Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages

Novel indigenous probiotic isolated from the healthy Pacific white shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approaches

The healthy intestinal microbiota of shrimp can be used as an indicator sustainable shrimp production. In this study, the integrated of metagenomic and screening probiotic approach from healthy Litopenaeus vannamei intestines in differing stages was studied to find novel indigenous probiotics. The microbiota from intestine of naupli, post larva (PL-10), juvenile (40 days), and adult (80 days) of Pacific white shrimp were characterized using a high-quality sequence of V3-V4 of 16S rRNA gene as the hypervariable region. The classifiable sequence number was detected in 54 phyla. Several core intestine bacteria, 35 of these 557 genera, have a prevalence >10 sequences across all samples. We found microbiota were different taxa in the difference stages, such as Proteobacteria, Firmicutes, and Bacteriodetes. The top 10 most abundant genera were Vibrio, Pseudoalteromonas, Spingomonas, Marinibacterium, Klebsiella, Alteromonas, Aestuaribacter, Shimia, Stenotrophomonas, and Ruegeria. Microbiota profiling based on a metagenomic approach was integrated with screening assessment for pathogenicity, antagonistic activity with Vibrio parahaemolyticus Vp5, antibiotic resistance, and digestive enzyme activities. As their assessment activity, several screened culturable bacteria were 19 of these 84 isolates. Three isolates with high activities (P < 0.05) found as novel indigenous probiotics were Shewanella algae A1, Shewanella algae A3, and Vibrio diabolicus UB3. Integrating metagenomic and screening methods was a new signature for the isolating novel indigenous probiotics in Pacific white shrimp.

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.

Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis

Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.

Shrimp microbiome and immune development in the early life stages

With its contribution to nutrition, development, and disease resistance, gut microbiome has been recognized as a crucial component of the animal's health and well-being. Microbiome in the gastrointestinal tract constantly interacts with the host animal's immune systems as part of the normal function of the intestines. Interactions between the microbiome and the immune system are complex and dynamic, with the microbiome shaping immune development and function. In contrast, the immune system modulates the composition and activity of the microbiome. In shrimp, as with all other aquatic animals, the interaction between the microbiome and the animals occurs at the early developmental stages. This early interaction is likely essential to the development of immune responses of the animal as well as many key physiological developments that further contribute to the health of shrimp. This review provides background knowledge on the early developmental stage of shrimp and its microbiome, examines the interaction between the microbiome and the immune system in the early life stage of shrimp, and discusses potential pitfalls and challenges associated with microbiome research. Understanding the interaction between the microbiome and shrimp immune system at this crucial developmental stage could have the potential to aid in the establishment of a healthy microbiome, improve shrimp survival, and provide ways to shape the microbiome with feed supplements or other strategies.

AssesSments of Vibrio parahaemolyticus and Vibrio vulnificus levels and microbial community compositions in blue crabs (Callinectes sapidus) and seawater harvested from the Maryland Coastal Bays

Introduction

Fluctuations in environmental physicochemical parameters can affect the diversity and prevalence of microbial communities, including vibrios, associated with aquatic species and their surrounding environments. This study aimed to investigate the population dynamics of two Vibrio species as well as the microbial community diversity of whole crab and seawater from the Maryland Coastal Bays (MCBs), using 16S rRNA sequencing.

Methods

During this study, three crabs and 1 L of seawater were collected monthly from two sites for 3 months. Crab tissue was extracted and pooled for each site. Extracted crab tissue and seawater were analyzed for Vibrio parahaemolyticus and V. vulnificus using Most Probable Number (MPN) real-time PCR. For 16S rRNA microbiome analysis, three different DNA extraction kits were evaluated to extract microbial DNA from individual crabs. Also, 500 mL of each seawater sample was filtered for DNA extraction.

Results

Results indicated that sample types and sampling periods had a significant effect on the alpha diversity of the microbial community of crabs and seawater (p < 0.05); however, no statistical difference was found between DNA extraction kits. Beta diversity analysis also found that the microbial compositions between sample types and temporal distributions were statistically significant. Taxonomic classification revealed that Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes were present in both crab and seawater samples. Vibrio parahaemolyticus and V. vulnificus were also detected in both crab and seawater samples, although crabs contained a higher concentration of the bacterium compared to the seawater samples. It was found that vibrios were not a dominant species in the microbial community of crab or seawater samples.

Discussion

Results from this study provide further insight into species diversity and phylogenetic compositions of blue crabs and seawater from the MCBs. These approaches will help in risk assessments that are essential in the overall advancement of public health.

Host gut-derived Bacillus probiotics supplementation improves growth performance, serum and liver immunity, gut health, and resistive capacity against Vibrio harveyi infection in hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus)

Several reports have revealed the vital role that probiotics play in fish growth and health. However, few works are available for host gut-derived probiotics on the growth, immunity, and gut microbiota of fish, especially in hybrid grouper (♀Epinephelus fuscoguttatus × ♂Epinephelus lanceolatus) due to their isolation difficulty and functional verification. This study aimed at assessing 3 host gut-derived Bacillus species' effects on the growth, immune and antioxidant-biochemical responses, haematological parameters, intestinal morphology, immune-related gene expression, gut microbiota, and disease resistance against Vibrio harveyi in hybrid grouper. A total of 480 hybrid grouper (initial weight = 9.03 ± 0.02 g) were randomly allotted into 4 groups, namely, the group fed a basal diet without probiotic inclusion (control, B0), the group fed the basal diet with Bacillus velezensis GPSAK4 (BV), the group fed the basal diet with Bacillus subtilis GPSAK9 (BS), and the group fed the basal diet with Bacillus tequilensis GPSAK2 (BT) strains at 1.0 × 10⁹ CFU/g. After a 6-week feeding trial, the results revealed significant improvements (P < 0.05) in the growth performance, whole fish-body proximate composition, blood haematological parameters, serum, liver, and intestinal biochemical indexes, intestinal morphology, and protection against V. harveyi pathogen in the probiotic-treated groups compared with the untreated. Additionally, the expressions of intestinal tight junction genes (occludin and ZO1), pro- and anti-inflammatory genes, including IL1β, IL6, IL8, TNFα, MyD88, IL10, and TGFβ, were upregulated (P < 0.05) after Bacillus species administration. Host gut-derived Bacillus supplementation shaped the gut microbiota by significantly increasing (P < 0.05) the relative abundance of Proteobacteria, Bacteroidetes, Actinobacteria (except the BS group), Acidobacteria (except the BT group), Cyanobacteria (except the BV and BT groups), and Verrucomicrobia phyla, as well as known beneficial genera (Romboutsia, Turicibacter, Epulopiscium, Clostridium_sensu_stricto 1 and 13, Lactobacillus, and Bacillus), but significantly decreased (P < 0.05) the abundance of Firmicutes, Chloroflexi, and Fusobacteria phyla, and purported pathogenic genera (Staphylococcus and Photobacterium) compared with the control group. Collectively, the results suggest that B. velezensis GPSAK4, B. subtilis GPSAK9 (especially this strain), B. tequilensis GPSAK2 dietary supplementation at 1.0 × 10⁹ CFU/g has positive effects on the intestinal health of hybrid grouper via microbial composition modulation, thus enhancing the assimilation and absorption of nutrients to boost fish growth, immunity, and disease resistance.

Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system

Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Comparative Analysis of the Symbiotic Microbiota in the Chinese Mitten Crab (Eriocheir sinensis): Microbial Structure, Co-Occurrence Patterns, and Predictive Functions

Symbiotic microorganisms in the digestive and circulatory systems are found in various crustaceans, and their essential roles in crustacean health, nutrition, and disease have attracted considerable interest. Although the intestinal microbiota of the Chinese mitten crab (Eriocheir sinensis) has been extensively studied, information on the symbiotic microbiota at various sites of this aquatic economic species, particularly the hepatopancreas and hemolymph, is lacking. This study aimed to comprehensively characterize the hemolymph, hepatopancreas, and intestinal microbiota of Chinese mitten crab through the high-throughput sequencing of the 16S rRNA gene. Results showed no significant difference in microbial diversity between the hemolymph and hepatopancreas (Welch t-test; p > 0.05), but their microbial diversity was significantly higher than that in the intestine (p < 0.05). Distinct differences were found in the structure, composition, and predicted function of the symbiotic microbiota at these sites. At the phylum level, the hemolymph and hepatopancreas microbiota were dominated by Proteobacteria, Firmicutes, and Acidobacteriota, followed by Bacteroidota and Actinobacteriota, whereas the gut microbiota was mainly composed of Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, Candidatus Hepatoplasma, Shewanella, and Aeromonas were dominant in the hepatopancreas; Candidatus Bacilloplasma, Roseimarinus, and Vibrio were dominant in the intestine; Enterobacter, norank_Vicinamibacterales, and Pseudomonas were relatively high-abundance genera in the hemolymph. The composition and abundance of symbiotic microbiota in the hemolymph and hepatopancreas were extremely similar (p > 0.05), and no significant difference in functional prediction was found (p > 0.05). Comparing the hemolymph in the intestine and hepatopancreas, the hemolymph had lower variation in bacterial composition among individuals, having a more uniform abundance of major bacterial taxa, a smaller coefficient of variation, and the highest proportion of shared genera. Network complexity varied greatly among the three sites. The hepatopancreas microbiota was the most complex, followed by the hemolymph microbiota, and the intestinal microbiota had the simplest network. This study revealed the taxonomic and functional characteristics of the hemolymph, hepatopancreas, and gut microbiota in Chinese mitten crab. The results expanded our understanding of the symbiotic microbiota in crustaceans, providing potential indicators for assessing the health status of Chinese mitten crab.

Supplementing artemisinin positively influences growth, antioxidant capacity, immune response, gut health and disease resistance against Vibrio parahaemolyticus in Litopenaeus vannamei fed cottonseed protein concentrate meal diets

Artemisinin (ART) is a kind of Chinese herbal medicine worth exploring, which obtains various physiological activities. In order to study the prebiotic effect of ART on Litopenaeus vannamei fed cottonseed protein concentrate meal diets, six groups of isonitrogenous and isolipid diets were prepared (including the fish meal control group, FM; cottonseed protein concentrate replacing 30% fishmeal protein and supplementing ART groups: ART0, ART0.3, ART0.6, ART0.9, and ART1.2). The feeding trials was lasted for 56 days. The results showed that the final body weight, weight gain and specific growth rate of the ART0.6 group were the highest, yet the feed coefficient rate of the ART0.6 group was the lowest significantly (P < 0.05). There was no significant difference in survival rate among treatments (P > 0.05). In serum, the content of malondialdehyde in ART0 group was the highest (P < 0.05); the activities of superoxide dismutase, catalase, phenol oxidase and lysozyme increased firstly and then decreased among the ARTs groups (P < 0.05). The activities of intestinal digestive enzymes (including the trypsin, lipase and amylase) showed an upward trend among the ARTs groups (P < 0.05). The histological sections showed that the intestinal muscle thickness, fold height and fold width in the FM group were significantly better than those in the ART0 group; while the mentioned above morphological indexes in the ART0 group were significantly lowest among the ARTs groups (P < 0.05). Sequencing of intestinal microbiota suggested that the microbial richness indexes firstly increased and then decreased (P < 0.05); the bacterial community structure of each treatment group was almost close; the relative abundance of pathogenic bacteria decreased significantly (P < 0.05), such as the Proteobacteria and Cyanobacteria at phylum level, besides the Vibrio and Candidatus Bacilloplasma at genus level. In intestinal tissue, the relative expression levels of TOLL1, TRAF6 and Pehaeidih3 showed up-regulated trends, while the expression of Crustin and LZM firstly up-regulated and then down-regulated (P < 0.05). The challenge experiment suggested that the cumulative mortality of FM group was significantly lower than that of ART0 group; besides the cumulative mortality firstly increased and then decreased between the ARTs groups (P < 0.05). In conclusion, the dietary supplementation of ART can improve the growth, antioxidant capacity, immune response, gut health and disease resistance of the shrimp. To be considered as a dietary immune enhancer, the recommended supplementation level of ART in shrimp's cottonseed protein concentrate meal diets is 0.43%.

Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages

Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.

Effects of Pelleted and Extruded Feed on Growth Performance, Intestinal Histology and Microbiota of Juvenile Red Swamp Crayfish (Procambarus clarkii)

The study was conducted to evaluate the extruded and pelleting feed production on growth performance, intestinal histology and microbiome analysis of juvenile red swamp crayfish, Procambarus clarkii. Crayfish were fed either pelleted or extruded feeds that were made using the same formula. Crayfish fed extruded feed had a lower feed conversion ratio, as well as significantly higher levels of trypsin and amylase (p < 0.05) than those fed pelleted feed. However, other growth indices and the activity of lipase were not significantly influenced by the feed processing technique (p > 0.05). In comparison with the pelleted feed group, the lamina propria thickness of crayfish fed extruded feed was significantly lower (p < 0.05). Additionally, the abundance of intestinal microbiota in the extruded feed group was higher than that in the pelleted feed group. The dominant phyla in the intestine of both groups were Proteobacteria, Tenericutes, and Firmicutes, and the relative abundance of Proteobacteria in the extruded feed group was significantly higher than that in the pelleted feed group (p < 0.05). These results revealed that P. clarkii fed extruded feed had higher feed utilization and better intestinal health.

Effects of sulfated β-glucan from Saccharomyces cerevisiae on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii)

The aim of this study was to examine the combined effects of sulfated β-Glucan from Saccharomyces cerevisiae (sGSC) on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii). Four experimental diets (sGSC25, sGSC50, sGSC100 and sGSC200) with different levels of sGSC (0.025%, 0.05%, 0.1% and 0.2% in diet, respectively) were fed to juvenile crayfish (average weight: 2.5 ± 0.5 g) for 8 weeks. The control diet was given with 2000 mg/kg GSC (GSC200 group). The based control diet was given without sGSC or GSC (blank group). Each group had 3 parallel test pools, 20 crayfish were reared in each pool. At the end of the growth trial, adding dietary 0.025%-0.1% sGSC could significantly improve the growth performance, antioxidant capacity and immunity of crayfish. Compared with GSC, sGSC had a better effect at lower concentration. Higher concentration of sGSC (>0.1%) would cause some side effects. sGSC also could improve the structure of the intestinal flora and optimize the function of the flora. sGSC would increase the abundances of probiotics such as Hafnia and Acinetobacter, and decreases the abundances of maleficent bacteria such as Enterobacteriaceae. Higher concentration of sGSC (>0.1%) would increase the abundance of Aeromonas. To conclude, 0.025%-0.1% sGSC can be used as a supplement in crayfish feed to increase growth, immunity, and antioxidant capacity and improve the structure of intestinal flora. These results provided a theoretical basis for the application of sGSC instead of GSC in crayfish breeding. It will be necessary to further study the optimal concentration of sGSC in feed additives in different growth stages of crayfish in the future.

The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission

The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.

Changes in the intestinal microbiota of Pacific white shrimp (Litopenaeus vannamei) with different severities of Enterocytozoon hepatopenaei infection

The intestinal microbiota of the Pacific white shrimp Litopenaeus vannamei during Enterocytozoon hepatopenaei (EHP) infection was investigated by 16S rRNA gene-based analysis. The results showed that bacterial diversity in the intestine of L. vannamei was high, but it decreased with increasing severity of EHP infection. The relative abundances of the phyla Planctomycetes, Actinobacteria and Acidobacteria decreased significantly with a decrease in body size or EHP infection severity (P<0.05). The most abundant genera were Pseudomonas, Methylobacterium, Bradyrhizobium, Bacteroides, Vibrio, Prevotella and so on. In addition, the relative abundances of some bacteria, such as Pseudomonas, Bradyrhizobium, Bacteroides and Vibrio, increased significantly with a decrease in body size or EHP infection severity (P<0.05). These findings suggest that changes in the intestinal microbiota occur depending on the severity of EHP infection.

A meta-analysis study of the robustness and universality of gut microbiota-shrimp diseases relationship

Intensive case study has shown dysbiosis in the gut microbiota-shrimp disease relationship, however, variability in experimental design and the diversity of diseases arise the question whether some gut indicators are robust and universal in response to shrimp health status, irrespective of causal agents. Through an unbiased subject-level meta-analysis framework, we re-analyzed 10 studies including 261 samples, 4 lifestages, 6 different diseases (the causal agents are virus, bacterial, eukaryotic pathogens, or unknown). Results showed that shrimp diseases reproducibly altered the structure of gut bacterial community, but not diversity. After ruling out the lifestage- and disease specific- discriminatory taxa (different diseases dependent indicators), we identify 18 common disease-discriminatory taxa (indicative of health status, irrespective of causal agents) that accurately diagnosed (90.0% accuracy) shrimp health status, regardless of different diseases. These optimizations substantially improved the performance (62.6% vs. 90.0%) diagnosing model. The robustness and universality of model was validated for effectiveness via leave-one-dataset-out validation and independent cohorts. Interspecies interaction and stability of the gut microbiotas were consistently compromised in diseased shrimp compared with corresponding healthy cohorts, while stochasticity and beta-dispersion exhibited the opposite trend. Collectively, our findings exemplify the utility of microbiome meta-analyses in identifying robust and reproducible features for quantitatively diagnosing disease incidence, and the downstream consequences for shrimp pathogenesis from an ecological prospective. This article is protected by copyright. All rights reserved.

New Insights into the Mechanism of Action of PirAB from Vibrio Parahaemolyticus

PirAB toxins secreted by Vibrio parahaemolyticus (Vp) harbor the pVA1 virulence plasmid, which causes acute hepatopancreatic necrosis disease (AHPND), an emerging disease in Penaeid shrimp that can cause 70–100% mortality and that has resulted in great economic losses since its first appearance. The cytotoxic effect of PirAB^Vp on the epithelial cells of the shrimp hepatopancreas (Hp) has been extensively documented. New insights into the biological role of the PirB^Vp subunit show that it has lectin-like activity and recognizes mucin-like O-glycosidic structures in the shrimp Hp. The search for toxin receptors can lead to a better understanding of the infection mechanisms of the pathogen and the prevention of the host disease by blocking toxin–receptor interactions using a mimetic antagonist. There is also evidence that Vp AHPND changes the community structure of the microbiota in the surrounding water, resulting in a significant reduction of several bacterial taxa, especially Neptuniibacter spp. Considering these findings, the PirAB^vp toxin could exhibit a dual role of damaging the shrimp Hp while killing the surrounding bacteria.

Microbial community composition associated with early developmental stages of the Indian white shrimp, Penaeus indicus

Gut microbiota is known to influence the physiology, health, nutrient absorption, reproduction, and other metabolic activities of aquatic organisms. Microbial composition can influence intestinal immunity and are considered as health indicators. Information on gut microbial composition provides potential application possibilities to improve shrimp health and production. In the absence of such information for Penaeus indicus, the present study reports the microbial community structure associated with its early developmental stages. Bacterial community associated with the early developmental stages (egg, nauplii, zoea, mysis, PL1, PL6 and PL12) from two hatchery cycles were analysed employing 16S rRNA high throughput sequencing. Proteobacteria and Bacteroidetes, were the two dominant phyla in P. indicus development stages. Sequential sampling revealed the constant change in the bacterial composition at genus level. Alteromonas was dominant in egg and nauplii stage, whilst Ascidiaceihabitans (formerly Roseobacter) was the dominant genera in both PL6 and PL12. The bacterial composition was highly dynamic in early stages and our study suggests that the mysis stage is the critical phase in transforming the microbial composition and it gets stabilised by early post larval stages. This is the first report on the composition of microbiota in early developmental stages of P. indicus. Based on these results the formation of microbial composition seems to be influenced by feeding at early stages. The study provides valuable information to device intervention strategies for healthy seed production.

Effect of functional diets on intestinal microbiota and resistance to Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) of Pacific white shrimp (Penaeus vannamei)

AIMS

The present study evaluated the effect of four functional diets and a reference diet on the survival and intestinal bacterial community of shrimp Penaeus vannamei infected with AHPND.

