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Aims This study used high-throughput sequencing to evaluate the intestinal microbiome dynamics in rainbow trout ( Oncorhynchus mykiss) fed commercial diets supplemented with either pre- or probiotics (0·6% mannan-oligosaccharides and 0·5% Saccharomyces cerevisiae respectively) or the mixture of both. Methods and Results A total of 57 fish whole intestinal mucosa and contents bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene, as well as the relationship between plasma biochemical health indicators and microbiome diversity. This was performed at 7, 14 and 30 days after start feeding functional diets, and microbiome diversity increased when fish fed functional diets after 7 days and it was positively correlated with plasma cholesterol levels. Dominant phyla were, in descending order, Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes and Fusobacteria. However, functional diets reduced the abundance of Gammaproteobacteria to favour abundances of organisms from Firmicutes and Fusobacteria, two phyla with members that confer beneficial effects. A dynamic shift of the microbiome composition was observed with changes after 7 days of feeding and the modulation by functional diets tend to cluster the corresponding groups apart from CTRL group. The core microbiome showed an overall stability with functional diets, except genus such as Escherichia-Shigella that suffered severe reductions on their abundances when feeding any of the functional diets. Conclusions Functional diets based on pre- or probiotics dynamically modulate intestinal microbiota of juvenile trout engaging taxonomical abundance shifts that might impact fish physiological performance. Significance and Impact of the Study This study shows for the first time the microbiome modulation dynamics by functional diets based on mannan-oligosaccharides and S. cerevisiae and their synergy using culture independent high-throughput sequencing technology, revealing the complexity behind the dietary modulation with functional feeds in aquatic organisms. [ABSTRACT FROM AUTHOR]

Abstract: The Toll and IMD signaling pathways represent one of the first lines of innate immune defense in invertebrates like Drosophila. However, for crustaceans like Caligus rogercresseyi, there is very little genomic information and, consequently, understanding of immune mechanisms. Massive sequencing data obtained for three developmental stages of C. rogercresseyi were used to evaluate in silico the expression patterns and presence of SNPs variants in genes involved in the Toll and IMD pathways. Through RNA-seq analysis, which used 20 contigs corresponding to relevant genes of the Toll and IMD pathways, an overexpression of genes linked to the Toll pathway, such as toll3 and Dorsal, were observed in the copepod stage. For the chalimus and adult stages, overexpression of genes in both pathways, such as Akirin and Tollip and IAP and Toll9, respectively, were observed. On the other hand, PCA statistical analysis inferred that in the chalimus and adult stages, the immune response mechanism was more developed, as evidenced by a relation between these two stages and the genes of both pathways. Moreover, 136 SNPs were identified for 20 contigs in genes of the Toll and IMD pathways. This study provides transcriptomic information about the immune response mechanisms of Caligus, thus providing a foundation for the development of new control strategies through blocking the innate immune response. [Copyright &y& Elsevier]

Salmon species cultured in Chile evidence different levels of susceptibility to the sea louse Caligus rogercresseyi. These differences have mainly been associated with specific immune responses. Moreover, iron regulation seems to be an important mechanism to confer immunity during the host infestation. This response called nutritional immunity has been described in bacterial infections, despite that no comprehensive studies involving in marine ectoparasites infestation have been reported. With this aim, we analysed the transcriptome profiles of Atlantic and coho salmon infected with C. rogercresseyi to evidence modulation of the iron metabolism as a proxy of nutritional immune responses. Whole transcriptome sequencing was performed in samples of skin and head kidney from Atlantic and coho salmon infected with sea lice. RNA-seq analyses revealed significant upregulation of transcripts in both salmon species at 7 and 14 dpi in skin and head kidney, respectively. However, iron regulation transcripts were differentially modulated, evidencing species-specific expression profiles. Genes related to heme degradation and iron transport such as hepcidin, transferrin and haptoglobin were primary upregulated in Atlantic salmon; meanwhile, in coho salmon, genes associated with heme biosynthesis were strongly transcribed. In summary, Atlantic salmon, which are more susceptible to infestation, presented molecular mechanisms to deplete cellular iron availability, suggesting putative mechanisms of nutritional immunity. In contrast, resistant coho salmon were less affected by sea lice, mainly activating pro-inflammatory mechanisms to cope with infestation. [ABSTRACT FROM AUTHOR]

