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

Updated roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence

Litopenaeus vannamei is the most extensively cultured shrimp species globally, recognized for its scale, production, and economic value. However, its aquaculture is plagued by frequent disease outbreaks, resulting in rapid and massive mortality. etiological research often lags behind the emergence of new diseases, leaving the causal agents of some shrimp diseases unidentified and leading to nomenclature based on symptomatic presentations, especially in cases involving co- and polymicrobial pathogens. Comprehensive data on shrimp disease statuses remain limited. In this review, we summarize current knowledge on shrimp diseases and their effects on the gut microbiome. Furthermore, we also propose a workflow integrating primary colonizers, "driver" taxa in gut networks from healthy to diseased states, disease-discriminatory taxa, and virulence genes to identify potential polymicrobial pathogens. We examine both abiotic and biotic factors (e.g., external and internal sources and specific-disease effects) that influence shrimp gut microbiota, with an emphasis on the "holobiome" concept and common features of gut microbiota response to diverse diseases. After excluding the effects of confounding factors, we provide a diagnosis model for quantitatively predicting shrimp disease incidence using disease common-discriminatory taxa, irrespective of the causal agents. Due to the conservation of functional genes used in designing specific primers, we propose a practical strategy applying qPCR-assayed abundances of disease common-discriminatory functional genes. This review updates the roles of the gut microbiota in exploring shrimp etiology, polymicrobial pathogens, and disease incidence, offering a refined perspective for advancing shrimp aquaculture health management.

The assembly of gut microbiota implicates shrimp acute hepatopancreas necrosis disease progression

Ample evidence shows dysbiosis in the gut microbiota when comparing healthy shrimp with those affected by severe acute hepatopancreatic necrosis disease (AHPND). However, the static comparison used in available studies leads to the uncertainties regarding how and to what extent the gut microbiota responds to the progressive severity of AHPND. In addition, shrimp AHPND is featured by rapid and massive mortality, thus the initiation of AHPND must be diagnosed for preemptive therapy. For these reasons, we explored the ecological assembly of gut microbiota over shrimp AHPND progression. Increasing AHPND severity was associated with linear increase in the copies of pirAB genes, relative abundance of gut Vibrio and potentially pathogenic, and reduction in the gut bacterial diversity, stability, and relative abundance of Bdellovibrio. Negative and significant association between gut Vibrio and Bdellovibrio were noted, indicating that compromised predation exerts a role in AHPND progression. Notably, the extents of departure to the healthy shrimp gut microbiota were positively coupled with the increasing severity of AHPND. After controlling the temporal variation in the gut microbiota as healthy shrimp age, we constructed a diagnosis model that accurately diagnosed the initial, progressed or moribund stages of AHPND, with an overall accuracy of 86.5%. Shrimp AHPND induced more stochastic gut microbiotas as a consequence of the attenuated ability of diseased shrimp to select their commensals, resulting in convergent bacterial communities between gut and rearing water over AHPND progression. Collectively, our findings provide important step toward the ecological assembly of gut microbiota implicating in AHPND etiology and in diagnosing AHPND stages. KEY POINTS: • The departure of shrimp gut microbiota positively linked with AHPND severity. • The diagnosis model accurately diagnosed the stages of AHPND. • Shrimp AHPND induced more stochastic gut microbiota.

Gut bacterial consortium enriched in a biofloc system protects shrimp against Vibrio parahaemolyticus infection

BACKGROUND

Shrimp cultured in a biofloc system (BFS) have a lower disease incidence than those farmed in a water exchange system (WES). Although a number of studies have reported that the gut bacterial community induced by BFS is highly associated with shrimp disease resistance, the causal relationship remains unknown. Here, the promotive roles of gut bacterial community induced by BFS in pathogenic Vibrio infection resistance and its potential micro-ecological and physiological mechanisms were investigated by gut bacterial consortium transplantation and synthetic community (SynCom) construction.

RESULTS

The BFS induced a more stable and resistant gut bacterial community, and significantly enriched some beneficial bacterial taxa, such as Paracoccus, Ruegeria, Microbacterium, Demequina, and Tenacibaculum. Transplantation of a gut bacterial consortium from BFS shrimp (EnrichBFS) greatly enhanced the stability of the bacterial community and resistance against pathogenic V. parahaemolyticus infection in WES shrimp, while transplantation of a gut bacterial consortium from WES shrimp significantly disrupted the bacterial community and increased pathogen susceptibility in both WES and BFS shrimp. The addition of EnrichBFS in shrimp postlarvae also improved the pathogen resistance through increasing the relative abundances of beneficial bacterial taxa and stability of bacterial community. The corresponding strains of five beneficial bacterial taxa enriched in BFS shrimp were isolated to construct a SynComBFS. The addition of SynComBFS could not only suppress disease development, but also improve shrimp growth, boost the digestive and immune activities, and restore health in diseased shrimp. Furthermore, the strains of SynComBFS well colonized shrimp gut to maintain a high stability of bacterial community.

CONCLUSIONS

Our study reveals an important role for native microbiota in protecting shrimp from bacterial pathogens and provides a micro-ecological regulation strategy towards the development of probiotics to ameliorate aquatic animal diseases. Video Abstract.

Gut microbiota of Pacific white shrimp (Litopenaeus vannamei) exhibits distinct responses to pathogenic and non-pathogenic Vibrio parahaemolyticus

Acute hepatopancreatic necrosis disease (AHPND), a high-mortality-rate shrimp disease, is caused by specific Vibrio parahaemolyticus (Vp) strains with a plasmid encoding the PirABVp toxins. As a bacterial pathogen, the invasion of AHPND-causing Vp might impose pressure on commensal microbiota in the shrimp gut, while the relationship between the pathogenesis of AHPND and the dysbiosis of gut bacterial communities remains unclear. Here we explored the temporal changes of shrimp gut microbiota in response to AHPND-causing and non-AHPND-causing Vp strains, with the non-infected controls as a baseline of the shrimp gut microbiota. The diversity and composition of bacterial communities from 168 gut samples (covering three treatments at seven time points with eight individuals per set) were investigated using 16S rRNA gene metabarcoding with high-throughput sequencing. The results showed that (i) species diversity of gut bacterial communities declined in Vp-infected shrimp, independent of the strain pathogenicity; (ii) taxonomic compositions of gut bacterial communities were significantly different between shrimp infected by AHPND-causing and non-AHPND-causing Vp strains; (iii) short-term (within 6 hours) compositional shifts in the gut microbiota were found only in AHPND-causing Vp-infected shrimp; (iv) the gut microbiota of AHPND-causing Vp-infected shrimp was enriched with genera Photobacterium and Vibrio, with a decline in Candidatus Bacilliplasma; and (v) functional predictions suggested the loss of normal metabolism due to compositional shifts in the gut microbiota. Our work reveals distinct features of community dynamics in shrimp gut microbiota, associated with pathogenic versus non-pathogenic Vibrio infections, providing a new perspective of the pathogenesis of AHPND. IMPORTANCE Shrimp production is continually threatened by newly emerging diseases, such as AHPND, which is caused by specific Vp strains. Previous studies on the pathogenesis of AHPND have mainly focused on the histopathology and immune responses of the host. However, more attention needs to be paid to the gut microbiota, which acts as the first barrier to pathogen colonization. In this study, we revealed that shrimp gut microbiota responded differently to pathogenic and non-pathogenic Vp strains, with bacterial genera Photobacterium and Vibrio enriched in pathogenic Vp-infected shrimp, and Candidatus Bacilliplasma enriched in non-pathogenic Vp-infected shrimp. Moreover, functional predictions suggested that changes in taxonomic compositions would further affect normal metabolic functions, emphasizing the importance of sustaining an equilibrium in the gut microbiota. Several biomarkers associated with specific microbial taxa and functional pathways were identified in our data sets, which help predict the incidence of disease outcomes.

