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Microbial communities, mainly those with probiotic characteristics, positively affect the culture of diverse organisms, including shrimp. In this study, three diets containing different types of probiotics were evaluated on the composition and diversity of the microbial community in the water column and gut of Litopenaeus vannamei, as well as on the expression of genes related to the immune system and resistance of the organisms after being challenged with WSSV and Vibrio parahaemolyticus. Results showed that probiotics affected the microbial community structure in water and shrimp. The expression of beta-glucan binding protein and prophenoloxidase increased in the treatments with probiotics compared to the control before and after the challenge. Overall the survival of shrimp was higher in all the treatments than in control. Results suggest that using probiotics in BFT systems could provide an extra benefit for these kinds of systems.

The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

La microbiota del tracto digestivo es diversa y provee grandes beneficios al hospedero; participando en múltiples funciones relacionadas con su estado de salud, nutrición y crecimiento. Recientemente ha cobrado relevancia el estudio del papel de la microbiota en organismos de importancia acuícola, incluyendo a camarones peneidos. Los estudios pioneros en conocer la relación de los microorganismos en el desarrollo de camarones peneidos utilizaron técnicas dependientes de cultivo. A pesar de los novedosos hallazgos, esto representó solo una pequeña fracción del total de la población; sin embargo, estas primeras aproximaciones permitieron vislumbrar el rol relevante de la microbiota en la biología de estos crustáceos. Más tarde, el desarrollo de métodos basados en técnicas moleculares extendió el panorama con nuevos registros de bacterias no cultivables en estos ambientes, elucidando el efecto de diversos factores incluyendo dieta, antibióticos, probióticos, prebióticos y enfermedades sobre la modulación de la microbiota del tracto digestivo. Sin embargo, el desarrollo de técnicas de secuenciación masiva de alto rendimiento, comenzó a proporcionar bases de datos más robustas, permitiendo conocer no solo qué microorganismos están presentes en un organismo dado, sino también conocer sus funciones y roles potenciales. Hasta el momento se cuenta con descripciones de la composición de la microbiota del tracto digestivo de camarones peneidos y del como el manejo de estos microorganimos tiene beneficios en la respuesta productiva y estado de salud; sin embargo, es necesario continuar comprendiendo la relación microbiotahospedero. La presente revisión analiza la situación actual y plantea las perspectivas futuras para el estudio de la microbiota de camarones peneidos.ABSTRACTThe digestive tract microbiota is diverse and can provide great benefits to the host, participating in multiple functions related to its health, nutrition and growth. Recently, the microbiota study of important aquaculture species including penaeid shrimp has gained relevance. The first research efforts in the knowledge of the relationship between microorganisms and penaeid shrimp development used culture-dependent techniques. In spite of the novel findings, this represented only a small fraction of the total population; however, these first approaches allowed knowing the relevant role of microbiota in the biology of these crustaceans. Later, the development of methods based on molecular techniques, increased the panorama with new records of nonculturable bacteria in these environments, elucidating the effect of diverse factors including diet, antibiotics, probiotics, prebiotics, and disease on the digestive tract microbiota modulation. However, the rise of high throughput sequencing, began providing robust datasets, allowing to know not only which microbes are present in a given organism, but reveal their functions and potential roles. So far, descriptions of the microbiota composition of the digestive tract of penaeid shrimp are available, as well as on how the management of these microorganisms benefits the productive response and health status; however, it is necessary to continue comprehending the microbiota-host relationship. The present review analyzes the current situation and future perspectives in the study of penaeid shrimp microbiota

The aim of this work was to study the functional properties of bacterial communities in shrimp-culture bioflocs produced with amaranth (BFT_Amaranth) and wheat (BFT_Wheat) as biofloc promoters. No significant differences between treatments were recorded for physical and chemical parameters of water. A total of 22 phyla were detected in the biofloc samples, but the taxonomic structure was based on four principal phyla (Planctomycetes, Proteobacteria, Bacteroidetes, and Firmicutes). Most of the predicted KEGG pathways of bacterial communities contained in both bioflocs were associated with metabolism (50–53%), genetic information processing (19–21%), environmental information processing (12–15%), cellular processes and signaling (4–6%), organismal systems (1–2%) and other (3–5%). Both, the taxonomic and functional profiles of the two bioflocs were different at the beginning of the trial, but similar at the end of it, suggesting that the micro-environmental conditions of the culture units shaped the microbiota of biofloc regardless the type of seed used. Evidence of methane (RuMP and Serine pathways) and nitrogen (via N fixation, denitrification, nitrification, and detoxification) metabolism was detected in both BFT_Amaranth and BFT_Wheat, regardless of the sampling date. Carbon dioxide fixation was also detected, including photosynthetic pathways such as the Calvin cycle; however, other carbon dioxide fixation pathways including the reductive citric acid cycle, dicarboxylate-hydroxybutyrate cycle, 3-hydroxypropionate-bicycle and the Wood-Ljungdahl pathway were detected in both bioflocs. These results represent a first insight into the functions exerted by bioflocs in aquacultural systems, and suggest that nitrogenous and carbonaceous compounds can be simultaneously processed through diverse pathways by bacteria thriving in bioflocs.

