Understanding the Relationship Between Hosts and their Microbiome

Microbes are bountiful and associated with every animal and plant kingdom. Furthermore, microbes can alter host phenotype, development, health and functioning. However, this is not a one-way interaction, hosts can structure microbial communities by changing the environment to be suitable for certain microbial species. Several studies have characterized microbial communities associated with hosts to answer two2 main questions in ecology: who’s there, and what are they doing? However, two questions from the field of community ecology are often ignored (1) what forces are structuring the microbial communities (how was the community formed) and (2) how stable are these communities. Vellend synthesized that all communities are governed by four main processes: drift, selection, speciation and dispersal. These processes can be grouped into 2 components of assembly, either deterministic (selection, speciation, dispersal) or stochastic (drift, dispersal limitation). The goal of my thesis was to (1) understand the relative contribution strengths of these processes on microbial communities and (2) how stable is the assemblage of microbial community over time and during an infection. In order to determine if microbial communities are structured deterministically or stochastically, I studied the root endophytic microbiome, which has been shown to directly impact plant physiology. By analyzing 252 root endophytic bacterial (REB) communities, which had been perturbed using antibiotics and sterilization, I show the communities are assembled deterministically. The strongest selective force structuring the REB communities was plant identity even in a perturbed state. I demonstrate show the interplay between REB communities and plant phenotype by linking the variation in the reduction of biomass in autoclaved soils to changes in the abundance of bacterial species. This suggests hosts can selectively increase or decrease the abundance of bacterial species that will increase the plant’s fitness. Consequently, this allows plants to co-exist by specializing on different bacterial species. To determine the stability of microbial community structure, I studied the urine microbiome of individuals who are do not have urinary symptoms and those who are suspected to have a healthy and who have a suspected Urinary Tract Infection (UTI). By analyzing the urine microbiome of 220 urine samples, microbiome, I show that the urine microbiome is in an altered state during an infection and is stable over time in asymptomatic women for healthy patients. Healthy individuals are enriched with Lactobacillus crispatus and L. iners while individuals with suspected UTIs are enriched with Ruminococcus torques, Propionibacterium acnes and Escherichia coli. There is a plethora of putative pathogens uncovered only with non-conventional culturing methods. Roughly 21% of individuals with suspected UTIs did not have the putative cultured pathogen at high relative abundance but a different known UTI pathogen . This suggests that UTIs could be caused by a dysbiosis of the urine microbiome rather than direct inoculation of an organism from the gastrointestinal tract. an invasion from a different body site. Collectively these studies show that microbial communities can be structured by the host and host state, and are deterministically assembled. Further work to investigate how the host can structure the microbial community possibly through changing environmental conditions or through immune response is warranted

Is there specificity in a defensive mutualism against soil versus lab nematodes, Dictyostelium discoideum farmers and their bacteria?

Background: The social amoeba Dictyostelium discoideum is a soil-dwelling microbe, which lives most of its life cycle in the vegetative stage as a predator of bacteria and as prey for nematodes. When bacteria are sparse, amoebae aggregate into a multicellular fruiting body. Some clones of D. discoideum have agriculture (Brock et al., 2011). They carry bacteria through the social stage, eat them prudently, and use some bacteria as defence against non-farming D. discoideum competitors. Caenorhabditis elegans preys on D. discoideum in the laboratory but does not encounter it in nature because C. elegans lives on rotten fruit. The nematode Oscheius tipulae is abundant in the soil. Questions: Do the defensive bacteria that farmers carry also protect farmers from nematodes? Is this protection specific to nematodes that reside with D. discoideum? Hypotheses: Many organisms evolve defensive mutualisms against predators. The natural habitat of D. discoideum is populated with nematodes. Therefore, we hypothesize that farming D. discoideum clones use non-food bacteria for protection from nematodes. We predicted higher fitness of farmers than non-farmers in the presence of nematodes. We also predicted to see this change of fitness only in the presence of the soil nematode, O. tipulae. Organisms: Amoeba Dictyostelium discoideum, nematodes Caenorhabditis elegans and Oscheius tipulae, bacteria Klebsiella pneumoniae and Burkholderia xenovorans. Methods: We compared spore production of D. discoideum farmers and non-farmers with and without nematodes. We also looked at nematode proliferation in the presence of farmers, non-farmers, K. pneumonia, and B. xenovorans. Results: Overall, farmer D. discoideum produced fewer spores than non-farmers. There was a decrease in the spore counts in the presence of nematodes for both farmers and non-farmers. There was a significant decrease in the percentage change in spore production for the farmers in the presence of soil nematodes but not laboratory nematodes. Nematode proliferation with the laboratory nematode and soil nematode did not vary in the presence of farmers, non-farmers, K. pneumoniae or B. xenovorans. Conclusion: The non-food bacteria that farmers carry do not provide defence against nematodes. In fact, it was a disadvantage for farmers to carry bacteria, since the soil nematode decreased spore production for farmers compared with non-farmers. However, the differences between the laboratory nematode and the soil nematode are marked enough to conclude that different species of nematodes respond differently to D. discoideum as a food source

