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Copyright of CyTA: Journal of Food is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Squid hydrolysates obtained by autolysis without addition of lactic acid at two different p H (5 and 7) and included at 25 and 50 g kg−1 in a commercial shrimp feed were evaluated. Shrimp fed on such diets were cultured under indoor and outdoor conditions. Diets containing both hydrolysates and included at both levels caused a higher feed consumption by shrimp. In general, shrimp fed on both hydrolysates, but particularly on that prepared at p H 7, exhibited similar or better production responses (survival, biomass, feed conversion ratio, specific growth rate) compared to those fed on diets without the inclusion of hydrolysates. Shrimp cultured outdoor showed a better growth performance compared to those cultured indoor. No significant differences were found regarding the proximate composition of shrimp of any treatment. Results suggest that the free amino acids provided by squid hydrolysates contributed to improve the feed consumption and growth performance of shrimp cultured under both indoor and outdoor conditions. [ABSTRACT FROM AUTHOR]

A 7-week study was performed to evaluate the partial and total replacement of formulated feed ( FF) by live insects ( Trichocorixa sp.), during intensive culture of Litopenaeus vannamei. Production response, physiological status and postharvest quality were evaluated. Five treatments consisting of 0%, 25%, 50%, 75% and 100% of FF replacement (T-0, T-25, T-50, T-75 and T-100) were performed. Better production responses were observed in T-50, followed by T-0 and T-75 respectively. Also, no negative effect of insect supplying was detected on the physiological status of shrimp (evaluated by haemolymph parameters). However, shrimp fed exclusively on insects (T-100) had poor growth and physiological performances, and lower postharvest quality compared with the rest of treatments. Regarding organoleptic characteristics, no effect of treatments was detected on the colour, odour and taste of shrimp muscle. In conclusion, the insect Trichocorixa sp. can contribute to the nutritional requirements of shrimp and could be used as complementary natural food, improving productive responses, without affecting the physiological status or the post mortem quality of shrimp; however the total substitution of FF by insects is not recommendable. [ABSTRACT FROM AUTHOR]

Copyright of Universidad & Ciencia is the property of Universidad Juarez Autonoma de Tabasco and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The effect of promoted biota on the production parameters, water quality, nutritional and immunological condition of Litopenaeus vannamei was assessed in semi-intensive ponds. Earthen ponds were used as experimental units: three with formulated + natural promoted feed + shrimp (T1), three with formulated feed + shrimp (T2), and three with promoted natural feed without shrimp (Control). The dissolved oxygen (DO) levels were optimal for all treatments (≥6 mg L) as well as the pH (8.4-8.6). Total ammonia nitrogen was greater in T2 (0.10 mg L) than T1 (0.07 mg L) and the Control (0.06 mg L). Phytoplankton, zooplankton and benthos were more abundant in T1 and the Control. The promotion of natural feed had a positive effect on all the production parameters of shrimp with an increase of 19.0%, 3.5% and 23.9% in weight gain, survival, and final biomass, respectively; also it was observed a decrease of 13.9% in feed conversion ratio. No differences in haemolymph parameters were observed for nutritional indicators (glucose, cholesterol, proteins, and triglycerides) nor for immunological response (phenoloxidase and prophenoloxidase). The results indicate that the promotion of biotic communities enhances the production parameters of farmed shrimp, without affecting the nutritional and immunological status. Also the water quality was improved by the presence of biota. [ABSTRACT FROM AUTHOR]

Endpoint responses identifying critical thermal maximum (CTMax) and minimum (CTMin) temperatures of the Pacific sardine Sardinops sagax caeruleus Girard 1854 were estimated, after acclimation to a summer (SC) and a winter (WC) thermal cycle, to establish a precise endpoint for this species. The initial response observed during critical thermal limits was the onset of muscle spasms (OS) which was followed by loss of equilibrium (LE). Significant differences were found between SC and WC acclimated sardines when LE was used as the CTM endpoint. No differences were observed when the OS endpoint was used, owing to the high variance of OS values. Sardines had a CTMax of 30.4 and 31.8 °C for fish that underwent the WC and SC, respectively, while the CTMin was 5.2 and 6.5 °C for WC and SC sardines, respectively. Sardines showed a marked tolerance to low temperatures and some capacity to modify their critical limits when acclimated to different cycling thermal regimes. The thermal limits can be useful to compare sub-populations of this species inhabiting the North Pacific Ocean. Moreover, loss of equilibrium (LE) was a more consistent response than onset of spasms (OS); thus, it can be used as a reliable endpoint in further studies. [ABSTRACT FROM AUTHOR]

