Microbiome interactions shape host fitness

Impact of gut microbial diversity on egg production performance in chickens

Chickens are one of the most economically important poultry species, and their egg-laying performance is a crucial economic trait. The intestinal microbiome plays a significant role in the egg-laying performance. To clarify the diversity of chicken intestinal microbiota and its connection to egg-laying performance, this study utilized 16S rRNA sequencing technology to characterize the intestinal microbiomes of 101 chickens from 13 breeds with varying levels of egg production. The results reveal significant differences in gut microbiota structure among chicken groups with varying egg production levels. High egg-producing chickens showed significantly higher abundances of Firmicutes, Proteobacteria, and Lactobacillus, while low egg-producing chickens displayed greater microbial α-diversity and more complex community structures. These differences in gut microbiota influence key physiological functions, including nutrient absorption and hormone regulation through metabolic pathways, and directly affect egg production performance. The low and medium production groups partially overlapped on the principal coordinates analysis plot, whereas the high-production group was distinctly separate. This study provides a scientific basis and intestinal microbiome data for selecting probiotics related to high egg production in chickens.

IMPORTANCE

This study elucidates the critical role of gut microbiota in the egg-laying performance of chickens, a key economic indicator in the poultry industry. By employing 16S rRNA sequencing, we uncovered distinct microbial profiles associated with varying levels of egg production. High egg-producing chickens exhibit a higher abundance of specific bacterial taxa, such as Firmicutes and Proteobacteria, which are linked to enhanced nutrient absorption and metabolic efficiency. Conversely, lower and medium egg-producing chickens display greater microbial diversity, suggesting a more complex but less efficient gut ecosystem. Our findings provide valuable insights into the relationship between gut microbiota and egg production, offering a scientific foundation for the selection of probiotics that could potentially improve the egg-laying performance of chickens. This research not only advances our understanding of avian gut microbiology but also has practical implications for optimizing poultry farming practices and enhancing economic outcomes.

Utilizing a novel fecal sampling method to examine resistance of the honey bee (Apis mellifera) gut microbiome to a low dose of tetracycline

Disruption of host-associated microbial communities can have detrimental impacts on host health. However, the capacity of individual host-associated microbial communities to resist disturbance has not been well defined. Using a novel fecal sampling method for honey bees (Apis mellifera), we examined the resistance of the honey bee gut microbiome to disruption from a low dose of the antibiotic, tetracycline (4.5 μg). Prior to the experiment, bacterial communities from fecal samples were compared to communities from dissected whole guts of the same individuals to ensure fecal samples accurately represented the gut microbiome. Fecal samples were collected from lab-caged honey bees prior to, and five days after, tetracycline exposure to assess how antibiotic disturbance affected the communities of individuals. We used metrics of alpha and beta diversity calculated from 16S rRNA gene amplicon sequences to compare gut community structure. Low dose tetracycline exposure did not consistently change honey bee gut microbiome structure, but there was individual variation in response to exposure and specific taxa (one ASV assigned to Lactobacillus kunkeei and one ASV in the genus Bombella) were differentially abundant following tetracycline treatment. To assess whether individual variation could be influenced by the presence of tetracycline resistance genes, we quantified the abundance of tet(B) and tet(M) with qPCR. The abundance of tet(M) prior to tetracycline treatment was negatively correlated with change in community membership, assessed by difference in Jaccard dissimilarity over the five-day experiment. Our results suggest that the honey bee gut microbiome has some ability to resist or recover from antibiotic-induced change, specific taxa may vary in their susceptibility to tetracycline exposure, and antibiotic resistance genes may contribute to gut microbiome resistance.

Microbiome transplants may not improve health and longevity in Drosophila melanogaster

The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.

Microbial communities associated with the skin, gill, and gut of large yellow croaker (Larimichthys crocea)

The microbiota inhabiting the surface of fish mucosal tissue play important roles in the nutrition, metabolism and immune system of their host. However, most investigations on microbial symbionts have focused on the fish gut, but the microbiota associated with external mucosal tissues (such as the skin and gill) is poorly understood. This study characterised the traits and dynamic of microbial communities associated with the skin, gill and gut of large yellow croaker (Larimichthys crocea) culturing with net enclosures or pens at different sampling times (with seasonal transition). Results revealed the structure and function of microbial communities differed according to the mucosal tissues of large yellow croaker. The richness and diversity of microbiota in the skin were significantly higher than that in the gill and gut. Discriminative microbial taxa such as Psychrobacter in the skin, Enterobacterales in the gill, and Fusobacterium in the gut, and discriminative predictive functions were identified in the skin, gill and gut. Furthermore, different environmental-related factors (such as sampling time/season and culture method) had impacts on the fish microbiota differently. The diversity and composition of microbiota associated with the skin, gill and gut changed over time, and the difference in skin microbiota across sampling times was most significant among the three tissues. The culture method significantly impacted the diversity and composition of skin microbiota, but no significant difference was found in the gill and gut microbiota between net enclosure and net pen. These results indicated that the skin microbiota of large yellow croaker was more diverse and affected by environmental-related factors than other tissues. This study provides new insights into the structure, environmental response pattern, and relationship with host health of microbiota associated with the mucosal tissues of large yellow croaker.