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states

BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota. RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as \u27insignificant\u27, \u27contaminated\u27, or \u27no-growth\u27 by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae. CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract

The gut microbiome defines social group membership in honey bee colonies

In the honey bee, genetically related colony members innately develop colony-specific cuticular hydrocarbon profiles, which serve as pheromonal nestmate recognition cues. Yet, despite high intracolony relatedness, the innate development of colony-specific chemical signatures by individual colony members is largely determined by the colony environment, rather than solely relying on genetic variants shared by nestmates. Therefore, it is puzzling how a nongenic factor could drive the innate development of a quantitative trait that is shared by members of the same colony. Here, we provide one solution to this conundrum by showing that nestmate recognition cues in honey bees are defined, at least in part, by shared characteristics of the gut microbiome across individual colony members. These results illustrate the importance of host-microbiome interactions as a source of variation in animal behavioral traits

Bogota River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes

The increase in antibiotic resistant bacteria has raised global concern regarding the future effectiveness of antibiotics. Human activities that influence microbial communities and environmental resistomes can generate additional risks to human health. In this work, we characterized aquatic microbial communities and their resistomes in samples collected at three sites along the Bogotá River and from wastewaters at three city hospitals, and investigated community profiles and antibiotic resistance genes (ARGs) as a function of anthropogenic contamination. The presence of antibiotics and other commonly used drugs increased in locations highly impacted by human activities, while the diverse microbial communities varied among sites and sampling times, separating upstream river samples from more contaminated hospital and river samples. Clinically relevant antibiotic resistant pathogens and ARGs were more abundant in contaminated water samples. Tracking of resistant determinants to upstream river waters and city sources suggested that human activities foster the spread of ARGs, some of which were co-localized with mobile genetic elements in assembled metagenomic contigs. Human contamination of this water ecosystem changed both community structure and environmental resistomes that can pose a risk to human health

Migration in the social stage of Dictyostelium discoideum amoebae impacts competition

Interaction conditions can change the balance of cooperation and conflict in multicellular groups. After aggregating together, cells of the social amoeba Dictyostelium discoideum may migrate as a group (known as a slug) to a new location. We consider this migration stage as an arena for social competition and conflict because the cells in the slug may not be from a genetically homogeneous population. In this study, we examined the interplay of two seemingly diametric actions, the solitary action of kin recognition and the collective action of slug migration in D. discoideum, to more fully understand the effects of social competition on fitness over the entire lifecycle. We compare slugs composed of either genetically homogenous or heterogeneous cells that have migrated or remained stationary in the social stage of the social amoeba Dictyostelium discoideum. After migration of chimeric slugs, we found that facultative cheating is reduced, where facultative cheating is defined as greater contribution to spore relative to stalk than found for that clone in the clonal state. In addition our results support previous findings that competitive interactions in chimeras diminish slug migration distance. Furthermore, fruiting bodies have shorter stalks after migration, even accounting for cell numbers at that time. Taken together, these results show that migration can alleviate the conflict of interests in heterogeneous slugs. It aligns their interest in finding a more advantageous place for dispersal, where shorter stalks suffice, which leads to a decrease in cheating behavior

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities.

Plant-soil feedback studies attempt to understand the interplay between composition of plant and soil microbial communities. A growing body of literature suggests that plant species can coexist when they interact with a subset of the soil microbial community that impacts plant performance. Most studies focus on the microbial community in the soil rhizosphere; therefore, the degree to which the bacterial community within plant roots (root-endophytic compartment) influences plant-microbe interactions remains relatively unknown. To determine if there is an interaction between conspecific vs heterospecific soil microbes and plant performance, we sequenced root-endophytic bacterial communities of five tallgrass-prairie plant species, each reciprocally grown with soil microbes from each hosts' soil rhizosphere. We found evidence of plant-soil feedbacks for some pairs of plant hosts; however, the strength and direction of feedbacks varied substantially across plant species pairs-from positive to negative feedbacks. Additionally, each plant species harbored a unique subset of root-endophytic bacteria. Conspecifics that hosted similar bacterial communities were more similar in biomass than individuals that hosted different bacterial communities, suggesting an important functional link between root-endophytic bacterial community composition and plant fitness. Our findings suggest a connection between an understudied component of the root-endophytic microbiome and plant performance, which may have important implications in understanding plant community composition and coexistence

ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs.