Different protocols were performed to evaluate their effectiveness to inoculate necrotizing hepatopancreatitis bacterium (NHPB) into Artemia sp. Protocol-A consisted of adding to water 0.2 mL•L-1 of bacterial inoculum composed of infected hepatopancreas (HPNHPB) and glycerol (1:1 w/v). Protocol-B consisted of adding the same inoculum but at a ratio of 2 mL•L-1, whereas protocol C consisted of adding 0.2 mL•L-1, of HPNHPB+glycerol+formulated feed (0.5:0.5:1 w/v/w). Controls for each treatment consisted of similar inoculums but using healthy hepatopancreas. Artemia from A and B treatments were negative for NHPB after four and eight days post-inoculation, whereas Artemia from treatment C resulted as positive to NHPB after four (75% of individuals) and eight (100%) days post-inoculation. The results suggest that the incorporation of formulated feed into the inoculums induced the bacteria’s consumption of Artemia.

Diverse protocols have been used in the shrimp industry to produce microalgae. In this work, we evaluated the effect of inoculation time (0600 and 1200) and initial microalgae density (0.4 and 0.8 x105cells mL-1) in static outdoor cultures of Tetraselmis chuii, using F/2 and 2-F media. A significant effect on cell density (> 6.7 x 105 cells mL-1) was found after treatments with a high initial density and in the F/2 medium. The higher productive responses were observed in treatments inoculated at 0600. The better productive response was found in treatments inoculated at 0600 with 0.8 x 105 cells•mL-1 in the F/2 medium.

A seven-week experiment was performed to evaluate the effect of supplying copepods (Acartia sp. and Calanus pacificus), as exogenous feed during the intensive pre-growout phase of white shrimp (Litopenaeus vannamei), on the productive parameters and water quality. Five treatments were tested in which shrimp were fed formulated feed and the addition of 0 (control), 1, 2, 4, or 8 copepods mL-1. Treatments with 1 and 4 copepods mL-1 had higher ammonia nitrogen levels than the rest of the treatments (>4 mg L-1). Nitrite levels were significantly higher in the treatment with 8 copepods mL-1, whereas nitrate levels were higher in all treatments relative to the control. Phosphate concentration was higher in the treatments with 4 and 8 copepods mL-1. Shrimp from the treatments with 2, 4, and 8 copepods mL-1 showed a higher survival (>93%), weight (>3.1 g), and final biomass (>77 g). The treatment with 2 copepods mL-1 had the best feed conversion ratio (1.19) compared with the rest (>1.7). The results suggest that the additional supply of copepods as exogenous feed during the intensive pre-growout phase of shrimp culture can have a negative effect on the water quality, although survival was not affected; however, the effect on the production parameters was positive, indicating that the use of copepods as exogenous live feed is feasible in the culture of white shrimp. [ABSTRACT FROM AUTHOR]

A meta-analytic approach deciphered the taxonomic profile of the zebrafish gut microbiota at different developmental stages. Data (16S rDNA) were systematically searched in databases, selecting those with intestine samples of fish not exposed to a particular treatment or challenge (e.g., pathogens, dietetic tests, xenobiotics, etc.) and obtaining 340 samples to be processed. Results revealed marked differences between the developmental phases. Proteobacteria was the dominant phylum in the larval phase, with a relative abundance of 90%, while the rest of the phyla did not exceed 2%. Vibrio, Aeromonas, Plesiomonas, Pseudomonas, Shewanella, and Acinetobacter were the dominant genera in this phase. Transitional changes were observed after the larvae stage. Proteobacteria still registered high abundance (48%) in the juvenile phase, but Fusobacteria (40%) and Bacteriodota (5.9%) registered considerable increases. Genera, including Cetobacterium, Plesiomonas, Aeromonas, Vibrio, and Flavobacterium, dominated this stage. The phyla Proteobacteria (48%) and Fusobacteria (35%) were strongly established in the adult phase. Cetobacterium was registered as the most abundant genus, followed by Aeromonas, Acinetobacter, Plesiomonas, Vibrio, and ZOR0006 (Firmicutes; 6%). In conclusion, the composition of the intestinal microbiota of zebrafish is consistently determined by two primary phyla, Proteobacteria and Fusobacteria; however, this composition varies depending on the developmental stage. Cetobacterium and Aeromonas are the most relevant genera in juveniles and adults. Finally, these results reveal a consistent pattern of certain bacterial groups in the zebrafish microbiota that could help shape gnotobiotic models (colonized with a specific known bacterial community) or synthetic microbiota (in vitro assembly of microbes), among other approaches., Competing Interests: Declaration of competing interest None., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Probiotics in aquaculture hold promise for enhancing fish health and growth. Due to their increased specificity and affinity for their host, indigenous probiotics may offer isolated and potentially amplified benefits. This study investigated the effects of Lactococcus lactis PH3-05, previously isolated from adults of tropical gar ( Atractosteus tropicus ), on the growth, survival, digestive enzyme activity, intestinal morphology, expression of barrier and immune genes, and intestinal microbiota composition in the larvae of tropical gar. Larvae were fed with live L. lactis PH3-05 concentrations of 10 4 , 10 6 , and 10 8 CFU/g for 15 days alongside a control diet without probiotics. Higher concentrations of L. lactis PH3-05 (10 6 and 10 8 CFU/g) positively influenced larval growth, increasing hepatocyte area and enterocyte height. The 10 6 CFU/g dose significantly enhanced survival (46%) and digestive enzyme activity. Notably, the 10 8 CFU/g dose stimulated increased expression of muc-2 and il-10 genes, suggesting enhanced mucosal barrier function and anti-inflammatory response. Although L. lactis PH3-05 did not significantly change the diversity, structure, or Phylum level composition of intestinal microbiota, which was constituted by Proteobacteria, Bacteroidota, Chloroflexi, and Firmicutes, an increase in Lactobacillus abundance was observed in fish fed with 10 6 CFU/g, suggesting enhanced probiotic colonization. These results demonstrate that administering L. lactis PH3-05 at 10 6 CFU/g promotes growth, survival, and digestive health in A. tropicus larvae, establishing it as a promising indigenous probiotic candidate for aquaculture applications.

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Nocardiosis has caused high mortalities among fish cultures; however, the effects of Nocardia infections in the fish gastrointestinal microbiota are unknown. In this research, tilapia was infected with Nocardia sp., to analyze the effect of infection on the gastrointestinal microbiota. Tilapia infected with Nocardia sp. reported a 46 % survival (100 % in non-infected). Moreover, the infection caused severe damage to the stomach microbiota, with a loss of diversity and a significant increase of Proteobacteria (94.8 %), resulting in a negative correlation network between Proteobacteria and other important phyla. Nocardia sp. is an emerging pathogen capable of inducing dysbiosis and causing significant mortalities., Competing Interests: Declaration of competing interest This manuscript has not been published previously in any form, and it is not under consideration for publication elsewhere. This publication is approved by all authors and tacitly by the responsible authorities where the work was carried out. Finally, if accepted, it will not be published elsewhere in the same form, in English, or any other language, including electronically, without the copyright holder's written consent., (Copyright © 2023 Elsevier Inc. All rights reserved.)

This work aimed to determine the presence of bacterial pathogens in fish with a clinical picture suggestive of infectious disease in Nile tilapia reared in Chiapas, Mexico. Blood and viscera samples were taken from healthy and diseased animals from commercial farms. Clinical and pathological examinations of each individual were performed and samples were collected for bacteriological studies. The bacterial isolates were identified and characterized by culture, biochemical tests, antibiogram, challenge tests and 16S rRNA sequencing. Staphylococcus haemolyticus and Providencia vermicola were isolated from various diseased organisms. The clinical picture caused by Staphylococcus haemolyticus was characterized by appetite disorders, neurological signs, nodulation or ulceration in different areas and congestion or enlargement of internal organs. Providenciosis in juvenile specimens caused a characteristic picture of hemorrhagic septicemia. Challenge tests performed in healthy organisms revealed that both infections caused higher mortality rates in fish ( p < 0.05) compared with non-infected specimens, with 100% survival. There was 100% mortality for animals infected with P. vermicola after three days post infection and 45% for those infected with S. haemolyticus . The isolation and identification of two pathogens involved in an infection process were achieved and cataloged as potential causal agents of disease outbreaks in tilapia farming in Mexico. This is the first report of possible bacterial infection caused by S. haemolyticus and P. vermicola in tilapia farms, which are two uncommon but potentially emerging pathogens for the species.

