachia in Drosophila fruit flies can cause a reduction in colonised host fertility, fecundity, and egg hatch rates, mediated by high symbiont densities [31]. A trade-off emerges in many host-microbe systems whereby increased conferred protection means the symbiont can become more pathogenic [34,35] (albeit, see Cayetano and colleagues [132]). Mathé-Hubert and colleagues [133] further showed that the cost of carrying a protective symbiont (Spiroplasma) in pea aphids can be alleviated by concurrent colonisation with a second symbiont (Regiella insecticola), as co-colonisation improves host lifetime reproduction and population growth.

Changes in the abiotic environment can also reveal the costs of these resident protectors in the microbiota. One extreme example is a species of the nematode-infecting bacterium Leucobacter, which under dry laboratory conditions is a protective bacterium against another highly virulent Leucobacter species, but in aqueous conditions causes hosts to become irreversibly fused by their tails leading to death [134]. The abiotic environment can therefore mediate host-associated microbe function to both favour and oppose pathogenicity.

Microbiota community structure as an early warning signal

Healthy microbiota community compositions can differ between individuals and population groups and also within individuals over time [135]. It is consequently not always feasible to establish what a “typical” dysbiotic microbiota looks like during infectious disease. However, a recent study in apiculture has demonstrated how early microbiota perturbations can have sustained negative consequences on host development and increase pathogen susceptibility within a population [116]. Schwarz and colleagues administered the commensal species Snodgrassella alvi to newly emerged worker bees as a potential probiotic therapy to protect against the parasite Lotmaria passim. Yet, despite S. alvi being part of the usual core microbiota of bees, inoculation of this species alone in young hosts led to microbiota perturbation, possibly reducing the protective benefits normally conferred and ultimately increasing parasite susceptibility [116].

While microbiota dysbiosis in general may correlate with infectious disease onset, microbial taxonomic signatures for specific infections may not always be a reliable indicator of disease [136]. The Anna Karenina principle [137] (“all happy families look alike, but each unhappy family is unhappy in its own way”) has been applied to explain observations in which microbiota community composition varies more between diseased individuals than healthy individuals. Nonetheless, in some instances, pathologies may be predicted by a specific reduction in certain key taxa. Bacterial vaginosis (BV) in humans is one such example, a condition caused by dysbiosis within the vaginal microbiota that affects approximately one-third of reproductive age women [138]. Vaginal microbiota composition varies across demographics [139], but onset of BV is typically associated with a reduction in Lactobacillus species, accompanied by the dominance of anaerobes and increased alpha diversity [140]. In these lactobacilli-depleted communities, the presence of biogenic amines can increase [141]. These amines, and the microbial community composition with which they are associated, could be useful biomarkers of disease in the early stages of BV development. Indeed, multi-omic approaches have been used to characterise the metabolic profiles corresponding to different symptomatic BV types [142]. Yeoman and colleagues [142] took this approach and identified distinct microbial taxa and metabolites which correlated to 2 different symptomatic BV types (and also to host behaviour). The characteristic odour of BV infection was linked to Dialister spp., the presence of discharge was linked with Mobiluncus spp., and Gardnerella spp. were linked with the symptom of pain. These findings provide both potential diagnostic markers for the onset of disease and insights into the determinants of BV.

Moving beyond correlative relationships between microbes and infections to establishing causation remains a major challenge [143–146]. Due to the complexities of microbial communities within a host, including the high species richness within a niche and the multitude of microbe–microbe and host–microbe interactions, it is often difficult to attribute specific microbes to a causative role in disease. Furthermore, in some cases, infection may not be attributable to one species, but to polymicrobial interactions which are difficult to pick apart [30]. Host heterogeneity in genotype, lifestyle, and diet further compounds the ability to infer causality. Not all components of the microbiota are culturable in the laboratory setting and are only identifiable as members of the community through sequencing. They are thus often excluded from culture-dependent laboratory experiments aiming to determine causality [86,147–150].

To bridge this gap between correlation and causation in elucidating the relationship between microbiota and infection, current research is benefitting from combining laboratory experiments with multidisciplinary and multi-omic approaches (see Table 2). Tractable, controlled experimental models of defined microbial communities will be important in this transition [151]. Synthetic microbial communities composed of native microbiota components are now being developed for use in model organisms [147,152–154]. Such resources will allow in-depth dissection of host–microbiota interactions in model organisms, using tools which are easily controlled while remaining representative of natural systems. The combination of experimental models with corresponding omics data will further allow functional verification of bacterial phenotypes within the microbiota [155]; this mechanistic insight will be essential in determining causality in microbial infections.

Microbiota manipulation: Always a silver bullet?

Microbial approaches to managing disease in both humans and animals are gaining traction. The application of protective microbes directly to a host, or into a host’s habitat or food source, has been investigated for the control of infectious disease in endangered amphibians [36], aquaculture [156], and apiculture [157] as well as in the prevention and treatment of infectious and noninfectious human disease [38].

Microbe-based solutions have huge potential as alternatives to synthetic drugs [156,158,159]. However, they can sometimes have off-target effects. Studies on amphibian infection reveal the need for identification of these effects associated with probiotic use. Inhibition of the amphibian fungal pathogen Batrachochtyrium dendrobatidis (Bd) by bacteria can differ based on pathogen genotype and microbial community composition [160,161]. Single bacterial strains show both growth inhibition or promotion depending on Bd genotype. Becker and colleagues [37] exposed the critically endangered Panamanian golden frog, Atelopus zeteki, to fungal Bd and candidate probiotic bacteria identified based on their Bd inhibitory activity in vitro. Results of the in vivo study showed no difference in Bd-induced mortality in probiotic-treated versus untreated groups. Several probiotics, however, showed a (nonsignificant) trend towards exacerbating Bd-induced mortality when compared to Bd alone. More recently, a probiotic treatment for the emerging fungal pathogen of amphibians Batrachochytrium salamandrivorans (Bsal) was shown to slow disease progression, but did not improve individual survival within populations [36]. A longer period of infection resulting from treatment was suggested to likely extend the shedding period of Bsal into the environment, increasing its transmission. Research has also shown that colonisation resistance of the native skin microbiota can be metabolically costly and cause amphibians to lose body mass during probiotic treatment for chytridiomycosis [162]. These amphibian studies demonstrate the difficulty in applying protective microbes in the natural environment. There could be a mismatch between in vitro and in vivo outcomes, genetic variation in the effectiveness of protective microbes, or probiotic treatment could alter the infection dynamics in a way that benefits transmission.