Resilience and probiotic interventions to prevent and recover from shrimp gut dysbiosis

To counter the recurrent outbreaks of bacterial (acute hepatopancreatic necrosis disease; AHPND) and viral (white spot disease; WSD) shrimp diseases, which still remain a threat to the global industry, shrimp gut microbiota research has been gaining more attention in recent years, and the use of probiotics in aquaculture has had promising results in improving shrimp gut health and immunity. In this review based on our studies on AHPND and WSD, we summarize our current understanding of the shrimp gastrointestinal tract and the role of the microbiota in disease, as well as effects of probiotics. We focus particularly on the concept of microbiota resilience, and consider strategies that can be used to restore shrimp gut health by probiotic intervention at a crucial time during gut microbiota dysbiosis. Based on the available scientific evidence, we argue that the use of probiotics potentially has an important role in controlling disease in shrimp aquaculture.

Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria

Huanglongbing (HLB), the most prevalent citrus disease worldwide, is responsible for substantial yield and economic losses. Phytobiomes, which have critical effects on plant health, are associated with HLB outcomes. The development of a refined model for predicting HLB outbreaks based on phytobiome markers may facilitate early disease detection, thus enabling growers to minimize damages. Although some investigations have focused on differences in the phytobiomes of HLB-infected citrus plants and healthy ones, individual studies are inappropriate for generating common biomarkers useful for detecting HLB on a global scale. In this study, we therefore obtained bacterial information from several independent datasets representing hundreds of citrus samples from six continents and used these data to construct HLB prediction models based on 10 machine learning algorithms. We detected clear differences in the phyllosphere and rhizosphere microbiomes of HLB-infected and healthy citrus samples. Moreover, phytobiome alpha diversity indices were consistently higher for healthy samples. Furthermore, the contribution of stochastic processes to citrus rhizosphere and phyllosphere microbiome assemblies decreased in response to HLB. Comparison of all constructed models indicated that a random forest model based on 28 bacterial genera in the rhizosphere and a bagging model based on 17 bacterial species in the phyllosphere predicted the health status of citrus plants with almost 100% accuracy. Our results thus demonstrate that machine learning models and phytobiome biomarkers may be applied to evaluate the health status of citrus plants.

Effects of anthropogenic stress on hosts and their microbiomes: Treated wastewater alters performance and gut microbiome of a key detritivore (Asellus aquaticus)

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host-microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater - potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Effects of high temperature stress on the intestinal histology and microbiota in Yesso scallop Patinopecten yessoensis

High temperature stress posed by global warming is considered as one of the greatest threats to marine ectotherms by altering their behavior and physiological functions. The intestine and its associated microbiota constitute the first defensive line for the animals against environmental stresses, but their responses to high temperature stress in mollusks are largely unknown. In the present study, the changes of intestinal histology and microbiota were investigated in Yesso scallop Patinopecten yessoensis, a cold-water bivalve species, after high temperature stress. The shrinkage of intestinal lumen, shortening of intestinal villi and increased goblet cells were observed in the intestines of scallops exposed to seawater temperatures of 20 °C (T20 group) and 23 °C (T23 group), compared to the control group (15 °C). High-throughput sequencing of 16S rRNA gene showed that the composition of intestinal microbiota rather than the alpha diversity indices changed significantly after high temperature stress. At the phylum level, the relative abundances of Proteobacteria and Firmicutes decreased progressively with increasing temperature, while that of Bacteroidetes increased by 1.18-fold in the T20 group and 0.95-fold in the T23 group. At the genus level, Tenacibaculum and Mycoplasma were significantly enriched after high temperature stress, and Mycoplasma exhibited highest abundance of 39.43% in the T23 group. Functional prediction revealed that the pathways related to amino acid biosynthesis were blocked after high temperature stress, while that of phospholipases showed the opposite trend. According to the results of network analysis, the network connectivity decreased with increasing temperature, while the percentages of negative correlations in the two high temperature groups were higher than that in the control group. Collectively, the intestinal histology and microbial community of P. yessoensis changed significantly after high temperature stress, which would hinder the nutrient absorption and promote the proliferation of pathogenic microorganisms in the intestine of scallops. Our results will provide novel insights into the occurrence mechanism of mass summer mortality in marine mollusks.

