The impact of interactions on invasion and colonization resistance in microbial communities

In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions of resident members with the invader. Here we study how interactions influence invasion outcomes in microbial communities, when interactions are primarily mediated by chemicals that are released into or consumed from the environment. We use a previously developed dynamic model which explicitly includes species abundances and the concentrations of chemicals that mediate species interaction. Using this model, we assessed how species interactions impact invasion by simulating a new species being introduced into an existing resident community. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or decreased and whether the invader was maintained in the community or went extinct. We found that as the number of invaders introduced into the resident community increased, disruption rather than augmentation became more prevalent. With more facilitation of the invader by the resident community, resistance outcomes were replaced by displacement and augmentation. By contrast, with more facilitation among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, the majority of augmentation outcomes turned into displacement, while when inhibition of residents by invaders was eliminated, invasion outcomes were largely unaffected. Our results suggest that a better understanding of interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities.     

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession

Successful microbial invasions are determined by a species’ ability to occupy a niche in the new habitat whilst resisting competitive exclusion by the resident community. Despite the recognised importance of biotic factors in determining the invasiveness of microbial communities, the success and impact of multiple concurrent invaders on the resident community has not been examined. Simultaneous invasions might have synergistic effects, for example if resident species need to exhibit divergent phenotypes to compete with the invasive populations. We used three phylogenetically diverse bacterial species to invade two compositionally distinct communities in a controlled, naturalised in vitro system. By initiating the invader introductions at different stages of succession, we could disentangle the relative importance of resident community structure, invader diversity and time pre‐invasion. Our results indicate that multiple invaders increase overall invasion success, but do not alter the successional trajectory of the whole community.     

Traits linked with species invasiveness and community invasibility vary with time,stage and indicator of invasion in a long‐term grassland experiment

Much uncertainty remains about traits linked with successful invasion – the establishment and spread of non‐resident species into existing communities. Using a 20‐year experiment, where 50 non‐resident (but mostly native) grassland plant species were sown into savannah plots, we ask how traits linked with invasion depend on invasion stage (establishment, spread), indicator of invasion success (occupancy, relative abundance), time, environmental conditions, propagule rain, and traits of invaders and invaded communities. Trait data for 164 taxa showed that invader occupancy was primarily associated with traits of invaders, traits of recipient communities, and invader‐community interactions. Invader abundance was more strongly associated with community traits (e.g. proportion legume) and trait differences between invaders and the most similar resident species. Annuals and invaders with high‐specific leaf area were only successful early in stand development, whereas invaders with conservative carbon capture strategies persisted long‐term. Our results indicate that invasion is context‐dependent and long‐term experiments are required to comprehensively understand invasions.     

Abiotic and biotic resistance to grass invasion in serpentine annual plant communities

Biological invasions severely impact native plant communities, causing dramatic shifts in species composition and the restriction of native species to spatially isolated refuges. Competition from resident species and the interaction between resource limitation and competition have been overlooked as mechanisms of community resistance in refugia habitats. We examined the importance of these factors in determining the resistance of California serpentine plant communities to invasion by three common European grasses, Avena barbata, Bromus diandrus, and Hordeum murinum. We added seeds of each of these grasses to plots subjected to six levels of resource addition (N, P, Ca, H₂O, all resources together, and a no-addition control) and two levels of competition (with resident community present or removed). Resource limitation and competition had strong effects on the biomass and reproduction of the three invaders. The addition of all resources together combined with the removal of the resident community yielded individual plants that were fourfold to 20-fold larger and sixfold to 20-fold more fecund than plants from control plots. Competitor removal alone yielded invaders that were twofold to sevenfold larger and twofold to ninefold more fecund. N addition alone or in combination with other resources led to a twofold to ninefold increase in the biomass and fecundity of the invaders. No other resource alone significantly affected native or invader performance, suggesting that N was the key limiting resource during our experiment. We found a significant interaction between abiotic and biotic resistance for Bromus, which experienced increased competitive suppression in fertilized plots. The threefold increase in resident biomass with N addition was likely responsible for this result. Our results confirm that serpentine plant communities are severely N limited, which, in combination with competition from resident species, promotes the resistance of these systems to invasions. Our work suggests that better understanding the relative sensitivities of invaders and residents to the physical environment is critical to predicting how abiotic and biotic factors interact to determine community resistance.     

