The evolution of the host microbiome as an ecosystem on a leash

Accessory microbiomes

In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host function. Much less attention has been paid to microbiome members that are present in only a subset of hosts. Such accessory microbiomes must in large part consist of species that have no effect on fitness, but some will have deleterious effects on fitness (pathogens), and it is also possible that some accessory microbiome members benefit an ecologically distinct subset of hosts. This short paper discusses what we know about accessory microbiomes, specifically by comparing it with the concept of accessory genomes.

Targeting the microbiota-mitochondria crosstalk in neurodegeneration with senotherapeutics

Neurodegenerative diseases are a group of age-related disorders characterized by a chronic and progressive loss of function and/or structure of synapses, neurons, and glial cells. The etiopathogenesis of neurodegenerative diseases is characterized by a complex network of intricately intertwined pathophysiological processes that are still not fully understood. Safe and effective disease-modifying treatments are urgently needed, but still not available. Accumulating evidence suggests that gastrointestinal dyshomeostasis and microbial dysbiosis might play an important role in neurodegeneration by acting as either primary or secondary pathophysiological factors. The research on the role of microbiota in neurodegeneration is in its early phase; however, accumulating evidence suggests that dysbiosis might promote neurodegenerative diseases by disrupting mitochondrial function and inducing mitochondrial dysfunction-associated senescence (MiDAS), possibly due to bidirectional crosstalk based on the common evolutionary origin of mitochondria and bacteria. Cellular senescence is an onco-supressive homeostatic mechanism that results in an irreversible cell cycle arrest upon exposure to noxious stimuli. Senescent cells resist apoptosis via senescent cell anti-apoptotic pathways (SCAPs) and transition into a state known as senescence-associated secretory phenotype (SASP) that generates a cytotoxic proinflammatory microenvironment. Cellular senescence results in the adoption of a detrimental vicious cycle driven by dysbiosis, mitochondrial dysfunction, inflammation, and oxidative stress - a pathophysiological positive feedback loop that results in neuroinflammation and neurodegeneration. Detrimental effects of MiDAS might be prevented and abolished by mitochondria-targeted senotherapeutics, a group of drugs specifically designed to alleviate senescence by inhibiting SCAPs (senolytics), or inhibiting SASP (senomorphics).

Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites

BACKGROUND

Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.

RESULTS

To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.

CONCLUSIONS

Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.

Discovery of Lactomodulin, a Unique Microbiome-Derived Peptide That Exhibits Dual Anti-Inflammatory and Antimicrobial Activity against Multidrug-Resistant Pathogens

The human body is a superorganism that harbors trillions of microbes, most of which inhabit the gut. To colonize our bodies, these microbes have evolved strategies to regulate the immune system and maintain intestinal immune homeostasis by secreting chemical mediators. There is much interest in deciphering these chemicals and furthering their development as novel therapeutics. In this work, we present a combined experimental and computational approach to identifying functional immunomodulatory molecules from the gut microbiome. Based on this approach, we report the discovery of lactomodulin, a unique peptide from Lactobacillus rhamnosus that exhibits dual anti-inflammatory and antibiotic activities and minimal cytotoxicity in human cell lines. Lactomodulin reduces several secreted proinflammatory cytokines, including IL-8, IL-6, IL-1β, and TNF-α. As an antibiotic, lactomodulin is effective against a range of human pathogens, and is most potent against antibiotic-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). The multifunctional activity of lactomodulin affirms that the microbiome encodes evolved functional molecules with promising therapeutic potential.

Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore (Asellus aquaticus)

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

The cecal ecosystem is a great contributor to intramuscular fat deposition in broilers

Intramuscular fat (IMF) content is a meat quality trait of major economic importance in animal production. Emerging evidence has demonstrated that meat quality can be improved by regulating the gut microbiota. However, the organization and ecological properties of the gut microbiota and its relationship with the IMF content remain unclear in chickens. Here, we investigated the microbial communities of 206 cecal samples from broilers with excellent meat quality. We noted that the cecal microbial ecosystem obtained from hosts reared under the same management and dietary conditions showed clear compositional stratification. Two enterotypes, in which the ecological properties, including diversity and interaction strengths, were significantly different, described the microbial composition pattern. Compared with enterotype 2, enterotype 1, distinguished by the Clostridia_vadinBB60_group, had a higher fat deposition, although no discrepancy was found in growth performance and meat yield. A moderate correlation was observed in the IMF content between 2 muscle tissues, despite the IMF content of thigh muscle was 42.76% greater than that of breast muscle. Additionally, the lower abundance of cecal vadinBE97 was related to higher IMF levels in both muscle tissues. Although vadinBE97 accounted for 0.40% of the total abundance of genera in the cecum, it exhibited significant and positive correlations with other genera (accounting for 25.3% of the tested genera). Our results highlight important insights into the cecal microbial ecosystem and its association with meat quality. Microbial interactions should be carefully considered when developing approaches to improve the IMF content by regulating the gut microbiota in broilers.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota: a Pilot Study

Bovine respiratory disease (BRD) remains the most significant health challenge affecting the North American beef cattle industry and results in $3 billion in economic losses yearly. Current BRD control strategies mainly rely on antibiotics, with metaphylaxis commonly employed to mitigate BRD incidence in commercial feedlots.