Transplantation of entire microbial communities has shown promise in treating human disease. Faecal microbiota transplants are currently used to successfully treat recurrent C. difficile infection [118]. However, the long-term and off-target effects of this intervention remain unknown [158]. One potential side effect is the unintentional transfer of pathobionts from donor to recipient [163], for which follow-up studies are lacking [164]. Evidence is also emerging of extra-intestinal and systemic effects of intestinal microbiota replacement [165], including obesity [166], autoimmune disorders [167], and depression [168]. Observations of such varied off-target effects reveal the complex and systemic consequences which microbiota manipulation may have on hosts.

The use of known protective microbes as probiotics also needs to be monitored for unexpected consequences. Bifidobacterium longum subsp. longum has been investigated for its potential to prevent lethal infection from enteric pathogens. This bacterium is a component of the human gut microbiota which positively modifies the metabolic environment within the gut to inhibit translocation of invading EHEC from the gut to the blood [169]. Severe and ultimately lethal infection is prevented in this manner, but cases of infection caused by this species have been reported [30]. Tena and colleagues [30] reflected that B. longum may often be overlooked as a cause of disease in polymicrobial infections due to being labelled as a commensal.

Administration of protective microbes used clinically as probiotics could be particularly problematic for immunocompromised, critically ill, or otherwise vulnerable hosts [170]. Safety concerns include the potential for a probiotic to cause infection by translocation [171], to pass antibiotic resistance genes or other virulence-associated genes onto other microbiota components, and the possibility for production of metabolites that can be toxic [172]. There is also the possibility of permanent colonisation [173] and long-term side effects. Such safety concerns will be essential to account for in cases where probiotic treatments are being investigated to treat vulnerable hosts. Furthermore, the applied probiotic will interact with host microbiota and invading pathogens. As probiotics are inherently “live microorganisms” [174], they retain the ability to evolve, and it is largely unclear how they might change in a new host [175].

Conclusions

The “microbiome revolution” is revealing the interconnectedness between a host’s health and its resident microbial species. Microbiota components can form an effective non-immunological line of defence against infection [11,17–20]. Although the microbiota can aid pathogens, worsen infection outcomes, or become harmful themselves in the situations we describe, overall it is acknowledged that the benefits of microbiota substantially outweigh any costs.

There is a need to distinguish the different conditions under which microbiota might facilitate infection. Some pathogens and pathobionts can directly exploit the metabolic and immunological environment shaped by the host microbiota. Whether these outcomes are specific to the interacting host and pathogen species/genotype is unclear. A change in host health status may dictate whether microbiota have the potential to allow for harmful infection [176,177]. Poor health, the application of antibiotics, or infection by invading pathogens might cause a loss of microbiota diversity (and thus protective traits) or physical disruption to the environment allowing for the expansion of harmful microbes. The integration of bioinformatics with lab experiments in model systems will help to characterise genomic, proteomic, and metabolic features of the microbiome in different contexts of infection [147,152,154,155,178,179]. Functional gene expression studies [180–182] and genome-scale metabolic models are also proving increasingly powerful in characterising the microbiota profiles of healthy versus diseased individuals [183,184]. Overall, these approaches will allow predictions to be made about microbial phenotypes (e.g., metabolic traits, toxin production, and antibiotic resistance) in different contexts and the relevance of these phenotypes to infectious disease.

There are further outstanding questions regarding the contribution of microbiota components to infection in real time. In vitro and in vivo coculture experiments using communities representative of native host microbiota [152] can reveal antagonistic, competitive, and beneficial interactions between species within the microbiota, as well as between microbiota and invading pathogens [185,186]. Interactions between microbiota and host immunity can also be more intricately explored in model animal systems to study the role of the immunological environment in infection promotion [187–189]. With a better understanding of the interactions and dynamic processes that govern the microbiota, it may be possible to predict when harmless components will promote invading pathogens or become pathogenic themselves. Direct experimental tests in tractable systems will help to move our understanding beyond correlations of microbiota structure with infection outcomes and host health.

Thinking on an evolutionary timescale is essential for tackling why pathogens can benefit from the host microbiota. Systems in which pathogenic invaders depend on microbiota to start replicating [47,48] may indicate a coevolutionary relationship in which host-associated microbial species and pathogens cooperate to promote their establishment within the host. The potential for coevolution between protective microbes and pathogens has been demonstrated experimentally [190]. The extent to which pathogen exploitation of microbiome metabolites and immune priming is incidental, or the product of adaptation, remains unclear. Perhaps pathogens can evolve to improve their exploitation of host microbiota. Pathogens might also gain a competitive advantage by modifying their within-host environment (“niche construction” [191]) to select host-associated microbes most favourable to their survival [192]. The long-term effectiveness of a manipulated microbiota will also be vulnerable to pathogen evolution. Does engineering the microbiota or therapeutically applying microbes drive unwanted evolutionary changes in the target pathogen? Reductions in pathogen virulence could be desirable. However, any pathogen adaptation and increased within-host fitness might enhance their transmissibility in the host population. Most of our current understanding of the evolutionary biology in this area is based on theory and empirical work in model systems. Its relevance to human infections is an open question.

Microbiota are an important driver of variation in the prevalence and severity of some infections. Pathogen-suppressive forces generally dominate, but the interactions within the microbiota and between microbiota and invading pathogens are complex and need more direct empirical investigation. Nevertheless, shining a light on the potential ways in which the microbiota can sometimes facilitate infection by pathogens or pathobionts is critical for understanding patterns of infection in natural and applied settings.

