Bacterial flora from the gut of the wild and cultured banana prawn, Penaeus merguiensis

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.

Maternal and environmental microbes dominate offspring microbial colonization in the giant freshwater prawn Macrobrachium rosenbergii

Microbial colonization is vital for physiological equilibrium in animals. However, the impact of maternal and environmental microbes on microbial succession in the early developmental stages of Macrobrachium rosenbergii remains elusive. In this study, the effects of maternal and environmental microbes on the embryonic and larval microbiota of M. rosenbergii were evaluated by high-throughput sequencing. The results showed that Proteobacteria and Firmicutes were the dominant phyla in the intestine, gonads, and hepatopancreases of maternal prawn. In addition, Actinobacteria was dominant in the intestine while Actinobacteria, Bacteroidetes, and Acidobacteria were dominant in gonads of maternal prawn. During the embryonic stages, Proteobacteria, Actinobacteria, and Bacteroidetes became the dominant phyla. In post-larval stages, Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes tended to dominate. In the water, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla at 7, 14, and 21 dph water. Maternal microbes prominently impacted the microbial composition during the embryonic stages. Specifically, microbial colonization during embryonic stages was directly related to the maternal hepatopancreas according to source-tracking models. When the post-larvae developed to 7 days, the high contribution to the larval microbiota mimicked the environment. These results indicated that microbial colonization in embryonic and post-larval stages was attributed to the maternal and environmental microbe community, respectively. This study provides a theoretical basis for microbial community manipulation to promote prawn growth and physiological health in aquaculture.

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.

The Intestinal Bacterial Community and Functional Potential of Litopenaeus vannamei in the Coastal Areas of China

Intestinal bacteria are crucial for the healthy aquaculture of Litopenaeus vannamei, and the coastal areas of China are important areas for concentrated L. vannamei cultivation. In this study, we evaluated different compositions and structures, key roles, and functional potentials of the intestinal bacterial community of L. vannamei shrimp collected in 12 Chinese coastal cities and investigated the correlation between the intestinal bacteria and functional potentials. The dominant bacteria in the shrimp intestines included Proteobacteria, Bacteroidetes, Tenericutes, Firmicutes, and Actinobacteria, and the main potential functions were metabolism, genetic information processing, and environmental information processing. Although the composition and structure of the intestinal bacterial community, potential pathogenic bacteria, and spoilage organisms varied from region to region, the functional potentials were homeostatic and significantly (p < 0.05) correlated with intestinal bacteria (at the family level) to different degrees. The correlation between intestinal bacteria and functional potentials further suggested that L. vannamei had sufficient functional redundancy to maintain its own health. These findings help us understand differences among the intestinal bacterial communities of L. vannamei cultivated in different regions and provide a basis for the disease management and healthy aquaculture of L. vannamei.

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.

Synergistic Antimicrobial Effect of a Seaweed-Probiotic Blend Against Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus

The outbreak of acute hepatopancreatic necrosis disease (AHPND) has caused great economic losses to the shrimp culture sector. However, the use of antibiotics to fight this disease has resulted in negative impacts on human health and the environment. Thus, the use of natural alternatives to antibiotics may be a better solution. In this study, four Bacillus species obtained from the guts of shrimps (Fenneropenaeus penicillatus and Penaeus monodon) showed antimicrobial activity against the AHPND-causing Vibrio parahaemolyticus strain 3HP using the cross-streaking and agar spot methods. Two of the Bacillus isolates, B2 and BT, also showed good probiotic properties, exhibiting tolerance to bile, good adhesion to shrimp mucus, non-hemolytic, susceptibility to antibiotics and being safe towards hosts. Moreover, a seaweed-probiotic blend (a combination of Bacillus B2 and 20 mg/ml of the red seaweed Gracilaria sp.) exhibited synergistic in vitro inhibition against V. parahaemolyticus strain 3HP, with an observed inhibition zone of 5.0 mm. The broth co-culture experiment results further indicated that the seaweed-probiotic blend inhibited V. parahaemolyticus through competitive exclusion. The in vivo challenge trials also confirmed that this seaweed-probiotic blend significantly reduced the mortality of shrimps post-challenge with the AHPND-causing V. parahaemolyticus strain 3HP (p < 0.05) compared to the negative control (mortality rate = 13.88% vs 72.19%). Thus, this seaweed-probiotic blend may serve as an alternative to antibiotics in controlling the outbreak of AHPND.

Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.

Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1

The spiny lobster Panulirus argus (Latreille, 1804) is currently affected by an unenveloped, icosahedral, DNA virus termed Panulirus argus virus 1 (PaV1), a virulent and pathogenic virus that produces a long-lasting infection that alters the physiology and behaviour of heavily infected lobsters. Gut-associated microbiota is crucial for lobster homeostasis and well-being, but pathogens could change microbiota composition affecting its function. In PaV1 infection, the changes of gut-associated microbiota are yet to be elucidated. In the present study, we used high-throughput 16S rRNA sequencing technology to compare the bacterial microbiota in intestines of healthy and heavily PaV1-infected male and female juveniles of spiny lobsters P. argus captured in Puerto Morelos Reef lagoon, Quintana Roo, Mexico. We found that basal gut-associated microbiota composition showed a sex-dependent bias, with females being enriched in amplicon sequence variants (ASVs) assigned to Sphingomonas, while males were enriched in the genus Candidatus Hepatoplasma and Aliiroseovarius genera. Moreover, the alpha diversity of microbiota decreased in PaV1-infected lobsters. A significant increase of the genus Candidatus Bacilloplasma was observed in infected lobsters, as well as a significant decrease in Nesterenkonia, Caldalkalibacillus, Pseudomonas, Cetobacterium and Phyllobacterium. We also observed an alteration in the abundances of Vibrio species. Results from this study suggest that PaV1 infection impacts intestinal microbiota composition in Panulirus argus in a sex-dependent manner.

