Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador

Characterization of Microbiome Diversity in the Digestive Tract of Penaeus vannamei Fed with Probiotics and Challenged with Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease

The microbiome of the shrimp's digestive tract shows differences between healthy and acute hepatopancreatic necrosis disease (AHPND)-affected shrimp. The present study aimed to evaluate the impact of probiotic consumption on the microbial community in experimentally AHPND-infected shrimp. Effective probiotics (EPs) Vibrio alginolyticus (Va32A), V. campbellii (VcHA), and Bacillus pumilus (BPY100) and non-effective probiotics (NEPs) B. pumilus (Bp43, and BpY119), were employed in bioassays with Penaeus vannamei and challenged with AHPND-causing V. parahaemolyticus (VpAHPND). Stomach (Sto), intestine (Int), and hepatopancreas (Hep) were analyzed by metabarcoding (16S rRNA gene) to characterize the microbiome and biomarkers. Hep-VcHA showed the highest alpha diversity (Shannon index = 5.88; 166 ASVs), whereas the lowest was for Hep-Bp43 (2.33; 7 ASVs). Proteobacteria, Actinobacteria, Bacteroidetes, and Saccharibacteria were the most abundant phyla. The relative abundance of Vibrio sp. was the highest in the Hep and Int of Bp43, BPY119 and the positive control, followed by Rhodobacteraceae in the EP group. Principle coordinate analysis (PCoA) showed a cluster grouped negative (Sto and Hep) control with almost all organs in the EP group causing 28.79% of the variation. The core microbiome of EP was mainly represented by Rhodobacteraceae, Caldilineaceae, Celeribacter indicus, Illumatobacter, Microbacterium, Ruegeria atlantica, Saccharibacteria sp., Shimia biformata, and Thalassobius mediterraneus, whose relative abundance was enriched by probiotics, which may explain their protective roles against VpAHPND, whereas the low survival in the NEP group was associated with a higher diversity of Vibrio spp. Our results present an ecosystem-friendly alternative based on beneficial microorganisms to prevent and control AHPND and probably other bacterial diseases in shrimp farming.

Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris

BACKGROUND

In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).

RESULTS

We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.

CONCLUSIONS

Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.

Unveiling the Bacterial Community across the Stomach, Hepatopancreas, Anterior Intestine, and Posterior Intestine of Pacific Whiteleg Shrimp

The gastrointestinal (GI) tract of shrimp, which is comprised of the stomach, hepatopancreas, and intestine, houses microbial communities that play crucial roles in immune defense, nutrient absorption, and overall health. While the intestine's microbiome has been well-studied, there has been limited research investigating the stomach and hepatopancreas. The present study addresses this gap by profiling the bacterial community in these interconnected GI segments of Pacific whiteleg shrimp. To this end, shrimp samples were collected from a local aquaculture farm in South Korea, and 16S rRNA gene amplicon sequencing was performed. The results revealed significant variations in bacterial diversity and composition among GI segments. The stomach and hepatopancreas exhibited higher Proteobacteria abundance, while the intestine showed a more diverse microbiome, including Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia. Genera such as Oceaniovalibus, Streptococcus, Actibacter, Ilumatobacter, and Litorilinea dominated the intestine, while Salinarimonas, Sphingomonas, and Oceaniovalibus prevailed in the stomach and hepatopancreas. It is particularly notable that Salinarimonas, which is associated with nitrate reduction and pollutant degradation, was prominent in the hepatopancreas. Overall, this study provides insights into the microbial ecology of the Pacific whiteleg shrimp's GI tract, thus enhancing our understanding of shrimp health with the aim of supporting sustainable aquaculture practices.