References

  1. 1. Rafaluk-Mohr C. The relationship between parasite virulence and environmental persistence: a meta-analysis. Parasitology. 2019;146:897–902. pmid:30777585
  2. 2. Leggett HC, Cornwallis CK, West SA. Mechanisms of Pathogenesis, Infective Dose and Virulence in Human Parasites. PLoS Pathog. 2012;8:e1002512. pmid:22359500
  3. 3. Brown SP, Cornforth DM, Mideo N. Evolution of virulence in opportunistic pathogens: generalism, plasticity. and control Trends in Microbiology. 2012;20:336–42. pmid:22564248
  4. 4. Bernardo-Cravo AP, Schmeller DS, Chatzinotas A, Vredenburg VT, Environmental Factors LA. Host Microbiomes Shape Host–Pathogen Dynamics. Trends Parasitol. 2020;36:616–33. pmid:32402837
  5. 5. Marquet S, Schurr E. Genetics of Susceptibility to Infectious Diseases: Tuberculosis and Leprosy as Examples. Drug Metab Dispos. 2001;29:479–83. pmid:11259336
  6. 6. Esper AM, Moss M, Lewis CA, Nisbet R, Mannino DM, Martin GS. The role of infection and comorbidity: Factors that influence disparities in sepsis. Crit Care Med. 2006;34:2576–82. pmid:16915108
  7. 7. Pinsky MR. Dysregulation of the Immune Response in Severe Sepsis. Am J Med Sci. 2004;328:220–9. pmid:15486537
  8. 8. Pallen MJ. The Human Microbiome and Host–Pathogen Interactions. In: Nelson KE, editor. Metagenomics of the Human Body. New York, NY: Springer; 2011. pp. 43–61. https://doi.org/10.1007/978-1-4419-7089-3_3
    • 9. Kurose D, Furuya N, Tsuchiya K, Tsushima S, Evans HC. Endophytic fungi associated with Fallopia japonica (Polygonaceae) in Japan and their interactions with Puccinia polygoni-amphibii var. tovariae, a candidate for classical biological control. Fungal Biol. 2012;116:785–91. pmid:22749165
    • 10. Ottman N, Smidt H, de Vos WM, Belzer C. The function of our microbiota: who is out there and what do they do? Front Cell Infect Microbiol. 2012;2. pmid:22919693
    • 11. Ford SA, King KC. Harnessing the Power of Defensive Microbes: Evolutionary Implications in Nature and Disease Control. PLoS Pathog. 2016;12:e1005465. pmid:27058881
    • 12. Michel Fons TK Ana Gomez. Mechanisms of Colonisation and Colonisation Resistance of the Digestive Tract Part 2. Bacteria/Bacteria Interactions. Microb Ecol Health Dis. 2000;12:240–6.
    • 13. Schneitz C. Competitive exclusion in poultry––30 years of research. Food Control. 2005;16:657–67.
    • 14. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 2008;453:620–5. pmid:18509436
    • 15. Chow J, Mazmanian SKA. Pathobiont of the Microbiota Balances Host Colonization and Intestinal Inflammation. Cell Host Microbe. 2010;7:265–76. pmid:20413095
    • 16. Pathogens HM, Symbionts C. Pathobionts: Discovery and Functional Effects on the Host. ILAR J. 2015;56:159–62. pmid:26323625
    • 17. Shanahan F. Gut Microbes: From Bugs to Drugs. Am J Gastroenterol. 2010;105:275–9. pmid:20068561
    • 18. Chiu L, Bazin T, Truchetet M-E, Schaeverbeke T, Delhaes L, Pradeu T. Protective Microbiota: From Localized to Long-Reaching Co-Immunity. Front Immunol. 2017;8. pmid:29270167
    • 19. Lamousé-Smith E, Kelly D, De Cremoux I. Designing bugs as drugs: exploiting the gut microbiome. Am J Physiol Gastrointest Liver Physiol. 2020 [cited. Feb 2021:3. pmid:33264062
    • 20. Britton RA, Cani PD. Bugs as Drugs: Therapeutic Microbes for Prevention and Treatment of Disease. John Wiley & Sons; 2020.
      • 21. Kamada N, Kim Y-G, Sham HP, Vallance BA, Puente JL, Martens EC, et al. Regulated Virulence Controls the Ability of a Pathogen to Compete with the Gut Microbiota. Science. 2012;336:1325–9. pmid:22582016
      • 22. Louca S, Doebeli M. Transient dynamics of competitive exclusion in microbial communities. Environ Microbiol. 2016;18:1863–74. pmid:26404023
      • 23. King KC, Brockhurst MA, Vasieva O, Paterson S, Betts A, Ford SA, et al. Rapid evolution of microbe-mediated protection against pathogens in a worm host. ISME J. 2016;10:1915–24. pmid:26978164
      • 24. Rooks MG, Garrett WS. Gut microbiota metabolites and host immunity Nat Rev Immunol. 2016;16:341–52. pmid:27231050
      • 25. Brown EM, Sadarangani M, Finlay BB. The role of the immune system in governing host-microbe interactions in the intestine. Nat Immunol. 2013;14:660–7. pmid:23778793
      • 26. Zeng H, Ishaq SL, Liu Z, Bukowski MR. Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet. J Nutr Biochem. 2018;54:18–27. pmid:29223827
      • 27. McMurtry VE, Gupta RW, Tran L, Blanchard EE, Penn D, Taylor CM, et al. Bacterial diversity and Clostridia abundance decrease with increasing severity of necrotizing enterocolitis. Microbiome. 2015;3. pmid:25810906
      • 28. Boutin S, Bernatchez L, Audet C, Derôme N. Network Analysis Highlights Complex Interactions between Pathogen Host and Commensal Microbiota. PLoS ONE. 2013;8. pmid:24376845
      • 29. Tovaglieri A, Sontheimer-Phelps A, Geirnaert A, Prantil-Baun R, Camacho DM, Chou DB, et al. Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites. Microbiome. 2019;7:43. pmid:30890187
      • 30. Tena D, Losa C, Medina MJ, Sáez-Nieto JA. Peritonitis caused by Bifidobacterium longum: Case report and literature review. Anaerobe. 2014;27:27–30. pmid:24657157
      • 31. Martinez J, Ok S, Smith S, Snoeck K, Day JP, Jiggins FM. Should Symbionts Be Nice or Selfish? Antiviral Effects of Wolbachia Are Costly but Reproductive Parasitism Is Not. PLoS Pathog. 2015;11. pmid:26132467
      • 32. Broderick NA, Raffa KF, Handelsman J. Midgut bacteria required for Bacillus thuringiensis insecticidal activity. PNAS. 2006;103:15196–9. pmid:17005725