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes.1,2,3,4,5,6 It is of interest to understand how perturbations, like the introduction of exogenous chemicals,7,8,9,10,11,12,13 impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.14,15,16,17,18,19 These alkaloids are antimicrobial20,21,22; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re-Analysis

Gut microbiota are fundamental for healthy animal function, but the evidence that host function can be predicted from microbiota taxonomy remains equivocal, and natural populations remain understudied compared to laboratory animals. Paired analyses of covariation in microbiota and host parameters are powerful approaches to characterise host-microbiome relationships mechanistically, especially in wild populations of animals that are also lab models, enabling insight into the ecological basis of host function at molecular and cellular levels. The fruitfly Drosophila melanogaster is a preeminent model organism, amenable to field investigation by 'omic analyses. Previous work in wild male D. melanogaster guts analysed paired measurements of (A) bacterial diversity and abundance, measured by 16S amplicon sequencing; and (B) the host gut transcriptome, but no signature of covariation was detected. Here, we re-analyse those data comprehensively. We find orthogonal axes of microbial genera, which correspond to differential expression of host genes. The differentially expressed gene sets were enriched in functions including protein translation, mitochondrial respiration, immunity and reproduction. Each gene set had a distinct functional signature, suggesting that wild flies exhibit a range of distinct axes of functional variation, which correspond to orthogonal axes of microbiome variation. These findings lay a foundation to better connect ecology and functional genetics of a leading host-microbiome model.

Environmental microbial reservoir influences the bacterial communities associated with Hydra oligactis

The objective to study the influence of microbiome on host fitness is frequently constrained by spatial and temporal variability of microbial communities. In particular, the environment serves as a dynamic reservoir of microbes that provides potential colonizers for animal microbiomes. In this study, we analyzed the microbiome of Hydra oligactis and corresponding water samples from 15 Hungarian lakes to reveal the contribution of environmental microbiota on host microbiome. Correlation analyses and neutral modeling revealed that differences in Hydra microbiota are associated with differences in environmental microbiota. To further investigate the influence of environmental bacterial community on the host microbiome, field-collected Hydra polyps from three populations were cultured in native water or foreign water. Our results show that lake water bacteria significantly contribute to Hydra microbial communities, but the compositional profile remained stable when cultured in different water sources. Longitudinal analysis of the in vitro experiment revealed a site-specific change in microbiome that correlated with the source water quality. Taken together, our findings demonstrate that while freshwater serves as a critical microbial reservoir, Hydra microbial communities exhibit remarkable resilience to environmental changes maintaining stability despite potential invasion. This dual approach highlights the complex interplay between environmental reservoirs and host microbiome integrity.

Exploring the Adaptation Process of Huso dauricus to High Temperatures Based on Changes in Intestinal Microbiota

Global warming has led to rising water temperatures, posing a significant threat to fish survival. Understanding the mechanisms by which fish respond to and adapt to temperature variations is thus of considerable importance. This study employed high-throughput 16S rRNA gene sequencing and bioinformatics to investigate changes in the intestinal microbiota of the kaluga sturgeon (Huso dauricus) under four temperature conditions (19 °C, 25 °C, 28 °C, and 31 °C) and its relationship with adaptation to high-temperature stress. The results indicated that temperature variations caused significant changes in the intestinal microbiota. Over time, differences in the microbiota structure became more pronounced under different temperature conditions, and within-group variability gradually decreased. At higher temperatures, the relative abundance of Sphingomonas significantly decreased, while that of Clostridium sensu stricto 1, Cetobacterium, and Plesiomonas exhibited a significant increase in relative abundance. Upon the cessation of rapid mortality under various high-temperature conditions, the intestinal microbiota structure and composition became highly similar, with Clostridium sensu stricto 1 dominating both in terms of composition and relative abundance, suggesting a central role in adaptation to high-temperature stress. This study preliminarily confirms that the high-temperature adaptability of Huso dauricus is closely related to the structure and composition of its intestinal microbiota, with bacteria such as Clostridium sensu stricto 1 playing an important role. These findings provide new scientific insights into enhancing fish adaptability to high-temperature stress.

Skin Bacterial and Fungal Microbiome Responses to Diet Supplementation and Rewilding in the Critically Endangered Southern Corroboree Frog

The composition and dynamics of the skin bacterial and fungal microbiome is thought to influence host-pathogen defence. This microbial community is shaped by host captivity, diet, and microbial interactions between bacterial and fungal components. However, there remains little understanding of how specific micronutrients influence bacterial and fungal microbiome composition and their inter-domain interactions during rewilding of captive-bred animals. This study experimentally investigated the effect of dietary beta-carotene supplementation and subsequent field release on bacterial and fungal microbiome composition and dynamics using the Southern Corroboree frog (Pseudophryne corroboree) as a model system. We found large-scale diversification of bacterial communities post-release and similar diversification of fungal communities. The rewilded fungal mycobiome was more transient and demonstrated stronger temporal and micro-spatial fluctuations than the bacterial microbiome. Accounting for temporal and spatial factors, we found strong residual associations between bacterial members, yet limited evidence for inter-domain associations, suggesting that co-occurrence patterns between bacterial and fungal communities are largely a result of shared responses to the environment rather than direct interactions. Lastly, we found supplementation of dietary beta-carotene in captivity had no impact on post-release microbiome diversity, yet was associated with approximately 15% of common bacterial and fungal genera. Our research demonstrates that environmental factors play a dominant role over dietary beta-carotene supplementation in shaping microbiome diversity post-release, and suggest inter-domain interactions may also only exert a minor influence. Further research on the function and ecology of skin bacterial and fungal microbiomes will be crucial for developing strategies to support survival of endangered amphibian species.

Unraveling host regulation of gut microbiota through the epigenome-microbiome axis

Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.