Host habitat shapes the core gut bacteria of decapod crustaceans: A meta-analysis

Gut microbiota is an essential determinant factor that drives the physiological, immunological, and metabolic functions of animals. A few meta-analysis studies identified crucial information about the gut microbiota of vertebrate animals in different habitats including fish while no report is yet available for the commercially cultured decapod crustaceans (DC). This meta-analysis investigated the gut microbiota of 11 commercially cultured DC species from five different groups-crab, crayfish, lobster, prawn, and shrimp to gain an overview of microbial diversity and composition and to find out core genera under two different host habitats: freshwater and saltwater. The analysis of 627 Illumina datasets from 25 published studies revealed selective patterns of diversity and compositional differences among groups and between freshwater and saltwater culture systems. The study found a salinity-dependent heterogeneous response of gut microbiota, specifically Vibrio in saltwater for white shrimp, a species that can be cultured with and without salt. Overall, the genera reared in freshwater showed higher diversity in the gut microbial communities than those reared in saltwater. An overwhelming abundance of Candidatus Bacilloplasma and Vibrio were identified for species cultured in freshwater and saltwater system, respectively and these two species were identified as the main core genera for nine out of 11 DC species, except freshwater prawn and river prawn. Together, these results demonstrate the effectiveness of the meta-analysis in identifying the robust and reproducible features of DC gut microbiota for different groups and host habitats. The diversity information curated here could be used as a reference for future studies to differentiate various DC species under two different rearing environments.

Bacterial community in Sinonovacula constricta intestine and its relationship with culture environment

Although the importance of intestinal microbes to aquaculture animals has been recognized, the intestinal bacteria of Sinonovacula constricta and its culture environment are rarely studied. In this study, high-throughput sequencing was used to explore the intestinal bacterial communities of pond water, sediment, and S. constricta intestine. Significance analysis and principal coordinates analysis (PCoA) showed that there were significant differences in bacterial communities among animals' intestine, pond water, and sediment (p < 0.05). Venn analysis showed that intestinal bacteria shared a considerable number of OTUs (operational taxonomic units) with the sediment and water. SourceTracker analysis suggested that the contribution of sediment to the intestinal bacteria of S. constricta was much larger than that of rearing water. The Kruskal-Wallis test showed that the dominant bacterial taxa differed significantly between animals' intestines and the pond environment, and each of them has a unique bacterial composition. A network diagram indicated the complex positive and negative interactions between intestinal bacteria at the OTU level. Furthermore, BugBase analysis indicated that the bacterial contribution to potential pathogens in the animals' intestines is similar to that in sediments, suggesting that sediment was the main source of potential pathogens in S. constricta intestine. This study provided a theoretical basis for environmental regulation and disease prevention of S. constricta in aquaculture. KEY POINTS: • Culture environment had a significant effect on the intestinal bacterial community in S. constricta. • Sediment was a major source of intestinal bacteria and potentially pathogenic bacteria. • Complex positive and negative interactions existed between intestinal bacteria.

Microbiome of Penaeus vannamei Larvae and Potential Biomarkers Associated With High and Low Survival in Shrimp Hatchery Tanks Affected by Acute Hepatopancreatic Necrosis Disease

Acute hepatopancreatic necrosis disease (AHPND) is an emerging bacterial disease of cultured shrimp caused mainly by Vibrio parahaemolyticus, which harbors the lethal PirAB toxin genes. Although Penaeus vannamei (P. vannamei) postlarvae are susceptible to AHPND, the changes in the bacterial communities through the larval stages affected by the disease are unknown. We characterized, through high-throughput sequencing, the microbiome of P. vannamei larvae infected with AHPND-causing bacteria through the larval stages and compared the microbiome of larvae collected from high- and low-survival tanks. A total of 64 tanks from a commercial hatchery were sampled at mysis 3, postlarvae 4, postlarvae 7, and postlarvae 10 stages. PirAB toxin genes were detected by PCR and confirmed by histopathology analysis in 58 tanks. Seven from the 58 AHPND-positive tanks exhibited a survival rate higher than 60% at harvest, despite the AHPND affectation, being selected for further analysis, whereas 51 tanks exhibited survival rates lower than 60%. A random sample of 7 out of these 51 AHPND-positive tanks was also selected. Samples collected from the selected tanks were processed for the microbiome analysis. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene of the samples collected from both the groups were sequenced. The Shannon diversity index was significantly lower at the low-survival tanks. The microbiomes were significantly different between high- and low-survival tanks at M3, PL4, PL7, but not at PL10. Differential abundance analysis determined that biomarkers associated with high and low survival in shrimp hatchery tanks affected with AHPND. The genera Bacillus, Vibrio, Yangia, Roseobacter, Tenacibaculum, Bdellovibrio, Mameliella, and Cognatishimia, among others, were enriched in the high-survival tanks. On the other hand, Gilvibacter, Marinibacterium, Spongiimonas, Catenococcus, and Sneathiella, among others, were enriched in the low-survival tanks. The results can be used to develop applications to prevent losses in shrimp hatchery tanks affected by AHPND.