Metabolic turnover rate, digestive enzyme activities, and bacterial communities in the white shrimp Litopenaeus vannamei under compensatory growth

The present work aimed to evaluate the effects promoted by a phase of compensatory growth on metabolic turnover rate, digestive enzyme activity, and bacterial biota of the Pacific white shrimp Litopenaeus vannamei kept under different feeding regimes. Three treatments were evaluated as follows: 70% feed restriction during 3 (T3) and 6 (T6) days, followed by a period of feeding to satiety, and a control treatment without restriction periods. The results showed a full compensatory growth in treatments T3 and T6 by day 35 of the bioassay. A significant increase in trypsin and lipase (T6) activities was observed during compensatory growth, whereas specific amylase activity was significantly lower in treatment T6 compared to T3 but not significantly different from the control group. To determine the metabolic turnover rate of nitrogen in muscle tissue, an analysis of nitrogen isotope values (δ¹⁵N) at natural abundance levels was performed. At the end of the experimental period, shrimp under feed restriction had lower metabolic turnover rates and longer nitrogen residence times (t ₅₀) in muscle tissue, as compared to individuals in the control treatment. Regarding the changes in the bacterial communities in shrimp gut, no significant differences were observed at the phylum level, with Proteobacteria being the most abundant bacteria, followed by Actinobacteria. At family taxa level, Rhodobacteraceae presented the highest relative abundance in all treatments, whereas a decrease in Vibrionaceae was observed in treatments T3 and T6 when compared to control shrimps during compensatory growth. At the genus level, a decrease in Celeribacter, Catenococcus, and Epibacterium, and an increase in Ruegeria and Shimia, were identified in shrimp subjected to feed restriction when compared to control organisms during compensatory growth (day 14). At the end of the experimental period, the evaluated parameters showed similar results as those observed in the control treatment, suggesting a normalization of the metabolism and the physiological state. The present findings contribute to a better understanding on the physiological effects produced during compensatory growth in shrimp, which in turn could assist in the development of improved feeding strategies in benefit of the aquaculture industry.

Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition

Supplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00124-9.

Gut Microbial Composition of Pacific Salmonids Differs across Oregon River Basins and Hatchery Ancestry

The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and as a function of ancestry. First, we measured this variation across watersheds using wild steelhead trout sampled from nine locations spanning three river basins. While gut microbial composition differs across basins, there exist bacterial clades that are ubiquitous across all populations. Correlating the phylogenetic composition of clades with geographic distance reveals 395 clades of bacteria whose ecological distribution implicates their co-diversification with steelheads. Second, we quantified how microbiome composition varies between first generation hatchery-reared steelhead and traditional hatchery-reared steelhead. Despite being subject to the same hatchery management strategies, fish bred from wild parents carry distinct microbiomes from those bred from hatchery broodstock, implicating the role of genotype on microbiome composition. Finally, we integrated all data from both studies to reveal two distinct, yet robust clusters of community composition. Collectively, our study documents for the first time how the steelhead gut microbiome varies by geography or broodstock and uncovers microbial taxa that may indicate the watershed or hatchery from which an individual was sourced.

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.

Occurrence and distribution of antibiotics and antibiotic resistance genes in the guts of shrimp from different coastal areas of China

With the continuous increase in shrimp (Litopenaeus vannamei) aquaculture production, the widespread use of antibiotics as a means of preventing and treating diseases has adversely affected the environment, animal health and symbiotic microorganisms in gut environments. At the same time, antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a great threat to aquatic organisms and humans. Therefore, in the present study, the occurrence and distribution of 17 antibiotics, ARGs and mobile genetic elements (MGEs) were detected in the guts of shrimp collected from 12 coastal regions of China. The results showed that sulfadiazine, ciprofloxacin and norfloxacin were detectable in the guts of L. vannamei at all sampling sites. Sul1, sul2, floR and intI-1 were also detected in the guts of L. vannamei at all sampling sites. The total relative abundances of ARGs and MGEs were significantly positively correlated according to Pearson correlation analysis. Sulfonamide resistance genes (sul1 and sul2) were significantly positively correlated with intI-1. These results indicated that MGEs could increase the risk of horizontal gene transfer of ARGs in a gut environment. MGEs are the most important factors promoting the spread of ARGs. Correlation analysis showed that sulfadiazine was significantly positively correlated with sul1 and sul2 and that fluoroquinolone antibiotics were significantly positively correlated with floR, indicating that antibiotics could induce the production of ARGs. Network analysis indicated that Iamia and Alkaliphilus species may harbor the most antibiotic resistance genes, and these bacteria were closely related to the proliferation and spread of ARGs in a gut environment. Antibiotic use and the spread of ARGs in mariculture systems may have negative effects on shrimp and human health. The use of antibiotics should be strictly regulated to control contaminants in mariculture systems, including pathogens and ARGs, thereby reducing potential risks to human health.