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

The processes to obtain value-added products from brewers' spent grain, a contaminant industrial waste, require alkaline non-ecofriendly pre-treatments. The arabinoxylans from brewers' spent grain were extracted by nixtamalization evaluating the extraction procedure, antioxidant capacity and molecular characteristics. The best arabinoxylans yields were those extracted with CaO at 100 °C and 25 °C (6.43% and 3.37%, respectively). The antioxidant capacity by 2,2-diphenyl-1-picrylhydrazyl assay of the arabinoxylans after thermal treatment and additional arabinoxylans after thermal treatment proteolysis were 434 and 118 mg TE/g, while by 2,20'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt assay the value was similar (380 μmol TE/g). The intrinsic viscosities and viscosimetric molecular weights were 69 mL/g and 13 kDa for arabinoxylans after thermal treatment, and 15 mL/g and 1.6 kDa for arabinoxylans after thermal treatment proteolysis, respectively. The protein and lignin contents were 3.1% and 6.4% for arabinoxylans after thermal treatment and, 0.9% and 4.6% for arabinoxylans after thermal treatment proteolysis, while their arabinose: xylose ratios were 0.39 and 0.36, with ferulic acid contents of 0.63 and 0.14 mg/g, respectively. Both products of arabinoxylans were molecularly identical by Fourier transform infra-red. Although the purity of the extracted arabinoxylans was improved with proteolysis, their intrinsic viscosity and viscosimetric molecular weight were affected. The extraction of arabinoxylans from brewers' spent grain by CaO nixtamalization alone or after additional proteolysis was successful to obtain purity and good antioxidant capacity.

Human intrusions into undisturbed wildlife areas greatly contribute to the emergence of infectious diseases. To minimize the impacts of novel emerging infectious diseases (EIDs) on human health, a comprehensive understanding of the microbial species that reside within wildlife species is required. The Gulf of California (GoC) is an example of an undisturbed ecosystem. However, in recent decades, anthropogenic activities within the GoC have increased. Zalophus californianus has been proposed as the main sentinel species in the GoC; hence, an assessment of sea lion bacterial microbiota may reveal hidden risks for human health. We evaluated the presence of potential human pathogenic bacterial species from the gastrointestinal (GI) tracts of wild sea lions through a metabarcoding approach. To comprehensively evaluate this bacterial consortium, we considered the genetic information of six hypervariable regions of 16S rRNA. Potential human pathogenic bacteria were identified down to the species level by integrating the RDP and Pplacer classifier outputs. The combined genetic information from all analyzed regions suggests the presence of at least 44 human pathogenic bacterial species, including Shigella dysenteriae and Bacillus anthracis. Therefore, the risks of EIDs from this area should be not underestimated., (© 2022. The Author(s).)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Bacterial diseases represent the main impediment to the development of fish aquaculture. Granulomatous diseases caused by bacteria lead to fish culture losses by high mortality rates and slow growth. Bacteria belonging to genera Streptococcus spp., Mycobacterium sp., Nocardia sp., Francisella sp., and Staphylococcus sp. have been implicated in the development of granulomatous processes. The granuloma formation and the fish's immune response continue to be the subject of scientific research. In fish, the first defense line is constituted by non-specific humoral factors through growth-inhibiting substances such as transferrin and antiproteases, or lytic effectors as lysozyme and antimicrobial peptides, and linking with non-specific phagocyte responses. If the first line is breached, fish produce antibody constituents for a specific humoral defense inhibiting bacterial adherence, as well as the mobilization of non-phagocytic host cells and counteracting toxins from bacteria. However, bacteria causing granulomatous diseases can be persistent microorganisms, difficult to eliminate that can cause chronic diseases, even using some immune system components to survive. Understanding the infectious process leading to granulomatosis and how the host's immune system responds against granulomatous diseases is crucial to know more about fish immunology and develop strategies to overcome granulomatous diseases., (Copyright © 2021 Elsevier Inc. All rights reserved.)