The taxonomy profiles of bacterial communities contained in bioflocs produced with amaranth (BFT_Amaranth) and wheat (BFT_Wheat) grains as substrates, and used for shrimp culture were evaluated. The proliferation of heterotrophic bacteria was promoted by maintaining a carbon:nitrogen ratio of 12:1. High throughput sequencing of the 16S-rRNA gene revealed that the maximum difference between BFT_Amaranth and BFT_Wheat was registered at the beginning of the trial, when BFT_Wheat was dominated by Bacteroidetes (80–85%), whereas BFT_ Amaranth was dominated by Planctomycetes (42%), Proteobacteria (26%) and Bacteroidetes (16%). However, the taxonomic profile of both biofloc types were similar at the end of the trial, suggesting that the type of substrate affected the initial biofouling process, but the similar physicochemical conditions maintained during the trial favored the same heterotrophic communities in both treatments; herein, only 97 were shared between BFT_Wheat and BFT_Amaranth at the beginning of the trial, but 185 at the end. Thereafter, a better productive response in terms of survival, growth rate and FCR was registered for shrimp reared with BFT_Wheat, which corresponded to the biofloc registering the highest protein content at the end of the trial (18.5%), compared to BFT_Amaranth (12.7%). Finally, despite the high similarity detected among both biofloc types, this may not be strongly associated with their nutritional composition, nor the massification rate of these microbial communities.

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.

The study of plant microbiota has been stimulated by recognizing the fundamental role that the genetic capacity of the associated microbial communities has to modulate the phenotypic expression of plants, which is crucial for its health, physiology, and productivity. All genes in a metagenome can be described by whole-metagenome shotgun sequencing, but it is time-consuming, and a high level of experience is required. Alternatively, the amplification and high-throughput sequencing of the16S-rRNA gene allow describing the microbial composition. Then functional activities can be inferred by listing the abundance of each gene. Also, the identification and the quantification of microbiome transcripts are now accessible to determine the profile and changes in gene expression occurring in a microbial community in response to environmental or experimental variations. Considering the beneficial role of microbial communities in soil environments, it is important increasing the understanding of plant-microbe relationships to provide biotechnological information for control and management with sustainable practices.

Even though Litopenaeus vannamei is one of the most important species used in aquaculture, little is known about the functions provided by the intestinal microbiota for host development. This study aims to determine the taxonomic and functional changes in the L. vannamei gut microbiota during postlarval development in a recirculation system under controlled conditions for 80 days. The results revealed that the Vibrionaceae family predominated at the beginning of the experiment, when the postlarvae weighed 0.5 to 1.5 g. The representativeness of the family Rhodobacteraceae increased to the detriment of Vibrionaceae, which showed a constant decrease as the shrimp reached the juvenile and adult stages. Finally, the Intrasporangiaceae family remained constant in postlarvae weighing 4 to 10 g. Differences in the taxonomic profile at the family level between culture days were observed through principal component analysis (PCA), where two main clusters were observed: a group of microbiota sampled at 0 D and 20 D and another of samples collected at 40 D, 60 D and 80 D, suggesting that the microbiota tend to be variable during the first postlarval phase but become more constant towards the adult phase. Microbial-mediated functions predicted by PICRUSt showed an overall functional redundancy, suggesting that gut conditions maintain the same microbiota functions regardless of changes in the taxonomic structure. These results also suggest that shrimp are under certain selective pressure favoring microbiota with specific functions according to their requirements.

The physiological and immune responses of adult shrimp (Litopenaeus vannamei) undergoing the acute phase of the necrotizing hepatopancreatitis (NHP) disease and the efficiency of oxytetracycline (OXI) and florfenicol (FF) to eliminate the pathogen were evaluated. Four shrimp groups were considered: three groups infected with necrotizing hepatopancreatitis bacteria (NHP-B) (two treated with antibiotics and a positive control) and one group non-infected (negative control). Hemolymph concentration of glucose, lactate, acylglycerides, cholesterol, total protein, aminotransferases, superoxide dismutase, and the transcriptional expression of several immune related genes were monitored at the acute phase of the disease, and at 15 and 20 days after administration of antibiotics (daa). Shrimp from the positive control registered a mortality of 100%. NHP-B infection affected the immu-nophysiological response of shrimp; herein, most of the parameters were significantly up regulated in infected shrimp before the use of antibiotics, compared to the negative control. Increased transcriptional levels of clotting protein, lipopolysaccharide and β-1-3-glucan binding protein (LGBP), serine protease, peroxinectin, lysozyme, heat shock proteins (HSP) 60 and 70 were detected in shrimp treated with OXI. At 20 daa NHP-B was still detected in FF-treated shrimp, but not in OXI-treated shrimp. It is hypothesized that despite none of the antibiotics per se eliminated the bacterium, both had a negative effect on its virulence. OXI seems to have a greater effect, allowing shrimp to integrate a better immune response at 15 daa.