Effects of dietary supplementation of Ulva pertusa and non-starch polysaccharide enzymes on gut microbiota of Siganus canaliculatus

Sun

et al. 2018

Appl Environ Microbiol

Self Cite

Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimps and oysters. Hemolymph is a critical site in host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies using selective media (e.g., TCBS, 2216E, and LB) for enumerating and isolating microbial cells. However, doubts remain about the "true" representation of the microbial abundance and diversity of symbiotic microorganisms in hemolymph, particularly for uncultivable microorganisms which are believed to be more abundant than the cultured. To explore this, we developed a culture-independent cell extraction method for separating microbial cells from the hemolymph of three aquatic invertebrates (, , and) involving filtration through a 5-μm mesh filter membrane (the Filtration Method). A combination of the Filtration Method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. More than 2.6 × 10 cells/mL of microbial cells dominated by and, and, and and, were detected in the hemolymph of ,, and , respectively. A parallel study for investigating the hemolymph microbiome by comparing the Filtration Method and a culture-dependent method (the Plate Count Method), showed significantly higher microbial abundances (between 26 and 369-folds difference; P<0.05) and less biased community structures of the Filtration Method than those of the Plate Count Method. Furthermore, hemolymph of the three invertebrates harbored many potential pathogens, including ,, and Finally, the Filtration Method provides a solution that improves understanding of the metabolic functions of uncultivable hemolymph microorganisms (e.g., metagenomics) devoid of host hemocytes contamination. Microorganisms are found in invertebrates' hemolymph, a critical site in host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies. However, doubts remain about the "true" representation of hemolymph microbiome. This study developed a culture-independent cell extraction method that could separate microbial cells from the hemolymph of three aquatic invertebrates (, , and) based on filtration through a 5-μm mesh filter membrane (the Filtration Method). A combination of the Filtration Method with fluorescence microscopy and high-throughput sequencing technique provides insight into the abundances and diversity of the total microbiota in the hemolymph of these three invertebrates. Our results demonstrate that the hemolymph of aquatic invertebrates harbors a much higher microbial abundance and distinct microbial community composition than previously estimated. Furthermore, this work provides a less biased solution for studying the metabolic functions of uncultivable hemolymph microbiota devoid of host hemocytes contamination.

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method

Sun

et al. 2018

Appl Environ Microbiol

Self Cite

“…Like surgeon sh intestinal microbiomes from the Red Sea [15], the damsel sh microbiomes presented here were dominated by members of Proteobacteria, Bacteroidetes, Firmicutes and Planctomycetes. Another dominant ASV in the damsel sh microbiome belonging to Mollicutes (Tenericutes) resembled bacteria detected in rabbit sh intestines [22]. The number of highly similar bacterial ASVs shared among pomacentrids, acanthurids and siganids may re ect the similar feeding behaviours of these coral reef shes.…”

Section: Discussionmentioning

confidence: 91%

“…These include host-related factors such as genetic attributes, size, age, sex [12][13][14], host phylogeny [15][16][17] and environmental factors such as water quality and diet [15][16][17][18][19]. Studies that investigate intestinal microbiome changes have concentrated on the impact of sh foods on species of aquaculture importance [20,21], although a few studies have investigated wild sh populations [15,22]. Bacterial symbiont diversi cation in wild herbivorous surgeon sh intestines is thought to be an important driver of host niche-partitioning [23,24], suggesting that intestinal microbiomes can in uence the trophic ecology of coral reefs.…”

Section: Introductionmentioning

confidence: 99%

Core intestinal microbiomes of planktivorous and algae-farming coral reef damselfishes (Actinopterygii: Pomacentridae) reflects feeding behaviour

