Label or Concept – What Is a Pathobiont?

Abstract

Pathobionts can cause or promote disease only when specific genetic or environmental conditions are altered in the host.Conditions under which pathobionts exhibit virulence include impaired host immune defenses and altered microbiota composition.Several microorganisms classified as pathobionts can also exert beneficial functions on their host in different scenarios.Currently the term 'pathobiont' does not comprise a well-defined concept and should therefore be revised. In this opinion article, we suggest an alternative terminology. An increasing number of microorganisms are classified as 'pathobionts' (i.e., organisms that can cause harm under certain circumstances) but there exist no universally used criteria for this definition. In particular, the term is often used for categorizing disease-associated taxa without proof of 'causality'. This creates confusion and distracts from explicitly searching for beneficial functions of these organisms that they may in fact have. Here, we discuss why this term in its current use, and its apparent simplicity, may obscure the complexity of microbe–host and microbe–microbe interactions that define (the status of) the gut ecosystem. An increasing number of microorganisms are classified as 'pathobionts' (i.e., organisms that can cause harm under certain circumstances) but there exist no universally used criteria for this definition. In particular, the term is often used for categorizing disease-associated taxa without proof of 'causality'. This creates confusion and distracts from explicitly searching for beneficial functions of these organisms that they may in fact have. Here, we discuss why this term in its current use, and its apparent simplicity, may obscure the complexity of microbe–host and microbe–microbe interactions that define (the status of) the gut ecosystem. Historically, infectious diseases have been the most significant causes of death. Research in this context eventually led to the discovery of the causal role of pathogenic bacteria in the etiology of infections. Thus, for a long time, bacteria were considered to have a largely negative impact on human health. However, particularly in recent decades, it has become clear that microorganisms carry out immensely important functions in every ecosystem on earth. Their positive impact on ecosystem functioning is now well known for members of the gut microbiome as research in this field has drastically increased over recent years. Scientists and media outlets spreading the news were quick to categorize bacteria as 'the good' and 'the bad' according to their impact on human health. However, solid evidence is accumulating that bacteria–host interactions are more complex than 'good' and 'bad'. In particular, members of the gut microbiome seem to resist this classification: they can provide essential functions to their mammalian host in one scenario yet be detrimental to health in another situation. Even though this comment may apply to other ecosystems, here we refer specifically to the gut ecosystem and its bacterial inhabitants. The recognition that bacterial classification requires concepts that are more flexible than 'good' and 'bad' has led to a shift in gut microbiome research from a medical disease-centered focus to a more ecological perspective [1.Costello E.K. et al.The application of ecological theory toward an understanding of the human microbiome.Science. 2012; 336: 1255-1262Crossref PubMed Scopus (925) Google Scholar,2.Proctor L. Priorities for the next 10 years of human microbiome research.Nature. 2019; 569: 623-625Crossref PubMed Scopus (58) Google Scholar]. Ecological theory is increasingly used to explain phenomena observed in microbe–microbe and microbe–host interactions. Phylogenetic analysis and measures of community diversity are standard in microbiome analysis [3.Gilbert J.A. Lynch S.V. Community ecology as a framework for human microbiome research.Nat. Med. 2019; 25: 884-889Crossref PubMed Scopus (57) Google Scholar], and concepts such as microbial interaction networks [4.Faust K. Raes J. Microbial interactions: from networks to models.Nat. Rev. Microbiol. 2012; 10: 538-550Crossref PubMed Scopus (1836) Google Scholar], nutrient niches [5.Pereira F.C. Berry D. Microbial nutrient niches in the gut.Environ. Microbiol. 2017; 19: 1366-1378Crossref PubMed Scopus (167) Google Scholar], or keystone species [6.Berry D. Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks.Front. Microbiol. 