The genomic era has increased the research effort to uncover how the genome of an organism, and specifically the transcriptome, is modulated after interplaying with pathogenic microorganisms and ectoparasites. However, the ever-increasing accessibility of sequencing technology has also evidenced regulatory roles of long non-coding RNAs (lncRNAs) related to several biological processes including immune response. This study reports a high-confidence annotation and a comparative transcriptome analysis of lncRNAs from several tissues of Salmo salar infected with the most prevalent pathogens in the Chilean salmon aquaculture such as the infectious salmon anemia (ISA) virus, the intracellular bacterium Piscirickettsia salmonis and the ectoparasite copepod Caligus rogercresseyi . Our analyses showed that lncRNAs are widely modulated during infection. However, this modulation is pathogen-specific and highly correlated with immuno-related genes associated with innate immune response. These findings represent the first discovery for the widespread differential expression of lncRNAs in response to infections with different types of pathogens in Atlantic salmon, suggesting that lncRNAs are pivotal player during the fish immune response. [ABSTRACT FROM AUTHOR]

Aim: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next‐generation sequencing (NGS). Methodology: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3–V4 variable regions of the 16S rRNA gene were amplified. The amplification was deep sequenced by Illumina technology to establish the metagenetic relationships among the bacterial species identified. The composition and diversity of microbial communities in the root canal and their relationships with clinical features were analysed. Parametric and nonparametric tests were used to analyse differences between patient characteristics and microbial data. Results: A total of 86 different operational taxonomic units (OTUs) were identified and Good's nonparametric coverage estimator method indicated that 99.9 ± 0.00001% diversity was recovered per sample. The largest number of bacteria belonged to the phylum Proteobacteria. According to the medical history from the American Society of Anesthesiologists (ASA) Classification System, ASA II–III had higher richness estimates and distinct phylogenetic relationships compared to ASA I individuals (P < 0.05). Periapical index (PAI) score 5 was associated with increased microbiota diversity in comparison to PAI score 4, and this index was reduced in symptomatic patients. Conclusions: Based on the findings of this study, it is possible to suggest a close relationship between several clinical features and greater microbiota diversity with persistent endodontic infections. This work provides a better understanding on how microbial communities interact with their host and vice versa. [ABSTRACT FROM AUTHOR]

The article focuses on the study of hydrogen peroxide (H2O2) treatment that changes transcription of sex-related genes in the sea lice Caligus rogercresseyi. It mentions that H2O2 is an antiparasitic chemical used to control adult sea lice in salmon farms. It states that detached adult lice shows the recovery after H2O2 treatment and could resettle hosts under laboratory conditions.

The rapid development of the aquaculture industry has global concerns with health management and control strategies to prevent and/or treat diseases and increase sustainability standards. Saprolegniosis is a disease caused by Saprolegnia parasitica, and is characterized by promoting an immunosuppression in the host. This study evaluated in vitro the extract and one active compound (polygodial) of Drimys winteri , a Chilean medicinal tree as a potential early immunostimulatory aid in Saprolegniosis control. Atlantic salmon ( Salmo salar ) head kidney cells (ASK-1) were incubated with both extract and pure polygodial before exposure to S. parasitica mycelium, and the expression of the immune-related genes interleukin 1β ( IL-1β ), interferon α ( IFNα ), and major histocompatibility complex II ( MHCII ) was evaluated. Both evidenced immunomodulatory capacities by increasing gene expressions. This immunomodulation related to a mitigatory action counteracting the immunosuppressing effects of S. parasitica . Despite that most immune-related genes were up-regulated, the down-regulation of MHCII , characteristic of S. parasitica infection, was lessened by pre-incubation with the compounds. This study provides the first insight on the potential of D. winteri bark extract as a possible immunomodulatory and defensive strategy against this oomycete infection in fish. [ABSTRACT FROM AUTHOR]