Nutrition influences immunity: Diet and host-parasite interactions

Nutrition plays a major role in host immune responses and in pathogen resistance. Understanding the network that modulates the relationship between nutrition and immunity remains a challenge. Several pathways govern the direct effects of nutrition on host immunity and the indirect effects mediated by pathogen populations. We note host microbiota also influence the intricate relationships between nutrition and immunity. The purpose of this review is to discuss recent findings from nutritional research in relation to insect immunology. We outline the relationship between diet, immunity, disease, and microbiota in insects and emphasize the significance of utilizing an integrative, multifaceted approach to grasping the influence of nutrition on immunity.

Microbial function matters: Microbiome-aware nano-ecotoxicology needs functional endpoints besides compositional data

The microbiome provides an active barrier to the external environment and aids in the metabolism of the host. Nanomaterials are known to interact with this microbiome host plane. Given the recent advances in techniques to study the microbiome, there has been a vast increase in studies trying to find causality in host response via the microbiome in nano-ecotoxicology. Our review integrates the latest advancements in understanding the microbiome's role in elucidating host health related to nanomaterial exposure, thereby explicitly emphasizing the gap between compositional and functional studies. Both the techniques used to interfere and the current understanding of microbiome-host relationships in nano-ecotoxicology are discussed. To further highlight the functional side of the microbiome, we performed an explorative meta-analysis to bridge the gap between top-down and bottom-up studies. This review gives a perspective on generalising microbiome-aware nano-ecotoxicology and discusses methodologies to enhance the interpretation of nanomaterial or chemical exposure to host-microbiome interactions. The current study discloses that correlations built on compositional data are not a good proxy for host outcome and more in-depth analysis coupled with functional analysis should be explored more in microbiome-aware nano-ecotoxicology.

Effects of plastic aging on biodegradation of polystyrene by Tenebrio molitor larvae: Insights into gut microbiome and bacterial metabolism

Plastics aging reduces resistance to microbial degradation. Plastivore Tenebrio molitor rapidly biodegrades polystyrene (PS, size: < 80 μm), but the effects of aging on PS biodegradation by T. molitor remain uncharacterized. This study examined PS biodegradation over 24 days following three pre-treatments: freezing with UV exposure (PS1), UV exposure (PS2), and freezing (PS3), compared to pristine PS (PSv) microplastic. The pretreatments deteriorated PS polymers, resulting in slightly higher specific PS consumption (602.8, 586.1, 566.7, and 563.9 mg PS·100 larvae-1·d-1, respectively) and mass reduction rates (49.6 %, 49.5 %, 49.2 %, and 48.7 %, respectively) in PS1, PS2, and PS3 compared to PSv. Improved biodegradation correlated with reduced molecular weights and the formation of oxidized functional groups. Larvae fed more aged PS exhibited greater gut microbial diversity, with microbial community and metabolic pathways shaped by PS aging, as supported by co-occurrence network analysis. These findings indicated that the aging treatments enhanced PS biodegradation by only limited extent but impacted greater on gut microbiome and bacterial metabolic genes, indicating that the T. molitor host have highly predominant capability to digest PS plastics and alters gut microbiome to adapt the PS polymers fed to them.

The gut microbiota of three avian species living in sympatry

BACKGROUND

Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

RESULTS

We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

CONCLUSION

While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.

Genetic evidence of bidirectional mendelian randomization study on the causality between gut microbiome and respiratory diseases contributes to gut-lung axis

Observational studies and clinical trials have suggested the relationship between the gut microbiome and respiratory diseases, but the causality between them remains unclear. Firstly, we selected eight respiratory diseases Genome-wide association study (GWAS) datasets mainly from the FinnGen collaboration as outcomes. The exposure was based on GWAS statistics about the gut microbiome, sourced from the MiBioGen consortium, including gut microbial taxa. The causal link between the gut microbiome and respiratory illnesses was then estimated using a Two-sample Mendelian randomization (MR) analysis, including the inverse-variance weighted (IVW), weighted median, MR-Egger, simple mode, and weighted mode. To ensure reliability, F-statistics and sensitivity tests were conducted. Furthermore, we performed a reverse MR analysis of the pre-Mendelian positive findings to possible reverse causality. For the 196 gut microbe taxa, the IVW analysis suggested 88 potential associations with eight clinically prevalent respiratory diseases. Among them, 30 causal associations were found in more than one MR method. Multiple statistical corrections have confirmed three causal associations: genus Holdemanella was a risk factor for chronic obstructive pulmonary disease (COPD) (P = 1.3 × 10-4, OR = 1.18), family FamilyXIII was a protective factor for COPD (P = 1.3 × 10-3, OR = 0.75), and genus Oxalobacter was a risk factor for asthma (P = 2.1 × 10-4, OR = 1.09). Our MR analysis results indicate that there would be a causal relationship between the gut microbiome and respiratory diseases, contributing to the gut-lung axis. This finding offers new insights into the gut microbiome's roles in respiratory diseases' clinical prevention, pathogenesis, and improvement of clinical symptoms. Further randomized controlled trials are necessary to clarify the protective effect of probiotics and fecal microbial transplantation on respiratory health.

Advancements in the Impact of Insect Gut Microbiota on Host Feeding Behaviors

With the application and development of high-throughput sequencing technology, the structure and function of insect gut microbiota have been analysed, which lays a foundation for further exploring the intricate relationships between gut microbiota and host feeding behaviour. The microbial community in the insect gut, as an important ecological factor, affects the host's food selection and nutritional metabolic processes through various mechanisms, which play a key role in population dynamics and ecosystems. The implications of these interactions are profound, affecting agricultural practices, biodiversity, and the broader environment, such as pollination and pest control. In-depth exploration of the molecular mechanism of the interaction between gut microbiota and hosts contributes to the grasp of insect biology and evolution and offers novel avenues for manipulating insect behaviour for practical applications in agriculture and environmental management. This paper focuses on the possible mechanisms of insect gut microbiota regulating host feeding behaviour. It inspires further research on the interaction between gut microbiota and insects affecting host behaviour.

Environment and diet shape the geography-specific Drosophila melanogaster microbiota composition

Geographic and environmental variation in the animal microbiota can be directly linked to the evolution and wild fitness of their hosts but often appears to be disordered. Here, we sought to better understand patterns that underlie wild variation in the microbiota composition of Drosophila melanogaster . First, environmental temperature predicted geographic variation in fly microbial communities better than latitude did. The microbiota also differed between wild flies and their diets, supporting previous conclusions that the fly microbiota is not merely a reflection of diet. Flies feeding on different diets varied significantly in their microbiota composition, and flies sampled from individual apples were exceptionally depauperate for the Lactic Acid Bacteria (LAB), a major bacterial group in wild and laboratory flies. However, flies bore significantly more LAB when sampled from other fruits or compost piles. Follow-up analyses revealed that LAB abundance in the flies uniquely responds to fruit decomposition, whereas other microbiota members better indicate temporal seasonal progression. Finally, we show that diet-dependent variation in the fly microbiota is associated with phenotypic differentiation of fly lines collected in a single orchard. These last findings link covariation between the flies' dietary history, microbiota composition, and genetic variation across relatively small (single-orchard) landscapes, reinforcing the critical role that environment-dependent variation in microbiota composition can play in local adaptation and genomic differentiation of a model animal host.

SIGNIFICANCE STATEMENT

The microbial communities of animals influence their hosts' evolution and wild fitness, but it is hard to predict and explain how the microbiota varies in wild animals. Here, we describe that the microbiota composition of wild Drosophila melanogaster can be ordered by temperature, humidity, geographic distance, diet decomposition, and diet type. We show how these determinants of microbiota variation can help explain lactic acid bacteria (LAB) abundance in the flies, including the rarity of LAB in some previous studies. Finally, we show that wild fly phenotypes segregate with the flies' diet and microbiota composition, illuminating links between the microbiota and host evolution. Together, these findings help explain how variation in microbiota compositions can shape an animal's life history.

Predicting and Prioritising Community Assembly: Learning Outcomes via Experiments

Community assembly provides the foundation for applications in biodiversity conservation, climate change, invasion, restoration and synthetic ecology. However, predicting and prioritising assembly outcomes remains difficult. We address this challenge via a mechanism-free approach useful when little data or knowledge exist (LOVE; Learning Outcomes Via Experiments). We carry out assembly experiments ('actions', here, random combinations of species additions) potentially in multiple environments, wait, and measure abundance outcomes. We then train a model to predict outcomes of novel actions or prioritise actions that would yield the most desirable outcomes. Across 10 single- and multi-environment datasets, when trained on 89 randomly selected actions, LOVE predicts outcomes with 0.5%-3.4% mean error, and prioritises actions for maximising richness, maximising abundance, or removing unwanted species, with 94%-99% mean true positive rate and 10%-84% mean true negative rate across tasks. LOVE complements existing mechanism-first approaches for community ecology and may help address numerous applied challenges.

Gut microbial factors predict disease severity in a mouse model of multiple sclerosis

Gut bacteria are linked to neurodegenerative diseases but the risk factors beyond microbiota composition are limited. Here we used a pre-clinical model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE), to identify microbial risk factors. Mice with different genotypes and complex microbiotas or six combinations of a synthetic human microbiota were analysed, resulting in varying probabilities of severe neuroinflammation. However, the presence or relative abundances of suspected microbial risk factors failed to predict disease severity. Akkermansia muciniphila, often associated with MS, exhibited variable associations with EAE severity depending on the background microbiota. Significant inter-individual disease course variations were observed among mice harbouring the same microbiota. Evaluation of microbial functional characteristics and host immune responses demonstrated that the immunoglobulin A coating index of certain bacteria before disease onset is a robust individualized predictor of disease development. Our study highlights the need to consider microbial community networks and host-specific bidirectional interactions when aiming to predict severity of neuroinflammation.

Comparative analysis of the microbiota of sand fly vectors of Leishmania major and L. tropica in a mixed focus of cutaneous leishmaniasis in southeast Tunisia; ecotype shapes the bacterial community structure

Phlebotomine sand flies are vectors of the protozoan parasite Leishmania spp. Although the intestinal microbiota is involved in a wide range of biological and physiological processes and has the potential to alter vector competence, little is known about the impact of host species and environment on the gut microbiome. To address this issue, a comparative analysis of the microbiota of sand fly vector populations of Leishmania major and L. tropica in a mixed focus of cutaneous leishmaniasis in Tunisia was performed. Bacterial 16S rRNA gene amplification and Illumina MiSeq sequencing were used to characterize and compare the overall bacterial and fungal composition of field-collected sand flies: Phlebotomus papatasi, Ph. perniciosus, Ph. riouxi, and Ph. sergenti. Thirty-eight bacterial genera belonging to five phyla were identified in 117 female specimens. The similarities and differences between the microbiome data from different samples collected from three collections were determined using principal coordinate analysis (PCoA). Substantial variations in the bacterial composition were found between geographically distinct populations of the same sand fly species, but not between different species at the same location, suggesting that the microbiota content was structured according to environmental factors rather than host species. These findings suggest that host phylogeny may play a minor role in determining the insect gut microbiota, and its potential to affect the transmission of the Leishmania parasite appear to be very low. These results highlight the need for further studies to decode sand fly Leishmania-microbiota interactions, as even the same bacterial species, such as Enterococcus faecalis, can exert completely opposite effects when confronted with different pathogens within various host insects and vice versa.