METHODS AND RESULTS

After 42 days of feeding trail, shrimp were inoculated with a Vibrio parahaemolyticus (CIB-0018-3) carrying the plasmid encoding for the PirAB toxins responsible for AHPND. After 120 h post-infection (hpi), shrimp fed with a diet containing 2% of a mix with Curcuma longa and Lepidium meyenii (TuMa) and a diet containing 0.2% of vitamin C (VitC) showed a significantly higher survival (85%) compared to the remaining treatments (50-55%) (p<0.05). Infected shrimp fed with TuMa diet, showed a significant reduction of Vibrionales; and VitC diet promoted an increase of Alteromonadales.

CONCLUSIONS

Our findings suggest that the TuMa diet conferred protection against AHPND and could be attributed to a combined effect of antibacterial properties against Vibrionales, and promoting a desirable bacterial community in the shrimp intestine, while the VitC diet protection could be attributed to their antioxidant capacity and in a lower proportion to a bacterial modulation in shrimp gut.

SIGNIFICANCE AND IMPACT OF THE STUDY

Acute Hepatopancreatic Necrosis Disease (AHPND) is a devastating disease that significantly affects aquaculture production of shrimps. Therefore, the use of functional diets that promotes resistance to AHPND, represents a valuable tool to reduce the mortality of farmed shrimp.

Micro-Aid Liquid 10 Promotes Growth Performance and Health Status of White Shrimp, Litopenaeus vannamei

An experiment was conducted to evaluate the effects of the Micro-Aid Liquid 10 (MAL10) (DPI Global, Porterville, CA, USA), a product made from yucca extract, on growth performance, gut microbiota, and resistance of white shrimp, Litopenaeus vannamei against infectious disease caused by Vibrio alginolyticus. MAL10 was added to shrimp rearing water at different levels of 0 (control), 0.25 mL m3−1 (W0.25), 0.5 mL m3−1 (W0.5), 1 mL m3−1 (W1), and 5 mL m3−1 (W5), respectively, once per week for 70 days. Growth performances, including final body weight, specific growth rate, average daily growth and percentage of weight gain, were significantly improved by adding the MAL10 at levels up to 5 mL m3−1, which may be due to the proliferation of B cells in hepatopancreas of MAL10-treated shrimp. No significant differences in the total viable count and Vibrio-like count in the gut of shrimp were recorded by spread plate method. In the challenge test, shrimp reared in the water supplemented with MAL10 at levels of 1–5 mL m3−1 had significantly lower cumulative mortality after a challenge test with V. alginolyticus compared to shrimp reared in the control, W0.25 and W0.5 groups. Next-generation sequencing indicated that the relative distribution of phylum Proteobacteria in control (80.4%) was higher than the W (77.4%). The proportion of Vibrio was primarily dominant genera in the shrimp intestine and highest in the control group compared to the W group, followed by Spongiimonas, Motilimonas, Demequina, and Shewanella genera. Although there was no statistically significant difference, higher α-diversity indices were recorded in the W5-treated group than in the control group. Therefore, it is considered that MAL10 could be used as a natural alternative in shrimp aquaculture to reduce the risk of infectious disease caused by pathogenic Vibrio and improve the growth performance of white shrimp.

Process optimization for fermented siwu decoction by multi-index-response surface method and exploration of the effects of fermented siwu decoction on the growth, immune response and resistance to Vibrio harveyi of Pacific white shrimp (Litopenaeus vannamei)

The purpose of this study was to explore the optimal fermentation technology of Chinese herbal medicine formula-Siwu Decoction and the effects of fermented Siwu Decoction (FSW) on the growth performance, immune response, intestinal microflora and anti microbial ability of Litopenaeus vannamei. Response to surface methodology (RSM) was used to optimize the fermentation process of Siwu Decoction. The optimal fermentation conditions were obtained as follows: inoculation amount of mixed strains was 4.5%, fermentation time was 36 h, and the ratio of material to liquid was 20%. A total of 1260 shrimps were selected and divided into seven groups, three in parallel in each group. The dietary level of each group was as follows: Control （No additions）, USW1 (0.2% unfermented herbal medicine), USW2 (0.5% unfermented herbal medicine), USW3 (0.8% unfermented herbal medicine), FSW1 (0.2% fermented herbal medicine), FSW2 (0.5% fermented herbal medicine), FSW3 (0.8% fermented herbal medicine). The immune response and antioxidant defense ability of hemocytes and intestine were measured at 21 and 42 days of feeding and the intestinal flora and growth performance were measured at 42 days of feeding, after that, a 7-day challenge test against Vibrio harveyi was conducted. The results showed that fermented Siwu Decoction significantly improved the growth performance and body composition of Litopenaeus vannamei; significantly increased the total number of hemocytes, phagocytic activity, antibacterial activity and bacteriolytic activity of Litopenaeus vannamei, and improved the antioxidant activity of Litopenaeus vannamei; the addition of fermented Siwu Decoction significantly increased the gene expression level of hemocytes and intestinal tract of Litopenaeus vannamei, and improved the antioxidant activity of Litopenaeus vannamei. The abundance of Bacillus increased, while the abundance of Vibrio decreased. After Vibrio harveyi challenge, the cumulative mortality of FSW group was significantly lower than that of control group. Fermented Siwu Decoction may be a potential physiological enhancer in aquaculture, and can be widely used in aquaculture.

Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp Litopenaeus stylirostris: possible influence of the rearing water and more

BACKGROUND

Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management.

METHOD

In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp (Litopenaeus stylirostris) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method.

RESULTS

We found a core microbiota made of taxa related to Aestuariibacter, Alteromonas, Vibrio, SAR11, HIMB11, AEGEAN 169 marine group and Candidatus Endobugula associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to Pseudomonas, Corynebacterium, Acinetobacter, Labrenzia, Rothia, Thalassolituus, Marinobacter, Aureispira, Oleiphilus, Profundimonas and Marinobacterium genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.

Comparison of the Intestinal Microbiota During the Different Growth Stages of Red Swamp Crayfish (Procambarus clarkii)

This study aimed to determine the effect of the growth stage of Procambarus clarkii on their intestinal microbiota. Intestinal samples of five different growth stages of P. clarkii (first instar, second instar, third instar, juvenile, and adult) from laboratory culture were analyzed through the Illumina MiSeq high-throughput sequencing platform to determine the intestinal microbiome of crayfish. The alpha diversity decreased along with the growth of the crayfish, with the relative abundance of the microbiota changing among stages; crayfish at closer development stages had a more comparable intestinal microbiota composition. A comparative analysis by principal component analysis and principal coordinate analysis showed that there were significant differences in the intestinal microbiota of crayfish among the different growth stages, except for the first two stages of larval crayfish, and the intestinal microbiota showed a consistent progression pattern from the larval stage to the juvenile stage. Some microbiota showed stage specificity, which might be the characteristic microbiota of different stages of growth. According to FAPROTAX functional clustering analysis, the three stages of larvae were clustered together, while the juvenile and adult stages were clustered separately according to the growth stage, indicating that, in the early stages of larval development, the function of the intestinal flora was similar; as the body grew and developed, the composition and function of the intestinal microbiota also changed.