The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of infectious diseases due to high-density farming. Antibiotic overuse and misuse in fish farming and its global health consequences have led to searching for more natural alternatives such as medicinal plants. In this sense, garlic (Allium sativum) has different bioactive compounds with biological properties for animal health. Among them are the ajoene, alliin, and allicin, which confer biological properties such as growth promotion, antimicrobial, antiviral, antioxidant, and antiparasitic. Ways to use garlic in aquaculture include oil, fresh mash, aqueous extract, and garlic powder. The powder presentation is the most used in aquaculture; it is generally applied by oral administration, adding to the feed, and the dose used ranges from 0.05 to 40 g/kg of feed. Garlic has been used in the aquaculture of different species such as rainbow trout (Oncorhynchus mykiss), spotted grouper (Epinephelus coioides), catfish (Clarias gariepinus), tilapia (Oreochromis niloticus), guppy fish (Poecilia reticulata), goldfish (Carassius auratus), and barramundi (Lates calcarifer). In addition to its properties, garlic's usage became popular, thanks to its low cost, easy incorporation into food, and little environmental impact. Therefore, its application can be an effective solution to combat diseases, improve organisms' health using natural supplies, and as an alternative to antibiotics. This review reports and discusses plant-derived products' beneficial properties, emphasizing garlic and its usages in fish aquaculture., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

In vivo evaluation of arabinoxylans (AX) microspheres showed to protect insulin from degradation in the upper gastrointestinal tract and carrier insulin to colon. Insulin-loaded AX microspheres (50 UI/kg) decreased blood glucose level by 39% in diabetic rats with a maximum effect at 18 h post-administration, indicating that insulin remains bioactive. The continuous administration (4 days) of insulin-loaded AX microspheres improved the polyuria and increased the production of short-chain fatty acids, as well as Bifidobacterium and Bacteroides in diabetic rats compared to untreated diabetic rats. AX microspheres are a potential microbiota-activated carrier for colon-specific drug delivery and could be useful as a complementary treatment for diabetes., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Proteolytic enzymes are widely distributed in nature, playing essential roles in important biological functions. Recently, the use of plant proteases at the industrial level has mainly increased in the food industry (e.g., cheesemaking, meat tenderizing, and protein hydrolysate production). Current technological and scientific advances in the detection and characterization of proteolytic enzymes have encouraged the search for new natural sources. Thus, this work aimed to explore the milk-clotting and proteolytic properties of different tissues of Vallesia glabra. Aqueous extracts from the leaves, fruits, and seeds of V. glabra presented different protein profiles, proteolytic activity, and milk-clotting activity. The milk-clotting activity increased with temperature (30-65 °C), but this activity was higher in leaf (0.20 MCU/mL) compared with that in fruit and seed extracts (0.12 and 0.11 MCU/mL, respectively) at 50 °C. Proteolytic activity in the extracts assayed at different pH (2.5-12.0) suggested the presence of different types of active proteases, with maximum activity at acidic conditions (4.0-4.5). Inhibitory studies indicated that major activity in V. glabra extracts is related to cysteine proteases; however, the presence of serine, aspartic, and metalloproteases was also evident. The hydrolytic profile of caseins indicated that V. glabra leaves could be used as a rennet substitute in cheesemaking, representing a new and promising source of proteolytic enzymes.

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.

This study evaluated the effect of using arabinoxylans (AX) and gelled arabinoxylans (AxGel) as anti-obesogenic agents on the faecal microbiota of rats fed with a high-fat (HF) diet. Results revealed that the HF content in diet caused obesity in rats and alterations in the taxonomic and functional profiles of faecal microbiota. However, these effects were lessened when AX and AxGel were used as ingredients of the HF diet. Metabolisms of amino acids and energy, as well as genetic information processing, were negatively affected when the rats consumed the HF diet; however, this effect was not observed if AX and AxGel were included as part of the diet formulation. Results suggest that AX may act as a prebiotic agent. Therefore, AX and AxGel could be considered as hypothetical protectors of the intestinal microbiota against HF consumption.