BackgroundSince the prolonged use of insecticidal proteins has led to toxin resistance, it is important to search for novel insecticidal protein genes (IPGs) that are effective in controlling resistant insect populations. IPGs are usually encoded in the genomes of entomopathogenic bacteria, especially in large plasmids in strains of the ubiquitous soil bacteria, Bacillus thuringiensis (Bt). Since there are often multiple similar IPGs encoded by such plasmids, their assemblies are typically fragmented and many IPGs are scattered through multiple contigs. As a result, existing gene prediction tools (that analyze individual contigs) typically predict partial rather than complete IPGs, making it difficult to conduct downstream IPG engineering efforts in agricultural genomics.MethodsAlthough it is difficult to assemble IPGs in a single contig, the structure of the genome assembly graph often provides clues on how to combine multiple contigs into segments encoding a single IPG.ResultsWe describe ORFograph, a pipeline for predicting IPGs in assembly graphs, benchmark it on (meta)genomic datasets, and discover nearly a hundred novel IPGs. This work shows that graph-aware gene prediction tools enable the discovery of greater diversity of IPGs from (meta)genomes.ConclusionsWe demonstrated that analysis of the assembly graphs reveals novel candidate IPGs. ORFograph identified both already known genes "hidden" in assembly graphs and potential novel IPGs that evaded existing tools for IPG identification. As ORFograph is fast, one could imagine a pipeline that processes many (meta)genomic assembly graphs to identify even more novel IPGs for phenotypic testing than would previously be inaccessible by traditional gene-finding methods. While here we demonstrated the results of ORFograph only for IPGs, the proposed approach can be generalized to any class of genes. Video abstract

Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone

Mesophotic reef-building coral communities (~30-120 m depth) remain largely unexplored, despite representing roughly three-quarters of the overall depth range at which tropical coral reef ecosystems occur. Although many coral species are restricted to shallow depths, several species occur across large depth ranges, including lower mesophotic depths. Yet, it remains unclear how such species can persist under extreme low-light conditions and how the different symbiotic partners associated with these corals contribute to facilitate such broad depth ranges. We assessed holobiont genetic diversity of the Caribbean coral Agaricia undata over depth in three localities of Colombia: San Andres Island (between 37 and 85 m), Cartagena (between 17 and 45 m) and "Parque Nacional Natural Corales de Profundidad" (between 77 and 87 m). We used a population genomics approach (NextRAD) for the coral host, and amplicon sequencing for the associated Symbiodinium (non-coding region of the plastid psbA minicircle) and prokaryotic (V4 region of the 16S rRNA gene) symbiont community. For the coral host, genetic structuring was only observed across geographic regions, but not between depths. Bayesian clustering and discriminant analysis of principal components revealed genetic structuring between the three regions, but not between shallow ( 60 m) depths. This pattern was confirmed when evaluating pairwise differentiation (FST) between populations, with much higher values between regions (0.0467-0.1034) compared to between depths [within location; -0.0075-(-0.0007)]. Symbiotic partners, including seven types of zooxanthellae and 325 prokaryotic OTUs, did not exhibit partitioning across depths. All samples hosted Symbiodinium clade C3 and the type C3psbA_e was present in all depths. Alpha microbial diversity was not significantly different between zones (upper vs. lower), which community composition between coral colonies was similar in the two zones (ANOSIM, R = -0.079, P > 0.05). The coral microbiome was dominated by Uncultured Betaproteobacteria in the order EC94 (16%), Unknown-Bacteria (15%), family Cenarchaeaceae (12 %), Burkholderiaceae (10%), and Hahellaceae (10%). The constant coral-holobiont composition along the studied depth range suggests that identity of the symbionts is not responsible for the coral's broad depth range and adaptation to low light environments

Migration in the social stage of Dictyostelium discoideum amoebae impacts competition.

Interaction conditions can change the balance of cooperation and conflict in multicellular groups. After aggregating together, cells of the social amoeba Dictyostelium discoideum may migrate as a group (known as a slug) to a new location. We consider this migration stage as an arena for social competition and conflict because the cells in the slug may not be from a genetically homogeneous population. In this study, we examined the interplay of two seemingly diametric actions, the solitary action of kin recognition and the collective action of slug migration in D. discoideum, to more fully understand the effects of social competition on fitness over the entire lifecycle. We compare slugs composed of either genetically homogenous or heterogeneous cells that have migrated or remained stationary in the social stage of the social amoeba Dictyostelium discoideum. After migration of chimeric slugs, we found that facultative cheating is reduced, where facultative cheating is defined as greater contribution to spore relative to stalk than found for that clone in the clonal state. In addition our results support previous findings that competitive interactions in chimeras diminish slug migration distance. Furthermore, fruiting bodies have shorter stalks after migration, even accounting for cell numbers at that time. Taken together, these results show that migration can alleviate the conflict of interests in heterogeneous slugs. It aligns their interest in finding a more advantageous place for dispersal, where shorter stalks suffice, which leads to a decrease in cheating behavior