A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia

Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often exhibit considerable shifts in response to environmental variation and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear how much shifts in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined phenotypic responses and microbiome composition in 20 genetically distinct Daphnia magna clones exposed to non-toxic and toxic diets containing Microcystis, a cosmopolitan cyanobacteria and common stressor for Daphnia. Daphnia exhibited significant plasticity in survival, reproduction, and population growth rates in response to Microcystis exposure. However, the effects of Microcystis exposure on the Daphnia microbiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.

Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles

There is experimental evidence that microbiomes have a strong influence on a range of host traits. Understanding the basis and importance of symbiosis between host and associated microorganisms is a rapidly developing research field, and we still lack a mechanistic understanding of ecological and genetic pressures affecting host-microbiome associations. Here Drosophila melanogaster lines from a large-scale artificial selection experiment were used to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions for two generations prior to assessment. Our findings provide strong evidence for symbiosis between host and microbiomes but we cannot reveal whether the interactions are adaptive, nor whether they are caused by genetic or ecological factors.

The plant-sucking insect selects assembly of the gut microbiota from environment to enhance host reproduction

Plant-sucking insects have intricate associations with a diverse array of microorganisms to facilitate their adaptation to specific ecological niches. The midgut of phytophagous true bugs is generally structured into four distinct compartments to accommodate their microbiota. Nevertheless, there is limited understanding regarding the origins of these gut microbiomes, the mechanisms behind microbial community assembly, and the interactions between gut microbiomes and their insect hosts. In this study, we conducted a comprehensive survey of microbial communities within the midgut compartments of a bean bug Riptortus pedestris, soybean plant, and bulk soil across 12 distinct geographical fields in China, utilizing high-throughput sequencing of the 16 S rRNA gene. Our findings illuminated that gut microbiota of the plant-sucking insects predominantly originated from the surrounding soil environment, and plants also play a subordinate role in mediating microbial acquisition for the insects. Furthermore, our investigation suggested that the composition of the insect gut microbiome was probably shaped by host selection and/or microbe-microbe interactions at the gut compartment level, with marginal influence from soil and geographical factors. Additionally, we had unveiled a noteworthy dynamic in the acquisition of core bacterial taxa, particularly Burkholderia, which were initially sourced from the environment and subsequently enriched within the insect midgut compartments. This bacterial enrichment played a significant role in enhancing insect host reproduction. These findings contribute to our evolving understanding of microbiomes within the insect-plant-soil ecosystem, shedding additional light on the intricate interactions between insects and their microbiomes that underpin the ecological significance of microbial partnerships in host adaptation.

Bifidobacterium longum subsp. longum BG-L47 boosts growth and activity of Limosilactobacillus reuteri DSM 17938 and its extracellular membrane vesicles

The aim of this study was to identify a Bifidobacterium strain that improves the performance of Limosilactobacillus reuteri DSM 17938. Initial tests showed that Bifidobacterium longum subsp. longum strains boosted the growth of DSM 17938 during in vivo-like conditions. Further characterization revealed that one of the strains, BG-L47, had better bile and acid tolerance compared to BG-L48, as well as mucus adhesion compared to both BG-L48 and the control strain BB536. BG-L47 also had the capacity to metabolize a broad range of carbohydrates and sugar alcohols. Mapping of glycoside hydrolase (GH) genes of BG-L47 and BB536 revealed many GHs associated with plant-fiber utilization. However, BG-L47 had a broader phenotypic fiber utilization capacity. In addition, B. longum subsp. longum cells boosted the bioactivity of extracellular membrane vesicles (MV) produced by L. reuteri DSM 17938 during co-cultivation. Secreted 5'-nucleotidase (5'NT), an enzyme that converts AMP into the signal molecule adenosine, was increased in MV boosted by BG-L47. The MV exerted an improved antagonistic effect on the pain receptor transient receptor potential vanilloid 1 (TRPV1) and increased the expression of the immune development markers IL-6 and IL-1ß in a peripheral blood mononuclear cell (PBMC) model. Finally, the safety of BG-L47 was evaluated both by genome safety assessment and in a human safety study. Microbiota analysis showed that the treatment did not induce significant changes in the composition. In conclusion, B. longum subsp. longum BG-L47 has favorable physiological properties, can boost the in vitro activity of L. reuteri DSM 17938, and is safe for consumption, making it a candidate for further evaluation in probiotic studies.

IMPORTANCE

By using probiotics that contain a combination of strains with synergistic properties, the likelihood of achieving beneficial interactions with the host can increase. In this study, we first performed a broad screening of Bifidobacterium longum subsp. longum strains in terms of synergistic potential and physiological properties. We identified a superior strain, BG-L47, with favorable characteristics and potential to boost the activity of the known probiotic strain Limosilactobacillus reuteri DSM 17938. Furthermore, we demonstrated that BG-L47 is safe for consumption in a human randomized clinical study and by performing a genome safety assessment. This work illustrates that bacteria-bacteria interactions differ at the strain level and further provides a strategy for finding and selecting companion strains of probiotics.

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses

Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.