16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus)

The endemic Indian white shrimp (Penaeus indicus) is an economically important crustacean species, distributed in the Indo-West Pacific region. Knowledge of its gut microbial composition helps in dietary interventions to ensure improved health and production. Here we analyzed V3-V4 hypervariable regions of the 16 S rRNA gene to examine intestinal microbiota in wild and domesticated farmed P. indicus. The study revealed that Proteobacteria, Fusobacteria, Tenericutes, and Bacteroidetes, were the dominant phyla in both the groups although there were differences in relative abundance. The dominant genera in case of the wild group were Photobacterium (29.5 %) followed by Propionigenium (13.9 %), Hypnocyclicus (13.7 %) and Vibrio (11.1 %); while Vibrio (46.5 %), Catenococcus (14 %), Propionigenium (10.3 %) and Photobacterium (8.7 %) were dominant in the farmed group. The results of the study suggest the role of environment on the relative abundance of gut bacteria. This is the first report characterizing gut microbial diversity in P. indicus, which can be used to understand the role of gut microbiota in health, nutrition, reproduction, and growth.

Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview

The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.

Molecular docking study of bio-inhibitors extracted from marine macro-alga Ulva fasciata against hemolysin protein of luminescence disease-causing Vibrio harveyi

Shrimp grow-out and hatchery systems are being affected by bacterial disease particularly Vibrios. The use of chemotherapeutic agents in aquaculture practices has to lead to the development of resistance among aquatic bacteria. Thus, health management becomes of major importance in aquaculture. Under this situation, progressing bio-inhibitors from marine resources are most appropriate to be considered against pathogenic bacteria. Molecular docking is an appropriate tool in structural biology and computer-assisted drug design to predict and neutralize a target protein of known diseases. In this study, marine macro-alga Ulva fasciata was aimed at developing inhibitors against luminescence disease-causing pathogenic bacteria Vibrio harveyi. U. fasciata was collected from Thoothukudi, Tamil Nadu, India. Extract of U. fasciata was tested against growth and virulence factors of V. harveyi during Penaeus monodon larviculture. Further U. fasciata extract was subjected to GC-MS analysis to identify the biomolecules. The homology modeling of virulent protein, hemolysin of V. harveyi was designed in this study. Hence, it was aimed for molecular docking against the biomolecules identified from U. fasciata extract. During shrimp larviculture, the extract of U. fasciata (200 μg mL^-1) exhibited reduction on Cumulative Percentage of Mortality (32.40%) in postlarvae against challenge of V. harveyi infection. Biomolecule Methyl dehydroabietate had showed highest binding affinity among the compounds was evaluated in molecular docking study. Statistical analysis had revealed significant differences (p < 0.05) in trials. Therefore, it was proved that the bio-inhibitors from U. fasciata will be a better option for controlling luminescence disease-causing V. harveyi in shrimp grow-out practices.

Comparative analysis of the intestinal bacterial communities in mud crab Scylla serrata in South India

Little is known about the functions of the crustacean gut microbiome, but environmental parameters and habitat are known to affect the composition of the intestinal microbiome, which may in turn affect the physiological status of the host. The mud crab Scylla serrata is an economically important species, and is wild‐caught, and farmed across the Indo‐Pacific region. In this study, we compared the composition of the gut microbiome (in terms of gut microbial species richness and abundance) of S. serrata collected from wild sites, and farms, from the east and west coast of India, and also tested the effects of the environment on the composition. The water temperature had a statistically significant effect on gut microbiome composition, with microbial biodiversity decreasing with increasing water temperature. This could have negative effects on both wild and farmed mud crabs under future climate change conditions, although further research into the effects of temperature on gut microbiomes is required. By comparison, salinity, crab mass and carapace width, geographical location as well as whether they were farmed or wild‐caught crabs did not have a significant impact on gut microbiome composition. The results indicate that farming does not significantly alter the composition of the gut microbiome when compared to wild‐caught crabs.

C-Type Lectin Maintains the Homeostasis of Intestinal Microbiota and Mediates Biofilm Formation by Intestinal Bacteria in Shrimp

Intestinal microbiota are closely related to host physiology. Over the long course of evolution and interaction, both commensal bacteria and their host have evolved multiple strategies to adapt to each other. However, in invertebrates, the regulatory mechanism of intestinal microbiota homeostasis is largely unknown. In the current study, a digestive tract-specific C-type lectin, designated as CTL33, was identified because of its abundance and response to bacteria in the intestine of kuruma shrimp (Marsupenaeus japonicus). Silencing of CTL33 expression led directly to intestinal dysbiosis, tissue damage, and shrimp death. CTL33 could facilitate biofilm formation by the intestinal bacteria. This function originated from its unique architecture, with a lectin domain responsible for bacteria recognition and a coiled coil region that mediated CTL33 dimerization and cross-linked the bacteria into a biofilm-like complex. By mediating the formation of a biofilm, CTL33 promoted the establishment of intestinal bacteria in intestine and maintained the homeostasis of the microbiota. Thus, to our knowledge, we demonstrated a new mechanism of C-type lectin-mediated biofilm formation by intestinal bacteria, providing new insights into intestinal homeostasis regulation in invertebrates.

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

Intestine microbiota is tightly associated with host health status. Increasing studies have focused on assessing how host intestine microbiota is affected by biotic factors but ignored abiotic factors. Here, we aimed to understand the effects of salinity on shrimp intestine microbiota, by comparing the differences of intestine bacterial signatures of shrimp under low-salinity (LS) and high-salinity (HS) culture conditions. Our results found that intestine core bacterial taxa of shrimp under LS and HS culture conditions were different and that under HS contained more opportunistic pathogen species. Notably, compared with LS culture conditions, opportunistic pathogens (e.g., Vibrio species) were enriched in shrimp intestine under HS. Network analysis revealed that shrimp under HS culture conditions exhibited less connected and lower competitive intestine bacterial interspecies interactions compared with LS. In addition, under HS culture conditions, several opportunistic pathogens were identified as keystone species of intestine bacterial network in shrimp. Furthermore, the ecological drift process played a more important role in the intestine bacterial assembly of shrimp under HS culture conditions than that under LS. These above traits regarding the intestine microbiota of shrimp under HS culture conditions might lead to host at a higher risk of disease. Collectively, this work aids our understanding of the effects of salinity on shrimp intestine microbiota and helps for shrimp culture.

Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp

Biofloc systems generate and accumulate microbial aggregates known as bioflocs. The presence of bioflocs has been shown to change gut bacterial diversity and stimulate innate immunity in shrimp. The microbial niche of bioflocs may therefore have the potential to drive shifts in the shrimp gut microbiota associated with stimulation of innate immunity. We performed shotgun metagenomic analysis and 16S rRNA-based amplicon sequencing to characterize complex bacterial members in bioflocs and the shrimp digestive tract, respectively. Moreover, we determined whether biofloc-grown shrimp with discrete gut microbiomes had an elevation in local immune-related gene expression and systemic immune activities. Our findings demonstrated that the bacterial community in bioflocs changed dynamically during Pacific white shrimp cultivation. Metagenomic analysis revealed that Vibrio comprised 90% of the biofloc population, while Pseualteromonas, Photobacterium, Shewanella, Alteromonas, Bacillus, Lactobacillus, Acinetobacter, Clostridium, Marinifilum, and Pseudomonas were also detected. In the digestive tract, biofloc-grown shrimp maintained the presence of commensal bacteria including Vibrio, Photobacterium, Shewanella, Granulosicoccus, and Ruegeria similar to control shrimp. However, Vibrio and Photobacterium were significantly enriched and declined, respectively, in biofloc-grown shrimp. The presence of bioflocs upregulated immune-related genes encoding serine proteinase and prophenoloxidase in digestive organs which are routinely exposed to gut microbiota. Biofloc-grown shrimp also demonstrated a significant increase in systemic immune status. As a result, the survival rate of biofloc-grown shrimp was substantially higher than that of the control shrimp. Our findings suggested that the high relative abundance of vibrios in bioflocs enriched the number of vibrios in the digestive tract of biofloc-grown shrimp. This shift in gut microbiota composition may be partially responsible for local upregulation of immune-related gene expression in digestive organs and systemic promotion of immune status in circulating hemolymph.

Effects of Yu-Ping-Feng polysaccharides (YPS) on the immune response, intestinal microbiota, disease resistance and growth performance of Litopenaeus vannamei

A 28-day feeding trial was conducted to investigate the effects of Yu-Ping-Feng polysaccharides (YPS) containing Astragalus polysaccharides (APS), Atractylodes macrocephala polysaccharides (AMP) and Saposhnikoviae polysaccharides (SPS) on the immune response, intestinal microbiota, disease resistance and growth performance of Litopenaeus vannamei. Seven hundred and twenty shrimp (3.04 ± 0.33 g) were fed the following diets: Control, YPS1 (0.13% APS + 0.0325% AMP + 0.0325% SPS), YPS2 (0.13% APS + 0.0325% AMP + 0.065% SPS) and YPS3 (0.13% APS + 0.0325% AMP+0.0975% SPS). After 14 and 28 days of feeding, the immune responses of hemocytes and intestine were measured. Intestinal microbiota and growth performance were measured after 28 days of feeding, after that, a 7-day challenge test against Vibrio harveyi was conducted. A significant (P < 0.05) increase of the total haemocyte count (THC), phagocytic activity, antibacterial activity and phenoloxidase (PO) activity was observed in shrimp fed YPS diets compared to the control. Also, dietary YPS supplementation particularly YPS3 group significantly increased the expressions of immune-related genes in the hemocytes and intestine. Regarding the intestinal microbiota, the microbial diversity and richness decreased and functional genes associated with short-chain fatty acids metabolism increased in YPS groups. After Vibrio harveyi challenge, the cumulative mortality in YPS groups was significantly lower than that of the control. Besides, dietary YPS had no significant effect on growth performance of shrimp (P > 0.05). The present results suggested that YPS could be considered as potential prebiotics for aquaculture farmed shrimp.

Developmental, Dietary, and Geographical Impacts on Gut Microbiota of Red Swamp Crayfish (Procambarus clarkii)

Red swamp crayfish (Procambarus clarkii) breeding is an important economic mainstay in Hubei province, China. However, information on the gut microbiota of the red swamp crayfish is limited. To address this issue, the effect of developmental stage, diet (fermented or non-fermented feed), and geographical location on the gut microbiota composition in the crayfish was studied via high-throughput 16S rRNA gene sequencing. The results revealed that the dominant phyla in the gut of the crayfish were Proteobacteria, Bacteroidetes,Firmicutes, Tenericutes, and RsaHF231. The alpha diversity showed a declining trend during development, and a highly comparable gut microbiota clustering was identified in a development-dependent manner. The results also revealed that development, followed by diet, is a better key driver for crayfish gut microbiota patterns than geographical location. Notably, the relative abundance of Bacteroidetes was significantly higher in the gut of the crayfish fed with fermented feed than those fed with non-fermented feed, suggesting the fermented feed can be important for the functions (e.g., polysaccharide degradation) of the gut microbiota. In summary, our results revealed the factors shaping gut microbiota of the crayfish and the importance of the fermented feed in crayfish breeding.

Insights into the microbiota of larval and postlarval Pacific white shrimp (Penaeus vannamei) along early developmental stages: a case in pond level

Increasing studies have revealed strong links among gut microbiota, health status, and shrimp development, but they mainly focus on the microbiota of Pacific white shrimp, Penaeus vannamei, during life stages from juveniles to adults. Little is known about shrimp microbiota dynamics at early developmental stages. In this study, with an aim to profile shrimp microbiota and its dynamics at stages nauplius, zoea, mysis, and early postlarva, we conducted a survey for the successful breeding processes in a commercial hatchery in China, sampled 33 samples including larval/postlarval shrimp, suspended substance in rearing water (SSRW), and nutrition supplements (i.e., algae and brine shrimp larvae) at stages N5, Z2, M2, and P2. The associated bacterial communities were sequenced and comparatively analyzed using high-throughput sequencing of bacterial 16S rRNA genes. Our case study results showed that bacterial community structures and compositions were strikingly different at stages N5, Z2, and P2, indicating the shift of microbiota at the three stages. Many taxa within Gamma-, Alphaproteobacteria, and Flavobacteriia classes were observed to be stage-specifically abundant and identified as taxonomic biomarkers potentially used to differentiate among shrimp at different early developmental stages. Summing up, these results shed light on larval/postlarval microbiota and its dynamics at different early developmental stages, highlighting the potential roles of shrimp development in microbiota formation and shifting.

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.

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle

BACKGROUND

Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.

RESULTS

Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.

CONCLUSIONS

Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

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.