Distinct bacterial communities in the environmental water, sediment and intestine between two crayfish-plant coculture ecosystems

Microorganisms are an important part of productivity, water quality, and biogeochemical cycles in an aquaculture ecosystems and play a key role in determining the growth and fitness of aquaculture animals. Coculture ecosystems are widely applied with great significance in agricultural production worldwide. The crayfish-rice coculture ecosystem (CRCE) and crayfish-waterweed coculture ecosystem (CWCE) are two high-profile artificial ecosystems for crayfish culture. However, the bacterial communities of the environmental water, sediment, and intestine in the CRCE and CWCE remain elusive. In this study, we investigated the diversity, composition, and function of bacterial communities in water, sediment, and intestine samples from the CRCE to CWCE. The physicochemical factors of water [such as ORP (oxidation-reduction potential), TC (total carbon), TOC (total oxygen carbon), and NO₃^--N] and sediment [such as TC, TOC, TN (total nitrogen), and TP (total phosphate)] were significantly different in the CRCE and CWCE. The abundances of Proteobacteria, Actinobacteria, Verrucomicrobia, Cyanobacteria, Chlorobi, Chloroflexi, and Firmicutes were significantly different in the water bacterial communities of the CRCE and CWCE. The abundance of Vibrio in the crayfish intestine was higher in the CRCE than in the CWCE. The most abundant phyla in the CRCE and CWCE sediment were Proteobacteria and Bacteroidetes. The abundances of genes involved in transporters and ABC transporters were different in water of CRCE and CWCE. The abundances of genes involved in oxidative phosphorylation were significantly higher in the crayfish intestine of the CRCE than in that of the CWCE. Furthermore, the functional genes associated with carbon metabolism were significantly more abundant in the sediment of the CRCE than in that of the CWCE. Spearman correlation analysis and redundancy analysis (RDA) showed that the bacterial communities of the water and sediment in the CRCE and CWCE were correlated with environmental factors (pH, total carbon (TC), total oxygen carbon (TOC), total nitrogen (TN), and total phosphorus (TP)). Our findings showed that the composition, diversity and function of the bacterial communities were distinct in the environmental water, sediment, and intestine of the CRCE and CWCE crayfish coculture ecosystems due to their different ecological patterns. These results can help guide healthy farming practices and deepen the understanding of bacterial communities in crayfish-plant coculture ecosystems from the perspective of bacterial ecology. KEY POINTS: • The composition of bacterial communities in the environmental water, sediment, and intestine of the CRCE and CWCE were distinct. ̉• The abundances of genes involved in transporters and ABC transporters were different in the water of the CRCE and CWCE. • The bacterial communities of the water and sediment in the CRCE and CWCE were correlated with some environmental factors.

Effects of metal ions on activity and structure of phenoloxidase in Penaeus vannamei

Phenoloxidase (PO) is a typical metal enzyme, which requires metal ions as prosthetic groups to enable the full exertion of its activity. To study how metal ions affected the activity and structure of PO enzymes, while providing reference materials for in-depth investigations, we examined the effects of different metal ions (Cu²⁺, Zn²⁺, Mg²⁺, Ca²⁺, and Ba²⁺) on their activities. Furthermore, Cu²⁺ and Mg²⁺ were selected for further investigation through UV spectra, intrinsic fluorescence spectroscopy, AFM, and FTIR. It was revealed that Cu²⁺ had a more obvious effect on PO compared to Mg²⁺. The PO could be activated when the concentrations of Cu²⁺ and Mg²⁺ were lower than 10^-3 and 10^-2 mol/L, respectively, and maximum PO activities (182.14% and 141.02%) were observed at 10^-4 mol/L concentrations of Cu²⁺ and Mg²⁺. When the concentrations of Cu²⁺ and Mg²⁺ were higher than 10^-2 and 10^-1 mol/L, the activities PO were inhibited. The results of the UV-vis and fluorescence spectra revealed that Cu²⁺ shaped the tertiary structure of PO, whereas the effect of Mg²⁺ was slight. The AFM results demonstrated that high concentrations of Cu²⁺ and Mg²⁺ resulted in PO aggregation. FTIR analysis indicated that the total content of PO α-helices and β-sheets decreased with higher concentrations of Cu²⁺ and Mg²⁺.