Microplastic exposure disturbs sleep structure, reduces lifespan, and decreases ovary size in Drosophila melanogaster

The organ-specific toxicity resulting from microplastic (MP) exposure has been extensively explored, particularly concerning the gut, liver, testis, and lung. However, under natural conditions, these effects are not restricted to specific organs or tissues. Investigating whether MP exposure presents a systemic threat to an entire organism, impacting factors such as lifespan, sleep, and fecundity, is essential. In this study, we investigated the effects of dietary exposure to two different doses of MPs (1-5 μm) using the terrestrial model organism Drosophila melanogaster. Results indicated that the particles caused gut damage and remained within the digestive system. Continuous MP exposure significantly shortened the lifespan of adult flies. Even short-term exposure disrupted sleep patterns, increasing the length of daytime sleep episodes. Additionally, one week of MP exposure reduced ovary size, with a trend towards decreased egg-laying in mated females. Although MPs did not penetrate the brain or ovaries, transcriptome analysis revealed altered gene expression in these tissues. In the ovary, Gene Ontology (GO) analysis indicated genotoxic effects impacting inflammation, circadian regulation, and metabolic processes, with significant impacts on extracellular structure-related pathways. In the brain, GO analysis identified changes in pathways associated with proteolysis and carbohydrate metabolism. Overall, this study provides compelling evidence of the systemic negative effects of MP exposure, highlighting the urgent need to address and mitigate environmental MP pollution.

Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant

Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes.

IMPORTANCE

There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.

Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity

The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.

Global epistasis and the emergence of function in microbial consortia

The many functions of microbial communities emerge from a complex web of interactions between organisms and their environment. This poses a significant obstacle to engineering microbial consortia, hindering our ability to harness the potential of microorganisms for biotechnological applications. In this study, we demonstrate that the collective effect of ecological interactions between microbes in a community can be captured by simple statistical models that predict how adding a new species to a community will affect its function. These predictive models mirror the patterns of global epistasis reported in genetics, and they can be quantitatively interpreted in terms of pairwise interactions between community members. Our results illuminate an unexplored path to quantitatively predicting the function of microbial consortia from their composition, paving the way to optimizing desirable community properties and bringing the tasks of predicting biological function at the genetic, organismal, and ecological scales under the same quantitative formalism.

Community assembly of ectomycorrhizal fungal communities in pure and mixed Pinus massoniana forests

Ectomycorrhizal (EcM) fungi play an important role in nutrient cycling and community ecological dynamics and are widely acknowledged as important components of forest ecosystems. However, little information is available regarding EcM fungal community structure or the possible relationship between EcM fungi, soil properties, and forestry activities in Pinus massoniana forests. In this study, we evaluated soil properties, extracellular enzyme activities, and fungal diversity and community composition in root and soil samples from pure Pinus massoniana natural forests, pure P. massoniana plantations, and P. massoniana and Liquidambar gracilipes mixed forests. The mixed forest showed the highest EcM fungal diversity in both root and bulk soil samples. Community composition and co-occurrence network structures differed significantly between forest types. Variation in the EcM fungal community was significantly correlated with the activities of β-glucuronidase and β-1,4-N-acetylglucosaminidase, whereas non-EcM fungal community characteristics were significantly correlated with β-1,4-glucosidase and β-glucuronidase activities. Furthermore, stochastic processes predominantly drove the assembly of both EcM and non-EcM fungal communities, while deterministic processes exerted greater influence on soil fungal communities in mixed forests compared to pure forests. Our findings may inform a deeper understanding of how the assembly processes and environmental roles of subterranean fungal communities differ between mixed and pure plantations and may provide insights for how to promote forest sustainability in subtropical areas.

The importance of host physical niches for the stability of gut microbiome composition

Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history

Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.

The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation

Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.

Gut Microbiota Affects Host Fitness of Fall Armyworm Feeding on Different Food Types

The fall armyworm (FAW), Spodoptera frugiperda, seriously threatens food and cash crops. Maize, wheat, and even rice damage by FAWs have been reported in many areas of China. It is urgent to clarify the mechanism which FAWs adapt to different feeding hosts and develop effective control technologies. Two-sex life tables and 16s rDNA sequencing were used to determine the host fitness and gut microbial diversity of FAWs when fed four different food types. Considering the life history parameters, pupa weight, and nutrient utilization indexes, the host fitness of FAWs when fed different food types changed in descending order as follows: artificial diet, maize, wheat, and rice. The gut microbial composition and the diversity of FAWs when fed different food types were significantly different, and those changes were driven by low-abundant bacteria. The gut microbes of FAWs that were fed with maize had the highest diversity. The functions of the gut microbes with significant abundance differences were enriched in nutrient and vitamin metabolism and other pathways that were closely related to host adaptation. Furthermore, we identified five genera (Acinetobacter, Variovorax, Pseudomonas, Bacillus, and Serratia) and one genus (Rahnella) that were positively and negatively correlated with the host fitness, respectively. This study revealed the possible role of gut microbes in the host adaptation of FAWs.

Microbiome-derived acidity protects against microbial invasion in Drosophila

Microbial invasions underlie host-microbe interactions resulting in pathogenesis and probiotic colonization. In this study, we explore the effects of the microbiome on microbial invasion in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival and lead to a reduction in microbial burden during infection. Using a microbial interaction assay, we report that L. plantarum inhibits the growth of invasive bacteria, while A. tropicalis reduces this inhibition. We further show that inhibition by L. plantarum is linked to its ability to acidify its environment via lactic acid production by lactate dehydrogenase, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid from the microbiome is a gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods and findings described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.

