Functional roles and metabolic niches in the honey bee gut microbiota.

Gut microbiota studies on diverse animals facilitate our understanding of the general principles governing microbiota-host interactions. The honey bee adds a relevant study system due to the simplicity and experimental tractability of its gut microbiota, but also because bees are important pollinators that suffer from population declines worldwide. The use of gnotobiotic bees combined with genetic tools, 'omics' analysis, and experimental microbiology has recently provided important insights about the impact of the microbiota on bee health and the general functioning of gut ecosystems

Characterisation of the British honey bee metagenome

Numerous microbial symbionts, both commensal and pathogenic, are associated with honey bees. Here, the authors genomically characterize this ‘metagenome’ of the British honey bee, identifying a diversity of commensal microbes as well as known and putative pathogen

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota.

The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member Bifidobacterium asteroides, but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities

External carbon addition for enhancing denitrification modifies bacterial community composition and affects CH₄ and N₂O production in sub-arctic mining pond sediments.

Explosives used in mining operations release reactive nitrogen (N) that discharge into surrounding waters. Existing pond systems at mine sites could be used for N removal through denitrification and we investigated capacity in tailings and clarification pond sediments at an iron-ore mine site. Despite differences in microbial community structure in the two ponds, the potential denitrification rates were similar, although carbon limited. Therefore, a microcosm experiment in which we amended sediment from the clarification pond with acetate, cellulose or green algae as possible carbon sources was conducted during 10 weeks under denitrifying conditions. Algae and acetate treatments showed efficient nitrate removal and increased potential denitrification rates, whereas cellulose was not different from the control. Denitrifiers were overall more abundant than bacteria performing dissimilatory nitrate reduction to ammonium (DNRA) or anaerobic ammonium oxidation, although DNRA bacteria increased in the algae treatment and this coincided with accumulation of ammonium. The algae addition also caused higher emissions of methane (CH <sub>4</sub> ) and nitrous oxide (N <sub>2</sub> O). The bacterial community in this treatment had a large proportion of Bacteroidia, sulfate reducing taxa and bacteria known as fermenters. Functional gene abundances indicated an imbalance between organisms that produce N <sub>2</sub> O in relation to those that can reduce it, with the algae treatment showing the lowest relative capacity for N <sub>2</sub> O reduction. These findings show that pond sediments have the potential to contribute to mitigating nitrate levels in water from mining industry, but it is important to consider the type of carbon supply as it affects the community composition, which in turn can lead to unwanted processes and increased greenhouse gas emissions

Suppression of High-Fat Diet-Induced Obesity by Platycodon Grandiflorus in Mice Is Linked to Changes in the Gut Microbiota.

The root of Platycodon grandiflorus (PG) has a long-standing tradition in the Asian diet and herbal medicine, because of its anti-inflammatory and antiobesity effects. Changes in the gut microbiota can have dietary effects on host health, which suggests a relation between the 2. The aim of our study was to investigate the relation between PG-mediated suppression of obesity and the composition and functioning of the gut microbiota. Six-week-old male C57BL/6J mice were fed either a control diet (CON, 10% kcal from fat), a high-fat diet (HFD, 60% kcal from fat), or a PG-supplemented HFD for 18 wk. PG was administered by oral gavage at 2 g · kg body weight-1 · d-1. Body weight and food intake were monitored. Lipid metabolism, inflammation, and intestinal barrier function were determined. Amplicon sequencing of the bacterial 16S ribosomal RNA gene was used to explore gut microbiota structure, and nontargeted metabolomics analysis was performed to investigate metabolite concentrations in fecal samples. We found that PG significantly ameliorated HFD-induced inflammation, recovered intestinal barrier integrity (reduced permeability by 39% , P = 0.008), reduced fat accumulation by 26% (P = 0.009), and changed the expression of key genes involved in the development of white adipose tissue (P < 0.05) in HFD-fed mice to similar levels in CON mice. Moreover, PG attenuated HFD-induced changes in the gut microbiota; it especially increased Allobaculum (7.3-fold, P = 0.002) relative to HFD, whereas CON was 15.2-fold of HFD (P = 0.002). These changes by PG were associated with an increase in the production of SCFAs (butyrate and propionate, P < 0.001) and other carbohydrate-related metabolites known to have a major role in disease suppression. Our study demonstrated that PG beneficially changed the gut microbiota and the gut metabolome in HFD-fed mice, and suggests that the antiobesity effects of PG may be mediated via changes in gut microbiota composition and metabolic activity

High dietary fat intake induces a microbiota signature that promotes food allergy.

Diet-induced obesity and food allergies increase in tandem, but a potential cause-and-effect relationship between these diseases of affluence remains to be tested. We sought to test the role of high dietary fat intake, diet-induced obesity, and associated changes in gut microbial community structure on food allergy pathogenesis. Mice were fed a high-fat diet (HFD) for 12 weeks before food allergen sensitization on an atopic dermatitis-like skin lesion, followed by intragastric allergen challenge to induce experimental food allergy. Germ-free animals were colonized with a signature HFD or lean microbiota for 8 weeks before induction of food allergy. Food-induced allergic responses were quantified by using a clinical allergy score, serum IgE levels, serum mouse mast cell protease 1 concentrations, and type 2 cytokine responses. Accumulation of intestinal mast cells was examined by using flow cytometry and chloroacetate esterase tissue staining. Changes in the gut microbial community structure were assessed by using high-throughput 16S ribosomal DNA gene sequencing. HFD-induced obesity potentiates food-induced allergic responses associated with dysregulated intestinal effector mast cell responses, increased intestinal permeability, and gut dysbiosis. An HFD-associated microbiome was transmissible to germ-free mice, with the gut microbial community structure of recipients segregating according to the microbiota input source. Independent of an obese state, an HFD-associated gut microbiome was sufficient to confer enhanced susceptibility to food allergy. These findings identify HFD-induced microbial alterations as risk factors for experimental food allergy and uncouple a pathogenic role of an HFD-associated microbiome from obesity. Postdieting microbiome alterations caused by overindulgence of dietary fat might increase susceptibility to food allergy

Bacterioplankton seasonality in deep high-mountain lakes.

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.

Bacteria that engage in long-standing associations with particular hosts are expected to evolve host-specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep-branching host-specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate-related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate-related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation.

There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant