Insects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.

Bactrocera tryoni (Froggatt) (Queensland fruit fly, or “Qfly”) is a highly polyphagous tephritid fruit fly and a serious economic pest in Australia. Qfly biology is intimately linked to the bacteria and fungi of its microbiome. While there are numerous studies of the microbiome in larvae and adults, the transition of the microbiome through the pupal stage remains unknown. To address this knowledge gap, we used high-throughput Next-Generation Sequencing (NGS) to examine microbial communities at each developmental stage in the Qfly life cycle, targeting the bacterial 16S rRNA and fungal ITS regions. We found that microbial communities were similar at the larval and pupal stage and were also similar between adult males and females, yet there were marked differences between the larval and adult stages. Specific bacterial and fungal taxa are present in the larvae and adults (fed hydrolyzed yeast with sugar) which is likely related to differences in nutritional biology of these life stages. We observed a significant abundance of the Acetobacteraceae at the family level, both in the larval and pupal stages. Conversely, Enterobacteriaceae was highly abundant (>80%) only in the adults. The majority of fungal taxa present in Qfly were yeasts or yeast-like fungi. In addition to elucidating changes in the microbiome through developmental stages, this study characterizes the Qfly microbiome present at the establishment of laboratory colonies as they enter the domestication process.

BackgroundEvidence is accumulating that nutritional exposures in utero can influence health outcomes in later life. Animal studies and human epidemiological studies have implicated epigenetic modifications as playing a key role in this process, but there are limited data from large well-controlled human intervention trials.This study utilized a large double-blind randomized placebo-controlled trial to test whether a defined nutritional exposure in utero, in this case docosahexaenoic acid (DHA), could alter the infant epigenome. Pregnant mothers consumed DHA-rich fish oil (800 mg DHA/day) or placebo supplements from 20 weeks’ gestation to delivery. Blood spots were collected from the children at birth (n = 991) and blood leukocytes at 5 years (n = 667). Global DNA methylation was measured in all samples, and Illumina HumanMethylation450K BeadChip arrays were used for genome-wide methylation profiling in a subset of 369 children at birth and 65 children at 5 years.ResultsThere were no differences in global DNA methylation levels between the DHA and control group either at birth or at 5 years, but we identified 21 differentially methylated regions (DMRs) at birth, showing small DNA methylation differences (<5%) between the treatment groups, some of which seemed to persist until 5 years. The number of DMRs at birth was greater in males (127 DMRs) and in females (72 DMRs) separately, indicating a gender-specific effect.ConclusionMaternal DHA supplementation during the second half of pregnancy had small effects on DNA methylation of infants. While the potential functional significance of these changes remains to be determined, these findings further support the role of epigenetic modifications in developmental programming in humans and point the way for future studies.Trial registrationAustralian New Zealand Clinical Trials Registry (ANZCTR), ACTRN12605000569606 and ACTRN12611001127998 Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0281-7) contains supplementary material, which is available to authorized users.

Bundera sinkhole, located in north-western Australia, is the only known continental anchialine system in the Southern Hemisphere. Anchialine environments are characterised by stratified water columns with complex physicochemical profiles spanning hypoxic and anoxic regions, often displaying high levels of endemism. Research on these systems has focused on eukaryotic fauna, however interest in the microbial diversity of these environments is growing, enabled by next-generation DNA sequencing. Here we report detailed analyses of the microbial communities across a depth profile within Bundera sinkhole (from 2 to 28 m), involving parallel physicochemical measurements, cell population counts and 16S rRNA amplicon analyses. We observed clear shifts in microbial cell counts, community diversity, structure and membership across the depth profile, reflecting changing levels of light, organic and inorganic energy sources as well as shifts in pH and salinity. While Proteobacteria were the most abundant phylum found, there was a high degree of taxonomic novelty within these microbial communities, with 13,028 unique amplicon sequence variants (ASVs) identified, belonging to 67 identifiable bacterial and archaeal phyla. Of these ~4,600, more than one third of the total, were unclassified below family level. A small number of ASVs were highly abundant at select depths, all of which were part of the set not classified below family level. The 2 m and 6 m samples had in common two highly abundant ASVs, belonging to the Ectothiorhodospiraceae and Thiotrichaceae families, while the 8 m community contained a single predominant ASV belonging to family Thioglobaceae. At lower depths a different Ectothiorhodospiraceae ASV comprised up to 68% relative abundance, peaking at 26 and 28 m. Canonical correspondence analyses indicated that community structure was strongly influenced by differences in key physicochemical parameters, particularly salinity, dissolved organic and inorganic carbon, phosphate and sulphate concentrations. This work highlights the potential for anchialine systems to house considerable microbial novelty, potentially driven by adaptations to the specific physicochemical makeup of their local environment. As only a small number of anchialine systems have been examined via microbial community studies to date, this work is particularly valuable, contributing new insight regarding the microbial residents of these important and sensitive environments.