2014; 5: 219Crossref PubMed Scopus (760) Google Scholar] have proven to be useful in understanding microbiome functions. Importantly, this framework and terminology are derived from eukaryotic systems; these differ from microbiological systems, as noted by Koskella et al. [7.Koskella B. et al.The microbiome beyond the horizon of ecological and evolutionary theory.Nat. Ecol. Evol. 2017; 1: 1606-1615Crossref PubMed Scopus (136) Google Scholar]. Quickly, the respective concepts were modified to meet the needs and requirements of gut microbiome researchers. This has led to an ambiguous use of terminology and a lack of comparability between studies, as neither terminology nor concepts have been unified and unambiguously defined for the field. Additionally, new terminology has been introduced to classify the myriad interactions observed between members of the gut microbiome themselves as well as between the microbiome and the host. Among the new concepts and terms introduced into gut microbiome research – needed because classical ecology did not quite fit the demand – is the identification of microorganisms as ‘pathobionts’. A ‘pathobiont’ was originally defined as 'a symbiont that is able to promote pathology only when specific genetic or environmental conditions are altered in the host' [8.Mazmanian S.K. et al.A microbial symbiosis factor prevents intestinal inflammatory disease.Nature. 2008; 453: 620-625Crossref PubMed Scopus (1696) Google Scholar,9.Chow J. Mazmanian S.K. A pathobiont of the microbiota balances host colonization and intestinal inflammation.Cell Host Microbe. 2010; 7: 265-276Abstract Full Text Full Text PDF PubMed Scopus (211) Google Scholar]. This definition implies that we know when normality exists – a balanced state, maybe, which, when altered, allows pathobionts to exert negative effects on the host. However, there is no consensus on what a healthy or unhealthy microbiome looks like [10.McBurney M.I. et al.Establishing what constitutes a healthy human gut microbiome: state of the science, regulatory considerations, and future directions.J. Nutr. 2019; 149: 1882-1895Crossref PubMed Scopus (107) Google Scholar]. By labeling something, we like to believe that we actually understand it. This explains why an increasing number of microorganisms are being classified as ‘pathobionts’: researchers observe sequence-based associations of specific microorganisms with disease and are quick to classify them as ‘pathobiont’, even while evidence of causality or a mechanistic understanding is lacking. Often, numerous studies and different models are needed to decipher the range of interactions between one microbe and its host. These interactions can be altered by the other resident microorganisms, further complicating conclusions on the function of one isolated microbe. By now, the term ‘pathobiont’ serves to describe multiple, different phenomena that hardly comprise a well-defined concept. The first bacterium termed ‘pathobiont’ was Helicobacter hepaticus, a common constituent of the murine gut microbiota [11.Mazmanian S.K. Capsular polysaccharides of symbiotic bacteria modulate immune responses during experimental colitis.J. Pediatr. Gastroenterol. Nutr. 2008; 46: E11-E12Crossref PubMed Google Scholar]. H. hepaticus has been causally linked to large-bowel inflammation in immunocompromised mice but it induces no overt pathology in wild-type animals [12.Cahill R.J. et al.Inflammatory bowel disease: an immunity-mediated condition triggered by bacterial infection with Helicobacter hepaticus.Infect. Immun. 1997; 65: 3126-3131Crossref PubMed Google Scholar,13.Kullberg M.C. et al.Helicobacter hepaticus triggers colitis in specific-pathogen-free interleukin-10 (IL-10)-deficient mice through an IL-12- and gamma interferon-dependent mechanism.Infect. Immun. 1998; 66: 5157-5166Crossref PubMed Google Scholar]. Later on, similar characteristics were discovered for other bacterial inhabitants of the gut, such as segmented filamentous bacteria (SFB), Escherichia coli, and Enterococcus faecalis [14.Stepankova R. et al.Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells.Inflamm. Bowel Dis. 2007; 13: 1202-1211Crossref PubMed Scopus (159) Google Scholar, 15.Waidmann M. et al.Bacteroides vulgatus protects against Escherichia coli-induced colitis in gnotobiotic interleukin-2-deficient mice.Gastroenterology. 2003; 125: 162-177Abstract Full Text Full Text PDF PubMed Scopus (179) Google Scholar, 16.Balish E. Warner T. Enterococcus faecalis induces inflammatory bowel disease in interleukin-10 knockout mice.Am. J. Pathol. 