Microbial community structure dynamics of invasive bullfrog with meningitis-like infectious disease

Meningitis-like infectious disease (MID) (also known as frog cataract and torticollis) is a disease prone to occur in amphibians and reptiles. It is highly contagious and has a high mortality rate. In this study, we sampled and sequenced microbiomes from oral and intestinal samples of five normal and five diseased bullfrogs. The analysis found that the richness, uniformity, and abundance of the microbial community of the diseased bullfrogs were significantly higher than those of the normal bullfrogs in both the oral cavity and the gut. In the diseased group, the abundance of Elizabethkingia significantly increased and that of Lactococcus significantly decreased. It showed that the structure of the microbial community had changed a lot in diseased frogs. After the pathogenic bacteria infected the body, it might be make the decline in the immune function of the body declined, and resulting in some conditional pathogenic bacteria in the water body further infecting the body. As a result, the richness and composition of the microbial community significantly changed. This study can provide a theoretical basis for the control of MID of bullfrogs.

Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus)

BACKGROUND

Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing.

RESULTS

The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity.

CONCLUSIONS

Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.

Reprogramming of the gut microbiota following feralization in Sus scrofa

BACKGROUND

Wild boar has experienced several evolutionary trajectories from which domestic (under artificial selection) and the feral pig (under natural selection) originated. Strong adaptation deeply affects feral population's morphology and physiology, including the microbiota community. The gut microbiota is generally recognized to play a crucial role in maintaining host health and metabolism. To date, it is unclear whether feral populations' phylogeny, development stages or lifestyle have the greatest impact in shaping the gut microbiota, as well as how this can confer adaptability to new environments. Here, in order to deepen this point, we characterized the gut microbiota of feral population discriminating between juvenile and adult samples, and we compared it to the microbiota structure of wild boar and domestic pig as the references. Gut microbiota composition was estimated through the sequencing of the partial 16S rRNA gene by DNA metabarcoding and High Throughput Sequencing on DNA extracted from fecal samples.

RESULTS

The comparison of microbiota communities among the three forms showed significant differences. The feral form seems to carry some bacteria of both domestic pigs, derived from its ancestral condition, and wild boars, probably as a sign of a recent re-adaptation strategy to the natural environment. In addition, interestingly, feral pigs show some exclusive bacterial taxa, also suggesting an innovative nature of the evolutionary trajectories and an ecological segregation in feral populations, as already observed for other traits.

CONCLUSIONS

The feral pig showed a significant change between juvenile and adult microbiota suggesting an influence of the wild environment in which these populations segregate. However, it is important to underline that we certainly cannot overlook that these variations in the structure of the microbiota also depended on the different development stages of the animal, which in fact influence the composition of the intestinal microbiota. Concluding, the feral pigs represent a new actor living in the same geographical space as the wild boars, in which its gut microbial structure suggests that it is mainly the result of environmental segregation, most different from its closest relative. This gives rise to interesting fields of exploration regarding the changed ecological complexity and the consequent evolutionary destiny of the animal communities involved in this phenomenon.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Metabolites of sea cucumber sulfated polysaccharides fermented by Parabacteroides distasonis and their effects on cross-feeding

Sea cucumber sulfated polysaccharide (SCSPsj) is one of the dietary components which effectively modulates gut microbiota; however, the underlying mechanism remains unclear. In the present study, the interaction between SCSPsj and its utilizer (Parabacteroides distasonis) was investigated. Further study was carried out to explore the cross-feeding between intestinal Bacteroidales mediated by SCSPsj. The results revealed that SCSPsj can be fermented by P. distasonis to produce various microbial metabolites, including organic acids and derivatives, lipids and lipid-like molecules, organoheterocyclic compounds. SCSPsj can regulate the succinate pathway and acetyl-CoA pathway to influence the production of propanoic acid and acetic acid, respectively. Moreover, the SCSPsj-fermented supernatants of P. distasonis can only promote the growth of B. stercoris, B. vulgatus and P. johnsonii among 8 intestinal Bacteroidales strains through cross-feeding. The effect of cross-feeding was related to spatial distances and bacterial species. Moreover, the cross-feeding was correlated with compounds belonging to organic acids and derivatives, lipids and lipid-like molecules. These findings could provide new insights into the interaction between SCSPsj and gut microbiota.

Sex, puberty, and the gut microbiome

In brief

Sex differences in the gut microbiome may impact multiple aspects of human health and disease. In this study, we review the evidence for microbial sex differences in puberty and adulthood and discuss potential mechanisms driving differentiation of the sex-specific gut microbiome.

Abstract

In humans, the gut microbiome is strongly implicated in numerous sex-specific physiological processes and diseases. Given this, it is important to understand how sex differentiation of the gut microbiome occurs and how these differences contribute to host health and disease. While it is commonly believed that the gut microbiome stabilizes after 3 years of age, our review of the literature found considerable evidence that the gut microbiome continues to mature during and after puberty in a sex-dependent manner. We also review the intriguing, though sparse, literature on potential mechanisms by which host sex may influence the gut microbiome, and vice versa, via sex steroids, bile acids, and the immune system. We conclude that the evidence for the existence of a sex-specific gut microbiome is strong but that there is a dearth of research on how host-microbe interactions lead to this differentiation. Finally, we discuss the types of future studies needed to understand the processes driving the maturation of sex-specific microbial communities and the interplay between gut microbiota, host sex, and human health.