      • 33. Wei G, Lai Y, Wang G, Chen H, Li F, Wang S. Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality. PNAS. 2017;114:5994–9. pmid:28533370
      • 34. Chrostek E, Marialva MSP, Esteves SS, Weinert LA, Martinez J, Jiggins FM, et al. Wolbachia Variants Induce Differential Protection to Viruses in Drosophila melanogaster: A Phenotypic and Phylogenomic Analysis. PLoS Genet. 2013;9:e1003896. pmid:24348259
      • 35. Vorburger C, Gouskov A. Only helpful when required: a longevity cost of harbouring defensive symbionts. J Evol Biol. 2011;24:1611–7. pmid:21569156
      • 36. Bletz MC, Kelly M, Sabino-Pinto J, Bales E, Van Praet S, Bert W, et al. Disruption of skin microbiota contributes to salamander disease. Proc R Soc B. 2018;20180758:285. pmid:30135150
      • 37. Becker MH, Walke JB, Cikanek S, Savage AE, Mattheus N, Santiago CN, et al. Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus. Proc R Soc B Biol Sci. 2015;282:20142881. pmid:25788591
      • 38. Crane J, Barthow C, Kang J, Hood F, Stanley T, Wickens K. Probiotics for humans: hoax, hype, hope, or help. J R Soc N Z. 2020;50:456–69. pmid:32366320
      • 39. Keeney KM, Finlay BB. Enteric pathogen exploitation of the microbiota-generated nutrient environment of the gut. Curr Opin Microbiol. 2011;14:92–8. pmid:21215681
      • 40. Bäumler AJ, Sperandio V. Interactions between the microbiota and pathogenic bacteria in the gut. Nature. 2016;535:85–93. pmid:27383983
      • 41. Cameron EA, Frenemies SV. Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions. Cell Host Microbe. 2015;18:275–84. pmid:26355214
      • 42. Pacheco AR, Sperandio V. Enteric Pathogens Exploit the Microbiota-generated Nutritional Environment of the Gut. Metabolism and Bacterial Pathogenesis. John Wiley & Sons, Ltd; 2015. pp. 279–296. https://doi.org/10.1128/9781555818883.ch13
        • 43. Li M, Wei Z, Wang J, Jousset A, Friman V-P, Xu Y, et al. Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett. 2019;22:149–58. pmid:30460736
        • 44. Salem H, Onchuru TO, Bauer E, Kaltenpoth M. Symbiont transmission entails the risk of parasite infection. Biol Lett. 2015;11:20150840. pmid:26673937
        • 45. Jia D, Mao Q, Chen Y, Liu Y, Chen Q, Wu W, et al. Insect symbiotic bacteria harbour viral pathogens for transovarial transmission. Nat Microbiol. 2017;2:1–7. pmid:28263320
        • 46. Robinson CM. Enteric viruses exploit the microbiota to promote infection. Curr Opin Virol. 2019;37:58–62. pmid:31284078
        • 47. Hayes KS, Bancroft AJ, Goldrick M, Portsmouth C, Roberts IS, Grencis RK. Exploitation of the Intestinal Microflora by the Parasitic Nematode Trichuris muris. Science. 2010;328:1391–4. pmid:20538949
        • 48. Kuss SK, Best GT, Etheredge CA, Pruijssers AJ, Frierson JM, Hooper LV, et al. Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis. Science. 2011;334:249–52. pmid:21998395
        • 49. Reynolds LA, Smith KA, Filbey KJ, Harcus Y, Hewitson JP, Redpath SA, et al. Commensal-pathogen interactions in the intestinal tract: lactobacilli promote infection with, and are promoted by. helminth parasites Gut Microbes. 2014;5:522–32. pmid:25144609
        • 50. Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517:205–8. pmid:25337874
        • 51. Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol. 2019;12:1–9. pmid:29988120
        • 52. Reeves AE, Theriot CM, Bergin IL, Huffnagle GB, Schloss PD, Young VB. The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. Gut Microbes. 2011;2:145–58. pmid:21804357
        • 53. Samarkos M, Mastrogianni E, Kampouropoulou O. The role of gut microbiota in Clostridium difficile infection. Eur J Intern Med. 2018;50:28–32. pmid:29428498
        • 54. Taur Y, Pamer EG. The Intestinal Microbiota and Susceptibility to Infection in Immunocompromised Patients. Curr Opin Infect Dis. 2013;26:332–7. pmid:23806896
        • 55. Rojas I-G, Padgett DA, Sheridan JF, Marucha PT. Stress-Induced Susceptibility to Bacterial Infection During Cutaneous Wound Healing. Brain Behav Immun. 2002;16:74–84. pmid:11846442
        • 56. Dai W-F, Zhang J-J, Qiu Q-F, Chen J, Yang W, Ni S, et al. Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities Fish Shellfish Immunol. 2018;80:191–9. pmid:29803665
        • 57. Kim E-K, Lee K-A, Hyeon DY, Kyung M, Jun K-Y, Seo SH, et al. Bacterial Nucleoside Catabolism Controls Quorum Sensing and Commensal-to-Pathogen Transition in the Drosophila Gut Cell Host Microbe. 2020;27:345–357.e6. pmid:32078802
        • 58. Lee K-A, Kim S-H, Kim E-K, Ha E-M, You H, Kim B, et al. Bacterial-Derived Uracil as a Modulator of Mucosal Immunity and Gut-Microbe Homeostasis in Drosophila. Cell. 2013;153:797–811. pmid:23663779
        • 59. Dogan B, Suzuki H, Herlekar D, Sartor RB, Campbell BJ, Roberts CL, et al. Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation. Inflamm Bowel Dis. 2014;20:1919–32. pmid:25230163
        • 60. Samant S, Lee H, Ghassemi M, Chen J, Cook JL, Mankin AS, et al. Nucleotide Biosynthesis Is Critical for Growth of Bacteria in Human Blood. PLoS Pathog. 2008;4. pmid:18282099
        • 61. Hopkins MJ, Sharp R, Macfarlane GT. Variation in human intestinal microbiota with age. Dig Liver Dis. 2002;34:S12–8. pmid:12408433
        • 62. Barreto HC, Sousa A, Gordo I. The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice. Curr Biol. 2020;30:1102–1109.e5. pmid:32142696
        • 63. Chatzigiannidou I, Teughels W, Van de Wiele T, Boon N. Oral biofilms exposure to chlorhexidine results in altered microbial composition and metabolic profile. NPJ Biofilms Microbiomes. 2020;6:1–8. pmid:31908831