Antimicrobial resistance in freshwater Plesiomonas shigelloides isolates: Implications for environmental pollution and risk assessment

Antibiotic resistance is known to impact treatment efficiency of Plesiomonas infections negatively with fatal outcomes. This study investigated antibiogram fingerprint of P. shigelloides (n = 182) isolated from three South Africa rivers using the disc diffusion technique. Environmental pollution and analogous health risk (given infections) that could associate with the freshwaters and empirical treatment of Plesiomonas were assessed using Antibiotic Resistance Index (ARI) and Multiple Antibiotic Resistance Indices (MARI), respectively. Thirteen EUCAST recommended (ERAs) and eleven non-recommended antibiotics (NAs) used as first line agents in the treatment of gastroenteritis and extraintestinal infections were tested. Resistance against ERAs decreased from cefoxitin (37.91%), cefuroxime (35.17%), cefepime (31.87%), ceftriaxone (29.67%), ciprofloxacin (18.13%), trimethoprim-sulfamethoxazole (10.44%), piperacillin/tazobactam (8.79%), ertapenem (4.95%), norfloxacin (4.40%), levofloxacin (2.75%), meropenem (1.10%) to imipenem (0.55%). The isolates had higher resistance (≥36.07%) against NAs but were susceptible to amikacin (67.58%), gentamycin (73.08%), and tetracycline (80.77%). MARI of the isolates were significantly different between ERAs and NAs (P-value < 0.05) and had an average of 0.17 ± 0.18 and 0.45 ± 0.13, respectively. About 33.87% and 95.63% of the isolates had MARI value from 0.23 to 0.62 and 0.27-0.82 to ERAs and NAs, respectively. Also, ERAs-based and NAs-based ARI across sampling units showed significantly different (P-value < 0.05) means of 0.18 ± 0.09 and 0.46 ± 0.05, respectively. MARI attributed low risk of empirical treatment to recommended antibiotics but higher risk to non-recommended antibiotics. Model estimated successful and unsuccessful empirical treatment of infections risks due to resistance in the isolates using recommended antibiotics as 65.93% and 34.07%, respectively; 1.65% and 98.35% in the case of non-recommended antibiotics, respectively. ARI based on recommended antibiotics identified potential environmental pollutions in a number of sites. Resistance in freshwater P. shigelloides especially against cephalosporin, quinolones and fluoroquinolones is distressing and might suggests high pollution of the freshwaters in the Eastern Cape Province.

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 effect of nitrite and sulfide on the antioxidant capacity and microbial composition of the intestines of red swamp crayfish, Procambarus clarkii

Nitrite and sulfide are harmful pollutants in water ecosystems that negatively influence the survival and growth of crayfish. It is currently known that the intestine of crustaceans acts as a significant immune organ, serving as the front line of defense against diseases. In this study, we investigated how the oxidative damage parameters, antioxidant status and microbial composition of the intestine of Procambarus clarkii were influenced under acute nitrite (60 mg/L) and sulfide (18 mg/L) stress for 72 h. Compared with the control, after exposure to nitrite and sulfide stress, the production of reactive oxygen species, and the lipid peroxide and malondialdehyde contents increased in the intestines and were significantly higher after 72 h of exposure. The superoxide dismutase, catalase and glutathione peroxidase activities increased to maximum levels at 6, 24 and 12 h, respectively. These activities then decreased gradually and were significantly lower than those of the control after 48 or 72 h of exposure. In the crayfish exposed to stress, the expression of antioxidant genes including heat shock protein 70, ferritin and metallothionein increased to their maximum values at 12, 48 and 12 h, respectively. The expression levels then decreased gradually, and after 72 h, were lower than, or lacked significant differences with, the expression levels in the control. Additionally, nitrite and sulfide exposure restructured the intestinal microbial community of P. clarkii. This led to decreases in the abundance of some genera such as Citrobacter. However, the abundance of other genera, such as Shewanella and Acinetobacter, increased. Therefore, the health of P. clarkii was seriously impaired when exposed to nitrite and sulfide stress.

Screening and selection of bacteria inhibiting white spot syndrome virus infection to Litopenaeus vannamei

A total of 173 bacterial strains were isolated from different sources at different regions such as fermented foods, shrimp guts, sea water, mangrove water, and sediments. These bacteria were screened against white spot syndrome virus (WSSV) infection in Palaemon paucidens. Based on mortality, white spot level, and healthiness, three bacterial strains were selected and identified using 16S rRNA gene sequencing. These bacterial strains were Bacillus subtilis KA1, B. licheniformis KA2, and B. subtilis KA3. WSSV challenge test in pilot scale was conducted using Litopenaeus vannamei with B. subtilis KA1 and B. subtilis KA3. The survival ratio of shrimp was 0% for WSSV control after 17th days, 84% for B. subtilis KA1 plus WSSV after 26th days, and 28% for B. subtilis KA3 with WSSV after 26th days. B. subtilis KA1 showed good growth at 18-37 °C in with and without 3% NaCl, and therefore can be applied to aquaculture at low to high temperatures. B. subtilis KA1 produced protease and lipase which can increase digestion to shrimp; exhibited antibacterial activity against Vibrio parahaemolyticus; and significantly increased the survival of WSSV challenged shrimps.