The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development

This work aimed to evaluate the link between the occurrence/abundance of Vibrio populations and bacterial composition in shrimp’s intestine (Litopenaeus vannamei) during post-larval ontogenetic development and in its culture water, and the correlation of these with environmental parameters. The total and metabolically active populations of Vibrio in the digestive tract of shrimp during its post-larval development were analysed using quantitative PCR (qPCR) and reverse transcription qPCR targeting the 16S rRNA gene sequence. A lab-scale shrimp bioassay was performed for 80 days in a recirculating aquarium under strictly controlled conditions. The results indicate that the Vibrio population from shrimp’s gut is associated with its developmental stage and the environment. Multivariate analyses revealed that the presence of Vibrio spp. drove the studied system, but their metabolically active performance was related to earlier developmental stages in an aqueous environment. Also, the samples taken from water of culture units to compare the influence of the aquatic environment on the intestinal microbial community during shrimp’s ontogenetic development showed significant differences. Finally, our results revealed that Vibrio is an important member of shrimp’s gut microbiota; however, its metabolic activity seems to be highly regulated, possibly by the host and by the rest of the microbiota.

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico

This study investigated the intestinal microbial community structure of Litopenaeus vannamei at six different stages during shrimp farming. Our goal was to elucidate the bacterial profile and the changes in the relative abundance of taxa during an atypical massive mortality event in Sonora, Mexico. High-throughput sequencing of the 16S rRNA gene and denaturing gradient gel electrophoresis showed that Vibrionaceae was persistent with high relative abundances in the intestine from cultivated shrimp during all the studied stages. The massive mortality observed at day 63 could be related to an overabundance of different Operational Taxonomic Units (OTUs) of Vibrio, Shewanella and Clostridium. Principal coordinate analysis (PCoA) showed variations in microbial structure at different culture times. These findings suggest that OTUs of different taxa contributed to the community switch from healthy to diseased individuals, questioning the hypothesis that single bacterial species is the cause of disease outbreaks. This study provided data to improve the understanding of disease outbreaks during shrimp farming.

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.

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes)

In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka (Oryzias latipes) were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (IL-1β), complement 1q subunit C (C1qc), transferrin a (Tfa), and G-type lysozyme (LyzG), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (pla2g1b), and elastase-1-like (CELA1), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae Plesiomonas shigelloides was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.

Effect of mannan oligosaccharides on the microbiota and productivity parameters of Litopenaeus vannamei shrimp under intensive cultivation in Ecuador

The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently emerged early mortality syndrome. Many bacterial pathogens have been identified but the L. vannamei microbiota is still poorly known. Using a next-generation sequencing (NGS) approach, this work evaluated the impact of the inclusion in the diet of mannan oligosaccharide, (MOS, 0.5% w/w), over the L. vannamei microbiota and production behavior of L. vannamei under intensive cultivation in Ecuador. The MOS supplementation lasted for 60 days, after which the shrimp in the ponds were harvested, and the production data were collected. MOS improved productivity outcomes by increasing shrimp survival by 30%. NGS revealed quantitative differences in the shrimp microbiota between MOS and control conditions. In the treatment with inclusion of dietary MOS, the predominant phylum was Actinobacteria (28%); while the control group was dominated by the phylum Proteobacteria (30%). MOS has also been linked to an increased prevalence of Lactococcus- and Verrucomicrobiaceae-like bacteria. Furthermore, under the treatment of MOS, the prevalence of potential opportunistic pathogens, like Vibrio, Aeromonas, Bergeyella and Shewanella, was negligible. This may be attributable to MOS blocking the adhesion of pathogens to the surfaces of the host tissues. Together, these findings point to the fact that the performance (survival) improvements of the dietary MOS may be linked to the impact on the microbiota, since bacterial lines with pathogenic potential towards shrimps were excluded in the gut.