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.

Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

BACKGROUND

Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut.

RESULTS

We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio.

CONCLUSIONS

Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota.

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.

Metabolic Alterations in Shrimp Stomach During Acute Hepatopancreatic Necrosis Disease and Effects of Taurocholate on Vibrio parahaemolyticus

Acute hepatopancreatic necrosis disease (AHPND), a recently emerged bacterial shrimp disease, has increased shrimp mortality and caused huge economic losses in many Asian countries. However, molecular factors underlying pathogenesis of this disease remain largely unknown. Our objective was to characterize metabolic alterations in shrimp stomach during AHPND and determine effects of taurocholate on AHPND-causing Vibrio parahaemolyticus. Based on metabolomics, pathways for lipid metabolism and for primary bile acid (BA) synthesis were majorly affected following AHPND infection. Bile acid metabolites, namely taurocholate, were downregulated in the metabolomics database. This prompted us to study effects of taurocholate on biofilm formation, PirAB ^vp toxin release and biofilm detachment capabilities in AHPND-causing V. parahaemolyticus. Treatment of this bacterium with high concentration of taurocholate, a primary bile acid, induced biofilm formation, PirAB ^vp toxin release and facilitated the dispersion of bacterial cells. Taken together, our findings suggest that AHPND infection can affect the lipid metabolites in shrimp stomach, and further suggest that the primary bile acid taurocholate is important for the virulence of AHPND-causing V. parahaemolyticus.

Identifying Potential Polymicrobial Pathogens: Moving Beyond Differential Abundance to Driver Taxa

It is now recognized that some diseases of aquatic animals are attributed to polymicrobial pathogens infection. Thus, the traditional view of "one pathogen, one disease" might mislead the identification of multiple pathogens, which in turn impedes the design of probiotics. To address this gap, we explored polymicrobial pathogens based on the origin and timing of increased abundance over shrimp white feces syndrome (WFS) progression. OTU70848 Vibrio fluvialis, OTU35090 V. coralliilyticus, and OTU28721 V. tubiashii were identified as the primary colonizers, whose abundances increased only in individuals that eventually showed disease signs but were stable in healthy subjects over the same timeframe. Notably, the random Forest model revealed that the profiles of the three primary colonizers contributed an overall 91.4% of diagnosing accuracy of shrimp health status. Additionally, NetShift analysis quantified that the three primary colonizers were important "drivers" in the gut microbiotas from healthy to WFS shrimp. For these reasons, the primary colonizers were potential pathogens that contributed to the exacerbation of WFS. By this logic, we further identified a few "drivers" commensals in healthy individuals, such as OUT50531 Demequina sediminicola and OTU_74495 Ruegeria lacuscaerulensis, which directly antagonized the three primary colonizers. The predicted functional pathways involved in energy metabolism, genetic information processing, terpenoids and polyketides metabolism, lipid and amino acid metabolism significantly decreased in diseased shrimp compared with those in healthy cohorts, in concordant with the knowledge that the attenuations of these functional pathways increase shrimp sensitivity to pathogen infection. Collectively, we provide an ecological framework for inferring polymicrobial pathogens and designing antagonized probiotics by quantifying their changed "driver" feature that intimately links shrimp WFS progression. This approach might generalize to the exploring disease etiology for other aquatic animals.

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.

Dynamic distribution of gut microbiota during embryonic development in chicken

The gut microbiota is a complex ecological community and widely recognized in many aspects of research, but little is known on the relation between gut microbiota and embryonic development in chickens. The aim of this study was to explore the dynamic distribution of gut microbiota in chickens' embryos during stages of developments (chicken embryos that had incubated until day 3 [E3], day 12 [E12], and day 19 [E19]). Here, 16S rRNA gene sequencing was performed on the gut microbiota in chicken embryos across different developmental stages. Twenty-one phyla and 601 genera were present in chicken embryos, and 96 genera such as Ochrobactrum, Phyllobacterium, and Amycolatopsis were the core microbiota in the 3 stages of development. Second, 94 genera of microbes were found to change significantly between E3 and E12, and 143 genera significantly differed between E12 and E19 in chicken embryos (P < 0.05). Ochrobactrum and Amycolatopsis decreased with growth changes: E3 (30.4%), E12 (25.1%), and E19 (13.6%) and E3 (11.5%), E12 (7.4%), and E19 (5.6%), respectively. Contrarily, Phyllobacterium increased to 47.9% at E19, indicating the growing trend of microbial diversity among the embryos' development. Moreover, the principal component analysis showed a high level of similarities between E3 and E12 compared with E19, whereas the alpha analysis showed more diversity of gut microbiota at E19. Furthermore, the functional predictions showed that metabolic pathways such as energy metabolism and genetic information processing were significantly enriched on day 3 and day 12 in our study, suggesting their strong influence on growth, development, and immunity of chicken embryos. Our findings provide insights into the understanding of dynamic shifts of gut microbiota during chicken embryonic growth.

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.

RNA-seq revealed the signatures of immunity and metabolism in the Litopenaeus vannamei intestine in response to dietary succinate

The intestine is important for nutrition, metabolism and immunity. Succinate (SA) plays a vital role in the physiological homeostasis of animal intestines. However, the effects of dietary SA on the intestinal immunity and metabolism in shrimp are not clear. In this study, we investigated the immune and metabolic responses in the intestine of Litopenaeus vannamei that were fed diets consisting of different levels of SA: 0 g/kg (Con) and 10 g/kg (SA) for 56 days. The results from a RNA-seq analysis identified 6005 differentially expressed genes (DEGs), including 2728 upregulated genes and 3277 downregulated genes, which were grouped into 312 pathways. The DEGs were most enriched in pathways related to protein synthesis and amino acid metabolism, including "ribosome", "aminoacyl-tRNA biosynthesis", "pyrimidine metabolism", and "arginine and proline metabolism"; additionally, carbohydrate and lipid metabolism pathways were also activated. A large number of immune-related genes were associated with mucus barrier modification, antimicrobial activity, pathogen attachment and recognition, antioxidant activity, and apoptosis. The expression patterns of several candidate genes involved in the immune response and nutrition metabolism were detected by qPCR. This study provides insight into the transcriptomic modulating mechanisms associated with intestinal immunity and the metabolism of L. vannamei in response to the intake of dietary SA.

Intestinal bacterial signatures of the "cotton shrimp-like" disease explain the change of growth performance and immune responses in Pacific white shrimp (Litopenaeus vannamei)

Imbalance of intestinal microbiota has been recognized in aquatic animals infected with various diseases. However, the signature of intestinal bacteria of the "cotton shrimp-like" disease in the Pacific white shrimp Litopenaeus vannamei remains unknown. This study investigates the composition, diversity, microbial-mediated function and interspecies interaction of intestinal microbiota on shrimp with different health status using 16S rRNA gene high-throughput sequencing. Meanwhile, the growth performance and the mRNA expression of innate immune gene in hepatopancreas were also investigated. The growth performance and the mRNA expression of innate immune genes (e.g., crustin, toll, and immune deficiency genes) in the hepatopancreas were significantly decreased in diseased shrimp compared with healthy shrimp. Bacteria of the family Rickettsiaceae and genus Tenacibaculum were exclusively enriched and significantly increased in diseased shrimp, respectively, whereas, the Actinobacteria class dramatically deceased. The diseased shrimp exhibited higher ACE and Chao1 indices and lower complexity of intestinal interspecies interaction than healthy shrimp. Microbial-mediated functions predicted by PICRUSt showed that 83% KEGG pathway including nutrient absorption and digestion significantly increased in diseased shrimp. This study provides an overview on the interplay among the "cotton shrimp-like" disease, intestinal microbiota, growth performance and host immune responses from an ecological perspective.