Vibriosis and Aeromonas infection in shrimp: Isolation, sequencing, and control

Background and Aim: Shrimp is one of the most commonly consumed types of seafood. It is a very nutritious healthy food. Shrimp is low in calories and rich in protein and healthy fats. It also contains a treasure trove of vitamins and minerals. On the negative side, it may be affected by many bacterial diseases which affect its health. Furthermore, it may be incriminated as a vector of foodborne illnesses that range from mild gastrointestinal upset to life-threatening diseases. This study was designed to assess the clinical picture and zoonotic importance of vibriosis and Aeromonas infection in live shrimp and to study the antibacterial effect of citric acid (lemon juice) and acetic acid (vinegar) on these pathogens. Materials and Methods: A total of 170 live shrimp (Metapenaeus monoceros) samples were collected from Suez City, Egypt. The samples were examined clinically, and then, they were enriched into alkaline peptone water and cultivated on thiosulfate-citrate-bile salts-sucrose agar and ampicillin MacConkey agar for the isolation of Vibrio and Aeromonas species, respectively. The recovered isolates were confirmed biochemically and genotypically using duplex polymerase chain reaction (PCR) and sequencing. The germicidal effects of vinegar and lemon on artificially contaminated shrimp samples with Aeromonas hydrophila and Vibrio parahaemolyticus at different times (0.25, 1, 1.5, and 24 h) and temperatures (5° and 30°C) were studied. Results: The results revealed that some of the infected shrimp were hypoxic, lethargic with abnormal swimming behavior. In most cases, body appendages, telsons, uropods, and gills took black coloration. In addition, the hepatopancreas appeared soft, swollen, and congested. The prevalence rates of vibriosis in each of the musculature and hepatopancreas were 4.7%, while the prevalence rates of Aeromonas infection in the musculature and hepatopancreas were 11.8% and 11.2%, respectively. Duplex PCR showed that Aeromonas isolates gave double bands: 237 bp specific for gcat and 500 bp specific for 16S rRNA, while Vibrio spp. and Plesiomonas shigelloides isolates gave single band at 500 bp. The effect of organic acid treatment showed that acetic acid (vinegar 5%) had increasing reduction rates that reached its maximum level after 24 h; where it caused (100% inhibition) for A. hydrophila at both temperatures and (33.63% and 60% inhibition) for V. parahaemolyticus at refrigerator and room temperatures, respectively. Moreover, acetic acid was more effective at room temperature than at refrigerator temperature. Concerning the effect of lemon juice (citric acid), it was more effective than acetic acid at short marination (0.25 and 1 h) at both temperatures for the two pathogens. Moreover, lemon was more effective at refrigerator temperature than at room temperature at the same aforementioned time. The difference between the reduction effects of the two acids on both pathogens was statistically significant (p<0.0001). Conclusion: Overall, the examined shrimp samples were found to be vectors for Vibrio and Aeromonas spp. Application of hygienic measures during handling and cooking of shrimp should be esteemed. The organic acid treatment trial showed that vinegar and lemon juice can be used as a safe and economic method to limit the microbial contamination in seafood.

Dietary supplementation of probiotic Bacillus coagulans ATCC 7050, improves the growth performance, intestinal morphology, microflora, immune response, and disease confrontation of Pacific white shrimp, Litopenaeus vannamei

The present study assessed the effects of probiotic bacterium Bacillus coagulans ATCC 7050 (BC) fed at different inclusion levels (0 (BO), 1 × 10⁶ (BC1), 1 × 10⁷ (BC2) and 1 × 10⁸ (BC3) CFU g^-1 feed) on growth, feed utilization, body composition, intestinal morphology, microflora, immune response, and resistance to Vibrio parahaemolyticus infection in Litopenaeus vannamei. After 56 days of the feeding trial, the survival rate ranged from 83.33 to 94.17% with no significant difference between dietary treatments (P > 0.05). Dietary probiotic supplementation also affected the intestinal microflora composition. At the phylum level, Proteobacteria accounted for the majority of bacteria followed by Bacteroidetes irrespective of the group. At the genus level, the abundance of opportunistic pathogenic bacteria, such as Vibrio, Tenacibaculum, and Photobacterium significantly decreased (P < 0.05) with an increasing probiotic concentration, and BC3 group experiencing the least. Additionally, increasing probiotic inclusion in diet downregulated the abundance of Muricauda, Kangiella, and Shewanella in shrimps, with the least, observed in the BC3 group. However, beneficial bacteria Pseudoalteromonas significantly increased (P < 0.05) in the intestines of shrimp fed BC3 diet (P < 0.05) compared to other groups including the control. Compared to the control, a significant increase (P < 0.05) of the probiotic treated groups in the final weight, weight gain rate (WGR), specific growth rate (SGR), condition factor (K), activity of lysozyme (LYZ), acid phosphatase (ACP), superoxide dismutase (SOD), total protein (TP), albumin (ALB) in serum, glutathione peroxidase (GSH-Px) in serum and liver, and a significant decrease (P < 0.05) in feed conversion ratio (FCR), triglyceride (TG) in serum, and Malondialdehyde (MDA) in serum and liver were achieved. Increasing probiotic treatment again improved the digestive ability, thus; a significant increase in the activities of lipase, amylase, trypsin, and an enhancement in the villus height, villus width, and muscle thickness of the intestines of the shrimps which correspondingly alleviated intestinal injury. Furthermore, the supplementation of probiotics in challenge test significantly (P < 0.05) enhanced the resistance of shrimp against V. parahaemolyticus infection recording BC3 to receive the highest relative percentage survival (RPS) value of 76%. In conclusion, higher inclusion levels of probiotic BC at 1 × 10⁸ CFU g^-1 feed (BC3) in diets can be considered to enhance the growth, intestinal morphology and microflora, immune response and resistance to Vibrio parahaemolyticus of L. vannamei.

Comparative analysis of the bacterial community compositions of the shrimp intestine, surrounding water and sediment

AIMS

To reveal the relationship of the bacterial communities in shrimp intestine and surrounding environments.