Self-organization, layered structure, and aggregation enhance persistence of a synthetic biofilm consortium

Microbial consortia constitute a majority of the earth's biomass, but little is known about how these cooperating communities persist despite competition among community members. Theory suggests that non-random spatial structures contribute to the persistence of mixed communities; when particular structures form, they may provide associated community members with a growth advantage over unassociated members. If true, this has implications for the rise and persistence of multi-cellular organisms. However, this theory is difficult to study because we rarely observe initial instances of non-random physical structure in natural populations. Using two engineered strains of Escherichia coli that constitute a synthetic symbiotic microbial consortium, we fortuitously observed such spatial self-organization. This consortium forms a biofilm and, after several days, adopts a defined layered structure that is associated with two unexpected, measurable growth advantages. First, the consortium cannot successfully colonize a new, downstream environment until it self-organizes in the initial environment; in other words, the structure enhances the ability of the consortium to survive environmental disruptions. Second, when the layered structure forms in downstream environments the consortium accumulates significantly more biomass than it did in the initial environment; in other words, the structure enhances the global productivity of the consortium. We also observed that the layered structure only assembles in downstream environments that are colonized by aggregates from a previous, structured community. These results demonstrate roles for self-organization and aggregation in persistence of multi-cellular communities, and also illustrate a role for the techniques of synthetic biology in elucidating fundamental biological principles.     

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.Subject terms: Microbiome, Microbial ecology     

Environmental stress alters native-nonnative relationships at the community scale

The invasion of natural habitats by nonnative species is affected by both native biodiversity and environmental conditions; however few tests of facilitation between native community members and nonnative species have been conducted along disturbance and stress gradients. There is strong evidence for an increase in facilitation between native plant species with increasing levels of natural environmental stress, however it is unknown whether these same positive interactions occur between nonnative invaders and native communities. I investigated the effects of natural stress on community interactions between native heathland species and nonnative species with two field studies conducted at the landscape and community scale. At the landscape scale of investigation, nonnative species richness was positively related to native species richness. At the community level, nonnative invaders experienced facilitation with natives in the most stressful zones, whereas they experienced competition with native plants in the less stressful zones of the heathlands. Due to the observational nature of the landscape scale data, it is unclear whether nonnative diversity levels are responding positively to extrinsic factors or to native biodiversity. The experimental component of this research suggests that native community members may ameliorate stressful environmental conditions and facilitate invasion into high stress areas. I present a conceptual model which is a modification of the Shea and Chesson diversity-invasibility model and includes both facilitation as well as competition between the native community and nonnative invaders at the community level, summing to an overall positive relationship at the landscape scale.     

Can limiting similarity increase invasion resistance? A meta‐analysis of experimental studies

Synthesis We used meta‐analyses to examine experimental evidence that functional similarity between invaders and resident communities reduces invasion. We synthesized evidence from studies that experimentally added seed to resident communities in which the functional group composition had been manipulated. We found communities containing functionally similar resident species reduced invasion of forb but not grass invaders. However, experimental design dramatically influenced the results – with evidence for limiting similarity only found in artificially assembled communities, and not when studies used functional group removal from more ‘natural communities’. We suggest that functional group similarity plays a limited role in biotic resistance in established communities. The principle of limiting similarity suggests that species must be functionally different to coexist; based on the assumption that inter‐specific competition should be greatest between functionally similar species. There has been controversy over the generality of this assembly rule for plant communities with some studies finding evidence for limiting similarity and others not. One approach to testing this is to examine the ‘invasion’ success of species into communities in which the functional group composition has been manipulated. Using a meta‐analysis approach, we examined the generality of limiting similarity for plant communities based on published experimental studies. We asked – is establishment of an invading species less successful if it belongs to a functional group that is already present in the community compared to a community in which that functional group is absent? We explored separately colonisation (i.e. germination, establishment or seedling survival) and performance (i.e. biomass, cover or growth) of different functional groups (forbs and grasses) and experimental designs (removal experiments of more or less natural communities and synthetic‐assemblage experiments). We found that communities containing functionally similar resident species did reduce invader colonisation and performance of forb invaders, but did not reduce colonisation or performance of grass invaders. Evidence in support of limiting similarity was only detected in synthetic‐assemblage experiments and not when studies used functional group removal from ‘natural’ communities. Functional similarity is an important aspect of biotic resistance for forb invaders, but was only found in artificial communities. This has implications for restoration ecology especially when communities are built de novo. However, we suggest that limiting similarity plays a limited role in biotic resistance, because no evidence was detected in established communities.     

Allelopathy of a native grassland community as a potential mechanism of resistance against invasion by introduced plants

Successful plant invasions depend, at least partly, on interactions between introduced plants and native plant communities. While allelopathic effects of introduced invaders on native resident species have received much attention, the reverse, i.e. allelopathic effects of native residents on introduced plants, have been largely neglected. Therefore, we tested whether allelopathy of native plant communities decreases their invasibility to introduced plant species. In addition, we tested among the introduced species whether the invasive ones are more tolerant to allelopathy of native plant communities than the non-invasive ones. To test these hypotheses, we grew nine pairs of related (congeneric or confamilial) invasive and non-invasive introduced plant species (i.e. 18 species) in the presence or absence of a native grassland community, which consisted of three common forbs and three common grasses, with or without activated carbon in the soil. Activated carbon reduced the survival percentage and growth of introduced plants in the absence of the native plant community. However, its net effect on the introduced plants was neutral or even slightly positive in the presence of the native community. This might suggest that the native plant community imposed allelopathic effects on the introduced plants, and that these effects were neutralized or reduced by activated carbon. The invasive and non-invasive introduced plants, however, did not differ in their tolerance to such allelopathic effects of the native plant community. Thus, although allelopathy of native plant communities might increase their resistance against introduced plants, there was no evidence that tolerance to allelopathy of native plant communities contributes to the degree of invasiveness of introduced plants.     

