Host Physiology Research Articles

Impact of host physiology and external stressors on the bacterial community of Schmidtea mediterranea.

To fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.

A phloem-limited RNA phytovirus infection does not positively modulate vector preference and fitness in primary and alternate hosts.

Colonizing aphids play an important role in the transmission of RNA phytoviruses in the family Solemoviridae. According to "host manipulation hypothesis," phloem limited and persistently transmitted Solemoviridae viruses modulate host physiology that positively affects vector behavior and fitness and facilitates virus spread. However, it is unclear if virus-modulated host effects on vectors across pathosystems involving Solemoviridae members are always positive. Cotton leafroll dwarf virus (CLRDV) is a recently introduced Solemoviridae member in the United States, and it is transmitted by the cotton aphid (Aphis gossypii). Effects of CLRDV infection on vector behavior and fitness were evaluated on its primary host plant, cotton (Gossypium hirsutum), and an alternate host plant, hibiscus (Hibiscus acetosella). In this study, changes to viruliferous and non-viruliferous aphid preference and aphid fitness on virus-infected and non-infected hosts were examined. In contrast to the hypothesized preference of non-viruliferous aphids for infected plants and vice-versa, both viruliferous and non-viruliferous A. gossypii preferred non-infected cotton and hibiscus plants over CLRDV-infected plants. This suggested that the preference of non-viruliferous vectors to non-infected plants might negatively impact virus acquisition, whereas the preference of viruliferous vectors toward non-infected plants could positively facilitate virus inoculation. The total fecundity and intrinsic rate of increase of aphids were higher on non-infected plants compared with CLRDV-infected plants. The lack of enhanced fitness benefits on CLRDV-infected hosts also could negatively impact virus spread. Overall, this study suggested that "host manipulation hypothesis" favoring vector attraction and enhanced fitness on infected plants does not apply to all pathosystems involving Solemoviridae members.

Population Dynamics and the Microbiome in a Wild Boreal Mammal: The Snowshoe Hare Cycle and Impacts of Diet, Season and Predation Risk.

The North American boreal forest is a massive ecosystem, and its keystone herbivore is the snowshoe hare (Lepus americanus). Hares are exposed to considerable environmental extremes in diet and weather, food availability, and predation risk. Gut microbiomes have been suggested to facilitate adaptive animal responses to environmental change, but severe environmental challenges to homeostasis can also disrupt host-microbiome relationships. To better understand gut microbiome contributions to animal acclimation, we studied the faecal bacterial microbiome of wild hares across two types of extreme environmental change that are integral to their natural history: (1) seasonal transitions between summer and winter, and (2) changes over the ~10 year 'boom-bust' population cycles that are characterised by shifting food resource availability and predation pressure. When compared to summer, hares in winter had lower bacterial richness and were depleted in 20 families (including Oxalobacteraceae and Christensenellaceae) but enriched for Ruminococcaceae (a family which contains plant fibre degrading bacteria) alongside nine other bacterial groups. Marked bacterial microbiome differences also occurred across phases of the population cycle. Bacterial microbiomes were lower in richness and compositionally distinct in the peak compared to the increase or decline phases of the population cycle. Direct measures of host physiology and diet quality (faecal fibre contents) most strongly supported food resource availability as a mechanism underlying phase-based differences in bacterial communities, but faecal fibre contents could not fully account for bacterial microbiome variation across phases.

Spiroplasma endosymbiont reduction of host lipid synthesis and Stomoxyn-like peptide contribute to trypanosome resistance in the tsetse fly Glossina fuscipes.