METHODS AND RESULTS

We examined bacterial communities in the intestine of pacific white shrimp, Litopenaeus vannamei, the surrounding water and sediment by high-throughput sequencing analysis. Sequences were clustered into operational taxonomic units (OTUs) at 97% similarity levels, which ranged from 4956 to 5976 in each sample. All OTUs were affiliated with at least 64 phyla. The 10 most abundant phyla were Proteobacteria, Cyanobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Planctomycetes, Gemmatimonadetes and Verrucomicrobia. The relationship of bacterial communities in the intestine and the surroundings was also investigated. A total of 1395 OTUs shared in the three habitats, accounting for 80, 65 and 77% in the intestine, the surrounding water and sediment respectively. There were 352, 891, 833 unique OTUs in intestine, surrounding water and sediment. Welch's t-test analysis showed that the abundances of some taxa were significantly different between the shrimp intestine and surroundings. Unweighted pair-group method with arithmetic mean analysis revealed that there was a generally similar bacterial community composition in three environments.

CONCLUSIONS

These results showed that the bacterial compositions are mostly the same in shrimp intestine, water and sediment, but with different relative abundances of the bacterial communities.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provided valuable findings on the relationship of the bacterial communities in shrimp intestine, the surrounding water and sediment, which can expand our knowledge of the broad trend on bacterial community in shrimp cultural ecosystems.

Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188

Plesiomonas shigelloides is a Gram-negative bacterium isolated from diverse environments. Here, we describe the complete genome sequence of the multidrug-resistant P. shigelloides strain MS-17-188, isolated from a diseased catfish. Availability of this genome will be beneficial for characterizing the molecular mechanisms of antibiotic resistance in this strain.

Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus

With recent technologies making it possible for commercial scale closed life-cycle aquaculture production of spiny lobster (Panulirus ornatus) comes a strong impetus to further understand aspects of lobster health. The gut microbiome plays a crucial role in host health, affecting growth, digestion, immune responses and pathogen resistance. Herein we characterise and compare gut microbiomes across different developmental stages (6-7 days post-emergence [dpe], 52 dpe and 13 months post-emergence [mpe]) and gut regions (foregut, midgut and hindgut) of cultured P. ornatus juveniles. Gut samples were analysed using 16S rRNA next-generation sequencing. Core gut microbiomes of P. ornatus comprised the phyla Tenericutes and Proteobacteria. Within class Gammaproteobacteria, families Pseudoalteromonadaceae and Vibrionaceae were dominant members across the majority of the gut microbiomes. Characterisation of bacterial communities from 13 mpe lobsters indicated that the hindgut microbiome was more diverse and compositionally dissimilar to the foregut and midgut. The bacterial composition of the hindgut was more similar among younger juveniles (6-7 dpe and 52 dpe) compared to 13 mpe lobsters. This is the first study to explore gut microbiomes of spiny lobster juveniles. We demonstrate that the composition of the gut microbiome was shaped by gut region, whereas the structure of the hindgut microbiome was influenced by developmental stage.

Intestinal bacterial signatures of white feces syndrome in shrimp

Increasing evidence suggests that the intestinal microbiota is closely correlated with the host's health status. Thus, a serious disturbance that disrupts the stability of the intestinal microecosystem could cause host disease. Shrimps are one of the most important products among fishery trading commodities. However, digestive system diseases, such as white feces syndrome (WFS), frequently occur in shrimp culture and have led to enormous economic losses across the world. The WFS occurrences are unclear. Here, we compared intestinal bacterial communities of WFS shrimp and healthy shrimp. Intestinal bacterial communities of WFS shrimp exhibited less diversity but were more heterogeneous than those of healthy shrimp. The intestinal bacterial communities were significantly different between WFS shrimp and healthy shrimp; compared with healthy shrimp, in WFS shrimp, Candidatus Bacilloplasma and Phascolarctobacterium were overrepresented, whereas Paracoccus and Lactococcus were underrepresented. PICRUSt functional predictions indicated that the relative abundances of genes involved in energy metabolism and genetic information processing were significantly greater in WFS shrimp. Collectively, we found that the composition and predicted functions of the intestinal bacterial community were markedly shifted by WFS. Significant increases in Candidatus Bacilloplasma and Phascolarctobacterium and decreases in Paracoccus and Lactococcus may contribute to WFS in shrimp.

Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages

Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage-specific community in the shrimp intestinal ecosystem.

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

Crustaceans form the second largest subphylum on Earth, which includes Litopeneaus vannamei (Pacific whiteleg shrimp), one of the most cultured shrimp worldwide. Despite efforts to study the shrimp microbiota, little is known about it from shrimp obtained from the open sea and the role that aquaculture plays in microbiota remodeling. Here, the microbiota from the hepatopancreas and intestine of wild type (wt) and aquacultured whiteleg shrimp and pond sediment from hatcheries were characterized using sequencing of seven hypervariable regions of the 16S rRNA gene. Cultured shrimp with AHPND/EMS disease symptoms were also included. We found that (i) microbiota and their predicted metagenomic functions were different between wt and cultured shrimp; (ii) independent of the shrimp source, the microbiota of the hepatopancreas and intestine was different; (iii) the microbial diversity between the sediment and intestines of cultured shrimp was similar; and (iv) associated to an early development of AHPND/EMS disease, we found changes in the microbiome and the appearance of disease-specific bacteria. Notably, under cultured conditions, we identified bacterial taxa enriched in healthy shrimp, such as Faecalibacterium prausnitzii and Pantoea agglomerans, and communities enriched in diseased shrimp, such as Aeromonas taiwanensis, Simiduia agarivorans and Photobacterium angustum.