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway., Competing Interests: The authors have declared that no competing interests exist.

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.

Vibrio parahaemolyticus has been recognized as the causal agent of early mortality syndrome and is currently considered an emerging shrimp disease causing losses of millions in the aquaculture industry. Integral membrane proteins are widely recognized as pathogenicity factors involved in essential mechanisms for V. parahaemolyticus infection, which makes them attractive as therapeutic targets. However, their physico-chemical properties and weak expression has resulted in under-representation of these proteins in conventional bottom-up proteomics, making integral membrane proteomics a challenging task. Integral membrane proteins from a bacterial strain isolated from the hepatopancreases of white shrimp with early mortality syndrome and identified by 16S rRNA sequencing as V. parahaemolyticus and an ATCC strain that is pathogenic for humans were obtained by a sequential extraction method and subjected to relative quantification and identification by isobaric Tags for Relative and Absolute Quantitation. A homology database search resulted in identification of more than two hundred proteins, 35 of which are recognized as pathogenic factors showed statistically significant differential accumulation between the strains. These proteins are mainly associated with adherence, secretion systems, cell division, transport, lysogenization, movement and virulence. Identification of pathogenicity-related proteins in V. parahaemolyticus provides valuable information for developing strategies based on molecular mechanisms that inhibit these proteins, which may be useful therapeutic targets for assisting the shrimp and aquaculture industry., (© 2017 The Societies and John Wiley & Sons Australia, Ltd.)

The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated. Overall, 513,309 sequences recorded in SILVA were used to estimate the size of hypervariable regions of the gene. Redundant sequences were treated as a single sequence to achieve a better representation of the molecular diversity. Nucleotides found in each position in 95% of the sequences were considered the consensus sequences for different size-groups (consensus95). The sizes of different regions ranged from 96.7 to 283.1 nucleotides and had similar distribution patterns, except for the V3 region, which exhibited a bimodal distribution composed of 2 main peaks of 161 and 186 nt. The alignment of Consensuses95 of fractions 161 and 186 showed a high degree of similarity and conservation, except for the central positions (gap zone), where the sequence was highly variable and several deletions were observed. Structurally, the gap zone forms the central part of helix 17 (H17), and its extension was directly reflected in the size of this helix. H17 is part of a multihelix conjunction known as the 5-way junction (5 WJ), which is indispensable for 30 S ribosome assembly. However, because a drastic variation in the sequence size of V3 region occurs at a central position in loop H17 without affecting the base of the loop, it has no apparent effect on 5 WJ. Finally, considering that these differences were detected in non-redundant sequences, it can be concluded that this is not an uncommon or isolated event and that the V3 region is possibly more likely to mutate than are other regions.

Crustins are considered effector molecules of innate immunity in arthropods, and classification schemes have been proposed over the last 10 years. However, classification problems have emerged: for example, proteins that have been well identified as members of a particular category have also been classified as crustins. Therefore, the objective of this manuscript was to analyze and, based on solid arguments, improve the original proposed nomenclature to make crustins a distinctive group of antibacterial proteins. The presence of WAP or 4DSC domain has been considered a distinctive feature of crustins; however, several antibacterial proteins containing WAP domains have been detected in diverse taxonomic groups (including mammals). Here, we present evidence supporting the idea that the Cys-rich region and the 4DSC domain can be considered a signature of crustins and, together with some distance arrangements occurring within this 12-Cys region, yield enough information for the classification of these proteins. Herein, the core characteristics to be considered for classification purposes are the length of the Gly-rich region and the repetitive tetrapeptides occurring within this region; these characteristics are then hierarchically followed by the F and A distances located within the 4DSC domain. Finally, the proposed system considers the crustin signature as the common structure in all members, which is a differentiator from other proteins containing WAP domains, separating crustins as a well-distinguished member of the superfamily of WAP-domain containing proteins., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The use of k- mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k- mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k- mer size was inversely proportional to the occurrence of k- mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k- mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.

