Host Evolution Research Articles

Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome.

Nucleotide sequence similarity, including k-mer plasmid composition, has been used for prediction of plasmid evolutionary host range, representing the hosts in which a plasmid has replicated at some point during its evolutionary history. However, the relationships between the bacterial taxa of experimentally identified transconjugants and the predicted evolutionary host ranges are poorly understood. Here, four different PromA group plasmids showing different k-mer compositions were used as model plasmids. Filter mating assays were performed with a donor harbouring plasmids and recipients of bacterial communities extracted from environmental samples. A broad range of transconjugants was obtained with different bacterial taxa. A calculation of the dissimilarities in k-mer compositions as Mahalanobis distance between the plasmid and its sequenced transconjugant chromosomes revealed that each plasmid and transconjugant were significantly more similar than the plasmid and other non-transconjugant chromosomes. These results indicate that plasmids with different k-mer compositions clearly have different host ranges to which the plasmid will be transferred and replicated. The similarity of the nucleotide compositions could be used for predicting not only the plasmid evolutionary host range but also future host ranges.

Ectotherm heat tolerance and the microbiome: current understanding, future directions and potential applications.

Climate change and increasing global temperatures are a leading threat to ectothermic animals worldwide. Ectotherm persistence under climate change will depend on a combination of host and environmental factors; recently it has become clear that host-associated microbial communities contribute significantly to the response of ectotherms to environmental warming. However, several unanswered questions about these relationships remain before accurate predictions can be made regarding the microbiome's influence on host ecology and evolution under climate warming. In this Commentary, we provide a brief background of what is currently known about the influence of the microbiome on heat tolerance in both invertebrate and vertebrate ectothermic animals, and the mechanisms behind these effects. We then outline what we feel are important priorities for future work in the field, and how these goals could be accomplished. We specifically highlight a need for more diversity in study systems, especially through increasing representation of vertebrate hosts and hosts across a variety of life-history traits and habitats, as well as a greater understanding of how these relationships manifest in field settings. Lastly, we discuss the implications of microbiome-mediated heat tolerance for animal conservation under climate change and the possibility of 'bioaugmentation' approaches to bolster host heat tolerance in vulnerable populations.

Study on the exciton dynamic processes of exciplex host–guest system by transient magnetic field effects

Utilizing exciplex as the host and fluorescence emitter with dopant materials has been proved successfully to fabricate highly-efficient organic light-emitting diodes. Exciton evolution and energy transfer in this exciplex host–guest system are complex. Gaining insight into the electroluminescence (EL) mechanisms in exciplex-based devices is key for further optimizing device configuration. Here, we have investigated exciton dynamics in devices with exciplex as host and 4-(dicyanomethylene)-2-tert-butyl-6-(1,1,7,7-tetramethyljulolidin-4-yl-vinyl)-4H-pyran (DCJTB) as red fluorescence emitter. Two exciplexes, 2,6-bis(3-(9H-carbazol-9-yl)phenyl)pyridine (26DCzPPY) doped 2,4,6-tris[3-(triphenylphosphine)phenyl]-1,3,5-triazine (POT2T), and 4,4′,4″-tris[3-methylphenyl(phenyl)amino]-triphenylamine (m-MTDATA) doped tris(8-hydroxyquinoline)aluminum(III) (Alq3), with different band energy are utilized as host materials. Combining the measurements of transient EL, transient photoluminescence and magnetic field effect (MFE), it is concluded that Dexter energy transfer, together with Förster resonance energy transfer, are confirmed in the pure fluorescence doped system. Meanwhile, it is found that DCJTB works with the hot excitons mechanism but not a traditional red fluorescence emitter as recognized previously. This work presents that the transient MFE is powerful for detecting excitonic dynamic processes in excipelx based host–guest EL systems.

In host evolution of Exophiala dermatitidis in cystic fibrosis lung micro-environment.

Individuals with cystic fibrosis (CF) are susceptible to chronic lung infections that lead to inflammation and irreversible lung damage. While most respiratory infections that occur in CF are caused by bacteria, some are dominated by fungi such as the slow-growing black yeast Exophiala dermatitidis. Here, we analyze isolates of E. dermatitidis cultured from two samples, collected from a single subject 2 years apart. One isolate genome was sequenced using long-read Nanopore technology as an in-population reference to use in comparative single nucleotide polymorphism and insertion-deletion variant analyses of 23 isolates. We then used population genomics and phylo-genomics to compare the isolates to each other as well as the reference genome strain E. dermatitidis NIH/UT8656. Within the CF lung population, three E. dermatitidis clades were detected, each with varying mutation rates. Overall, the isolates were highly similar suggesting that they were recently diverged. All isolates were MAT 1-1, which was consistent with their high relatedness and the absence of evidence for mating or recombination between isolates. Phylogenetic analysis grouped sets of isolates into clades that contained isolates from both early and late time points indicating there are multiple persistent lineages. Functional assessment of variants unique to each clade identified alleles in genes that encode transporters, cytochrome P450 oxidoreductases, iron acquisition, and DNA repair processes. Consistent with the genomic heterogeneity, isolates showed some stable phenotype heterogeneity in melanin production, subtle differences in antifungal minimum inhibitory concentrations, and growth on different substrates. The persistent population heterogeneity identified in lung-derived isolates is an important factor to consider in the study of chronic fungal infections, and the analysis of changes in fungal pathogens over time may provide important insights into the physiology of black yeasts and other slow-growing fungi in vivo.

Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.

Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium.

The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of microbial virus researchers in Belgium. The sixteen founders are affiliated to fourteen different research entities across academia, industry and government. Its inaugural symposium was held on 23 September 2022 in the Thermotechnical Institute at KU Leuven. The meeting program covered three thematic sessions launched by international keynote speakers: (1) virus-host interactions, (2) viral ecology, evolution and diversity and (3) present and future applications. During the one-day symposium, four invited keynote lectures, ten selected talks and eight student pitches were given along with 41 presented posters. The meeting hosted 155 participants from twelve countries.

Global Spread Dynamics and Intrinsic Evolutionary Dynamics of Apple Chlorotic Leaf Spot Virus Whole-Genome Sequences over the Last 30 Years

Apple chlorotic leaf spot virus (ACLSV; genus Trichovirus) is an economically important virus. Approximately 101 ACLSV whole-genome sequences were obtained from NCBI and used to explore the evolutionary dynamics of ACLSV. The time to the most recent common ancestor of ACLSV based on BEAST analysis appeared on an apple host from Canada in 1918 and then spread around the world in three ways concurrent with host spread. The maximum clade credibility tree of ACLSV shows that the mean evolution rate was 4.92 × 10-4 substitutions per site per year (subs/site/year), and we found that, during host evolution, the rate of evolution was mostly 2.31 × 10-4 to 2.72 × 10-4 subs/site/year. The rate of geographic evolution was 5.51 × 10-4 to 6.17 × 10-4 subs/site/year. To further explore the intrinsic changes in ACLSV during the process of geographic and host spread, we explored the secondary structural changes of the ACLSV coat protein (CP), which were mainly concentrated in four regions-20 to 40, 70 to 90, 120 to 140, and 180 to 193-which are related to the presence or absence and change in length of the β-turn, β strand, coil, and α helix, respectively. We then explored the codon usage preference within the CP across the migration pathways of ACLSV. These comprehensive analyses not only reveal the changes in ACLSV in the last 30 years but also further elucidate the intrinsic evolutionary dynamics of ACLSV. This is also the first report on the intrinsic evolutionary dynamics of ACLSV.

Emergence of a novel reassortant H3N6 canine influenza virus.

Although the natural hosts of avian influenza viruses (AIVs) are wild birds, multiple subtypes of AIVs have established epidemics in numerous mammals due to their cross-species spillover. Replication and evolution in intermedia mammalian hosts may facilitate AIV adaptation in humans. Because of their large population and intimacy with humans, dogs could act as such an intermedia host. To monitor the epidemiology of canine influenza viruses (CIVs) in Liaoning, China, we performed three surveillances in November 2018, March 2019, and April 2019. Five H3N2 and seven novel H3N6 CIVs had been isolated. Since the N6 neuraminidase (NA) genes were clustered with the H5N6 AIV, there is a high possibility that these H3N6 CIVs were generated from a H3N2 CIVs and H5N6 AIVs reassortment case. In addition, the H3N6 CIV showed increased mammalian adaptation ability compared to all the H3N2 strains in both in vitro and in vivo studies. Even though isolated 3 months later, the March 2019 isolated H3N2 viruses replicated more efficiently than the November 2018 isolated viruses. Our study indicated that H3 CIVs were undergoing an evolution process, through both genetic mutations and gene reassortment, at an incredible speed.