Dietary supplementation of probiotic Bacillus PC465 isolated from the gut of Fenneropenaeus chinensis improves the health status and resistance of Litopenaeus vannamei against white spot syndrome virus

This study conducted a 30-day feeding trial and a subsequent 20-day anti-virus infection trial to determine the effects of probiotic Bacillus PC465 on the growth, health status, and disease resistance of Litopenaeus vannamei. Shrimp samples were fed with three practical diets prepared from shrimp feed containing varying probiotic doses [0 (control), 10(7), and 10(9) CFU g(-1)]. Probiotic supplementation significantly increased the weight gain and survival of L. vannamei (p < 0.05). The effect of 10(9) CFU g(-1) on the growth rate was higher than that of 10(7) CFU g(-1). Compared with those in the control group, the activities of digestive enzymes, such as amylase, protease, and lipase, in the shrimp mid-gut significantly increased in the probiotic-fed groups on days 15 and 30, except lipase on day 30. The influence of 10(9) CFU g(-1) on enzyme activities was also greater than that of 10(7) CFU g(-1). Scanning electron microscopy revealed folds and large ravines across the interior surface of the mid-gut, and the number of these folds and ravines increased significantly after the probiotic was administered. The probiotic treatment significantly (p < 0.05) enhanced the transcription of penaeidin 3a (Pen-3a), peroxinectin, C-type lectin 3 (Lec-3), and thioredoxin (Trx) in the hemocytes of L. vannamei. Likewise, probiotic treatment increased the transcription of hemocyanin in the hepatopancreas of L. vannamei. The probiotic treatment also significantly increased the transcription of prophenoloxidase (proPO) but decreased the transcription of crustin in hemocytes. By contrast, the same treatment failed to increase the transcription of Ras-related protein (Rab-6) in hemocytes. The number of species and biomass of Bacillus in the mid-gut were higher in the probiotic-fed group than in the control group. The total biomass of microbes was higher in the shrimp fed with 10(7) CFU g(-1) than in the shrimp fed with 10(9) CFU g(-1) and the control group on days 15 and 30 post-feeding. In two white spot syndrome virus (WSSV) infections, the weight gain, survival, and WSSV copies within the gills of the probiotic-treated shrimp significantly differed (p < 0.05) from those of the control group. Relatively efficient protection was associated with probiotic feeding. Results suggested that Bacillus PC465 feeding improves the growth performance, survival, digestion, and nutrient absorption of L. vannamei. Probiotic treatment also enhances the microbial structures in the gut, promotes the immune status of shrimp, and provides protection against viral infection. The supplementation with 10(9) CFU g(-1) can also improve the growth and survival of L. vannamei.

Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective

High-density aquaculture has led to increasing occurrences of diseases in shrimp. Thus, it is imperative to establish effective and quantitative strategies for preventing and predicting these diseases. Water quality indices and investigations of specific pathogen abundance provide only a qualitative evaluation of the risk of shrimp disease and can be inaccurate. To address these shortcomings, we introduced intestinal indicative assemblages as independent variables with which to quantitatively predict incidences of shrimp disease. Given the ignorance regarding the niches differences in the shrimp intestine throughout its developmental stages, the use of probiotics in aquaculture has had limited success. Therefore, we propose the exploration of effective probiotic bacteria from shrimp intestinal flora and the establishment of therapeutic strategies dependent on shrimp age. Following ecological selection principles, we hypothesize that the larval stage provides the best opportunity to establish a desired gut microbiota through preemptive colonization of the treated rearing water with known probiotics. To employ this strategy, however, substantial barriers must be overcome.

Plesiomonas shigelloides Revisited

After many years in the family Vibrionaceae, the genus Plesiomonas, represented by a single species, P. shigelloides, currently resides in the family Enterobacteriaceae, although its most appropriate phylogenetic position may yet to be determined. Common environmental reservoirs for plesiomonads include freshwater ecosystems and estuaries and inhabitants of these aquatic environs. Long suspected as being an etiologic agent of bacterial gastroenteritis, convincing evidence supporting this conclusion has accumulated over the past 2 decades in the form of a series of foodborne outbreaks solely or partially attributable to P. shigelloides. The prevalence of P. shigelloides enteritis varies considerably, with higher rates reported from Southeast Asia and Africa and lower numbers from North America and Europe. Reasons for these differences may include hygiene conditions, dietary habits, regional occupations, or other unknown factors. Other human illnesses caused by P. shigelloides include septicemia and central nervous system disease, eye infections, and a variety of miscellaneous ailments. For years, recognizable virulence factors potentially associated with P. shigelloides pathogenicity were lacking; however, several good candidates now have been reported, including a cytotoxic hemolysin, iron acquisition systems, and lipopolysaccharide. While P. shigelloides is easy to identify biochemically, it is often overlooked in stool samples due to its smaller colony size or relatively low prevalence in gastrointestinal samples. However, one FDA-approved PCR-based culture-independent diagnostic test system to detect multiple enteropathogens (FilmArray) includes P. shigelloides on its panel. Plesiomonads produce β-lactamases but are typically susceptible to many first-line antimicrobial agents, including quinolones and carbapenems.

Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment

This study aimed at determining bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and their surrounding brackish waters and sediment. Freshly caught shrimp, water and sediment samples were collected in Lakes Nokoue and Aheme in Benin (West Africa) during two periods with different water salinity and temperature. We used complementary culture-dependent and culture-independent methods for microbiota analysis. During both sampling periods, total mesophilic aerobic counts in shrimp samples ranged between 4.4 and 5.9 log CFU/g and were significantly higher than in water or sediment samples. In contrast, bacterial diversity was higher in sediment or water than in shrimps. The dominant phyla were Firmicutes and Proteobacteria in shrimps, Firmicutes, Proteobacteria, and Actinobacteria in water, and Proteobacteria and Chloroflexi in sediment. At species level, distinct bacterial communities were associated with sediment, water and shrimps sampled at the same site the same day. The study suggests that the bacterial community of tropical brackish water shrimps cannot be predicted from the microbiota of their aquatic environment. Thus, monitoring of microbiological quality of aquatic environments might not reflect shrimp microbiological quality.