Although iron has been proved as a vital element for the development of living organisms, high levels of this element can impact the normal function of different biological processes, including immune response. Therein, this study aimed to characterize the transcriptional changes in Atlantic salmon during the exposure to iron overload, evaluating the susceptibility to bacterial infection. Atlantic salmon were injected with 1 or 5 mg of iron dextran and an iron chelator (DFOM), and subsequently challenged with the intracellular bacterium Piscirickettsia salmonis. Iron levels in plasma and the transcriptional responses of the head kidney, liver, and spleen during the infection processes were evaluated. Here, iron transport, response to oxidative stress, and immune related genes were strongly modulated in individuals exposed to the metal. Fish overloaded with iron showed significant downregulation of CD83 , IL-17 , IL-1 , Toll-like receptors , immunoglobulin, and T-cell receptors genes, suggesting an overall deleterious effect on the immune system. Furthermore, histopathological analysis evidenced that iron overdoses can strongly increase the clinical signs during the P. salmonis infection. Notably, fish exposed to 1 mg of iron and infected with P. salmonis evidenced high mortality and bacterial burden. Also, this group showed significant downregulation of immune-related genes comparing with fish with 5 mg of iron. In addition, Atlantic salmon injected with deferoxamine mesylate salt (DFOM) showed high tolerance to P. salmonis infection and an increase of IL-1b expression, suggesting a cytokines response activation. These results suggest that iron overload disrupts fish immune response although not in a doses dependent manner, and when a chelator is injected, fish present higher resistance to P. salmonis. This study reveals novel insights about teleost's immune system modulation by iron availability. • Iron overdose in salmon disrupts the fish transcriptome responses. • Fish immune system is disrupted by iron overdose. • Atlantic salmon exposed to iron overload exhibit high susceptibility to P. salmonis. [ABSTRACT FROM AUTHOR]

The marine copepodid Caligus rogercresseyi is the causative agent of Caligidosis, the most important parasitic disease for the Chilean salmon industry. Historically, C. rogercresseyi has been widely distributed in coastal waters of northern Patagonia (40°15′S to 49°16′ S), where close to 90% of salmon farms are located. In 2017, sea lice were detected in farmed Atlantic salmon in the Magallanes region (south of 49°16′ S), affecting salmon farms for the first time. This study aimed to identify the sea louse C. rogercresseyi infecting Atlantic salmon, and also to report measures and activities conducted by the Chilean Fisheries and Aquaculture Service (SERNAPESCA) in conjunction with the Caligidosis Reference Laboratory (University of Concepción). The main actions were diagnosis and outbreak confirmation, case definition, surveillance, and implementation of control strategies. Here, the identification of C. rogercresseyi was confirmed through morphological and genetic analyses. In total, there were eight farms in the Magallanes region where at least one C. rogercresseyi individual was detected during 2017. Only in three case farms, C. rogercresseyi presented an epidemic behavior, reaching maximum levels of 24.5 adult lice/fish and 14 juvenile lice/fish. SERNAPESCA implemented different measures aimed to improve the sensitivity of the surveillance system, which yielded new case farms. The two farms with higher sea lice levels were treated with the organophosphate azamethiphos, resulting in a dramatic reduction of both adult and juvenile lice, although fish were re-infected a few weeks later. Further research is needed to determine the causes of this outbreak and evaluate its consequences for the local salmon industry. • The sea louse Caligus rogercresseyi was identified in Magallanes region infesting Atlantic salmon farms. • Outbreak was confirmed in 2017 for the first time for Chilean salmon farms located in Magallanes region. • Control measures and surveillance were implement based on the current study. [ABSTRACT FROM AUTHOR]