Host insect specificity and interspecific competition drive parasitoid diversification in a plant-insect community.

Ecological interactions among plants, insect herbivores, and parasitoids are pervasive in nature and play important roles in community assembling, but the codiversification of tri-trophic interactions has received less attention. Here we compare pairwise codiversification patterns between a set of 22 fig species, their herbivorous pollinating and galling wasps, and their parasitoids. The parasitoid phylogeny showed significant congruence and more cospeciation events with host insects phylogeny than with host plants. These results suggest that parasitoid phylogeny and speciation is more closely related to their host insects than to their host plants. The pollinating wasps hosted more parasitoid species than gallers and indicated a more intense interspecific competition among parasitoids associated with pollinators. Closer matching and fewer evolutionary host shifts were found between parasitoids and galler hosts than between parasitoids and pollinator hosts. These results suggest that interspecific competition among parasitoids, rather than resource availability of host wasps, is the main driver of the codiversification pattern in this community. Therefore, our study highlights the important role of interspecific competition among high trophic level insects in plant-insect tri-trophic community assembling.

Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.

Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed. Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method. Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.

The Timing and Magnitude of the Type I Interferon Response Are Correlated with Disease Tolerance in Arbovirus Infection.

Infected hosts possess two alternative strategies to protect themselves against the negative impact of virus infections: resistance, used to abrogate virus replication, and disease tolerance, used to avoid tissue damage without controlling viral burden. The principles governing pathogen resistance are well understood, while less is known about those involved in disease tolerance. Here, we studied bluetongue virus (BTV), the cause of bluetongue disease of ruminants, as a model system to investigate the mechanisms of virus-host interactions correlating with disease tolerance. BTV induces clinical disease mainly in sheep, while cattle are considered reservoirs of infection, rarely exhibiting clinical symptoms despite sustained viremia. Using primary cells from multiple donors, we show that BTV consistently reaches higher titers in ovine cells than cells from cattle. The variable replication kinetics of BTV in sheep and cow cells were mostly abolished by abrogating the cell type I interferon (IFN) response. We identified restriction factors blocking BTV replication, but both the sheep and cow orthologues of these antiviral genes possess anti-BTV properties. Importantly, we demonstrate that BTV induces a faster host cell protein synthesis shutoff in primary sheep cells than cow cells, which results in an earlier downregulation of antiviral proteins. Moreover, by using RNA sequencing (RNA-seq), we also show a more pronounced expression of interferon-stimulated genes (ISGs) in BTV-infected cow cells than sheep cells. Our data provide a new perspective on how the type I IFN response in reservoir species can have overall positive effects on both virus and host evolution. IMPORTANCE The host immune response usually aims to inhibit virus replication in order to avoid cell damage and disease. In some cases, however, the infected host avoids the deleterious effects of infection despite high levels of viral replication. This strategy is known as disease tolerance, and it is used by animal reservoirs of some zoonotic viruses. Here, using a virus of ruminants (bluetongue virus [BTV]) as an experimental system, we dissected virus-host interactions in cells collected from species that are susceptible (sheep) or tolerant (cow) to disease. We show that (i) virus modulation of the host antiviral type I interferon (IFN) responses, (ii) viral replication kinetics, and (iii) virus-induced cell damage differ in tolerant and susceptible BTV-infected cells. Understanding the complex virus-host interactions in disease tolerance can allow us to disentangle the critical balance between protective and damaging host immune responses.

Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees.

Pathogens and parasites of solitary bees have been studied for decades, but the microbiome as a whole is poorly understood for most taxa. Comparative analyses of microbiome features such as composition, abundance, and specificity, can shed light on bee ecology and the evolution of host-microbe interactions. Here we study microbiomes of ground-nesting cellophane bees (Colletidae: Diphaglossinae). From a microbial point of view, the diphaglossine genus Ptiloglossa is particularly remarkable: their larval provisions are liquid and smell consistently of fermentation. We sampled larval provisions and various life stages from wild nests of Ptiloglossa arizonensis and two species of closely related genera: Caupolicana yarrowi and Crawfordapis luctuosa. We also sampled nectar collected by P. arizonensis. Using 16S rRNA gene sequencing, we find that larval provisions of all three bee species are near-monocultures of lactobacilli. Nectar communities are more diverse, suggesting ecological filtering. Shotgun metagenomic and phylogenetic data indicate that Ptiloglossa culture multiple species and strains of Apilactobacillus, which circulate among bees and flowers. Larval lactobacilli disappear before pupation, and hence are likely not vertically transmitted, but rather reacquired from flowers as adults. Thus, brood cell microbiomes are qualitatively similar between diphaglossine bees and other solitary bees: lactobacilli-dominated, environmentally acquired, and non-species-specific. However, shotgun metagenomes provide evidence of a shift in bacterial abundance. As compared with several other bee species, Ptiloglossa have much higher ratios of bacterial to plant biomass in larval provisions, matching the unusually fermentative smell of their brood cells. Overall, Ptiloglossa illustrate a path by which hosts can evolve quantitatively novel symbioses: not by acquiring or domesticating novel symbionts, but by altering the microenvironment to favor growth of already widespread and generalist microbes.

Tracking life cycles of parasites across a broad taxonomic scale in a marine ecosystem

Parasitic helminths exhibit remarkable diversity in their life cycles, although few parasite species have their whole life cycles resolved. Owing to the fact that parasite life stages within hosts are often not comparable using morphological data, genetic data provides convincing evidence of transmission pathways between intermediate and definitive hosts. We took this approach to an ecosystem level, genetically matching parasite (acanthocephalan, cestode, nematode and trematode) life stages across a broad taxonomic range of intermediate and definitive hosts (invertebrates, seabirds, elasmobranchs and teleost fish) in Otago’s (New Zealand) coastal marine ecosystem. We identified which transmission routes are utilized by the most parasite species and assessed which intermediate hosts are most important in facilitating the transmission of parasites in this ecosystem. Our findings reveal 59 new records of larval parasites infecting their respective intermediate hosts and 289 transmission pathways utilized by 35 helminth species to complete their life cycles. Sprat, triplefin and arrow squid all hosted the highest number of larval parasite species, suggesting they play important roles as intermediate hosts. We then used the new life cycle data to provide a synthetic overview of the life cycles known for various parasite groups in New Zealand. This study highlights how studying parasite life cycles can enhance our understanding of the ecology and evolution of parasites and hosts in natural systems, beyond simply resolving life cycles.

Real-time insight into the multistage mechanism of nanoparticle exsolution from a perovskite host surface

In exsolution, nanoparticles form by emerging from oxide hosts by application of redox driving forces, leading to transformative advances in stability, activity, and efficiency over deposition techniques, and resulting in a wide range of new opportunities for catalytic, energy and net-zero-related technologies. However, the mechanism of exsolved nanoparticle nucleation and perovskite structural evolution, has, to date, remained unclear. Herein, we shed light on this elusive process by following in real time Ir nanoparticle emergence from a SrTiO3 host oxide lattice, using in situ high-resolution electron microscopy in combination with computational simulations and machine learning analytics. We show that nucleation occurs via atom clustering, in tandem with host evolution, revealing the participation of surface defects and host lattice restructuring in trapping Ir atoms to initiate nanoparticle formation and growth. These insights provide a theoretical platform and practical recommendations to further the development of highly functional and broadly applicable exsolvable materials.

The biogeography of host‐associated bacterial microbiomes: Revisiting classic biodiversity patterns

AbstractBackgroundThe question of which ecological and evolutionary processes structure the distribution of biodiversity has intrigued scientists for centuries, and historically, inferences have been gained predominantly by studying animals and plants. Although substantial progress has been made towards understanding the multitude of factors that shape host‐associated microbial communities (i.e., microbiomes), it remains largely unknown whether large‐scale geographical patterns in diversity observed for macroorganisms also apply for their microbiomes and whether microbiomes are shaped by the same processes that appear key for determining biogeographical patterns in their hosts.The geographical distribution of microbiome diversityWe discuss challenges and potential approaches for studying microbiome biogeography, with the goal of inspiring future lines of research that can stimulate the development of new ecological and evolutionary theory in the microbiome field. The theory and examples presented here focus specifically on bacterial microbiomes, and we give an overview of host‐associated bacterial microbiome research beginning to examine some of the classic biodiversity patterns central to the fields of ecology and evolution.Potential impacts of microbiome variation for host ecology and evolutionMicrobiome diversity patterns are particularly important to consider because microbes are crucial for many aspects of the biology of their hosts. We discuss how more comprehensive knowledge of the geographical variation of microbiome diversity at the host individual and population levels might be crucial for understanding host ecology and evolution.

High-Quality Complete Genome Resource of Pectobacterium brasiliense Strain TS20HJ1 Causing Rhizome Rot on Ginger

Pectobacterium brasiliense is a worldwide distributed bacterial pathogen causing soft rot and blackleg of a wide range of economically important crops. Here, we present the complete, high-quality genome of P. brasiliense strain TS20HJ1, which was isolated from a ginger ( Zingiber officinale) rhizome showing soft rot symptoms. The genome assembly consists of a circular 4,766,353-bp chromosome with 52.1% GC content. The genome harbors 4,128 protein-coding genes, 22 rRNA genes, and 77 tRNA genes. We believe that the complete genome sequence of P. brasiliense TS20HJ1 will provide a valuable resource for understanding the molecular basis of host adaptation and evolution of pathogenesis. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Diversity and dynamics of endosymbionts in a single population of sweet potato weevil, Cylas formicarius (Coleoptera: Brentidae): a preliminary study.

Endosymbionts live symbiotically with insect hosts and play important roles in the evolution, growth, development, reproduction, and environmental fitness of hosts. Weevils are one of the most abundant insect groups that can be infected by various endosymbionts, such as Sodalis, Nardonella, and Wolbachia. The sweet potato weevil, Cylas formicarius (Coleoptera: Brentidae), is a notorious pest in sweet potato (Ipomoea batatas L.) cultivation. Currently, little is known about the presence of endosymbionts in C. formicarius. Herein, we assessed the endosymbiont load of a single geographic population of C. formicarius. The results showed that Nardonella and Rickettsia could infect C. formicarius at different rates, which also varied according to the developmental stages of C. formicarius. The relative titer of Nardonella was significantly related to C. formicarius developmental stages. The Nardonella-infecting sweet potato weevils were most closely related to the Nardonella in Sphenophorus levis (Coleoptera, Curculionidae). The Rickettsia be identified in bellii group. These results preliminarily revealed the endosymbionts in C. formicarius and helped to explore the diversity of endosymbionts in weevils and uncover the physiological roles of endosymbionts in weevils.

A compilation of virulence-associated genes that are frequently reported in avian pathogenic Escherichia coli (APEC) compared to other E. coli.

Escherichia coli (E. coli) survive in various hosts and environments due to their highly diversified genome. These bacteria have co-evolved with human, colonized a broad range of hosts and survive as a commensal organism or pathogen. E. coli that adopted a pathogenic lifecycle in avian hosts typically belong to phylogroups B2 and D. Phylogenic investigations discovered these E. coli are noticeably overlapped with the phylogroup of E. coli infecting humans. This overlapping is possibly due to a parallel evolution in both hosts from a common ancestor, which indicates a high zoonotic potential of avian pathogenic E. coli (APEC). However, some contrasting evidence of other phylogroups infecting the avian host has also been reported in recent studies indicating phylogroups of E. coli are not definitive, only suggestive to their virulence in chickens. Furthermore, virulence-associated genes that contribute to bacterial features necessary to establish APEC infection, are predominantly located in plasmids. Therefore, phylogenetic classification based on chromosomal markers is often inadequate to identify APEC. Moreover, E. coli can obtain virulent plasmids from other bacteria which further complicates the link between phylogenetic classification and pathotype. Previous research has reported an array of virulence-associated genes highly prevalent only in APEC isolates. Function of these genes are possibly a prerequisite to establishing APEC infections in chickens. Consequently, these genes can be used to distinguish APEC from environmental, commensal, intestinal and other extra-intestinal E. coli. Therefore, we have extensively reviewed previous literature to compile the virulence-associated genes that are highly prevalent in APEC compared to other E. coli. From this review, we have identified 10 key virulence-associated genes (iss, tsh, iroN, episomal/chromosomal ompT, iutA, cvaC, hlyF, iucD, papG allel (II/III) and papC) that are frequently reported in APEC isolates than non-pathogenic E. coli. A compilation of these research findings can be crucial to the molecular identification of APEC. Furthermore, it can serve as a guideline for future investigation and aid in formulation of intervention strategies.

Infectious disease ecology and evolution in a changing world.

Infectious disease ecology and evolution in a changing world.

Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis

IntroductionHost-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.MethodsWe report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.Results and DiscussionThe phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated ‘Candidatus’ superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with ‘Candidatus Heimdallarchaeota’ were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb’s pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.