Kavazos

Leggat

Casey

et al. 2020

Preprint

Abstract Background: Fish harbour diverse microbiomes within their gastro-intestinal system that effect the host’s digestion, nutrition and immunity. Despite the great taxonomic diversity of fish, little is understood about fish microbiome diversity and the factors that determine its structure and composition. Damselfish are important coral reef fish species that play a strong role in determining algae and coral structure of reefs. Broadly, damselfish belong to either of two trophic guilds based on whether they are planktivorous or algae-farming. In this study, we use 16s rRNA sequencing to interrogate the intestinal microbiome of 10 damselfish species (Pomacentridae) from the Great Barrier Reef to compare the composition of their intestinal bacterial assemblages across the planktivorous and algae-farming trophic guilds.Results: We identify core intestinal bacterial taxa for each host fish species. Gammaproteobacteria, belonging to the genus Actinobacillus, were detected in 80 % of sampled individuals and suggests a possible core member of pomacentrid microbiomes. Core microbiomes of algae-farming species were more diverse than planktivorous species with farming species sharing 35 ± 22 ASVs and planktivorous sharing 7 ± 3 ASVs. We also provide evidence for significant shifts in bacterial community composition along the intestines. We show that Bacteroidia, Clostridia and Mollicutes bacteria are more abundant in the anterior intestinal regions while Gammaproteobacteria are generally highest in the stomach. Finally, we highlight differences in microbiomes associated with both trophic guilds. Algae-farming and planktivorous damselfish host species significantly differed in their composition of bacteria belonging to Vibrionaceae, Lachnospiraceae and Pasteurellaceae.Conclusions: Our results demonstrate that core intestinal bacterial communities of damselfish reflect host species diet and feeding behaviour, whereby algae-farming hosts have larger and more diverse core microbiomes than planktivorous hosts. We suggest that the trophic guild of a host fish species is a strong determinant of microbiome structure.

“…seaweeds, microalgae and their derivatives) have been investigated and overall have resulted in enhanced microbial diversity within GI tracts and sometimes also enhanced disease resistance [35]. However, dietary changes are not always correlated with changes in the microbiomes of farmed sh species [38] and we know very little about effects of diet on GI microbiomes of non-carnivorous or new candidate aquaculture sh species [35,[39][40][41][42]. This is of interest because there is an increasing push for farmers to move away from carnivorous species (e.g.…”

Section: Introductionmentioning

confidence: 99%

Influence of Seaweed Supplements on the Intestinal Bacteria in the Rabbitfish Siganus Fuscescens: Evidence for a Core Microbiome

Thépot

Slinger

Rimmer

et al. 2020

Preprint

BackgroundWe know very little about natural variation in microbiomes of marine herbivorous fish in the wild or in captivity (aquaculture). Understanding how the consumption of seaweed influences intestinal microbial communities will shed light on how such phytobiotics could enhance the health and productivity of farmed fish. Here we screened the effects of supplementing the diets of mottled rabbitfish (Siganus fuscescens), a candidate species for international aquaculture development, with 15 different species of seaweeds and functional supplements currently used in aquaculture, on the bacterial communities that colonised their hindguts. ResultsRemarkably, the second most abundant phylum and the majority (53%) of the bacterial genera were not assigned, highlighting a significant knowledge gap for the field of animal microbiomes. Dietary supplementation increased alpha diversity by up to 23% relative to the control fish. Furthermore, most supplements significantly increased the relative abundance of Firmicutes, with similar trends for Proteobacteria and consistent decreases in Bacteroides. Seaweed supplementation also had important effects at the genus level, including significant increases in Fusobacterium sp. in fish fed seaweed - especially the green Caulerpa taxifolia – and overall trends for reduced levels of Arcobacter sp., a genus that includes fish and human pathogens. When we compared microbiomes in our fish to those from two recently published studies of conspecific populations sampled many thousands of kilometres away, the populations were clearly distinct, however there were 55 ASVs that were shared across the three fish populations, of which 35 were present in 50% of all fish sampled.ConclusionThe identification of a core microbiome suggests that a host organism relies on certain microbes for key functions and our findings suggest that this candidate aquaculture species has a core microbiome in its hindgut which is robust to dietary manipulations and broad geographical and temporal variation. This insight will help guide future work investigating the functional and mechanistic bases of these relationships, as will improvements in microbial taxonomic resolution. Supplementation with seaweeds did have subtle influences on bacteria in the hindgut of Siganus fuscescens which could have important impacts on fish health and should be considered as aquaculture systems are developed for this species.