        • 64. Vötsch D, Willenborg M, Weldearegay YB, Valentin-Weigand P. Streptococcus suis–The “Two Faces” of a Pathobiont in the Porcine Respiratory Tract. Front Microbiol. 2018;9. pmid:29599763
        • 65. Ryu J-H, Kim S-H, Lee H-Y, Bai JY, Nam Y-D, Bae J-W, et al. Innate Immune Homeostasis by the Homeobox Gene Caudal and Commensal-Gut Mutualism in Drosophila. Science. 2008;319:777–82. pmid:18218863
        • 66. Meylan P, Lang C, Mermoud S, Johannsen A, Norrenberg S, Hohl D, et al. Skin Colonization by Staphylococcus aureus Precedes the Clinical Diagnosis of Atopic Dermatitis in Infancy. J Investig Dermatol. 2017;137:2497–504. pmid:28842320
        • 67. Hajishengallis G, Liang S, Payne MA, Hashim A, Jotwani R, Eskan MA, et al. Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement. Cell Host Microbe. 2011;10:497–506. pmid:22036469
        • 68. Hube B. From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. Curr Opin Microbiol. 2004;7:336–41. pmid:15288621
        • 69. Duell BL, Su Y-C, Riesbeck K. Host–pathogen interactions of nontypeable Haemophilus influenzae: from commensal to pathogen. FEBS Lett. 2016;590:3840–53. pmid:27508518
        • 70. Marks LR, Davidson BA, Knight PR, Hakansson AP. Interkingdom Signaling Induces Streptococcus pneumoniae Biofilm Dispersion and Transition from Asymptomatic Colonization to Disease. MBio. 2013;4:e00438–13, mBio.00438-13. pmid:23882016
        • 71. Theriot CM, Koenigsknecht MJ, Carlson PE, Hatton GE, Nelson AM, Li B, et al. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun. 2014;5:3114. pmid:24445449
        • 72. Becattini S, Taur Y, Pamer EG. Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends Mol Med. 2016;22:458–78. pmid:27178527
        • 73. Casals-Pascual C, Vergara A, Vila J. Intestinal microbiota and antibiotic resistance: Perspectives and solutions. Hum Microb J. 2018;9:11–5.
        • 74. Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. J Clin Invest. 2014;124:4212–8. pmid:25271726
        • 75. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, et al. Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. J Pediatr. 2014;165:23–9. pmid:24529620
        • 76. Mason KL, Stepien TA, Blum JE, Holt JF, Labbe NH, Rush JS, et al. From Commensal to Pathogen: Translocation of Enterococcus faecalis from the Midgut to the Hemocoel of Manduca sexta. MBio. 2011;2. pmid:21586646
        • 77. Kitamoto S, Nagao-Kitamoto H, Jiao Y, Gillilland MG, Hayashi A, Imai J, et al. The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis. Cell. 2020;182:447–462.e14. pmid:32758418
        • 78. Soares FS, Amaral FC, Silva NLC, Valente MR, Santos LKR, Yamashiro LH, et al. Antibiotic-Induced Pathobiont Dissemination Accelerates Mortality in Severe Experimental Pancreatitis. Front Immunol. 2017;8. pmid:29375557
        • 79. Caccia S, Lelio ID, Storia AL, Marinelli A, Varricchio P, Franzetti E, et al. Midgut microbiota and host immunocompetence underlie Bacillus thuringiensis killing mechanism. PNAS. 2016;113:9486–91. pmid:27506800
        • 80. Wardwell LH, Huttenhower C, Garrett WS. Current Concepts of the Intestinal Microbiota and the Pathogenesis of Infection. Curr Infect Dis Rep 2011;13:28–34. pmid:21308452
        • 81. McCarville JL, Chen GY, Cuevas VD, Troha K, Ayres JS. Microbiota Metabolites in Health and Disease. Annu Rev Immunol. 2020;38:147–70. pmid:32340573
        • 82. Hryckowian AJ, Van Treuren W, Smits SA, Davis NM, Gardner JO, Bouley DM, et al. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat Microbiol. 2018;3:662–9. pmid:29686297
        • 83. Roman MS, Wagner A. An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PLoS Comput Biol. 2018;14:e1006340. pmid:30040834
        • 84. Curtis MM, Hu Z, Klimko C, Narayanan S, Deberardinis R, Sperandio V. The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape. Cell Host Microbe. 2014;16:759–69. pmid:25498343
        • 85. Lustri BC, Sperandio V, Moreira CG. Bacterial Chat: Intestinal Metabolites and Signals in Host-Microbiota-Pathogen Interactions. Andrews-Polymenis HL, editor. Infect Immun. 2017;85:e00476–17e00476-17. pmid:28947641
        • 86. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569:655–62. pmid:31142855
        • 87. Zierer J, Jackson MA, Kastenmüller G, Mangino M, Long T, Telenti A, et al. The fecal metabolome as a functional readout of the gut microbiome. Nat Genet. 2018;50:790–5. pmid:29808030
        • 88. Zhang X, Li L, Butcher J, Stintzi A, Figeys D. Advancing functional and translational microbiome research using meta-omics approaches. Microbiome. 2019;7:154. pmid:31810497
        • 89. Kwong WK, Mancenido AL, Moran NA. Immune system stimulation by the native gut microbiota of honey bees. R Soc Open Sci. 2017;4:170003. pmid:28386455
        • 90. Muhammad A, Habineza P, Ji T, Hou Y, Shi Z. Intestinal Microbiota Confer Protection by Priming the Immune System of Red Palm Weevil Rhynchophorus ferrugineus Olivier (Coleoptera: Dryophthoridae). Front Physiol. 2019;10. pmid:31681013
        • 91. Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JN. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nat Med. 2010;16:228–31. pmid:20081863
        • 92. Ogawa M, Shimizu K, Nomoto K, Takahashi M, Watanuki M, Tanaka R, et al. Protective effect of Lactobacillus casei strain Shirota on Shiga toxin-producing Escherichia coli O157:H7 infection in infant rabbits. Infect Immun. 2001;69:1101–8. pmid:11160007