Within-host evolution of the gut microbiome

Gut bacteria inhabit a complex environment that is shaped by interactions with their host and the other members of the community. While these ecological interactions have evolved over millions of years, mounting evidence suggests that gut commensals can evolve on much shorter timescales as well, by acquiring new mutations within individual hosts. In this review, we highlight recent progress in understanding the causes and consequences of short-term evolution in the mammalian gut, from experimental evolution in murine hosts to longitudinal tracking of human cohorts. We also discuss new opportunities for future progress by expanding the repertoire of focal species, hosts, and surrounding communities, and by combining deep-sequencing technologies with quantitative frameworks from population genetics.

Gut-joint axis: Gut dysbiosis can contribute to the onset of rheumatoid arthritis via multiple pathways

Rheumatoid Arthritis (RA) is an autoimmune disease characterized by loss of immune tolerance and chronic inflammation. It is pathogenesis complex and includes interaction between genetic and environmental factors. Current evidence supports the hypothesis that gut dysbiosis may play the role of environmental triggers of arthritis in animals and humans. Progress in the understanding of the gut microbiome and RA. has been remarkable in the last decade. In vitro and in vivo experiments revealed that gut dysbiosis could shape the immune system and cause persistent immune inflammatory responses. Furthermore, gut dysbiosis could induce alterations in intestinal permeability, which have been found to predate arthritis onset. In contrast, metabolites derived from the intestinal microbiota have an immunomodulatory and anti-inflammatory effect. However, the precise underlying mechanisms by which gut dysbiosis induces the development of arthritis remain elusive. This review aimed to highlight the mechanisms by which gut dysbiosis could contribute to the pathogenesis of RA. The overall data showed that gut dysbiosis could contribute to RA pathogenesis by multiple pathways, including alterations in gut barrier function, molecular mimicry, gut dysbiosis influences the activation and the differentiation of innate and acquired immune cells, cross-talk between gut microbiota-derived metabolites and immune cells, and alterations in the microenvironment. The relative weight of each of these mechanisms in RA pathogenesis remains uncertain. Recent studies showed a substantial role for gut microbiota-derived metabolites pathway, especially butyrate, in the RA pathogenesis.

Multi stress system: Microplastics in freshwater and their effects on host microbiota

Microplastics are persistent and complex contaminants that have recently been found in freshwater systems, raising concerns about their presence in aquatic organisms. Plastics tend to be seen as an inert material; however, it is not well known if exposure to plastics for a prolonged time, in combination with organic chemicals, causes organism mortality. Ingestion of microplastics in combination with another pollutant may affect a host organism's fitness by altering the host microbiome. In this study, we investigated how microplastics interact with other pollutants in this multi-stress system, and whether they have a synergistic impact on the mortality of an aquatic organism and its microbiome. We used wild water boatmen Hemiptera (Corixidae) found at lake Erken located in east-central Sweden in a fully factorial two-way microcosm experiment designed with polystyrene microspheres and a commonly used detergent. The microplastic-detergent interaction is manifested as a significant increase in mortality compared to the other treatments at 48 h of exposure. The diversity of the microbial communities in the water was significantly affected by the combined treatment of microplastics and the detergent while the microbial communities in the host were affected by the treatments with microplastics and the detergent alone. Changes in relative abundance in Gammaproteobacteria (family Enterobacteriaceae), were observed in the perturbed treatments mostly associated with the presence of the detergent. This confirms that microplastics can interact with detergents having toxic effects on wild water boatmen. Furthermore, microplastics may impact wild organisms via changes in their microbial communities.

The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish's bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended.

The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling

Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the Akkermansia genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of Akkermansia induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower Akkermansiaceae/Lachnospiraceae (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.

Experimental temperatures shape host microbiome diversity and composition

Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.

Host's genetic background determines the outcome of reciprocal faecal transplantation on life-history traits and microbiome composition

BACKGROUND

Microbes play a role in their host's fundamental ecological, chemical, and physiological processes. Host life-history traits from defence to growth are therefore determined not only by the abiotic environment and genotype but also by microbiota composition. However, the relative importance and interactive effects of these factors may vary between organisms. Such connections remain particularly elusive in Lepidoptera, which have been argued to lack a permanent microbiome and have microbiota primarily determined by their diet and environment. We tested the microbiome specificity and its influence on life-history traits of two colour genotypes of the wood tiger moth (Arctia plantaginis) that differ in several traits, including growth. All individuals were grown in the laboratory for several generations with standardized conditions. We analyzed the bacterial community of the genotypes before and after a reciprocal frass (i.e., larval faeces) transplantation and followed growth rate, pupal mass, and the production of defensive secretion.

RESULTS

After transplantation, the fast-growing genotype grew significantly slower compared to the controls, but the slow-growing genotype did not change its growth rate. The frass transplant also increased the volume of defensive secretions in the fast-growing genotype but did not affect pupal mass. Overall, the fast-growing genotype appeared more susceptible to the transplantation than the slow-growing genotype. Microbiome differences between the genotypes strongly suggest genotype-based selective filtering of bacteria from the diet and environment. A novel cluster of insect-associated Erysipelotrichaceae was exclusive to the fast-growing genotype, and specific Enterococcaceae were characteristic to the slow-growing genotype. These Enterococcaceae became more prevalent in the fast-growing genotype after the transplant, which suggests that a slower growth rate is potentially related to their presence.