Exploring the immune-inflammatory mechanism of Maxing Shigan Decoction in treating influenza virus A-induced pneumonia based on an integrated strategy of single-cell transcriptomics and systems biology

BACKGROUND

Influenza is an acute respiratory infection caused by influenza virus. Maxing Shigan Decoction (MXSGD) is a commonly used traditional Chinese medicine prescription for the prevention and treatment of influenza. However, its mechanism remains unclear.

METHOD

The mice model of influenza A virus pneumonia was established by nasal inoculation. After 3 days of intervention, the lung index was calculated, and the pathological changes of lung tissue were detected by HE staining. Firstly, transcriptomics technology was used to analyze the differential genes and important pathways in mouse lung tissue regulated by MXSGD. Then, real-time fluorescent quantitative PCR (RT-PCR) was used to verify the changes in mRNA expression in lung tissues. Finally, intestinal microbiome and intestinal metabolomics were performed to explore the effect of MXSGD on gut microbiota.

RESULTS

The lung inflammatory cell infiltration in the MXSGD group was significantly reduced (p < 0.05). The results of bioinformatics analysis for transcriptomics results show that these genes are mainly involved in inflammatory factors and inflammation-related signal pathways mediated inflammation biological modules, etc. Intestinal microbiome showed that the intestinal flora Actinobacteriota level and Desulfobacterota level increased in MXSGD group, while Planctomycetota in MXSGD group decreased. Metabolites were mainly involved in primary bile acid biosynthesis, thiamine metabolism, etc. This suggests that MXSGD has a microbial-gut-lung axis regulation effect on mice with influenza A virus pneumonia.

CONCLUSION

MXSGD may play an anti-inflammatory and immunoregulatory role by regulating intestinal microbiome and intestinal metabolic small molecules, and ultimately play a role in the treatment of influenza A virus pneumonia.

Host evolution shapes gut microbiome composition in Astyanax mexicanus

The ecological and genetic changes that underlie the evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics, and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, Astyanax mexicanus, in their natural environments and under controlled laboratory conditions. Field-collected samples were dominated by very few taxa and showed considerable interindividual variation. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish evolution shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrated that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.

Host genetics and larval host plant modulate microbiome structure and evolution underlying the intimate insect-microbe-plant interactions in Parnassius species on the Qinghai-Tibet Plateau

Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.

Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition

Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C). The results showed that heat stress and cold stress caused injury and swelling, terminal congestion, cell vacuolation, and necrosis of the gill tissue of L. longirostris. For intestinal microbiota, the abundances of Pseudomonadota and Bacillota increased at the cold stress, while the abundances of Fusobacteriota and Bacteroidota increased at the heat stress. The number of opportunistic bacteria, mainly Aeromonas and Acinetobacter, was the highest under cold stress. In addition, the richness of the intestinal microbiota decreased significantly at heat and cold stresses, while evenness increased. Prediction of intestinal microbiota function showed that most common functions, such as metabolism of cofactors and vitamins, energy metabolism and replication and repair, were decreased significantly at heat stress and cold stress, and phylogenetic relationship analysis revealed significant differences among the groups. In conclusion, the change of temperature altered the gill tissue structure, and affected the structure and homeostasis of the intestinal microbiota, thus affecting the survival time of L. longirostris, and cold stress had a greater effect than heat stress.

Cold exposure, gut microbiota and health implications: A narrative review

Temperature has been recognized as an important environmental factor affecting the composition and function of gut microbiota (GM). Although research on high-temperature impacts has been well studied, knowledge about the effect of cold exposure on GM remains limited. This narrative review aims to synthesize the latest scientific findings on the impact of cold exposure on mammalian GM, and its potential health implications. Chronic cold exposure could disrupt the α-diversity and the composition of GM in both experimental animals and wild-living hosts. Meanwhile, cold exposure could impact gut microbial metabolites, such as short-chain fatty acids. We also discussed plausible biological pathways and mechanisms by which cold-induced changes may impact host health, including metabolic homeostasis, fitness and thermogenesis, through the microbiota-gut-brain axis. Intriguingly, alterations in GM may provide a tool for favorably modulating the host response to the cold temperature. Finally, current challenges and future perspectives are discussed, emphasizing the need for translational research in humans. GM could be manipulated by utilizing nutritional strategies, such as probiotics and prebiotics, to deal with cold-related health issues and enhance well-being in populations living or working in cold environments.

Host-related traits influence the microbial diversity of the invasive signal crayfish Pacifastacus leniusculus

The microbiome influences a variety of host-environment interactions, and there is mounting evidence of its significant role in biological invasions. During invasion, shifts in microbial diversity and function can occur due to both changing characteristics of the novel environment and physiological condition of the host. The signal crayfish (Pacifastacus leniusculus) is one of the most successful crayfish invaders in Europe. During range expansion, its populations often exhibit differences in many traits along the invasion range, including sex-composition, size-structure and aggressiveness, but to date it was not studied whether crayfish traits can also drive changes in the host microbiome. Thus, we used 16S rRNA gene amplicon sequencing to examine the effects of host-related traits, namely total length (TL), body condition index (FCF), hepatosomatic index (HSI) and sex on the microbial diversity of the signal crayfish. We examined both external (exoskeletal) and internal (intestinal, hepatopancreatic, hemolymph) microbiomes of 110 signal crayfish individuals from four sites along its invasion range in the Korana River, Croatia. While sex did not exhibit a significant effect on the microbial diversity in any of the examined tissues, exoskeletal, intestinal and hemolymph microbial diversity significantly decreased with increasing crayfish size. Additionally, significant effects of signal crayfish condition (FCF, HSI) on microbial diversity were recorded in the hepatopancreas, a main energy storage organ in crayfish that supports reproduction and growth and also regulates immune response. Our findings provide a baseline for evaluating the contribution of microbiome to an invader's overall health, fitness and subsequent invasion success.