Effect of dietary formic acid and astaxanthin on the survival and growth of Pacific white shrimp (Litopenaeus vannamei) and their resistance to Vibrio parahaemolyticus

A 90-day feeding trial was conducted to evaluate the effects of formic acid (FA) and astaxanthin (AX) on growth, survival, immune parameters, and tolerance to Vibrio infection in Pacific white shrimp. The study was divided into two experiments. In experiment 1, postlarvae-12 were randomly distributed into six groups and then fed four times daily with six experimental diets contained 0.3 % FA, 0.6 % FA, 50 ppm AX, 0.3 % FA + 50 ppm AX, 0.6 % FA + 50 ppm AX, or none of these supplements (control diet). After 60 days of the feeding trials, the body weight of all treatment groups was not significantly different from the control group, although shrimp fed formic acid had significantly lower body weight than shrimp fed 50 ppm AX. However, the 0.6 % FA + 50 ppm AX group had a significantly higher survival rate (82.33 ± 8.32 %) than the control group (64.33 ± 10.12 %). In experiment 2, Vibrio parahaemolyticus was added to each tank to obtain a final concentration of 10(4) colony-forming units/mL. Each treatment group received the aforementioned diets for another 30 days. At the end of this experiment, there was no difference in the weight gain among all experimental groups. However, the survival rate of shrimps whose diet included FA, AX, and their combination (in the range of 45.83-67.50 %) was significantly higher than the control group (20.00 ± 17.32 %). FA-fed shrimps also had significantly lower total intestinal bacteria and Vibrio spp. counts, while immune parameters [total hemocyte count (THC), phagocytosis activity, phenoloxidase (PO) activity, and superoxide dismutase (SOD) activity] of AX-fed groups were significantly improved compared with the other groups. In conclusion, FA, AX, and their combination are useful in shrimp aquaculture.

Interaction of Vibrio spp. with the Inner Surface of the Digestive Tract of Penaeus monodon

Several species of Vibrio are the causative agent of gastroenteritis in humans. In aquaculture, Vibrio harveyi (Vh) and V. parahaemolyticus (Vp) have long been considered as shrimp pathogens in freshwater, brackish and marine environments. Here we show by using scanning electron microscopy (SEM) that Penaeus monodon orally inoculated with each of these two pathogens via an Artemia diet had numerous bacteria attached randomly across the stomach surface, in single and in large biofilm-like clusters 6 h post-infection. A subsequent marked proliferation in the number of V. harveyi within the biofilm-like formations resulted in the development of infections in the stomach, the upper and middle midgut, but neither in the posterior midgut nor the hindgut. SEM also revealed the induced production of peritrichous pili-like structures by the Vp attaching to the stomach lining, whilst only a single polar fibre was seen forming an apparent physical bridge between Vh and the host’s epithelium. In contrast to these observations, no such adherences or linkages were seen when trials were conducted with non-pathogenic Vibrio spp. or with Micrococcus luteus, with no obvious resultant changes to the host’s gut surface. In naive shrimp, the hindgut was found to be a favorable site for bacteria notably curved, short-rod shaped bacteria which probably belong to Vibrio spp. Data from the current study suggests that pathogens of P. monodon must be able to colonize the digestive tract, particularly the stomach, where chitin is present, and then they use an array of virulent factors and enzymes to infect their host resulting in disease. Oral infection is a better way of mimicking natural routes of infection; investigating the host-bacteria interactions occurring in the digestive tract may lead to new strategies for the prevention or control of bacterial infections in penaeids.

Dietary supplementation of Avicennia marina extract on immune protection and disease resistance in Amphiprion sebae against Vibrio alginolyticus

The effect of Avicennia marina aqueous leaf extract on innate immune mechanisms such as total white blood cell counts (WBC), serum lysozyme activity, respiratory burst assay, alternative complement (ACH50) assay, phagocytic activity assay, disease resistance, gut bacteria, and survival rate of clownfish (Amphiprion sebae) against Vibrio alginolyticus is reported. Healthy fish challenged with V. alginolyticus (1 × 10(7) cells ml(-1)) were fed with diets supplemented (0, 1, 2, and 4%) with A. marina extract. The survival rate was 85% and 80% in infected fish fed with 4% and 8% supplementation diet; with 1% diet it was 70% while in the infected untreated group it was only 10%. The total gut bacteria flora was high in 8% and 4% supplementation diet groups with 2.8 × 10(5) and 4.7 × 10(4) cfu/g while it was 8.9 × 10(3) cfu/g in 1% diet group. The immunological parameters significantly increased on weeks 6 and 8 when infected fish were fed with 1% or 4% supplementation diet. This study reports that in clownfish challenged with V. alginolyticus, dietary administration of the 1% or 4% of A. marina extract improved the immune status and survival rate.

Microbiota from Litopenaeus vannamei: digestive tract microbial community of Pacific white shrimp (Litopenaeus vannamei)

Bacteria capable of producing different extracellular enzymes of potential relevance in digestive processes were isolated from the stomach, hepatopancreas and intestine of Pacific white shrimp Litopenaeus vannamei. A total of 64 strains with proteolytic activity were isolated and grouped into 16 clusters based on morphological characteristics: 4 groups were isolated from the intestine; 5 from the hepatopancreas; and 7 from the stomach. Molecular methods (16S rRNA gene amplification and sequencing) and phenotypic criteria (Gram stain, catalase and oxidase tests, cell and colony morphology) were used to identify strains, which corresponded to Pseudoalteromonas and Vibrio genera. These genera are reported to form part of the digestive tract microbial community in shrimp. Both genera were isolated from all three tested tissues. One member of each morphologic group was selected for analysis of the presence of amylases, lipases/esterases and chitinases. Most of the strains had all the tested enzymes, indicating that the L. vannamei digestive tract microbiotic flora includes groups which have the potential to contribute to the degradation of dietary components.

Isolation of lactic acid bacteria from kuruma shrimp (Marsupenaeus japonicus) intestine and assessment of immunomodulatory role of a selected strain as probiotic

Fifty-one lactic acid bacteria (LAB) strains were isolated and identified based on 16S ribosomal DNA sequence from the intestinal tracts of 142 kuruma shrimps (Marsupenaeus japonicus) collected from Kanmon Strait, Fukuoka and Tachibana Bay, Nagasaki, Japan. Cellular immunomodulatory function of 51 isolated LAB strains was assessed by measuring the level of interferon (IFN)-γ induction in mouse spleen cell culture. The strain Lactococcus lactis D1813 exhibited the highest amount of IFN-γ production and also bactericidal activity and was selected for testing its immunomodulatory role as a probiotic in kuruma shrimp. We also assessed the effect of dietary incorporation of this probiotic on resistance to Vibrio penaeicida infection in the kuruma shrimp. Our results demonstrate that probiotic L. lactis D1813-containing diet-fed (10⁵ cfu g⁻¹) shrimps displayed a significant up-regulation of lysozyme gene expressions in the intestine and hepatopancreas. However, insignificantly higher expression of anti-lipopolysaccharide factor, super oxide dismutase, prophenoloxidase, and toll-like receptor 1 was recorded in the intestine of shrimps fed the probiotic diet. Moreover, significantly increased (P < 0.01) resistance to the bacterial pathogen in term of better post-infection survival (61.7 %) was observed in the shrimps fed with the probiotic-incorporated diet compared with the control diet-fed group (28.3 %). The present study indicates the immunomodulatory role of the LAB L. lactis D1813 on the kuruma shrimp immune system and supports its potential use as an effective probiotic in shrimp aquaculture.

Characterization of intestinal bacteria in wild and domesticated adult black tiger shrimp (Penaeus monodon)

The black tiger shrimp (Penaeus monodon) is a marine crustacean of economic importance in the world market. To ensure sustainability of the shrimp industry, production capacity and disease outbreak prevention must be improved. Understanding healthy microbial balance inside the shrimp intestine can provide an initial step toward better farming practice and probiotic applications. In this study, we employed a barcode pyrosequencing analysis of V3-4 regions of 16S rRNA genes to examine intestinal bacteria communities in wild-caught and domesticated P. monodon broodstock. Shrimp faeces were removed from intestines prior to further analysis in attempt to identify mucosal bacterial population. Five phyla, Actinobacteria, Fusobacteria, Proteobacteria, Firmicutes and Bacteroidetes, were found in all shrimp from both wild and domesticated environments. The operational taxonomic unit (OTU) was assigned at 97% sequence identity, and our pyrosequencing results identified 18 OTUs commonly found in both groups. Sequences of the shared OTUs were similar to bacteria in three phyla, namely i) Proteobacteria (Vibrio, Photobacterium, Novosphingobium, Pseudomonas, Sphingomonas and Undibacterium), ii) Firmicutes (Fusibacter), and iii) Bacteroidetes (Cloacibacterium). The shared bacterial members in P. monodon from two different habitats provide evidence that the internal environments within the host shrimp also exerts selective pressure on bacterial members. Intestinal bacterial profiles were compared using denaturing gradient gel electrophoresis (DGGE). The sequences from DGGE bands were similar to those of Vibrio and Photobacterium in all shrimp, consistent with pyrosequencing results. This work provides the first comprehensive report on bacterial populations in the intestine of adult black tiger shrimp and reveals some similar bacterial members between the intestine of wild-caught and domesticated shrimp.

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

Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.

Bacterial community associated with the intestinal tract of P. monodon in commercial farms

The potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp Penaeus monodon have been increasingly investigated. However, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. In this study, the intestinal bacterial communities of juvenile P. monodon (70 individuals) from eight commercial farms in Thailand were examined using 16S rDNA PCR-DGGE, and seven 16S rDNA clone libraries from representative DGGE profiles were constructed. Bacteria in the γ-Proteobacteria class were the only common bacteria group found in the intestinal tracts of shrimp from all farms. The dominant bacterial genera in the intestinal population of each shrimp varied among different farms, and these genera were Vibrio, Photobacterium, Aeromonas, or Propionigenium (phylum Fusobacteria). Other commonly found genera included Actinomyces, Anaerobaculum, Halospirulina, Pseudomonas, Mycoplasma, and Shewanella. Twelve phyla of bacteria including Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria, Tenericutes, Deinococcus-Thermus, Planctomycetes, Spirochaetes, Synergistetes, Thermotogae, and Verrucomicrobia were represented in the sequences. Additionally, strictly anaerobic bacteria such as Propionigenium and Fusibacter were found. These intestinal bacterial communities varied significantly among different commercial farms and were distinct from their rearing water. The results provide descriptive structures of the intestinal bacterial communities of P. monodon in commercial farms, which can further be applied to areas of research on the immunity, disease resistance, and nutrition of shrimp to improve aquaculture of the black tiger shrimp.