Tsetse flies (Glossina spp.) vector African trypanosomes that cause devastating diseases in humans and domestic animals. Within the Glossina genus, species in the Palpalis subgroup exhibit greater resistance to trypanosome infections compared to those in the Morsitans subgroup. Varying microbiota composition and species-specific genetic traits can significantly influence the efficiency of parasite transmission. Notably, infections with the endosymbiotic bacterium Spiroplasma have been documented in several Palpalis subgroup species, including Glossina fuscipes fuscipes (Gff). While Spiroplasma infections in Gff are known to hinder trypanosome transmission, the underlying mechanisms remain unknown. To investigate Spiroplasma-mediated factors affecting Gff vector competence, we conducted high-throughput RNA sequencing of the gut tissue along with functional assays. Our findings reveal elevated oxidative stress in the gut environment in the presence of Spiroplasma, evidenced by increased expression of nitric oxide synthase, which catalyzes the production of trypanocidal nitric oxide. Additionally, we observed impaired lipid biosynthesis leading to a reduction of this important class of nutrients essential for parasite and host physiologies. In contrast, trypanosome infections in Gff's midgut significantly upregulated various immunity-related genes, including a small peptide, Stomoxyn-like, homologous to Stomoxyn first discovered in the stable fly, Stomoxys calcitrans. We observed that the Stomoxyn-like locus is exclusive to the genomes of Palpalis subgroup tsetse species. GffStomoxyn is constitutively expressed in the cardia (proventriculus) and synthetic GffStomoxyn exhibits potent activity against Escherichia coli and bloodstream form of Trypanosoma brucei parasites, while showing no effect against insect stage procyclic forms or tsetse's commensal endosymbiont Sodalis in vitro. Reducing GffStomoxyn levels significantly increased trypanosome infection prevalence, indicating its potential trypanocidal role in vivo. Collectively, our results suggest that the enhanced resistance to trypanosomes observed in Spiroplasma-infected Gff may be due to the reduced lipid availability necessary for parasite metabolic maintenance. Furthermore, GffStomoxyn could play a crucial role in the initial immune response(s) against mammalian parasites early in the infection process in the gut and prevent gut colonization. We discuss the molecular characteristics of GffStomoxyn, its spatial and temporal expression regulation and its microbicidal activity against Trypanosome parasites. Our findings reinforce the nutritional influences of microbiota on host physiology and host-pathogen dynamics.

Parasitoid wasp venoms degrade Drosophila imaginal discs for successful parasitism.

Parasitoid wasps, one of the most diverse and species-rich animal groups on Earth, produce venoms that manipulate host development and physiology to exploit resources. However, mechanisms of actions of these venoms remain poorly understood. Here, we discovered that the endoparasitoid wasp, Asobara japonica, induces apoptosis, autophagy, and mitotic arrest in the adult tissue precursors of its host Drosophila larvae. We termed this phenomenon imaginal disc degradation (IDD). A multi-omics approach facilitated identification of two venom proteins of A. japonica necessary for IDD, which is critical for parasitism success. Our study highlights a venom-mediated hijacking strategy of the parasitoid wasp that allows the host larvae to grow, but ultimately prevents their metamorphosis.

Real-world of Limosilactobacillus reuteri in mitigation of acute experimental colitis

Probiotics have been proposed as a potential strategy for managing ulcerative colitis (UC). However, the underlying mechanisms mediating microbiota-host crosstalk remain largely elusive. Here, we report that Limosilactobacillus reuteri (L. reuteri), as a probiotic, secretes cytoplasmic membrane vesicles (CMVs) that communicate with host cells, alter host physiology, and alleviate dextran sulfate sodium (DSS)-induced colitis. First, L. reuteri-CMVs selectively promoted the proliferation of the beneficial bacterium Akkermansia muciniphila (AKK) by upregulating the expression of glycosidases (beta-N-acetylhexosaminidase and alpha-N-acetylglucosaminidase) involved in glycan degradation and metabolic pathways and restored the disrupted gut microbiota balance. Second, L. reuteri-CMVs were taken up by intestinal epithelial cells (IECs), elevated the expression of ZO-1, E-cadherin (Cdh1), and Occludin (Ocln), decreased intestinal permeability, and exerted protective effects on epithelial tight junction functionality. RNA sequencing analysis demonstrated that L. reuteri-CMVs repaired intestinal barrier by activating the HIF-1 signaling pathway and upregulating HMOX1 expression. Third, L. reuteri-CMVs increased the population of double positive (DP) CD4+CD8+ T cells in the intestinal epithelial layer, suppressing gut inflammation and maintaining gut mucosal homeostasis. Finally, L. reuteri-CMVs exhibited satisfactory stability and safety in the gastrointestinal tract and specifically targeted the desired sites in colitis mice. Collectively, these findings shed light on how L. reuteri interact with the host in colitis, and provide new insights into potential strategies for alleviating colitis.Graphical

Wolbachia Infection Alters the Microbiota of the Invasive Leaf-Miner Liriomyza huidobrensis (Diptera: Agromyzidae)

Microbe–microbe interactions within a host drive shifts in the host’s microbiota composition, profoundly influencing host physiology, ecology, and evolution. Among these microbes, the maternally inherited endosymbiont Wolbachia is widespread in the invasive pest Liriomyza huidorbrensis (Diptera: Agromyzidae). However, its influence on the host microbiota remains largely unexplored. In the study presented herein, we investigated the bacterial communities of Wolbachia wLhui-infected (wLhui+) and -uninfected lines (wLhui−) of L. huidorbrensis using 16S rRNA gene high-throughput sequencing. For both leaf-miner lines, Bacteroidota was the dominant phylum (relative abundance: 59.18%), followed by Pseudomonadota (36.63%), Actinomycetota (2.42%), and Bacillota (0.93%). We found no significant differences in alpha-diversity indices between the wLhui+ and wLhui− lines (p > 0.05). However, principal coordinates analysis revealed significant differences in microbiota composition between the wLhui+ and wLhui− lines (PERMANOVA: p < 0.001), explaining 76.70% of the variance in microbiota composition. Correlation network analysis identified robust negative and positive associations between Wolbachia and several genera, suggesting that Wolbachia shapes microbial composition through competitive or cooperative interactions with specific taxa. Overall, our study suggests that Wolbachia plays a key role in shaping the leaf-miner microbiome, potentially affecting host fitness.

Biodiversity within phytoplankton-associated microbiomes regulates host physiology, host community ecology, and nutrient cycling.

As evidence is emerging of the key roles that host-associated microbiomes often play in regulating the physiology, fitness, and ecology of their eukaryotic hosts, human activities are causing declines in biological diversity, including within the microbial world. Here, we use a multifactorial manipulative experiment to test the effects of declining diversity within host microbiomes both alone and in tandem with the effects of emerging global changes, including climate warming and shifts in nutrient bioavailability, which are inflicting increasing abiotic stress on host organisms. Using single-celled eukaryotic phytoplankton that harbor an external microbiome as a model system, we demonstrate that diversity within host-associated microbiomes impacts multiple tiers of biological organization, including host physiology, the host population and community ecology, and ecosystem nutrient cycling. Notably, these microbiome diversity-driven effects became magnified in abiotically stressful environments, suggesting that the importance of microbiome diversity may have increased over time during the Anthropocene.

Activation and modulation of the host response to DNA damage by an integrative and conjugative element.

Mobile genetic elements help drive horizontal gene transfer and bacterial evolution. Conjugative elements and temperate bacteriophages can be stably maintained in host cells. They can alter host physiology and regulatory responses and typically carry genes that are beneficial to their hosts. We found that ICEBs1, an integrative and conjugative element (ICE) of Bacillus subtilis, inhibits the host response to DNA damage (the SOS response). Activation of ICEBs1 before DNA damage reduced host cell lysis that was caused by SOS-mediated activation of two resident prophages. Further, activation of ICEBs1 itself activated the SOS response in a subpopulation of cells, and this activation was attenuated by the functions of the ICEBs1 genes ydcT and yddA (now ramT and ramA; ram for RecA modulator). Double-mutant analyses indicated that RamA functions to inhibit and RamT functions to both inhibit and activate the SOS response. Both RamT and RamA caused a reduction in RecA filaments, one of the early steps in activation of the SOS response. We suspect that there are several different mechanisms by which mobile genetic elements that generate single-stranded DNA (ssDNA) during their life cycle inhibit the host SOS response and RecA function, as RamT and RamA differ from the known SOS inhibitors encoded by conjugative elements.IMPORTANCEBacterial genomes typically contain mobile genetic elements, including bacteriophages (viruses) and integrative and conjugative elements, that affect host physiology. ICEs can excise from the chromosome and undergo rolling-circle replication, producing ssDNA, a signal that indicates DNA damage and activates the host SOS response. We found that following excision and replication, ICEBs1 of B. subtilis stimulates the host SOS response and that ICEBs1 encodes two proteins that limit the extent of this response. These proteins also reduce the amount of cell killing caused by resident prophages following their activation by DNA damage. These proteins are different from those previously characterized that inhibit the host SOS response and represent a new way in which ICEs can affect their host cells.

Gut microbiota-derived metabolites and chronic inflammatory diseases

The gut microbiota, a complex ecosystem of microorganisms, plays an essential role in maintaining immune and metabolic homeostasis. Disruption of this microbial balance, known as dysbiosis, has been increasingly implicated in the pathogenesis of chronic inflammatory conditions, including cardiovascular, gastrointestinal, and autoimmune diseases, as well as metabolic disorders such as diabetes and obesity. A crucial mechanism through which the gut microbiota exerts its effects on host physiology is via the production of bioactive metabolites. These metabolites, including short-chain fatty acids, bile acids, and tryptophan derivatives, are key in modulating immune responses and regulating metabolic functions. Dysbiosis disrupts the production and function of these metabolites, thereby contributing to immune dysregulation, chronic inflammation, and disease progression. This review examines the role of gut microbiota-derived metabolites in chronic inflammatory diseases, with a focus on their immunomodulatory and metabolic effects. A deeper understanding of these mechanisms may open the way for novel therapeutic strategies aimed at restoring immune homeostasis and mitigating the global burden of chronic inflammatory diseases.

Effects of Microbes on Insect Host Physiology and Behavior Mediated by the Host Immune System.

Innate immunity is critical for insects to adjust to complicated environments. Studying the insect immune system can aid in identifying novel insecticide targets and provide insights for developing novel pest control strategies. Insects recognize environmental pathogens through pattern recognition receptors, thus activating the innate immune system to eliminate pathogens. The innate immune system of insects primarily comprises cellular immunity and humoral immunity. Toll, immune deficiency, and Janus kinase/signal transducers and activators of transcription are the main signaling pathways regulating insect humoral immunity. Nevertheless, increasing research has revealed that immune signaling activated by microbes also performs non-immune roles while exerting immune roles, and insulin signaling performs a key role in mediating the connection between the immune system and non-immune physiological activities. Therefore, this paper first briefly reviews the main innate immune signaling and insulin signaling of insects, then summarizes the relationship between immune signaling activated by microbes and insect growth and development, reproduction, pesticide resistance, chemical communication, cell turnover, lifespan, sleep, energy generation pathways and their possible underlying mechanisms. Future research directions and methodologies are also proposed, aiming to provide insights into further study on the physiological mechanism linking microbes and insect hosts.

Technical Advances Drive the Molecular Understanding of Effectors from Wheat and Barley Powdery Mildew Fungi.

Pathogens manipulate host physiology through the secretion of virulence factors (effectors) to invade and proliferate on the host. The molecular functions of effectors inside plant hosts have been of interest in the field of molecular plant-microbe interactions. Obligate biotrophic pathogens, such as rusts and powdery mildews, cannot proliferate outside of plant hosts. In addition to the inhibition of the plant's immune components, these pathogens are under particular pressure to efficiently extract nutrients from the host. Understanding the molecular basis of infections mediated by obligate biotrophic pathogens is of significance because of their impact in modern agriculture. In addition, powdery mildews serve as excellent models for obligate biotrophic cereal pathogens. Here, we summarise the current knowledge on the effectorome of the barley and wheat powdery mildews and putative molecular virulence functions of effectors. We emphasise the availability of comprehensive genomic, transcriptomic and proteomic resources and discuss the methodological approaches used for identifying candidate effectors, assessing effector virulence traits and identifying effector targets in the host. We highlight established and more recently employed methodologies, discuss limitations and suggest additional strategies. We identify open questions and discuss how addressing them with current available resources will enhance our understanding of Blumeria CSEPs.

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens' antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of an Akkermansia muciniphila isolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.

Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota.

Dietary protein has been shown to impact long-term health outcomes differentially depending on its amount and source. It has been suggested that interactions of the gut microbiota with dietary proteins mediate some of the effects of dietary protein on health outcomes. However, it remains unclear what specific host responses drive the health effects of dietary proteins from different plant and animal sources. Additionally, which specific host responses are mediated by interactions of dietary protein source with the gut microbiota and which host responses are caused by dietary proteins directly is not well understood. We used metaproteomics to quantify dietary, host, and microbial proteins in fecal samples of conventional and germ-free mice fed purified dietary protein from six different plant and animal sources, including casein, egg-white, soy, brown rice, pea, and yeast. We characterized differences in the host fecal proteome across the six dietary protein sources as well as between the conventional and germ-free mice for each source to determine how the host responds to the different dietary protein sources and the role of the gut microbiota in mediating these responses. We found that both the source of dietary protein and the presence or absence of the gut microbiota drive the host response to dietary protein source in the fecal host proteome. Host proteins pertaining to immune response, digestion, and barrier function were differentially abundant in different protein sources with and without the gut microbiota. These changes in the host response correlated with changes in microbial composition and differences in protein digestibility. Our results show how dietary protein sources, through their interactions with the gut microbiota, impact several aspects of host physiology.

Validation of Monilinia fructicola Putative Effector Genes in Different Host Peach (Prunus persica) Cultivars and Defense Response Investigation.

Monilinia fructicola is the most common and destructive brown rot agent on peaches. Knowledge of gene expression mediating host-pathogen interaction is essential to manage fungal plant diseases. M. fructicola putative virulence factors have been predicted by genome investigations. The pathogen interaction with the host was validated. Five M. fructicola isolates were inoculated on two cultivars (cv.s) of peach (Prunus persica (L.) Batsch) 'Royal Summer' and 'Messapia' with intermediate and late ripening periods, respectively. The expression pattern of 17 candidate effector genes of M. fructicola with functions linked to host invasion and fungal life, and seven peach genes involved in the immune defense system were monitored at 0, 2, 6, 10, and 24 h-post inoculation (hpi). All fungal isolates induced similar brown rot lesions on both cv.s whereas the modulation of effector genes was regulated mainly at 2, 6, and 10 hpi, when disease symptoms appeared on the fruit surface, confirming the involvement of effector genes in the early infection stage. Although differences were observed among the fungal isolates, the principal component investigation identified the main differences linked to the host genotype. The salicylic acid and jasmonate/ethylene signaling pathways were differently modulated in the host independent from the fungal isolate used for inoculation. On plants susceptible to brown rot, the pathogen may have adapted to the host's physiology by modulating its effectors as weapons.