CONCLUSIONS

We show that reciprocal frass transplantation can reverse some genotype-specific life-history traits in a lepidopteran host. The results indicate that genotype-specific selective filtering can fine-tune the bacterial community at specific life stages and tissues like the larval frass, even against a background of a highly variable community with stochastic assembly. Altogether, our findings suggest that the host's genotype can influence its susceptibility to being colonized by microbiota, impacting key life-history traits.

Immunological pathogenesis of Bovine E. coli infection in a model of C. elegans

BACKGROUND

Cattle industry is critical for China's livestock industry, whereas E. coli infection and relevant diseases could lead huge economic loss. Traditional mammalian models would be costly, time consuming and complicated to study pathological changes of bovine E. coli. There is an urgent need for a simple but efficient animal model to quantitatively evaluate the pathological changes of bovine-derived E. coli in vivo. Caenorhabditis elegans (C. elegans) has a broad host range of diverse E. coli strains with advantages, including a short life cycle, a simple structure, a transparent body which is easily visualized, a well-studied genetic map, an intrinsic immune system which is conservable with more complicated mammalians.

RESULTS

Here, we considered that O126 was the dominant serotype, and a total of 19 virulence factors were identified from 41 common E. coli virulence factors. Different E. coli strains with diverse pathogenicity strengths were tested in C. elegans in E. coli with higher pathogenicity (EC3/10), Nsy-1, Sek-1 and Pmk-1 of the p38 MAPK signaling pathway cascade and the expression of the antimicrobial peptides Abf-3 and Clec-60 were significantly up-regulated comparing with other groups. E. coli with lower pathogenicity (EC5/13) only activated the expression of Nsy-1 and Sek-1 genes in the p38 MAPK signaling pathway, Additionally, both groups of E. coli strains caused significant upregulation of the antimicrobial peptide Spp-1.

CONCLUSION

Thirteen E. coli strains showed diverse pathogenicity in nematodes and the detection rate of virulence factors did not corresponding to the virulence in nematodes, indicating complex pathogenicity mechanisms. We approved that C. elegans is a fast and convenient detection model for pathogenic bacteria virulence examinations.

Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations

Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are vulnerable to environmental stressors, particularly anthropogenic disturbance such as antibiotics, resulting in dysbiosis. In cases where microbiome transmission occurs, a disrupted microbiome may then become a contagious pathology causing harm to the host across generations. We tested this hypothesis using the specialized socially transmitted gut microbiome of honey bees as a model system. By experimentally passaging tetracycline-treated microbiomes across worker 'generations' we found that an environmentally acquired dysbiotic phenotype is heritable. As expected, the antibiotic treatment disrupted the microbiome, eliminating several common and functionally important taxa and strains. When transmitted, the dysbiotic microbiome harmed the host in subsequent generations. Particularly, naïve bees receiving antibiotic-altered microbiomes died at higher rates when challenged with further antibiotic stress. Bees with inherited dysbiotic microbiomes showed alterations in gene expression linked to metabolism and immunity, among other pathways, suggesting effects on host physiology. These results indicate that there is a possibility that sublethal exposure to chemical stressors, such as antibiotics, may cause long-lasting changes to functional host-microbiome relationships, possibly weakening the host's progeny in the face of future ecological challenges. Future studies under natural conditions would be important to examine the extent to which negative microbiome-mediated phenotypes could indeed be heritable and what role this may play in the ongoing loss of biodiversity.

Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.

Spatial differences in Casuarina equisetifolia L. endophyte community structure

Purpose

Casuarina equisetifolia, a fast-growing, abundant tree species on the southeastern coast of China, plays an important role in protecting the coastal environment, but the ecological processes that govern microbiome assembly and within-plant microorganism transmission are poorly known.

Methods

In this paper, we used ITS and 16S amplification techniques to study the diversity of fungal and bacterial endophytes in critical plant parts of this species: seeds, branchlets, and roots. Additionally, we examined the litter of this species to understand the process of branchlets from birth to litter.

Result

We uncovered a non-random distribution of endophyte diversity in which branchlets had the greatest and seeds had the lowest endophytic fungal diversity. In contrast, litter endophytic bacteria had the highest diversity, and branchlets had the lowest diversity. As for fungi, a large part of the seed microbiome was transmitted to the phyllosphere, while a large part of the bacterial microbiome in the seed was transmitted to the root.

Conclusion

Our study provides comprehensive evidence on diversity, potential sources, and transmission pathways for non-crop microbiome assembly and has implications for the management and manipulation of the non-crop microbiome in the future.

The Gill Microbiota of Argopecten purpuratus Scallop Is Dominated by Symbiotic Campylobacterota and Upwelling Intensification Differentially Affects Their Abundance