Why do hosts malfunction without microbes? Missing benefits versus evolutionary addiction

Microbes are widely recognized to be vital to host health. This new consensus rests, in part, on experiments showing how hosts malfunction when microbes are removed. More and more microbial dependencies are being discovered, even in fundamental processes such as development, immunity, physiology, and behavior. But why do they exist? The default explanation is that microbes are beneficial; when hosts lose microbes, they also lose benefits. Here I call attention to evolutionary addiction, whereby a host trait evolves a need for microbes without having been improved by them. Evolutionary addiction should be considered when interpreting microbe-removal experiments, as it is a distinct and potentially common process. Further, it may have unique implications for the evolution and stability of host-microbe interactions.

Catabolic Network of the Fermentative Gut Bacterium Phocaeicola vulgatus (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective

INTRODUCTION

Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary-fiber-fueled, fermentative metabolism the microbial community as well as the host health. Moreover, the fermentative metabolism of P. vulgatus bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the P. vulgatus physiology.

METHODS

P. vulgatus was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics.

RESULTS

The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (gCDW/mmolS) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (mMATP/mMC) from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one sided (with rhamnose or fucose: mainly propane-1,2-diol). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to d-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, Sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected.

CONCLUSIONS

The present study provides insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols.

On the limits to invasion prediction using coexistence outcomes

The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes relevant to systems in nature. Here, we study the limits to this predictability under a geometric and probabilistic Lotka-Volterra framework. We show that while individual survival probability in coexistence dynamics can be fairly closely translated into invader colonization probability in invasion dynamics, the translation is less precise between community persistence and community augmentation, and worse between exclusion probability and replacement probability. These results provide a guiding and testable theoretical framework regarding the translatability of outcomes between coexistence and invasion outcomes when communities are represented by Lotka-Volterra dynamics under environmental uncertainty.

A toxic environment selects for specialist microbiome in poison frogs

Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

Bacterial and fungal components of the microbiome have distinct roles in Hawaiian drosophila reproduction

The microbiome provides numerous physiological benefits for host animals. The role of bacterial members of microbiomes to host physiology is well-documented. However, much less is known about the contributions and interactions of fungal members, even though fungi are integral components of many microbiomes, including those of humans and insects. Here, we used antibacterial and antifungal drugs to manipulate the gut microbiome of a Hawaiian picture-wing Drosophila species, Drosophila grimshawi, and identified distinct effects for each treatment on microbiome community stability, reproduction, and lipid metabolism. Female oogenesis, fecundity, and mating drive were significantly diminished with antifungal treatment. In contrast, male fecundity was affected by antibacterial but not antifungal treatment. For males and females, simultaneous treatment with both antibacterial and antifungal drugs resulted in severely reduced fecundity and changes in fatty acid levels and composition. Microbial transplants using frass harvested from control flies partially restored microbiome composition and female fecundity. Overall, our results reveal that antibacterial and antifungal treatments have distinct effects on host fecundity, mating behavior, and lipid metabolism, and that interkingdom interactions contribute to microbial community stability and reproduction.

Drosophila melanogaster as a model to study polymicrobial synergy and dysbiosis

The fruit fly Drosophila melanogaster has emerged as a valuable model for investigating human biology, including the role of the microbiome in health and disease. Historically, studies involving the infection of D. melanogaster with single microbial species have yielded critical insights into bacterial colonization and host innate immunity. However, recent evidence has underscored that multiple microbial species can interact in complex ways through physical connections, metabolic cross-feeding, or signaling exchanges, with significant implications for healthy homeostasis and the initiation, progression, and outcomes of disease. As a result, researchers have shifted their focus toward developing more robust and representative in vivo models of co-infection to probe the intricacies of polymicrobial synergy and dysbiosis. This review provides a comprehensive overview of the pioneering work and recent advances in the field, highlighting the utility of Drosophila as an alternative model for studying the multifaceted microbial interactions that occur within the oral cavity and other body sites. We will discuss the factors and mechanisms that drive microbial community dynamics, as well as their impacts on host physiology and immune responses. Furthermore, this review will delve into the emerging evidence that connects oral microbes to systemic conditions in both health and disease. As our understanding of the microbiome continues to evolve, Drosophila offers a powerful and tractable model for unraveling the complex interplay between host and microbes including oral microbes, which has far-reaching implications for human health and the development of targeted therapeutic interventions.

Microbes control Drosophila germline stem cell increase and egg maturation through hormonal pathways

Reproduction is highly dependent on environmental and physiological factors including nutrition, mating stimuli and microbes. Among these factors, microbes facilitate vital functions for host animals such as nutritional intake, metabolic regulation, and enhancing fertility under poor nutrition conditions. However, detailed molecular mechanisms by which microbes control germline maturation, leading to reproduction, remain largely unknown. In this study, we show that environmental microbes exert a beneficial effect on Drosophila oogenesis by promoting germline stem cell (GSC) proliferation and subsequent egg maturation via acceleration of ovarian cell division and suppression of apoptosis. Moreover, insulin-related signaling is not required; rather, the ecdysone pathway is necessary for microbe-induced increase of GSCs and promotion of egg maturation, while juvenile hormone contributes only to increasing GSC numbers, suggesting that hormonal pathways are activated at different stages of oogenesis. Our findings reveal that environmental microbes can enhance host reproductivity by modulating host hormone release and promoting oogenesis.