Visual analytics of surveillance data on foodborne vibriosis, United States, 1973-2010

Foodborne illnesses caused by microbial and chemical contaminants in food are a substantial health burden worldwide. In 2007, human vibriosis (non-cholera Vibrio infections) became a notifiable disease in the United States. In addition, Vibrio species are among the 31 major known pathogens transmitted through food in the United States. Diverse surveillance systems for foodborne pathogens also track outbreaks, illnesses, hospitalization and deaths due to non-cholera vibrios. Considering the recognition of vibriosis as a notifiable disease in the United States and the availability of diverse surveillance systems, there is a need for the development of easily deployed visualization and analysis approaches that can combine diverse data sources in an interactive manner. Current efforts to address this need are still limited. Visual analytics is an iterative process conducted via visual interfaces that involves collecting information, data preprocessing, knowledge representation, interaction, and decision making. We have utilized public domain outbreak and surveillance data sources covering 1973 to 2010, as well as visual analytics software to demonstrate integrated and interactive visualizations of data on foodborne outbreaks and surveillance of Vibrio species. Through the data visualization, we were able to identify unique patterns and/or novel relationships within and across datasets regarding (i) causative agent; (ii) foodborne outbreaks and illness per state; (iii) location of infection; (iv) vehicle (food) of infection; (v) anatomical site of isolation of Vibrio species; (vi) patients and complications of vibriosis; (vii) incidence of laboratory-confirmed vibriosis and V. parahaemolyticus outbreaks. The additional use of emerging visual analytics approaches for interaction with data on vibriosis, including non-foodborne related disease, can guide disease control and prevention as well as ongoing outbreak investigations.

Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes

We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group.

Diversity and characterization of oxytetracycline-resistant bacteria associated with non-native species, white-leg shrimp (Litopenaeus vannamei), and native species, black tiger shrimp (Penaeus monodon), intensively cultured in Thailand

AIMS

This study aimed at surveying prevalence of oxytetracycline (OTC)-resistant bacteria in the white-leg shrimp Litopenaeus vannamei, and the black tiger shrimp Penaeus monodon, intensively cultured in Thailand. We investigated the phylogenetic diversity of the bacterial isolates, as well as the minimum inhibitory concentration (MIC) of OTC, the occurrence of major OTC-resistant genes and multiple-antibiotic resistance in the isolates.

METHODS AND RESULTS

Shrimps were collected from culture ponds, and the homogenates of whole bodies were plated on tryptic soy agar supplemented with or without OTC. Percentages of OTC-resistant bacteria were 0·3-52·1% in white-leg samples and 0·008-22·3% in black tiger samples. Analyses of 16S rDNA sequences indicated that most OTC-resistant isolates were closely related to Aeromonas spp. and Lactococcus garvieae. MICs of OTC were 4-128 μg ml(-1) in the OTC-resistant aeromonads and 128-256 μg ml(-1) in OTC-resistant L. garvieae. OTC resistance was found to be conferred by the genes tet(A), tet(C), tet(D), tet(E), tet(M) and tet(S), detected either singly or in pairs. No resistance to ceftazidime, imipenem or chloramphenicol was observed in any isolate.

CONCLUSIONS

Both species of shrimp are associated with OTC-resistant bacteria, occasionally at high densities exceeding 10(6) cfu g(-1). The associated bacteria, predominantly Lactococcus and Aeromonas genera, are potential pathogens and are reservoirs of a variety of OTC-resistant genes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Cultured shrimps can be vehicle to carry OTC-resistant bacteria to domestic and foreign consumers via the food chain. Very low populations of OTC-resistant bacteria observed in the several ponds suggest that levels of the resistant bacteria are artificially high and should be reduced in farmed shrimps.

Horizontal gene transfers with or without cell fusions in all categories of the living matter

This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

Abdominal setae and midgut bacteria of the mudshrimp Pestarella tyrrhena

We investigated the diversity of the bacterial 16S rRNA genes occurring on the abdominal setal tufts and in the emptied midgut of the marine mudshrimp Pestarella tyrrhena (Decapoda: Thalassinidea). There were no dominant phylotypes on the setal tufts. The majority of the phylotypes belonged to the phylum Bacteroidetes, frequently occurring in the water column. The rest of the phylotypes were related to anoxygenic photosynthetic α-Proteobacteria and to Actinobacteria. This bacterial profile seems more of a marine assemblage rather than a specific one suggesting that no specific microbial process can be inferred on the setal tufts. In the emptied midgut, 64 clones were attributed to 16 unique phylotypes with the majority (40.6%) belonging to the γ-Proteobacteria, specifically to the genus Vibrio, a marine group with known symbionts of decapods. The next most abundant group was the ɛ-Proteobacteria (28.1%), with members as likely symbionts related to the processes involving redox reactions occurring in the midgut. In addition, phylotypes related to the Spirochaetes (10.9%) were also present, with relatives capable of symbiosis conducting a nitrite associated metabolism. Entomoplasmatales, Bacteroidetes and Actinobacteria related phylotypes were also found. These results indicate a specific bacterial community dominated by putative symbiotic Bacteria within the P. tyrrhena’s midgut.

New phospholipase A1-producing bacteria from a marine fish

Phospholipase A1 is a hydrolytic enzyme that catalyzes the removal of the acyl group from position 1 of glycerophospholipids to form 2-acyl lysophospholipids. Lysophospholipids are used in foods, cosmetics, and pharmaceuticals as surfactants. Novel forms of phospholipase A1 that function at low temperatures are desirable for use in lipophilic systems in food processing. However, there is currently little variety in the available sources of phospholipase A1. Given this situation, we screened the intestinal contents of marine animals for phospholipase A1-producing bacteria. Colonies that formed a halo on K28CP screening medium and that grew in K28 medium were cultured in liquid K28 medium, and the supernatant was retrieved for analysis. Phosphatidylcholine was added to the culture supernatant, and the product of the reaction was analyzed by using TLC. For culture supernatants that were able to generate lysophosphatidylcholine, synthetic phosphatidylcholines were added, and the site of the reaction was determined by analyzing the fatty acid compositions of the lysophosphatidylcholines generated by GLC. A bacterial isolate from a flatfish, which we named HFKI0020, was found to have phospholipase A1 activity at low temperatures. We determined that the isolate HFKI0020 is closely related to Pseudomonas by using 16S rDNA sequence analysis and by characterizing the isolate with respect to its physiologic and biochemical properties. From the intestinal contents of a marine fish, we successfully isolated a bacterium that secretes phospholipase A1 that is active at low temperatures.