Effects on development and microbial community of shrimp Litopenaeus vannamei larvae with probiotics treatment

Shrimp production is the second ranked of the most-traded production in these decades and the whiteleg shrimp Litopenaeus vannamei is the sixth most cultured species. Probiotics are alternative strategy for the promotion of growth and prevention of diseases in aquaculture. To confirm the effects of the probiotics on development and microbial community of L. vannamei larvae during different development stages, five kinds of probiotics (10⁸ ~ 10⁹ CFU/g) were added into the rearing environment of shrimp larvae, and the effects of probiotics on bacterial community and water quality, larval growth and immune index were determined from nauplius larval stage to post larval stage. Results suggested that probiotics treated groups showed larger survival rate than the control groups from Z1 stage to P5 stage. Lactobacillus could improve the larvae's survival ability, especially in the larval stages M2, M3, P1, P5 stage. It was confirmed that probiotics could promote the growth and development of shrimp larvae and prevent the incomplete molting in their growing process, particularly for EM-treated group. Results suggested that all the probiotics-treated groups had shown significant decreasing trend in the quantity of vibrios, except for the SA-treated group. And different probiotics could inhibit vibrios during different life periods. Among these probiotics, LA, EM and PB had shown the best effects, including improving survival rate of the larvae, promoting the larval metamorphosis, reducing the quantity of vibrios and NH₄-N and NO₂-N levels, and increasing bacterial diversity.

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.

Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon)

Microbial colonization is an essential process in the early life of animal hosts—a crucial phase that could help influence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profiles exhibited different patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identified as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day-old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the first report on bacteria establishment and assembly in early developmental stages of P. monodon. Our findings showed that the bacterial compositions could be shaped by different host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong influence.

Fermented Animal Source Protein as Substitution of Fishmeal on Intestinal Microbiota, Immune-Related Cytokines and Resistance to Vibrio mimicus in Freshwater Crayfish (Cherax cainii)

A feeding trial was carried out to evaluate the effects of substitution of fishmeal (FM) by dietary poultry by-product meal, fermented by Lactobacillus casei and Saccharomyces cerevisiae on growth, intestinal health, microbial composition, immune related cytokines and disease resistance of freshwater crayfish, marron (Cherax cainii) against Vibrio mimicus. Two isonitrogenous and isocaloric diets were formulated by replacing FM protein with fermented poultry by-product meal (FPBM) protein at 0% (Control) and 75% (FPBM), and fed marron for 70 days. The results indicated no significant difference (P > 0.05) in final body weights between two groups of marron, whilst intestinal microvilli number per fold was increased in marron fed FPBM than the control. The 16S rRNA sequences revealed an increased number of Lactobacillus and Streptococcus, and decreased number of Aeromonas at genus level in the distal intestine of marron fed FPBM. Marron fed FPBM showed up-regulated expression of IL-8, IL-10, and IL-17F genes in the distal intestine. Significantly (P < 0.05) increased lysozyme and phagocytic activity, and higher survival was found in marron fed FPBM following a bacterial challenge with Vibrio mimicus. Therefore, it is concluded that FPBM is beneficial to marron in terms of microbial community, immune-related cytokines and disease resistance against V. mimicus.

Bacterial Community Dynamics During Nursery Rearing of Pacific White Shrimp (Litopenaeus vannamei) Revealed via High-Throughput Sequencing

A 20-day trial was conducted to reveal bacterial community dynamics in a commercial nursery of larval Litopenaeus vannamei larvae. The bacterial communities in the ambient water were profiled by high-throughput sequencing of the V4-V5 hypervariable region of the 16S rRNA gene. The results indicated that the dominant bacterial phyla between the metamorphosis stage and postlarval stage were Bacteroidetes, Proteobacteria, Cyanobacteria, and Firmicutes, representing more than 80.09% of the bacterial operational taxonomic units. The relative abundance among bacterial phyla notably differed between the two stages. The relative abundance of Cyanobacteria was higher in the metamorphosis stage, while that of Bacteroidetes was higher and more stable in the postlarval stage. At the class level, the relative abundance of Sphingobacteriia and Alphaproteobacteria increased markedly in the postlarval stage, while that of Flavobacteriia decreased. Redundancy analysis showed that bacterial composition in the metamorphosis stage was positively correlated with salinity, alkalinity, and pH, while in the postlarval stage, it was positively correlated with ammonium nitrogen and nitrite nitrogen. Thus, microbial community diversity in the nursery phase varies per rearing stage.

The intestinal bacterial community of healthy and diseased animals and its association with the aquaculture environment

Although increasing levels of attention have been targeted towards aquaculture-associated bacteria, the bacterial community of animal intestines and its relationship with the aquaculture environment need to be further investigated. In this study, we used high-throughput sequencing to analyze the bacterial community of pond water, sediment, and the intestines of diseased and healthy animals. Our data showed that Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes were the dominant taxa of bacteria across all samples and accounted for more than 90% of the total sequence. Difference analysis and Venn diagrams showed that most of the intestinal bacterial OTUs (operational taxonomic units) of diseased and healthy animals were the same as those of sediment and water, indicating that the aquaculture environment was the main source of intestinal bacteria. Compared with healthy animals, a considerable reduction of OTUs was evident in diseased animals. Welch's t test showed that the dominant bacterial taxa in sediment, water, and animal intestine were significantly different (p < 0.05) and each had its own unique dominant microorganisms. In addition, differences between the intestinal bacteria of healthy and diseased animals were represented by potential probiotics and pathogens, such as Bacillus, Vibrio, Oceanobacillus, and Lactococcus. Principal component analysis (PcoA) showed that a similar environment shaped a similar microbial structure. There was a large difference in the spectrum of intestinal bacteria in diseased animals; furthermore, the spectrum of intestinal bacteria in diseased animals was very different from the environment than in healthy animals. This study provides a theoretical basis for a relationship between the intestinal bacteria of healthy and diseased animals and the environment and provides guidance for environmental regulation and disease prevention in aquaculture areas.

Assessing interactions, predicting function, and increasing degradation potential of a PAH-degrading bacterial consortium by effect of an inoculant strain

A natural phenanthrene-degrading consortium CON was inoculated with an exogenous strain Sphingobium sp. (ex Sp. paucimobilis) 20006FA yielding the consortium called I-CON, in order to study ecological interactions into the bacterial community. DGGE and proteomic profiles and analyses by HTS (High-Throughput Sequencing) technologies demonstrated inoculant establishment and changes on CON composition. Inoculation increased degradation efficiency in I-CON and prevented intermediate HNA accumulation. This could be explained not only by the inoculation, but also by enrichment in Achromobacter genus at expense of a decrease in Klebsiella genus. After inoculation, cooperation between Sphingobium and Achromobacter genera were improved, thereby, some competition could have been generated, and as a consequence, species in minor proportion (cheaters), as Inquilinus sp. and Luteibacter sp., were not detected. Sequences of Sphingobium (corresponding to the inoculated strain) did not vary. PICRUSt predicted a network with bacterial phylotypes connected with enzymes, showing functional redundancy in the phenanthrene pathway, with exception of the first enzymes biphenyl-2,3-diol 1,2-dioxygenase and protocatechuate 4,5-dioxygenase that were only encoded in Sphingobium sp. This is the first report where a natural consortium that has been characterized by HTS technologies is inoculated with an exogenous strain in order to study competitiveness and interactions.

Overfeeding a High-Fat Diet Promotes Sex-Specific Alterations on the Gut Microbiota of the Zebrafish (Danio rerio)

Diet modulates the gut microbiota and is one of the main factors promoting obesity and overweight. In the present study, we investigated the effect of a high-fat diet (HFD) on the gut microbiota of the zebrafish (Danio rerio). Fish were separated into three groups and fed in different regimes: low fat, high fat, and high fat overfed; the experiments were performed on males and females separately. We analyzed more than 2.6 million sequences of variable region V3 of the 16S rRNA gene generated by the Illumina Miniseq platform, clustered to 97% similarity with vsearch and classified with the EzBioCloud database. The weight gain, condition factor (K), and body mass index were calculated as indicators of obesity. Multivariate analysis (PERMANOVA and ANOSIM) and diversity indices (Shannon and Dominance) revealed that overfeeding a HFD disturbs the gut microbiota differently in males and females suggesting that sex is a significant factor (p < 0.05) for the composition of the gut microbiota of zebrafish. The results also indicate that a HFD provided in a basal caloric regime does not promote obesity or alterations in the gut microbiota.

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei

The interactions of microbiota in the intestines play an important role in promoting or maintaining the health of hosts. The present study aim to investigate the effects of the surface proteins of Lactobacillus pentosus HC-2 on the immune response and the bacterial composition of Litopenaeus vannamei, thus, the immune-related genes, surface condition, HC-2 numbers and the bacteria diversity in midgut were explored after shrimp feeding the normal HC-2 and 5 M -  lithium chloride (LiCl) treated HC-2 for four weeks. Obvious improvements in the intestinal surface were observed in R group than the control group and L group. qPCR analysis demonstrated that the selected immune-related genes of lysozyme, proPO, LGBP, PEN-3α, crustin, and lvLec were significantly up-regulated in group R than in group L. Meanwhile, in the challenge test, shrimp in R group received 72% relative percent survival, which was significantly higher than the L group (RPS = 9%). The bacteria composition analysis showed that the abundance of Proteobacteria were significantly higher in group R and L than in group C, and the Bacteroidetes were significantly higher in group C than in group R and L, whereas the numbers of Chloroflexi were significantly higher in group R than in group C and L. The bacterial community difference analysis revealed that the harmful bacteria such as genus of Vibrio, Tenacibaculu and Thalassobius were decreased and the beneficial bacterium as Ruegeria and Lactobacillus were increased in R group, whereas this phenomenon were not found in L group. Taken together, above results indicating that the surface proteins were indispensable for L. pentosus HC-2 adhesion and colonization in shrimp intestines to improve intestine condition, enhance immune response, competitively exclude the pathogens, and promote the beneficial bacteria growth to protect the shrimp from pathogens infection. The findings in this work will help to promote the understanding of the roles of probiotics in shrimp intestines displaying probiotic-function by regulating the intestinal bacteria.

Change in the intestinal bacterial community structure associated with environmental microorganisms during the growth of Eriocheir sinensis

As an important organ to maintain the host's homeostasis, intestinal microbes play an important role in development of the organism. In contrast to those of terrestrial animals, the intestinal microbes of aquatic organisms are affected by environmental microorganisms (including water microorganisms and sediment microorganisms). In the present study, the compositional differences of intestinal microbes in three representative developmental stages of the Chinese mitten crab (Eriocheir sinensis) were studied. Meanwhile, network association analysis, and visualization of the water microorganisms of the crabs’ habitat, the environment microorganisms in the pond, and the intestinal microbes, was carried out. The results showed that the gut microbiota diversity index decreased continuously with age, and the four bacteria of Aeromonas (Proteobacteria), Defluviitaleaceae (Firmicutes), Candidatus Bacilloplasma (Tenericutes), and Dysgonomonas (Bacteroidetes) were the “indigenous” flora of the crab. In the network‐related analysis with the environment, we found that as the culture time increased, the effect of environmental microorganisms on the intestinal microbes of crabs gradually decreased, and the four “indigenous” bacteria were always unaffected by the environmental microorganisms. The results of this study identified the core bacteria of the crab and, for the first time, studied the relationship between intestinal environmental microorganisms, which will aid the practical production of crabs and will promote research into the relationship between specific bacteria and the physiological metabolism of crabs.

Persistence and spatial variation of antibiotic resistance genes and bacterial populations change in reared shrimp in South China

More attention has been paid to the abundance and diversity of antibiotic resistance genes (ARGs) in aquatic environments. However, few studies have investigated the persistence and spatial variation of ARGs in aquatic organisms. This study investigated the occurrence and abundance of ARGs and the bacterial populations in shrimp intestinal tracts during the rearing period in different regions of Guangdong, South China. The results showed that sul1, sul2, qnrD, and floR were the predominant ARGs. Compared with those of juvenile shrimp, the total concentrations of ARGs in the intestinal tract of adult shrimp in three shrimp farms were 2.45-3.92 times higher (p < 0.05), and the bacterial populations in the adult shrimp intestinal tract changed considerably. Redundancy analysis (RDA) showed that the abundance of Proteobacteria, Firmicutes, and Verrucomicrobia in Farms A, B, and C, respectively, were strongly positively correlated with the most abundant and predominant genes (sul1 and qnrD for Farm A; floR and sul2 for Farm B; floR and sul2 for Farm C) in the shrimp intestinal tract. The results of this study indicated that ARGs gained persistence in the developmental stages of the reared shrimp. Different phyla of predominant bacteria were responsible for the increase of ARGs abundance in the shrimp intestinal tract in different regions. This study represents a case study of the persistence and spatial variation of ARGs in aquaculture and can be a reference for the determination of harmful impacts of ARGs on food safety and human health.

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.

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota

Increasing evidence has emerged supporting a tight link between gut bacterial community and shrimp health. However, the knowledge about the variation of gut bacterial community, especially with different disease onset time, remains elusive. Here, healthy and diseased shrimps were collected at 3 disease-outbreak times (day 70, 80 and 85) to investigate the variation of gut bacterial community and its underlying ecological process with 16S rRNA gene amplicon sequencing. The gut bacterial community of diseased shrimp was distinct from the healthy one and temporally less stable, characterized by decreased alpha-diversity and dispersive structure. And its dominant ecological process experienced a transition with disease onset time, although deterministic process mainly governed the healthy gut bacterial assembly. In addition, the core microbiota of healthy shrimp gut harbored more diverse bacterial taxa with more cooperative interactions, while the diseased core microbiota showed opposite pattern with significantly higher abundance of opportunistic pathogens as well. These findings indicate that shrimp heath is highly relevant to the homeostasis of its gut bacterial community. Preservation and restoration of the bacterial community equilibrium could represent an effective strategy for shrimp disease prevention.