Increasing global population and the consequent increase in demand for food are not a new story. Agroindustrial activities such as livestock help meet this demand. Aquaculture arose decades ago and revolutionized the agroindustrial activity as a significant food generator. However, like livestock, aquaculture is based on finite resources and has been accused of being unsustainable. Abandoning aquaculture is not an option considering the food, foreign exchange, and employment it generates, and therefore must be reinvented. Among the many alternatives suggested to make aquaculture more sustainable, microorganisms have been highlighted as a direct food source for cultured fish and crustaceans, a strategy that promises to revolutionize aquaculture by eliminating waste. Considering waste, as part of a cycle, it can increase stock densities and reduce emissions of contaminants and operational costs.

The classification performance of Kraken was evaluated in terms of sensitivity and specificity when using short and long 16S rRNA sequences. A total of 440,738 sequences from bacteria with complete taxonomic classifications were downloaded from the high quality ribosomal RNA database SILVA. Amplicons produced (86,371 sequences; 1450 bp) by virtual PCR with primers covering the V1-V9 region of the 16S-rRNA gene were used as reference. Virtual PCŔs of internal fragments V3-V4, V4-V5 and V3-V5 were performed. A total of 81,523, 82,334 and 82,998 amplicons were obtained for regions V3-V4, V4-V5 and V3-V5 respectively. Differences in depth of taxonomic classification were detected among the internal fragments. For instance, sensitivity and specificity of sequences classified up to subspecies level were higher when the largest internal fraction (V3-V5) was used (54.0 and 74.6% respectively), compared to V3-V4 (45.1 and 66.7%) and V4-V5 (41.8 and 64.6%) fragments. Similar pattern was detected for sequences classified up to more superficial taxonomic categories (i.e. family, order, class…). Results also demonstrate that internal fragments lost specificity and some could be misclassified at the deepest taxonomic levels (i.e. species or subspecies). It is concluded that the larger V3-V5 fragment could be considered for massive high throughput sequencing reducing the loss of sensitivity and sensibility.

Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated when using Kraken. Kraken cumulates the information of both sequence senses, providing additional elements for the classification. In conclusion, the results demonstrate that Kraken is an excellent choice for use in the taxonomic assignment of sequences obtained by Sanger sequencing or based on third generation sequencing, of which the main goal is to generate larger sequences., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Necrotizing hepatopancreatitis bacterium (NHPB) is an obligated intracellular bacteria causing severe hepatopancreatic damages and mass mortalities in penaeid shrimp. The worldwide distribution of penaeid shrimp as alien species threatens the life cycle of other crustacean species. The aim of the experiment was to evaluate the possibility of experimentally infecting the American lobster (Homarus americanus) with NHPB extracted from shrimp hepatopancreas. Homogenates from infected shrimp were fed by force to lobsters. Other group of lobsters was fed with homogenates of NHPB-free hepatopancreas. After the 15th day from initial inoculation, the presence of NHPB was detected by polymerase chain reaction in feces and hepatopancreas from lobsters inoculated with infected homogenates. Necrotized spots were observed in the surface of lobster hepatopancreas. In contrast, lobsters fed on NHPB-free homogenates resulted negative for NHPB. Evidence suggests the plasticity of NHPB which can infect crustacean from different species and inhabiting diverse latitudes. Considering the results, the American lobster could be a good candidate to maintain available NHPB in vivo.

Shrimp postlarvae were reared into different microcosm systems without water exchange; a traditional system based on simple fertilization to improve microalgae concentration (control), an autotrophic system (AS) based on the promotion of biofloc and biofilm by the addition of fertilizer and artificial substrates and a heterotrophic system (HS) based on the promotion of heterotrophic bacteria by the addition of nitrogenous and carbonaceous sources and artificial substrates. Better growth performance and survival were registered in shrimp from the AS and HS compared to the control. Feed conversion ratios were below 0.7 for all treatments, but AS and HS were significantly lower than the control. Regarding digestive performance, no significant differences were observed for trypsin, amylase and lipase activities among AS and control shrimp; however, shrimp from HS showed a higher trypsin and amylase activities, suggesting a higher digestive activity caused by the presence of microbial bioflocs. The presence of biofilm and bioflocs composed by either autotrophic or heterotrophic organisms in combination with formulated feed improved the growth performance and survival of shrimp. Apparently, such combination fits the nutritional requirements of shrimp.