Despite the great importance of gills for bivalve mollusks (respiration, feeding, immunity), the microbiota associated with this tissue has barely been characterized in scallops. The scallop Argopecten purpuratus is an important economic resource that is cultivated in areas where coastal upwelling is intensifying by climate change, potentially affecting host-microbiota interactions. Thus, we first characterized the bacterial community present in gills from cultivated scallops (by 16S rRNA gene amplicon sequencing) and assessed their stability and functional potential in animals under farm and laboratory conditions. Results showed that under both conditions the gill bacterial community is dominated by the phylum Campylobacterota (57%), which displays a chemoautotrophic potential that could contribute to scallop nutrition. Within this phylum, two phylotypes, namely symbionts A and B, were the most abundant; being, respectively, taxonomically affiliated to symbionts with nutritional functions in mussel gills, and to uncultured bacteria present in coral mucus. Additionally, in situ hybridization and scanning electron microscopy analyses allowed us to detect these symbionts in the gills of A. purpuratus. Given that shifts in upwelling phenology can cause disturbances to ecosystems, affecting bacteria that provide beneficial functions to the host, we further assessed the changes in the abundance of the two symbionts (via qPCR) in response to a simulated upwelling intensification. The exposure to combined decreasing values in the temperature, pH, and oxygen levels (upwelling conditions) favored the dominance of symbiont B over symbiont A; suggesting that symbiont abundances are modulated by these environmental changes. Overall, results showed that changes in the main Campylobacterota phylotypes in response to upwelling intensification could affect its symbiotic function in A. purpuratus under future climate change scenarios. These results provide the first insight into understanding how scallop gill-microbial systems adapt and respond to climate change stressors, which could be critical for managing health, nutrition, and scallop aquaculture productivity.

Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity

BACKGROUND

Identifying meaningful ecological associations between host and components of the microbiome is challenging. This is especially true for hosts such as marine macroalgae where the taxonomic composition of the microbiome is highly diverse and variable in space and time. Identifying core taxa is one way forward but there are many methods and thresholds in use. This study leverages a large dataset of microbial communities associated with the widespread brown macroalga, Fucus distichus, across sites and years on one island in British Columbia, Canada. We compare three different methodological approaches to identify core taxa at the amplicon sequence variant (ASV) level from this dataset: (1) frequency analysis of taxa on F. distichus performed over the whole dataset, (2) indicator species analysis (IndVal) over the whole dataset that identifies frequent taxa that are enriched on F. distichus in comparison to the local environment, and (3) a two-step IndVal method that identifies taxa that are consistently enriched on F. distichus across sites and time points. We then investigated a F. distichus time-series dataset to see if those core taxa are seasonally consistent on another remote island in British Columbia, Canada. We then evaluate host-specificity of the identified F. distichus core ASVs using comparative data from 32 other macroalgal species sampled at one of the sites.

RESULTS

We show that a handful of core ASVs are consistently identified by both frequency analysis and IndVal approaches with alternative definitions, although no ASVs were always present on F. distichus and IndVal identified a diverse array of F. distichus indicator taxa across sites on Calvert Island in multiple years. Frequency analysis captured a broader suit of taxa, while IndVal was better at identifying host-specific microbes. Finally, two-step IndVal identified hundreds of indicator ASVs for particular sites/timepoints but only 12 that were indicators in a majority (> 6 out of 11) of sites/timepoints. Ten of these ASVs were also indicators on Quadra Island, 250 km away. Many F. distichus-core ASVs are generally found on multiple macroalgal species, while a few ASVs are highly specific to F. distichus.

CONCLUSIONS

Different methodological approaches with variable set thresholds influence core identification, but a handful of core taxa are apparently identifiable as they are widespread and temporally associated with F. distichus and enriched in comparison to the environment. Moreover, we show that many of these core ASVs of F. distichus are found on multiple macroalgal hosts, indicating that most occupy a macroalgal generalist niche rather than forming highly specialized associations with F. distichus. Further studies should test whether macroalgal generalists or specialists are more likely to engage in biologically important exchanges with host.

Rewilding plant microbiomes

Microbiota of crop ancestors may offer a way to enhance sustainable food production

Linking pathogen-microbiome-host interactions to explain amphibian population dynamics

Symbiotic interactions can determine the evolutionary trajectories of host species, influencing genetic variation through selection and changes in demography. In the context of strong selective pressures such as those imposed by infectious diseases, symbionts providing defences could contribute to increase host fitness upon pathogen emergence. Here, we generated genome-wide data of an amphibian species to find evidence of evolutionary pressures driven by two skin symbionts: a batrachochytrid fungal pathogen and an antifungal bacterium. Using demographic modelling, we found evidence of decreased effective population size, probably due to pathogen infections. Additionally, we investigated host genetic associations with infection status, antifungal bacterium abundance and overall microbiome diversity using structural equation models. We uncovered relatively lower nucleotide diversity in infected frogs and potential heterozygote advantage to recruit the candidate beneficial symbiont and fight infections. Our models indicate that environmental conditions have indirect effects on symbiont abundance through both host body traits and microbiome diversity. Likewise, we uncovered a potential offsetting effect among host heterozygosity-fitness correlations, plausibly pointing to different ecological and evolutionary processes among the three species due to dynamic interactions. Our findings revealed that evolutionary pressures not only arise from the pathogen but also from the candidate beneficial symbiont, and both interactions shape the genetics of the host. Our results advance knowledge about multipartite symbiotic relationships and provide a framework to model ecological and evolutionary dynamics in wild populations. Finally, our study approach can be applied to inform conservation actions such as bioaugmentation strategies for other imperilled amphibians affected by infectious diseases.