In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM¹²) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM¹² interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM¹² interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.Subject terms: Microbiome, Microbial ecology     

A meta-analysis of biotic resistance to exotic plant invasions

Biotic resistance describes the ability of resident species in a community to reduce the success of exotic invasions. Although resistance is a well‐accepted phenomenon, less clear are the processes that contribute most to it, and whether those processes are strong enough to completely repel invaders. Current perceptions of strong, competition‐driven biotic resistance stem from classic ecological theory, Elton's formulation of ecological resistance, and the general acceptance of the enemies‐release hypothesis. We conducted a meta‐analysis of the plant invasions literature to quantify the contribution of resident competitors, diversity, herbivores and soil fungal communities to biotic resistance. Results indicated large negative effects of all factors except fungal communities on invader establishment and performance. Contrary to predictions derived from the natural enemies hypothesis, resident herbivores reduced invasion success as effectively as resident competitors. Although biotic resistance significantly reduced the establishment of individual invaders, we found little evidence that species interactions completely repelled invasions. We conclude that ecological interactions rarely enable communities to resist invasion, but instead constrain the abundance of invasive species once they have successfully established.     

Community history affects the predictability of microbial ecosystem development

Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community''s previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.     

Facilitation promotes invasions in plant‐associated microbial communities

While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant–pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.     

Effects of small-scale disturbance on invasion success in marine communities

Introductions of non-indigenous species have resulted in many ecological problems including the reduction of biodiversity, decline of commercially important species and alteration of ecosystems. The link between disturbance and invasion potential has rarely been studied in the marine environment where dominance hierarchies, dynamics of larval supply, and resource acquisition may differ greatly from terrestrial systems. In this study, hard substrate marine communities in Long Island Sound, USA were used to assess the effect of disturbance on resident species and recent invaders, ascidian growth form (i.e. colonial and solitary growth form), and the dominant species-specific responses within the community. Community age was an additional factor considered through manipulation of 5-wk old assemblages and 1-yr old assemblages. Disturbance treatments, exposing primary substrate, were characterized by frequency (single, biweekly, monthly) and magnitude (20%, 48%, 80%) of disturbance. In communities of different ages, disturbance frequency had a significant positive effect on space occupation of recent invaders and a significant negative effect on resident species. In the 5-wk community, magnitude of disturbance also had a significant effect. Disturbance also had a significant effect on ascidian growth form; colonial species occupied more primary space than controls in response to increased disturbance frequency and magnitude. In contrast, solitary species occupied significantly less space than controls. Species-specific responses were similar regardless of community age. The non-native colonial ascidian Diplosoma listerianum responded positively to increased disturbance frequency and magnitude, and occupied more primary space in treatments than in controls. The resident solitary ascidian Molgula manhattensis responded negatively to increased disturbance frequency and magnitude, and occupied less primary space in treatments than in controls. Small-scale biological disturbances, by creating space, may facilitate the success of invasive species and colonial organisms in the development of subtidal hard substrate communities.     

Mechanisms determining the fate of dispersed bacterial communities in new environments

Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed ‘functional overachievement''. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.     

Alteration of microbial community composition and changes in decomposition associated with an invasive intertidal macrophyte

Data demonstrating the effects of biological invaders on microbial communities and microbial processes are scarce, especially in marine environments. Research was conducted at Padilla Bay, Washington, to examine the effect that an invasive intertidal eelgrass, Zostera japonica Aschers & Graebn, has on rates of decomposition, microbial community composition, and the possible implications for associated ecosystem processes in this estuarine environment. A series of observational and experimental studies were conducted in beds of Z. japonica, beds of its native congener, Zostera marina, and mixed eelgrass beds. These studies assessed decomposition of invasive and native eelgrass, enumerated bacterial abundance, and examined sole source carbon usage (SSCU) by microbial assemblages. Z. japonica decomposed more rapidly than its native congener throughout the study period although rates of decomposition were variable. Microbial abundance did not differ among different vegetation compositions although differences in SSCU by microbial assemblages were detected among beds of invasive, native, and mixed eelgrass. These results indicate that this abundant invasive species can accelerate rates of decomposition and alter the associative decomposer community, which may lead to higher carbon and nutrient turnover within Padilla Bay.     

