Understanding the role of the shrimp gut microbiome in health and disease.

With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.

Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus).

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.

The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae.

Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.

Tart Cherry Concentrate Does Not Alter the Gut Microbiome, Glycaemic Control or Systemic Inflammation in a Middle-Aged Population.

Limited evidence suggests that the consumption of polyphenols may improve glycaemic control and insulin sensitivity. The gut microbiome produces phenolic metabolites and increases their bioavailability. A handful of studies have suggested that polyphenol consumption alters gut microbiome composition. There are no data available investigating such effects in polyphenol-rich Montmorency cherry (MC) supplementation. A total of 28 participants (aged 40-60 years) were randomized to receive daily MC or glucose and energy-matched placebo supplementation for 4 wk. Faecal and blood samples were obtained at baseline and at 4 wk. There was no clear effect of supplementation on glucose handling (Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and Gutt indices), although the Matsuda index decreased significantly in the MC group post-supplementation, reflecting an increase in serum insulin concentration. Contrastingly, placebo, but not MC supplementation induced a 6% increase in the Oral Glucose Insulin Sensitivity (OGIS) estimate of glucose clearance. Serum IL-6 and C reactive protein were unaltered by either supplement. The faecal bacterial microbiome was sequenced; species richness and diversity were unchanged by MC or placebo and no significant correlation existed between changes in Bacteroides and Faecalibacterium abundance and any index of insulin sensitivity. Therefore, 4 weeks of MC supplementation did not alter the gut microbiome, glycaemic control or systemic concentrations of IL-6 and CRP in a middle-aged population.

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans.

Imbalances in the oral microbial community have been associated with reduced cardiovascular and metabolic health. A possible mechanism linking the oral microbiota to health is the nitrate (NO3-)-nitrite (NO2-)-nitric oxide (NO) pathway, which relies on oral bacteria to reduce NO3- to NO2-. NO (generated from both NO2- and L-arginine) regulates vascular endothelial function and therefore blood pressure (BP). By sequencing bacterial 16S rRNA genes we examined the relationships between the oral microbiome and physiological indices of NO bioavailability and possible changes in these variables following 10 days of NO3- (12 mmol/d) and placebo supplementation in young (18-22 yrs) and old (70-79 yrs) normotensive humans (n = 18). NO3- supplementation altered the salivary microbiome compared to placebo by increasing the relative abundance of Proteobacteria (+225%) and decreasing the relative abundance of Bacteroidetes (-46%; P < 0.05). After NO3-supplementation the relative abundances of Rothia (+127%) and Neisseria (+351%) were greater, and Prevotella (-60%) and Veillonella (-65%) were lower than in the placebo condition (all P < 0.05). NO3- supplementation increased plasma concentration of NO2- and reduced systemic blood pressure in old (70-79 yrs), but not young (18-22 yrs), participants. High abundances of Rothia and Neisseria and low abundances of Prevotella and Veillonella were correlated with greater increases in plasma [NO2-] in response to NO3- supplementation. The current findings indicate that the oral microbiome is malleable to change with increased dietary intake of inorganic NO3-, and that diet-induced changes in the oral microbial community are related to indices of NO homeostasis and vascular health in vivo.

Halioticida noduliformans infection in eggs of lobster (Homarus gammarus) reveals its generalist parasitic strategy in marine invertebrates.

A parasite exhibiting Oomycete-like morphology and pathogenesis was isolated from discoloured eggs of the European lobster (Homarus gammarus) and later found in gill tissues of adults. Group-specific Oomycete primers were designed to amplify the 18S ribosomal small subunit (SSU), which initially identified the organism as the same as the 'Haliphthoros' sp. NJM 0034 strain (AB178865.1) previously isolated from abalone (imported from South Australia to Japan). However, in accordance with other published SSU-based phylogenies, the NJM 0034 isolate did not group with other known Haliphthoros species in our Maximum Likelihood and Bayesian phylogenies. Instead, the strain formed an orphan lineage, diverging before the separation of the Saprolegniales and Pythiales. Based upon 28S large subunit (LSU) phylogeny, our own isolate and the previously unidentified 0034 strain are both identical to the abalone pathogen Halioticida noduliformans. The genus shares morphological similarities with Haliphthoros and Halocrusticida and forms a clade with these in LSU phylogenies. Here, we confirm the first recorded occurrence of H. noduliformans in European lobsters and associate its presence with pathology of the egg mass, likely leading to reduced fecundity.

An [Fe] hydrogenase from the anaerobic hydrogenosome-containing fungus Neocallimastix frontalis L2.

Hydrogenases, oxygen-sensitive enzymes that can make hydrogen gas, are key to the function of hydrogen-producing organelles (hydrogenosomes), which occur in anaerobic eukaryotes scattered throughout the eukaryotic tree. All of the eukaryotic enzymes characterized so far are iron-only [Fe] hydrogenases. In contrast, it has previously been suggested that hydrogenosomes of the best-studied anaerobic fungus Neocallimastix frontalis L2 contain an unrelated iron-nickel-selenium [NiFeSe] hydrogenase. We have isolated a gene from strain L2 that encodes a putative protein containing all of the characteristic features of an iron-only [Fe] hydrogenase, including the cysteine residues required for the co-ordination of the unique 'hydrogen cluster'. As is the case for experimentally verified hydrogenosomal matrix enzymes from N. frontalis, the [Fe] hydrogenase encodes a plausible amino terminal extension that resembles mitochondrial targeting signals. Phylogenetic analyses of an expanded [Fe] hydrogenase dataset reveal a complicated picture that is difficult to interpret in the light of current ideas of species relationships. Nevertheless, our analyses cannot reject the hypothesis that the novel [Fe] hydrogenase gene of Neocallimastix is specifically related to other eukaryote [Fe] hydrogenases, and thus ultimately might be traced to the same ancestral source.