Psycho-Microbiology, a New Frontier for Probiotics: An Exploratory Overview

Probiotics are gradually gaining importance in the field of psychiatry in the form of psychobiotics. Psychobiotics' studies examine the existing relationship between gut microbiota and mental phenomena; the intake of certain strains of probiotics, such as Bifidobacterium and Lactobacillus, for example, allow the gut microbial system to be modified in order to provide benefits at the psychic, immune, hormonal, and mental levels. Those who suffer from forms of depression, anxiety disorders, chronic stress, low mood, but also people who do not suffer from such disorders, can therefore benefit from the use of psychobiotics. Thanks to probiotics, neurochemicals can in fact be produced within the gut microbiota and interact with receptors of the enteric nervous system that innervate the entire gastrointestinal tract. Once they enter the portal circulation, these substances go on to influence components of the nervous system and ultimately the brain, through what is called the gut-brain axis. This article proposes an exploratory overview of the proven effects of probiotics on brain activity and psycho-related diseases, focusing on clinical studies and measurable outcomes. The search was conducted using two different online tools: ClinicalTrials.gov and PubMed.

Phenomenology and dynamics of competitive ecosystems beyond the niche-neutral regimes

Structure, composition, and stability of ecological populations are shaped by the inter- and intraspecies interactions within their communities. It remains to be fully understood how the interplay of these interactions with other factors, such as immigration, controls the structure, the diversity, and the long-term stability of ecological systems in the presence of noise and fluctuations. We address this problem using a minimal model of interacting multispecies ecological communities that incorporates competition, immigration, and demographic noise. We find that a complete phase diagram exhibits rich behavior with multiple regimes that go beyond the classical "niche" and "neutral" regimes, extending and modifying the "rare biosphere" or "niche-like" dichotomy. In particular, we observe regimes that cannot be characterized as either niche or neutral where a multimodal species abundance distribution is observed. We characterize the transitions between the different regimes and show how these arise from the underlying kinetics of the species turnover, extinction, and invasion. Our model serves as a minimal null model of noisy competitive ecological systems, against which more complex models that include factors such as mutations and environmental noise can be compared.

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

BACKGROUND

Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.

RESULTS

In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.

CONCLUSIONS

We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.

Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L

The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.

Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic

The gastrointestinal (GI) tract is the reservoir for multidrug resistant (MDR) pathogens, specifically carbapenem-resistant (CR) Klebsiella pneumoniae and other Enterobacteriaceae, which often lead to the spread of antimicrobial resistance genes, severe extraintestinal infections, and lethal outcomes. Selective GI decolonization has been proposed as a new strategy for preventing transmission to other body sites and minimizing spreading to susceptible individuals. Here, we purify the to-date uncharacterized class IIb microcin I47 (MccI47) and demonstrate potent inhibition of numerous Enterobacteriaceae, including multidrug-resistant clinical isolates, in vitro at concentrations resembling those of commonly prescribed antibiotics. We then genetically modify the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to produce MccI47 from a stable multicopy plasmid by using MccI47 toxin production in a counterselection mechanism to engineer one of the native EcN plasmids, which renders provisions for inducible expression and plasmid selection unnecessary. We then test the clinical relevance of the MccI47-producing engineered EcN in a murine CR K. pneumoniae colonization model and demonstrate significant MccI47-dependent reduction of CR K. pneumoniae abundance after seven days of daily oral live biotherapeutic administration without disruption of the resident microbiota. This study provides the first demonstration of MccI47 as a potent antimicrobial against certain Enterobacteriaceae, and its ability to significantly reduce the abundance of CR K. pneumoniae in a preclinical animal model, when delivered from an engineered live biotherapeutic product. This study serves as the foundational step toward the use of engineered live biotherapeutic products aimed at the selective removal of MDR pathogens from the GI tract.

Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome

Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

BACKGROUND

The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

RESULTS

Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

CONCLUSIONS

Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.

Intestinal Microbiome Richness of Coral Reef Damselfishes (Actinopterygii: Pomacentridae)

Fish gastro-intestinal system harbors diverse microbiomes that affect the host's digestion, nutrition, and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome and the factors that determine its structure and composition. Damselfish are important coral reef species that play pivotal roles in determining algae and coral population structures of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we used 16S rRNA gene sequencing to investigate the intestinal microbiome of 5 planktivorous and 5 algae-farming damselfish species (Pomacentridae) from the Great Barrier Reef. We detected Gammaproteobacteria ASVs belonging to the genus Actinobacillus in 80% of sampled individuals across the 2 trophic guilds, thus, bacteria in this genus can be considered possible core members of pomacentrid microbiomes. Algae-farming damselfish had greater bacterial alpha-diversity, a more diverse core microbiome and shared 35 ± 22 ASVs, whereas planktivorous species shared 7 ± 3 ASVs. Our data also highlight differences in microbiomes associated with both trophic guilds. For instance, algae-farming damselfish were enriched in Pasteurellaceae, whilst planktivorous damselfish in Vibrionaceae. Finally, we show shifts in bacterial community composition along the intestines. ASVs associated with the classes Bacteroidia, Clostridia, and Mollicutes bacteria were predominant in the anterior intestinal regions while Gammaproteobacteria abundance was higher in the stomach. Our results suggest that the richness of the intestinal bacterial communities of damselfish reflects host species diet and trophic guild.

Gut–Kidney Axis Investigations in Animal Models of Chronic Kidney Disease

Chronic kidney disease (CKD) is an incurable disease in which renal function gradually declines, resulting in no noticeable symptoms during the early stages and a life-threatening disorder in the latest stage. The changes that accompany renal failure are likely to influence the gut microbiota, or the ecosystem of micro-organisms resident in the intestine. Altered gut microbiota can display metabolic changes and become harmful to the host. To study the gut–kidney axis in vivo, animal models should ideally reproduce the disorders affecting both the host and the gut microbiota. Murine models of CKD, but not dog, manifest slowed gut transit, similarly to patient. Animal models of CKD also reproduce altered intestinal barrier function, as well as the resulting leaky gut syndrome and bacterial translocation. CKD animal models replicate metabolic but not compositional changes in the gut microbiota. Researchers investigating the gut–kidney axis should pay attention to the selection of the animal model (disease induction method, species) and the setting of the experimental design (control group, sterilization method, individually ventilated cages) that have been shown to influence gut microbiota.