        • 93. Cross ML. Microbes versus microbes: immune signals generated by probiotic lactobacilli and their role in protection against microbial pathogens. FEMS Immunol Med Microbiol. 2002;34:245–53. pmid:12443824
        • 94. García-Bayona L, Comstock LE. Bacterial antagonism in host-associated microbial communities. Science. 2018;361. pmid:30237322
        • 95. Brown SP, Le Chat L, Taddei F. Evolution of virulence: triggering host inflammation allows invading pathogens to exclude competitors. Ecol Lett. 2008;11:44–51. pmid:18021245
        • 96. Li RW, Wu S, Li W, Navarro K, Couch RD, Hill D, et al. Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Infect Immun. 2012;80:2150–7. pmid:22493085
        • 97. Grassl N, Kulak NA, Pichler G, Geyer PE, Jung J, Schubert S, et al. Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome. Genome Med. 2016;8:44. pmid:27102203
        • 98. Campbell LJ, Hammond SA, Price SJ, Sharma MD, Garner TWJ, Birol I, et al. A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations. Mol Ecol. 2018;27:1413–27. pmid:29420865
        • 99. Phalak P, Henson MA. Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota. PRO. 2019;7:97.
        • 100. Barroso-Batista J, Demengeot J, Gordo I. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat Commun. 2015;6:8945. pmid:26615893
        • 101. Koskella B, Parr N. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140297. pmid:26150663
        • 102. Tso GHW, Reales-Calderon JA, Tan ASM, Sem X, Le GTT, Tan TG, et al. Experimental evolution of a fungal pathogen into a gut symbiont. Science. 2018;362:589–95. pmid:30385579
        • 103. Gandon S, Michalakis Y. Evolution of parasite virulence against qualitative or quantitative host resistance. Philos Trans R Soc Lond B Biol Sci. 2000;267:985–90. pmid:10874747
        • 104. Hughes JM. Preserving the lifesaving power of antimicrobial agents. JAMA. 2011;305:1027–8. pmid:21343545
        • 105. Bacterial Vaccines LM. Serotype Replacement: Lessons from Haemophilus influenzae and Prospects for Streptococcus pneumoniae. Emerg Infect Dis. 1999;5:336–45. pmid:10341170
        • 106. Brown SP, Fredrik Inglis R, Taddei F. Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence. Evol Appl. 2009;2:32–9. pmid:25567845
        • 107. Martinez J, Bruner-Montero G, Arunkumar R, Smith SCL, Day JP, Longdon B, et al. Virus evolution in Wolbachia-infected Drosophila. Proc R Soc B Biol Sci. 2117;286 (2019):2019. pmid:31662085
        • 108. Rouchet R, Vorburger C. Experimental Evolution of Parasitoid Infectivity on Symbiont-Protected Hosts Leads to the Emergence of Genotype Specificity. Evolution. 2014;68:1607–1616. pmid:24495148
        • 109. McNally L, Vale PF, Brown SP. Microbiome engineering could select for more virulent pathogens. bioRxiv. 2015;027854.
        • 110. Ford SA, Kao D, Williams D, King KC. Microbe-mediated host defence drives the evolution of reduced pathogen virulence. Nat Commun. 2016;7:1–9. pmid:27845328
        • 111. Gamage SD, Patton AK, Hanson JF, Diversity WAA. Host Range of Shiga Toxin-Encoding Phage. Infect Immun. 2004;72:7131–9. pmid:15557637
        • 112. Rodemann JF, Dubberke ER, Reske KA, Seo DH, Stone CD. Incidence of Clostridium difficile infection in inflammatory bowel disease. Clin Gastroenterol Hepatol. 2007;5:339–44. pmid:17368233
        • 113. Lima AA, Lyerly DM, Wilkins TD, Innes DJ, Guerrant RL. Effects of Clostridium difficile toxins A and B in rabbit small and large intestine in vivo and on cultured cells in vitro. Infect Immun. 1988;56:582–8. pmid:3343050
        • 114. Drew et al. (In press). Microbial evolution and transitions along the parasite–mutualist continuum. Nat Rev Microbiol. 2021.
        • 115. Ayres JS, Trinidad NJ, Vance RE. Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota. Nat Med. 2012;18:799–806. pmid:22522562
        • 116. Schwarz RS, Moran NA, Evans JD. Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers. Proc Natl Acad Sci U S A. 2016;113:9345–50. pmid:27482088
        • 117. Broderick NA, Robinson CJ, McMahon MD, Holt J, Handelsman J, Raffa KF. Contributions of gut bacteria to Bacillus thuringiensis-induced mortality vary across a range of Lepidoptera. BMC Biol. 2009;7:11. pmid:19261175
        • 118. Kelly CR, Khoruts A, Staley C, Sadowsky MJ, Abd M, Alani M, et al. Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection. Ann Intern Med. 2016;165:609–16. pmid:27547925
        • 119. Ramsey MM, Rumbaugh KP, Whiteley M. Metabolite Cross-Feeding Enhances Virulence in a Model Polymicrobial Infection. PLoS Pathog. 2011;7:e1002012. pmid:21483753
        • 120. Stacy A, Fleming D, Lamont RJ, Rumbaugh KP, Whiteley M. A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration. MBio. 2016;7:e00782–16, /mbio/7/3/e00782-16.atom. pmid:27353758
        • 121. Proença JT, Barral DC, Gordo I. Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli -macrophage interaction. Sci Rep. 2017;7:4504. pmid:28674418
        • 122. Huang G. Regulation of phenotypic transitions in the fungal pathogen Candida albicans. Virulence. 2012;3:251–61. pmid:22546903
        • 123. Armistead B, Oler E, Adams Waldorf K, Rajagopal L. The Double Life of Group B Streptococcus: Asymptomatic Colonizer and Potent Pathogen. J Mol Biol. 2019;431:2914–31. pmid:30711542
        • 124. Franklin L, Nobbs AH, Bricio-Moreno L, Wright CJ, Maddocks SE, Sahota JS, et al. The AgI/II Family Adhesin AspA Is Required for Respiratory Infection by Streptococcus pyogenes. PLoS ONE. 2013;8. pmid:23638083
        • 125. Schmitt CK, Meysick KC, O’Brien AD. Bacterial toxins: friends or foes? Emerg Infect Dis. 1999;5:224–34. pmid:10221874
        • 126. Rudkin JK, McLoughlin RM, Preston A, Massey RC. Bacterial toxins: Offensive, defensive, or something else altogether? PLoS Pathog. 2017;13. pmid:28934339
        • 127. King KC. Defensive symbionts. Curr Biol. 2019;29:R78–80. pmid:30721677
        • 128. Martinez J, Cogni R, Cao C, Smith S, Illingworth CJR, Jiggins FM. Addicted? Reduced host resistance in populations with defensive symbionts Proc R Soc B Biol Sci. 2016;283:20160778. pmid:27335421
        • 129. Osborne SE, Iturbe-Ormaetxe I, Brownlie JC, O’Neill SL, Johnson KN. Antiviral Protection and the Importance of Wolbachia Density and Tissue Tropism in Drosophila simulans. Appl Environ Microbiol. 2012;78:6922–9. pmid:22843518
        • 130. Ye YH, Woolfit M, Rancès E, O’Neill SL, McGraw EA. Wolbachia-Associated Bacterial Protection in the Mosquito Aedes aegypti. PLoS Negl Trop Dis. 2013;7:e2362. pmid:23951381
        • 131. Kambris Z, Cook PE, Phuc HK, Sinkins SP. Immune activation by life-shortening Wolbachia and reduced filarial competence in mosquitoes. Science. 2009;326:134–6. pmid:19797660
        • 132. Cayetano L, Rothacher L, Simon J-C, Vorburger C. Cheaper is not always worse: strongly protective isolates of a defensive symbiont are less costly to the aphid host. Proc Biol Sci. 2015;282. pmid:25473015
        • 133. Mathé-Hubert H, Kaech H, Ganesanandamoorthy P, Vorburger C. Evolutionary costs and benefits of infection with diverse strains of Spiroplasma in pea aphids*. Evolution. 2019;73:1466–81. pmid:30990223
        • 134. Hodgkin J, Félix M-A, Clark LC, Stroud D, Gravato-Nobre MJ. Two Leucobacter Strains Exert Complementary Virulence on Caenorhabditis Including Death by Worm-Star Formation. Curr Biol. 2013;23:2157–61. pmid:24206844
        • 135. Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014;15:531. pmid:25517225
        • 136. Ma Z. (Sam), Li L, Gotelli NJ. Diversity-disease relationships and shared species analyses for human microbiome-associated diseases. ISME J. 2019;13:1911–9. pmid:30894688
        • 137. Zaneveld JR, McMinds R, Vega Thurber R. Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat Microbiol. 2017;2:1–8. pmid:28836573
        • 138. Koumans EH, Sternberg M, Bruce C, McQuillan G, Kendrick J, Sutton M, et al. The Prevalence of Bacterial Vaginosis in the United States, 2001–2004; Associations With Symptoms, Sexual Behaviors, and Reproductive Health. Sex Transm Dis. 2007;34: 864–869. pmid:17621244
        • 139. Xu J, Peng J-J, Yang W, Fu K, Zhang Y. Vaginal microbiomes and ovarian cancer: a review. Am J Cancer Res. 2020;10:743–56. pmid:32266088
        • 140. Nasioudis D, Linhares IM, Ledger WJ, Witkin SS. Bacterial vaginosis: a critical analysis of current knowledge. BJOG. 2017;124:61–9. pmid:27396541
        • 141. Nelson TM, Borgogna J-LC, Brotman RM, Ravel J, Walk ST, Yeoman CJ. Vaginal biogenic amines: biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis? Front Physiol. 2015;6. pmid:26483694
        • 142. Yeoman CJ, Thomas SM, Miller MEB, Ulanov AV, Torralba M, Lucas S, et al. A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease. PLoS ONE. 2013;8:e56111. pmid:23405259
        • 143. Lynch KE, Parke EC, O’Malley MA. How causal are microbiomes? A comparison with the Helicobacter pylori explanation of ulcers. Biol Philos. 2019;34:1–24.
        • 144. Walter J, Armet AM, Finlay BB, Shanahan F. Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents. Cell. 2020;180:221–32. pmid:31978342
        • 145. Microbiome FMA. Focus on Causation and Mechanism. Cell. 2018;174:785–90. pmid:30096310
        • 146. Giovanni MY, Schneider JS, Calder T, Fauci AS. Refocusing Human Microbiota Research in Infectious and Immune-mediated Diseases: Advancing to the Next Stage. J Infect Dis 2020 [cited 1 Feb 2021]. pmid:33188418
        • 147. Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. PNAS. 2011;108:6252–7. pmid:21436049
        • 148. Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res. 2015;6:269–82. pmid:26257925
        • 149. Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, et al. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30. pmid:31388130
        • 150. Gordon JI, Klaenhammer TR. A rendezvous with our microbes PNAS. 2011;108:4513–5. pmid:21406595
        • 151. Mooser C, Gomez de Agüero M, Ganal-Vonarburg SC. Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool. and perspective Curr Opin Microbiol. 2018;44:50–60. pmid:30056329
        • 152. Dirksen P, Assié A, Zimmermann J, Zhang F, Tietje A-M, Marsh SA, et al. CeMbio—The Caenorhabditis elegans Microbiome Resource. G3 Genes|Genomes|. Genetics. 2020;10:3025–39. pmid:32669368
        • 153. Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature. 2015;528:364–9. pmid:26633631
        • 154. Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, et al. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol. 2016;1:1–15. pmid:27670113
        • 155. Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol. 2019;37:186–92. pmid:30718869
        • 156. Hoseinifar SH, Sun Y-Z, Wang A, Zhou Z. Probiotics as Means of Diseases Control in Aquaculture, a Review of Current Knowledge and Future Perspectives. Front Microbiol. 2018;9. pmid:30369918
        • 157. Audisio MC. Gram-Positive Bacteria with Probiotic Potential for the Apis mellifera L. Honey Bee: The Experience in the Northwest of Argentina. Probiotics Antimicrob Proteins. 2017;9:22–31. pmid:27655068
        • 158. Sanders ME, Merenstein DJ, Reid G, Gibson GR, Rastall RA. Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Nat Rev Gastroenterol Hepatol. 2019;16:605–16. pmid:31296969
        • 159. Silva DR, Sardi J de CO, Pitangui NdeS, Roque SM, Silva ACB da, Rosalen PL. Probiotics as an alternative antimicrobial therapy: Current reality and future directions. J Funct Foods. 2020;73:104080.
        • 160. Antwis RE, Harrison XA. Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates. Mol Ecol. 2018;27:577–89. pmid:29218845
        • 161. Harrison XA, Sewell T, Fisher M, Antwis RE. Designing Probiotic Therapies With Broad-Spectrum Activity Against a Wildlife Pathogen. Front Microbiol. 2020;10. pmid:32038568
        • 162. Küng D, Bigler L, Davis LR, Gratwicke B, Griffith E, Woodhams DC. Stability of Microbiota Facilitated by Host Immune Regulation: Informing Probiotic Strategies to Manage Amphibian Disease. PLoS ONE. 2014;9. pmid:24489847
        • 163. Lo Vecchio A, Cohen MB. Fecal microbiota transplantation for Clostridium difficile infection: benefits and barriers. Curr Opin Gastroenterol. 2014;30:47–53. pmid:24275671
        • 164. Li Y-T, Cai H-F, Wang Z-H, Xu J, Fang J-Y. Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection. Aliment Pharmacol Ther. 2016;43:445–57. pmid:26662643
        • 165. Cryan JF, O’Mahony SM. The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil. 2011;23:187–92. pmid:21303428
        • 166. Lee P, Yacyshyn BR, Yacyshyn MB. Gut microbiota and obesity: An opportunity to alter obesity through faecal microbiota transplant (FMT). Diabetes Obes Metab. 2019;21:479–90. pmid:30328245
        • 167. Rosser EC, Mauri C. A clinical update on the significance of the gut microbiota in systemic autoimmunity. J Autoimmun. 2016;74: 85–93. pmid:27481556
        • 168. Kurokawa S, Kishimoto T, Mizuno S, Masaoka T, Naganuma M, Liang K, et al. The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study. J Affect Disord. 2018;235:506–12. pmid:29684865
        • 169. Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature. 2011;469:543–7. pmid:21270894
        • 170. Sotoudegan F, Daniali M, Hassani S, Nikfar S, Abdollahi M. Reappraisal of probiotics’ safety in human. Food Chem Toxicol. 2019;129:22–9. pmid:31009735
        • 171. Liong M-T. Safety of probiotics: translocation and infection. Nutr Rev. 2008;66:192–202. pmid:18366533
        • 172. Butel M-J. Probiotics, gut microbiota and health. Med Mal Infect. 2014;44:1–8. pmid:24290962
        • 173. Marteau P, Shanahan F. Basic aspects and pharmacology of probiotics: an overview of pharmacokinetics, mechanisms of action and side-effects. Best Pract Res Clin Gastroenterol. 2003;17:725–40. pmid:14507584
        • 174. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11:506–14. pmid:24912386
        • 175. Swain Ewald HA, Ewald PW, Selection N. The Microbiome. and Public Health Yale J Biol Med. 2018;91:445–55. pmid:30588210
        • 176. Chen YE, Fischbach MA, Belkaid Y. Skin microbiota–host interactions. Nature. 2018;553:427–36. pmid:29364286
        • 177. Shanahan F. The gut microbiota—a clinical perspective on lessons learned. Nat Rev Gastroenterol Hepatol. 2012;9:609–14. pmid:22890109
        • 178. Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, et al. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet. 2019;51:600–5. pmid:30778224
        • 179. Surana NK, Kasper DL. Moving beyond microbiome-wide associations to causal microbe identification. Nature. 2017;552:244–7. pmid:29211710
        • 180. Eloe-Fadrosh EA, Brady A, Crabtree J, Drabek EF, Ma B, Mahurkar A, et al. Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption. MBio. 2015;6. pmid:25873374
        • 181. Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T. Bacterial community assembly based on functional genes rather than species. PNAS. 2011;108: 14288–14293. pmid:21825123
        • 182. Armour CR, Nayfach S, Pollard KS, Sharpton TJA. Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. mSystems. 2019;4. pmid:31098399
        • 183. Levy R, Borenstein E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc Natl Acad Sci U S A. 2013;110:12804–9. pmid:23858463
        • 184. Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun. 2019;10:3586. pmid:31395883
        • 185. Frisan T. Co- and polymicrobial infections in the gut mucosa: The host–microbiota–pathogen perspective. Cell Microbiol. 2021;23:e13279. pmid:33040471
        • 186. Hajishengallis G, Lamont RJ. Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts. Trends Microbiol. 2016;24:477–89. pmid:26968354
        • 187. Ford SA, King KC. In Vivo Microbial Coevolution Favors Host Protection and Plastic Downregulation of Immunity. Mol Biol Evol. 2020 [cited 22 Feb 2021]. pmid:33179739
        • 188. Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, et al. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019;365. pmid:31371577
        • 189. Kissoyan KAB, Drechsler M, Stange E-L, Zimmermann J, Kaleta C, Bode HB, et al. Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group. Curr Biol. 2019;29:1030–1037.e5. pmid:30827913
        • 190. Ford SA, Williams D, Paterson S, King KC. Co-evolutionary dynamics between a defensive microbe and a pathogen driven by fluctuating selection. Mol Ecol. 2017;26:1778–89. pmid:27862515
        • 191. Odling-Smee J, Erwin DH, Palkovacs EP, Feldman MW, Laland KN. Niche construction theory: a practical guide for ecologists. Q Rev Biol. 2013;88:4–28. pmid:23653966
        • 192. Goddard MR. Quantifying the complexities of Saccharomyces cerevisiae’s ecosystem engineering via fermentation. Ecology. 2008;89:2077–82. pmid:18724717