Effect of sheep urine deposition on the bacterial community structure in an acidic upland grassland soil

The effect of the addition of synthetic sheep urine (SSU) and plant species on the bacterial community composition of upland acidic grasslands was studied using a microcosm approach. Low, medium, and high concentrations of SSU were applied to pots containing plant species typical of both unimproved (Agrostis capillaris) and agriculturally improved (Lolium perenne) grasslands, and harvests were carried out 10 days and 50 days after the addition of SSU. SSU application significantly increased both soil pH (P < 0.005), with pH values ranging from pH 5.4 (zero SSU) to pH 6.4 (high SSU), and microbial activity (P < 0.005), with treatment with medium and high levels of SSU displaying significantly higher microbial activity (triphenylformazan dehydrogenase activity) than treatment of soil with zero or low concentrations of SSU. Microbial biomass, however, was not significantly altered by any of the SSU applications. Plant species alone had no effect on microbial biomass or activity. Bacterial community structure was profiled using bacterial automated ribosomal intergenic spacer analysis. Multidimensional scaling plots indicated that applications of high concentrations of SSU significantly altered the bacterial community composition in the presence of plant species but at different times: 10 days after application of high concentrations of SSU, the bacterial community composition of L. perenne-planted soils differed significantly from those of any other soils, whereas in the case of A. capillaris-planted soils, the bacterial community composition was different 50 days after treatment with high concentrations of SSU. Canonical correspondence analysis also highlighted the importance of interactions between SSU addition, plant species, and time in the bacterial community structure. This study has shown that the response of plants and bacterial communities to sheep urine deposition in grasslands is dependent on both the grass species present and the concentration of SSU applied, which may have important ecological consequences for agricultural grasslands.     

Variation in the impact of non‐native seaweeds along gradients of habitat degradation: a meta‐analysis and an experimental test

Biological invasions are acknowledged among the main drivers of global changes in biodiversity. Despite compelling evidence of species interactions being strongly regulated by environmental conditions, there is a dearth of studies investigating how the effects of non‐native species vary among areas exposed to different anthropogenic pressures. Focusing on marine macroalgae, we performed a meta‐analysis to test whether and how the direction and magnitude of their effects on resident communities and species varies in relation to cumulative anthropogenic impact levels. The relationship between human impact levels and non‐native species impact intensity emerged only for a reduced subset of the response variables examined. Yet, there was a trend for the effects of non‐native species on community biomass and abundance and on species abundance to become less negative at heavily impacted sites. By contrast, the magnitude of negative effects of seaweed on community evenness tended to increase with human impact levels. The hypothesis of decreasing severity of invader’ impacts along a gradient of habitat degradation was also tested experimentally at a regional scale by comparing the effects of the removal of non‐native alga, Caulerpa cylindracea, on resident assemblages among rocky reefs exposed to different anthropogenic pressures. Assemblages at urban and pristine site did not differ when invaded, but did so when C. cylindracea was removed. Our results suggest that, despite the generally weak relationship between human impacts levels and non‐native species impacts, more negative impacts can be expected in less stressful environments (i.e. less degraded or pristine sites), where competitive interactions are presumably the driving force structuring resident communities. Implementing strategies for controlling the establishment of non‐native seaweeds should be, thus, considered a priority for preserving biodiversity in relatively pristine areas. On the other hand, control of invaders at degraded sites could be warranted to lessen their role as propagule sources. Synthesis Local anthropogenic stressors that severely alter biotic and abiotic conditions may underpin context‐dependency in the impacts of biological invasions. We used a meta‐analysis and an experimental test to examine the relationship between cumulative human impacts and ecological impact of non‐native seaweeds on resident assemblages. Our results suggest that more negative impacts of non‐native seaweeds on the abundance and biomass of resident assemblages can be expected in less degraded or pristine sites. Possibly, stronger impacts prevail at pristine sites, where assemblages are mainly structured by biotic interactions. Hence, management efforts should be mostly directed to prevent the establishment and spread of non‐native seaweeds in pristine areas. On the other hand, weak, but positive effects of seaweeds at the most degraded sites add to the ongoing debate on the role of non‐native species in rehabilitation plans.     

Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members

Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant community members in biogas reactors fed with manure.     

Incoming pathogens team up with harmless 'resident' bacteria

Microbial diseases occur as a result of multifarious host-pathogen interactions. However, invading pathogens encounter a large number of different harmless and beneficial bacterial species, which colonize and reside in the host. Surprisingly, there has been little study of the possible interactions between incoming pathogens and the resident bacterial community. Recent studies have revealed that resident bacteria assist different types of incoming pathogens via a wide variety of mechanisms including cell-cell signaling, metabolic interactions, evasion of the immune response and a resident-to-pathogen switch. This calls for serious consideration of pathogen-microbe interactions in the host with respect to disease severity and progression.