Species identity and combinations differ in their overall benefits to Astragalus adsurgens plants inoculated with single or multiple endophytic fungi under drought conditions

Although desert plants often establish multiple simultaneous symbiotic associations with various endophytic fungi in their roots, most studies focus on single fungus inoculation. Therefore, combined inoculation of multiple fungi should be applied to simulate natural habitats with the presence of a local microbiome. Here, a pot experiment was conducted to test the synergistic effects between three extremely arid habitat-adapted root endophytes (Alternaria chlamydospora, Sarocladium kiliense, and Monosporascus sp.). For that, we compared the effects of single fungus vs. combined fungi inoculation, on plant morphology and rhizospheric soil microhabitat of desert plant Astragalus adsurgens grown under drought and non-sterile soil conditions. The results indicated that fungal inoculation mainly influenced root biomass of A. adsurgens, but did not affect the shoot biomass. Both single fungus and combined inoculation decreased plant height (7-17%), but increased stem branching numbers (13-34%). However, fungal inoculation influenced the root length and surface area depending on their species and combinations, with the greatest benefits occurring on S. kiliense inoculation alone and its co-inoculation with Monosporascus sp. (109% and 61%; 54% and 42%). Although A. chlamydospora and co-inoculations with S. kiliense and Monosporascus sp. also appeared to promote root growth, these inoculations resulted in obvious soil acidification. Despite no observed root growth promotion, Monosporascus sp. associated with its combined inoculations maximally facilitated soil organic carbon accumulation. However, noticeably, combined inoculation of the three species had no significant effects on root length, surface area, and biomass, but promoted rhizospheric fungal diversity and abundance most, with Sordariomycetes being the dominant fungal group. This indicates the response of plant growth to fungal inoculation may be different from that of the rhizospheric fungal community. Structural equation modeling also demonstrated that fungal inoculation significantly influenced the interactions among the growth of A. adsurgens, soil factors, and rhizospheric fungal groups. Our findings suggest that, based on species-specific and combinatorial effects, endophytic fungi enhanced the plant root growth, altered soil nutrients, and facilitated rhizospheric fungal community, possibly contributing to desert plant performance and ecological adaptability. These results will provide the basis for evaluating the potential application of fungal inoculants for developing sustainable management for desert ecosystems.

Stochastic variation in gut bacterial community affects reproductive rates in the water flea Daphnia magna

It is well-documented that perturbation of the gut bacterial community can influence the reproductive rates of the host. Less is known about how natural ecological processes can change the bacterial composition in the gut and how such changes influence the reproductive rate of the host. Here, we provide novel experimental insights into such processes using the clonally reproducing water flea, Daphnia magna. A total of 20 replicate cultures were reared for 5 weeks (Phase 1) to allow for divergence of bacterial communities through stochastic processes (i.e. drift, founder effects, and/or colonization). Duplicate cultures created from each of these were reared for 21 days (Phase 2) while recording reproductive rates. There was a significant repeatability in reproductive rates between these duplicates, suggesting that divergence of the bacterial communities during Phase 1 translated into reproductive rate effects during Phase 2. This was further supported by significant differences in the relative abundance of gut bacteria (investigated by amplicon sequencing of a part of the 16S rRNA gene) between cultures with high and low reproductive rate in Phase 2. These results are consistent with the hypothesis that stochastic processes can cause natural variation in the bacterial composition in the gut, which in turn affect host reproductive rates.

Gut mutualists can persist in host populations despite low fidelity of vertical transmission

Humans harbour diverse microbial communities, and this interaction has fitness consequences for hosts and symbionts. Understanding the mechanisms that preserve host-symbiont association is an important step in studying co-evolution between humans and their mutualist microbial partners. This association is promoted by vertical transmission, which is known to be imperfect. It is unclear whether host-microbial associations can generally be maintained despite 'leaky' vertical transmission. Cultural practices of the host are expected to be important in bacterial transmission as they influence the host's interaction with other individuals and with the environment. There is a need to understand whether and how cultural practices affect host-microbial associations. Here, we develop a mathematical model to identify the conditions under which the mutualist can persist in a population where vertical transmission is imperfect. We show with this model that several factors compensate for imperfect vertical transmission, namely, a selective advantage to the host conferred by the mutualist, horizontal transmission of the mutualist through an environmental reservoir and transmission of a cultural practice that promotes microbial transmission. By making the host-microbe association more likely to persist in the face of leaky vertical transmission, these factors strengthen the association which in turn enables host-mutualist co-evolution.

