Aims/hypothesis: To investigate the longitudinal relationship between the gut microbiome, circulating short chain fatty acids (SCFAs) and intestinal permeability in children with islet autoimmunity or type 1 diabetes and controls. Methods:We analyzed the gut bacterial microbiome, plasma SCFAs, small intestinal permeability and dietary intake in 47 children with islet autoimmunity or recentonset type 1 diabetes and in 41 unrelated or sibling controls over a median (range) of 13 (2-34) months follow-up.Results: Children with multiple islet autoantibodies (≥2 IA) or type 1 diabetes had gut microbiome dysbiosis. Anti-inflammatory Prevotella and Butyricimonas genera were less abundant and these changes were not explained by differences in diet. Small intestinal permeability measured by blood lactulose:rhamnose ratio was higher in type 1 diabetes. Children with ≥2 IA who progressed to type 1 diabetes (progressors), compared to those who did not progress, had higher intestinal permeability (mean [SE] difference +5.14 [2.0], 95% confidence interval [CI] 1.21, 9.07, P = .006), lower within-sample (alpha) microbial diversity (31.3 [11.2], 95% CI 9.3, 53.3, P = .005), and lower abundance of SCFA-producing bacteria. Alpha diversity (observed richness) correlated with plasma acetate levels in all groups combined (regression coefficient [SE] 0.57 [0.21], 95% CI 0.15, 0.99 P = .008). Conclusions/Interpretation: Children with ≥2 IA who progress to diabetes, like those with recent-onset diabetes, have gut microbiome dysbiosis associated with increased intestinal permeability. Interventions that expand gut microbial diversity, in particular ABBREVIATIONS: ACAES, Australian child and adolescent eating survey; CSS, cumulative sum scaling; IA, islet autoantibody; IAA, insulin autoantibody; IA2, tyrosine phosphatase-like insulinoma antigen; GAD, glutamic acid decarboxylase 65; PCoA, principal coordinates analysis; SCFA, short chain fatty acid; SNP, single nucleotide polymorphism; TGAb, transglutaminase autoantibody.

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity.

To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6–24 h, before transfer and storage at −80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.

Bacterial communities play an essential role for the function of marine macroalgae. Recent work has shown that bacterial communities associated with individual macroalgae possess on a local scale a functional core that is likely derived from diverse members of functional guilds. It is not known whether such functional cores also exist across large spatial scales or between closely related host species. To address this, we studied here the bacterial communities on three species of the green macroalgal genus Ulva from different geographic locations. While the taxonomic composition was too variable to describe a community core, we identified genes that were enriched across all Ulva samples as compared to the communities of the surrounding seawater. Of these core functions, 70% were consistently found and independent of the Ulva species and biogeography, while the remaining functions (~30%) are possibly involved in local or host-specific adaptations. For each host individual, the core functions are provided by bacteria with distinct phylogenetic origin and these bacteria could constitute a global guild of Ulva-associated bacteria. Together, our results demonstrate the presence of a stable core set of functional genes in the bacterial communities associated with closely related host species and across large biogeographies.

Disease is increasingly viewed as a major factor impacting the health of both natural and cultured populations of marine organisms, including macroalgae. The red macroalga Delisea pulchra suffers from a bleaching disease resulting from host stress and infection by opportunistic bacterial pathogens. However, how pathogens cause the disease and how the entire macro algal-associated community is involved in the process is unclear. Here, we perform a metagenomic analysis of microbial communities associated with diseased and healthy D. pulchra across multiple bleaching events. Analysis of reconstructed 16S rRNA gene sequences showed that bacteria belonging to the families Rhodobacteraceae, Saprospiraceae and Flavobacteriaceae, including bacteria previously implicated in algal bleaching, to be enriched in diseased D. pulchra. Genes with predicted functions related to chemotaxis, motility, oxidative stress response, vitamin biosynthesis and nutrient acquisition were also prevalent in microbiomes of bleached algae, which may have a role in pathogenicity. Reconstruction of genomes that were abundant on bleached samples revealed that no single organism contains all bleaching-enriched functional genes. This observation indicates that potential virulence traits are distributed across multiple bacteria and that the disease in D. pulchra may result from a consortium of opportunistic pathogens, analogous to dysbiotic or polymicrobial diseases.

In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga’s chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.

Background The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D. Results Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage. Conclusions Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means.

Caulerpa taxifolia is a pantropical green benthic marine macroalga, and one of the best known marine invasive species in temperate coastal habitats. In Australia, this species has been introduced to seven estuaries along New South Wales and one in South Australia. How this alga will perform under future climate change scenarios is however not well defined. This study experimentally assessed the effects of ocean acidification and global warming on the growth, photosynthetic performance and the bacterial community on two populations of C. taxifolia, one native and one invasive. A range of complex significant interactive effects between pH, temperature, and initial plant size on the growth of C. taxifolia were observed, but no effect of population origin and photosystem II (PSII) fluorescence quantum yield parameters were detected. No significant effects of the treatment combinations were observed on bacterial community richness or diversity. Only one bacterial species out of 1087 present on the algae showed significant changes between pH treatments at high temperature (24°C). This bacterium belonged to the genus Planctomyces and its relative abundance was more than 10 times higher in samples with low pH compared to the control. Higher plant growth was observed under all higher pCO2 and lower pH conditions suggesting that C. taxifolia will benefit from climate change, posing a potential higher risk in invaded locations.