Evidence for microbially-mediated tradeoffs between growth and defense throughout coral evolution

BackgroundEvolutionary tradeoffs between life-history strategies are important in animal evolution. Because microbes can influence multiple aspects of host physiology, including growth rate and susceptibility to disease or stress, changes in animal-microbial symbioses have the potential to mediate life-history tradeoffs. Scleractinian corals provide a biodiverse, data-rich, and ecologically-relevant host system to explore this idea.ResultsUsing a comparative approach, we tested if coral microbiomes correlate with disease susceptibility across 425 million years of coral evolution by conducting a cross-species coral microbiome survey (the “Global Coral Microbiome Project”) and combining the results with long-term global disease prevalence and coral trait data. Interpreting these data in their phylogenetic context, we show that microbial dominance predicts disease susceptibility, and traced this dominance-disease association to a single putatively beneficial symbiont genus, Endozoicomonas. Endozoicomonas relative abundance in coral tissue explained 30% of variation in disease susceptibility and 60% of variation in microbiome dominance across 40 coral genera, while also correlating strongly with high growth rates.ConclusionsThese results demonstrate that the evolution of Endozoicomonas symbiosis in corals correlates with both disease prevalence and growth rate, and suggest a mediating role. Exploration of the mechanistic basis for these findings will be important for our understanding of how microbial symbioses influence animal life-history tradeoffs.

Fungi in the Gut Microbiota: Interactions, Homeostasis, and Host Physiology.

The mammalian gastrointestinal tract is a stage for dynamic inter-kingdom interactions among bacteria, fungi, viruses, and protozoa, which collectively shape the gut micro-ecology and influence host physiology. Despite being a modest fraction, the fungal community, also referred to as mycobiota, represents a critical component of the gut microbiota. Emerging evidence suggests that fungi act as early colonizers of the intestine, exerting a lasting influence on gut development. Meanwhile, the composition of the mycobiota is influenced by multiple factors, with diet, nutrition, drug use (e.g., antimicrobials), and physical condition standing as primary drivers. During its establishment, the mycobiota forms both antagonistic and synergistic relationships with bacterial communities within the host. For instance, intestinal fungi can inhibit bacterial colonization by producing alcohol, while certain bacterial pathogens exploit fungal iron carriers to enhance their growth. However, the regulatory mechanisms governing these complex interactions remain poorly understood. In this review, we first introduce the methodologies for studying the microbiota, then address the significance of the mycobiota in the mammalian intestine, especially during weaning when all 'primary drivers' change, and, finally, discuss interactions between fungi and bacteria under various influencing factors. Our review aims to shed light on the complex inter-kingdom dynamics between fungi and bacteria in gut homeostasis and provide insights into how they can be better understood and managed to improve host health and disease outcomes.

Microbes put drugs in(action)

Interactions between the gut microbiome, nutrients, drugs, and host physiology are inherently complex. Gut microbes contribute significantly towards host homeostasis and can modulate host-targeted drugs, affecting therapeutic outcomes. Finding ways to harness the gut microbiome to improve drug efficacy can be a promising strategy to advance precision medicine.

Effects of gastrointestinal parasites on fecal glucocorticoids and behaviour in vervet monkeys (Chlorocebus pygerythrus).

Relationships between parasites, host physiology, and behaviours are complex. Parasites can influence host hormonal microenvironment and behaviour through "sickness behaviours" that generally conserve energy. Using a parasite removal experiment, we examined the effects of gastrointestinal parasites on fecal glucocorticoid metabolites (fGC) and behaviours of vervet monkeys (Chlorocebus pygerythrus) at Lake Nabugabo, Uganda. We collected parasitological, hormonal, and behavioural data from adult and subadult male and female vervets (N = 19) in 2014 across four study phases: pre-deworming, post-deworming, early reinfection, and late reinfection as well as in 2015. Overall, there was no decrease in fGC after deworming, but there was an increase following natural reinfection. There was no change in feeding across study phases; however, moving, grooming, and resting changed between the post-deworming and late reinfection phases, but not always in the predicted direction. Comparing behaviour across the same months in the following year as in the 2014 experimental study period, we found no differences in moving, feeding, grooming, and resting events. Despite behavioural variation between study phases, we cannot conclude that behavioural changes are due to parasitism rather than other seasonal variation. However, fGC increased following reinfection, which is consistent with parasitism being costly for hosts.

Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.

Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B.subtilis, shedding light on bacterial genome evolution and phage-host dynamics.