Microbiome and Cervical Cancer – A Review

Cervical cancer (CC) contributes to 6%-29% of all cancers in women. In India, 527,624 new cases of CC are added every year. India contributes to ¼ of deaths worldwide to CC it occurs often in women around the age of 30 yrs which is contributed by a specific kind of human papillomavirus causes long-term infection and inflammation (HPV) which result in morphological changes in the cells of cervix the region that connect vagina and uterus. Cervicovaginal microbiome is observed to be highly diverse among patients with CC where there is reduced number of Latobacillus spp that leads to dysbiosis and decrease in pH and eventually colonised by other anaerobic bacteria. The shift in community state types (CST) is highly associated with the Human Papillomavirus infection and its further progression to cervical dysplasia or CIN i.e. ‘Cervical intraepithelial neoplasia’ and malignant tumour of the cervix uteri. The purpose of this research is to figure out if there’s a link between the cervico-vaginal microbiota and gynaecological cancer and the review also focuses whether cervical microbiome signatures can predict the severity of infection leading to development of CC? Probiotics can be used as a potential alternative to balance the dysbiosis of the cervicovaginal environment. Hence the review summarizes the current knowledge and the interaction of different bacterial groups with Human Papilloma Virus infection and development of CC.

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties

Microbe–microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM’s followed the Taylor’s power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.

Rapid evolution of a novel protective symbiont into keystone taxon in Caenorhabditis elegans microbiota

Protective microbes have a major role in shaping host-pathogen interactions, but their relative importance in the structure of the host microbiota remains unclear. Here, we used a network approach to characterize the impact of a novel, experimentally evolved 'protective microbial symbiont' (Enterococcus faecalis) on the structure and predicted function of the natural microbiota of the model organism Caenorhabditis elegans. We used microbial network analysis to identify keystone taxa and describe the hierarchical placement of protective and non-protective symbionts in the microbiota. We found that early colonization with symbionts produce statistically significant changes in the structure of the community. Notably, only the protective E. faecalis became a keystone taxon in the nematode microbiota. Non-protective lineages of the same bacterial species remained comparatively unimportant to the community. Prediction of functional profiles in bacterial communities using PICRUSt2 showed that the presence of highly protective E. faecalis decreased the abundance of ergothioneine (EGT) biosynthesis pathway involved in the synthesis of the antioxidant molecule EGT, a potential public good. These data show that in addition to direct antagonism with virulent pathogens, keystone protective symbionts are linked to modified bacterial community structure and possible reductions in public goods, potentially driving decreased antioxidant defense. We suggest that this response could suppress infection via wholesale microbial community changes to further benefit the host. These findings extend the concept of protective symbionts beyond bodyguards to ecosystem engineers.

Cell death in skin function, inflammation, and disease

Cell death is an essential process that plays a vital role in restoring and maintaining skin homeostasis. It supports recovery from acute injury and infection and regulates barrier function and immunity. Cell death can also provoke inflammatory responses. Loss of cell membrane integrity with lytic forms of cell death can incite inflammation due to the uncontrolled release of cell contents. Excessive or poorly regulated cell death is increasingly recognised as contributing to cutaneous inflammation. Therefore, drugs that inhibit cell death could be used therapeutically to treat certain inflammatory skin diseases. Programmes to develop such inhibitors are already underway. In this review, we outline the mechanisms of skin-associated cell death programmes; apoptosis, necroptosis, pyroptosis, NETosis, and the epidermal terminal differentiation programme, cornification. We discuss the evidence for their role in skin inflammation and disease and discuss therapeutic opportunities for targeting the cell death machinery.

Attention-Deficit/Hyperactivity Disorder and the Gut Microbiota–Gut–Brain Axis: Closing Research Gaps through Female Inclusion in Study Design

The gastrointestinal tract harbors a densely populated community of microbes that exhibits sexual dimorphism. Dysbiosis of this community has been associated with chronic human disease states ranging from metabolic diseases to neuropsychiatric disorders (NPDs). The gut microbiota–gut–brain axis (GMGBA) is a bi-directional pathway that facilitates the interaction of the gut microflora with host physiological functions. Recently, research surrounding the potential roles of the GMGBA in the development of NPDs (e.g., depression, anxiety, and autism spectrum disorders (ASDs)) has increased. However, the role of the GMGBA in attention-deficit/hyperactivity disorder (ADHD), an NPD that affects an estimated 8.4% of children (5.1% of female and 11.5% of male children) and 4% of adults (with a male–female odds ratio of 1.6) in the United States, remains understudied. Herein, we synthesize the current literature regarding the GMGBA, ADHD, and the potentially relevant intersections between the GMGBA and ADHD. Recommendations are presented for pathways of future research into the role(s) of the GMGBA in ADHD etiology and symptomatology. Particular focus is given to the potential for the variable of host sex to act as an outcome modifier of the relationship between the GMGBA and ADHD.

Modeling spatial interaction networks of the gut microbiota

How the gut microbiota is organized across space is postulated to influence microbial succession and its mutualistic relationships with the host. The lack of dynamic or perturbed abundance data poses considerable challenges for characterizing the spatial pattern of microbial interactions. We integrate allometric scaling theory, evolutionary game theory, and prey-predator theory into a unified framework under which quasi-dynamic microbial networks can be inferred from static abundance data. We illustrate that such networks can capture the full properties of microbial interactions, including causality, the sign of the causality, strength, and feedback loop, and are dynamically adaptive along spatial gradients, and context-specific, characterizing variability between individuals and within the same individual across time and space. We design and conduct a gut microbiota study to validate the model, characterizing key spatial determinants of the microbial differences between ulcerative colitis and healthy controls. Our model provides a sophisticated means of unraveling a complete atlas of how microbial interactions vary across space and quantifying causal relationships between such spatial variability and change in health state.