The effect of dietary supplementation with Clostridium butyricum on the growth performance, immunity, intestinal microbiota and disease resistance of tilapia (Oreochromis niloticus)

This study was conducted to assess the effects of dietary Clostridium butyricum on the growth, immunity, intestinal microbiota and disease resistance of tilapia (Oreochromis niloticus). Three hundreds of tilapia (56.21 ± 0.81 g) were divided into 5 groups and fed a diet supplemented with C. butyricum at 0, 1 x 10⁴, 1 x 10⁵, 1 x 10⁶ or 1 x 10⁷ CFU g^-1 diet (denoted as CG, CB1, CB2, CB3 and CB4, respectively) for 56 days. Then 45 fish from each group were intraperitoneally injected with Streptococcus agalactiae, and the mortality was recorded for 14 days. The results showed that dietary C. butyricum significantly improved the specific growth rate (SGR) and feed intake in the CB2 group and decreased the cumulative mortality post-challenge with S. agalactiae in the CB2, CB3 and CB4 groups. The serum total antioxidant capacity and intestinal interleukin receptor-associated kinase-4 gene expression were significantly increased, and serum malondialdehyde content and diamine oxidase activity were significantly decreased in the CB1, CB2, CB3 and CB4 groups. Serum complement 3 and complement 4 concentrations and intestinal gene expression of tumour necrosis factor α, interleukin 8, and myeloid differentiation factor 88 were significantly higher in the CB2, CB3 and CB4 groups. Intestinal toll-like receptor 2 gene expression was significantly upregulated in the CB3 and CB4 groups. Dietary C. butyricum increased the diversity of the intestinal microbiota and the relative abundance of beneficial bacteria (such as Bacillus), and decreased the relative abundance of opportunistic pathogenic bacteria (such as Aeromonas) in the CB2 group. These results revealed that dietary C. butyricum at a suitable dose enhanced growth performance, elevated humoral and intestinal immunity, regulated the intestinal microbial components, and improved disease resistance in tilapia. The optimal dose was 1 x 10⁵ CFU g^-1 diet.

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Multiple factors modulate microbial community assembly in the vertebrate gut, though studies disagree as to their relative contribution. One cause may be a reliance on captive animals, which can have very different gut microbiomes compared to their wild counterparts. To resolve this disagreement, we analyze a new, large, and highly diverse animal distal gut 16 S rRNA microbiome dataset, which comprises 80% wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decouple the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor modulates different aspects of diversity. Moreover, we resolve particular microbial taxa associated with host phylogeny or diet and show that Mammalia have a stronger signal of cophylogeny. Finally, we find that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment

Environmental microbiota plays important roles in the intestinal microbiota of aquatic animals. The Pacific white shrimp with high commercial value and euryhaline property has become the most important commercial species of shrimp in the world. However, the association between shrimp intestine and sediment at freshwater and marine cultured environment should be investigated to reveal the microbiota differences. In the present study, Miseq sequencing technology and bioinformatics were used to comprehensively compare the bacterial communities and all samples' V3-V4 regions of 16S rRNA gene were sequenced. Results showed that 55 phyla and 789 genera were identified due to the classifiable sequence. Sequencing data demonstrated statistically significant diverse microbiota compositions in the shrimp intestine and sediment at freshwater and marine cultured environment at the phylum and genus level. At the phylum level, the dominant phyla in all groups were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, Saccharibacteria. Proteobacteria were the most abundant and largest phylum except in the intestine of marine cultured shrimp and Actinobacteria may be enriched in the shrimp intestine from sediment. At the genus level, nine out of the twelve dominant genera exhibited statistically significant differences among all groups. Moreover, Lactobacillus tend to be enriched in the freshwater cultured shrimp intestine, while Synechococcus and Vibrio extremely abundance in the marine cultured shrimp intestine. These results showed that the bacterial compositions are mostly the same in shrimp intestine and sediment, while with different relative abundances of the bacterial communities. In conclusion, this study may greatly enhance our understanding of the microbiota characteristics between shrimp and sediment. Moreover, it provided guidance for the healthy aquaculture at freshwater and marine cultured environment.

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.