2002; 160: 2253-2257Abstract Full Text Full Text PDF PubMed Scopus (247) Google Scholar]. Seemingly, these organisms fit the criteria of being ‘pathobionts’ but, as was noted, their pathogenicity is dependent on an additional factor besides genetic susceptibility of the host: the microbial context. When inducing disease, these bacteria use different and sometimes contrasting ways of interacting with the other members of the gut microbiota. E. coli induces colitis in immunocompromised gnotobiotic mice – unless Bacteroides vulgatus is also present [15.Waidmann M. et al.Bacteroides vulgatus protects against Escherichia coli-induced colitis in gnotobiotic interleukin-2-deficient mice.Gastroenterology. 2003; 125: 162-177Abstract Full Text Full Text PDF PubMed Scopus (179) Google Scholar]. Conversely, SFB require a complex microbiota for triggering intestinal inflammation in severely immune-deficient mice [14.Stepankova R. et al.Segmented filamentous bacteria in a defined bacterial cocktail induce intestinal inflammation in SCID mice reconstituted with CD45RBhigh CD4+ T cells.Inflamm. Bowel Dis. 2007; 13: 1202-1211Crossref PubMed Scopus (159) Google Scholar]. Adherent and invasive E. coli provoke gut inflammation in genetically susceptible infant mice, which, in turn, leads to a more colitogenic microbiota, which further drives gut inflammation [17.Chassaing B. et al.AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition.Gut. 2014; 63: 1069-1080Crossref PubMed Scopus (138) Google Scholar]. These different influences of the microbiota further blurred the pathobiont concept as the term alone no longer allowed for definite conclusions on a specific disease-causing microorganism. Additionally, evidence has started to accumulate that a given bacterial strain termed 'a pathobiont' could also exert beneficial and health-promoting functions on its host in another context. E. faecalis can act as both a colitogenic and a protective microbe – depending on the composition of the remaining bacterial community in the gut [18.Lengfelder I. et al.Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis.Front. Immunol. 2019; 10: 1420Crossref PubMed Scopus (26) Google Scholar]. H. hepaticus produces soluble polysaccharides that activate an anti-inflammatory and repair-gene signature [19.Danne C. et al.A large polysaccharide produced by Helicobacter hepaticus induces an anti-inflammatory gene signature in macrophages.Cell Host Microbe. 2017; 22e5Abstract Full Text Full Text PDF PubMed Scopus (66) Google Scholar]. SFB also promote immune defenses and can protect against infections [20.Ivanov I.I. et al.Induction of intestinal Th17 cells by segmented filamentous bacteria.Cell. 2009; 139: 485-498Abstract Full Text Full Text PDF PubMed Scopus (3171) Google Scholar]. Most recently, Mucispirillum schaedleri, another so-called pathobiont, was reported to cause colitis in severely immunocompromised hosts [21.Caruso R. et al.A specific gene-microbe interaction drives the development of Crohn's disease-like colitis in mice.Sci. Immunol. 2019; 4 (pii: eaaw4341)Crossref PubMed Scopus (64) Google Scholar] while it can protect against Salmonella-induced colitis by interfering with the expression of Salmonella virulence factors in immunocompetent hosts [22.Herp S. et al.Mucispirillum schaedleri antagonizes salmonella virulence to protect mice against colitis.Cell Host Microbe. 2019; 25 (e8): 681-694Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar]. Evidently, the term ‘pathobiont’ has readily been attached to a variety of microorganisms at a stage when we do not completely understand their behavior because of their variable impact on the host. The examples listed earlier involve bacteria that have been causally linked to a specific host phenotype but this is not always the case. The term ´pathobiont´ has already been widely used to label bacteria that have been linked to a disease merely based on sequence-based correlations with diseased individuals [23.Armstrong H. et al.Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases.Microbiome. 2019; 7: 1Crossref PubMed Scopus (33) Google Scholar]. This is inherently error-prone as microbial community shifts can also occur as a consequence of disease [24.Byndloss M.X. Baumler A.J. The germ-organ theory of non-communicable diseases.Nat. Rev. Microbiol. 2018; 16: 103-110Crossref PubMed Scopus (82) Google Scholar] and are not necessarily involved in the etiology. Conceivably, it is important to identify microorganisms that can potentially harm their host in order to prevent complications during, for example, microbiome-directed therapy in immunocompromised patients or to limit exposure of immune-deficient patients to such microorganisms. However, hasty classification of these organisms as pathobionts does not serve the purpose as it quickly labels them as ‘bad’ and distracts from searching for beneficial functions that these organisms may in fact have. As a matter of fact, categorization of microorganisms without knowledge of their entire capacity will inevitably lead to confusion and incoherent terminology. To avoid this, rigorous experiments to establish causality [25.Surana N.K. Kasper D.L. Moving beyond microbiome-wide associations to causal microbe identification.Nature. 2017; 552: 244-247Crossref PubMed Scopus (140) Google Scholar] are of great importance. It has long been known that microorganisms have context-dependent functions and a changing metabolism, depending on the microbial context and environmental conditions. These characteristics are clinically relevant with regard to microbiota-driven diseases. As a matter of fact, symbionts are of potential danger to their host, and hosts have evolved sophisticated defense systems to prevent microorganisms from gaining access to deeper tissues and systemic sites. For this reason, we must assume that all human symbionts may potentially exhibit pathogenic behavior, and this can vary in the context of a yet unknown genetic predisposition or microbial environment. Previous studies support this hypothesis: mice with defects in the innate and adaptive arms of the immune system exhibit stunted growth and increased mortality when exposed to a 'clean SPF microbiota' [26.Slack E. et al.Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism.Science. 2009; 325: 617-620Crossref PubMed Scopus (383) Google Scholar]. In a human cardiosurgical patient, the probiotic Lactobacillus rhamnosus was shown to cause sepsis [27.Kochan P. et al.Lactobacillus rhamnosus administration causes sepsis in a cardiosurgical patient – is the time right to revise probiotic safety guidelines?.Clin. Microbiol. Infect. 2011; 17: 1589-1592Abstract Full Text Full Text PDF PubMed Scopus (71) Google Scholar]. So, the big question will in fact be: can we draw a clear line between pathogenic and non-pathogenic symbionts? To take this into account, we propose to refrain from using the term 'pathobiont' in the future. Instead, we recommend adapting the concept of pathogenic potential to members of the gut microbiome. This concept was recently introduced, by Arturo Casadevall, to quantify the capacity for virulence of a focal pathogen [28.Casadevall A. The pathogenic potential of a microbe.mSphere. 2017; 2e00015-17Crossref PubMed Scopus (60) Google Scholar]. Virulence is a microbial property that takes effect only in susceptible hosts. The pathogenic potential (PP) is proportional to the fraction of individuals who become symptomatic after infection (Fs) with a defined inoculum (I): PP α Fs/I. It can include attributes such as mortality, communicability, and the time between infection and disease onset. Importantly, this concept is open to including situations in which the microbe in question changes its relationship with a host, from commensal to pathogenic, as a result of a change in the host or in the microbiome [28.Casadevall A. The pathogenic potential of a microbe.mSphere. 2017; 2e00015-17Crossref PubMed Scopus (60) Google Scholar]. Therefore, it could well be adapted to grade human symbionts with regard to their potential to cause harm to their host, depending on the environmental conditions. Deciphering causal relationships and precise mechanisms of microbial interaction are crucial for a better understanding of the gut microbiome and its function in human health. It will be important to elucidate whether the pathogenic potential of symbionts is correlated with general characteristics (e.g., nutrient preference, antimicrobial resistance) or common themes pertaining to their position in microbial interaction networks. This can be clarified only when we obtain a detailed mechanistic understanding of the functioning of every possible member of the microbiome in every possible host under every possible environmental circumstance. Until then, categorization of microorganisms – without knowledge of their entire capacity – will inevitably lead to confusion and incoherent terminology. We conclude that we need to come to an understanding of the gut ecosystem not by categorizing its components but by taking individuality, interactions, and – for now – the unknown into account. Bärbel Stecher acknowledges funding by the German Center of Infection Research (DZIF), the DFG Priority Program SPP1656, the Collaborative Research Center CRC1371 and the European Research Council.

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