Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

The microorganisms within the intestinal tract (termed gut microbiota) have been shown to interact with the gut-brain axis, a bidirectional communication system between the gut and the brain mediated by hormonal, immune, and neural signals. Through these interactions, the microbiota might affect behaviors, including feeding behavior, digestive/absorptive processes (e.g., by modulating intestinal motility and the intestinal barrier), metabolism, as well as the immune response, with repercussions on the energy homeostasis and health of the host. To date, research in this field has mostly focused on mammals. Studies on non-mammalian models such as fish may provide novel insights into the specific mechanisms involved in the microbiota-brain-gut axis. This review describes our current knowledge on the possible effects of microbiota on feeding, digestive processes, growth, and energy homeostasis in fish, with emphasis on the influence of brain and gut hormones, environmental factors, and inter-specific differences.

/pdf/gut-microbiota-and-energy-homeostasis-in-fish-20ma2uvxjc.pdf

Gut Microbiota and Energy Homeostasis in Fish.

Fish immunization has been carried out for over 50 years and is generally accepted as an effective method for preventing a wide range of bacterial and viral diseases. Vaccination efforts contribute to environmental, social, and economic sustainability in global aquaculture. Most licensed fish vaccines have traditionally been inactivated microorganisms that were formulated with adjuvants and delivered through immersion or injection routes. Live vaccines are more efficacious, as they mimic natural pathogen infection and generate a strong antibody response, thus having a greater potential to be administered via oral or immersion routes. Modern vaccine technology has targeted specific pathogen components, and vaccines developed using such approaches may include subunit, or recombinant, DNA/RNA particle vaccines. These advanced technologies have been developed globally and appear to induce greater levels of immunity than traditional fish vaccines. Advanced technologies have shown great promise for the future of aquaculture vaccines and will provide health benefits and enhanced economic potential for producers. This review describes the use of conventional aquaculture vaccines and provides an overview of current molecular approaches and strategies that are promising for new aquaculture vaccine development.

https://www.mdpi.com/2076-2607/7/11/569/pdf

A Review of Fish Vaccine Development Strategies: Conventional Methods and Modern Biotechnological Approaches.

Among immunostimulants used in aquaculture, herbal is promising due to their propensities to improve growth performance, fish immunity, and their antimicrobial properties, as they are good alternat...

Herbal Immunomodulators in Aquaculture

Can dietary ginger (Zingiber officinale) alter biochemical and immunological parameters and gene expression related to growth, immunity and antioxidant system in zebrafish (Danio rerio)?

Processed soybean meal ingredients have become an emerging plant-based protein used in aquafeed formulations and have been shown to influence gastrointestinal health and microbiota in cultured species. Two 60-day feeding trials with juvenile rainbow trout (Oncorhynchus mykiss, Walbaum) were conducted to compare the effects of fishmeal (FMC), defatted soybean meal (SBM), bioprocessed soybean meal (BSBM) and commercial soy protein concentrate (CSPC) ingredients on intestinal histology, innate immunity and microbiota profiles. Results indicated no significant differences in intestinal immunoglobulin concentrations (p = .41) or gut leukocyte phagocytosis at day 15 samplings (p = .41). Intestinal lysozyme content was found to be highest at day 60 in the BSBM treatment group (p < .01). No significant differences across treatments were observed in histological profiles at day 0 (p = .75), day 15 (p = .08) and day 60 (p = .22). ANOSIM analysis for microbiota beta diversity showed differences among all treatment groups, with the exception of the high and low levels of BSBM (p = .40). There were also differences observed in the alpha diversity ratios, with significant differences in gut communities among dietary groups as demonstrated by Chao-1 (p < .01) and Shannon indices (p = .02). The incorporation of processed soy-based proteins alters the microbial community composition within the distal intestine, and modulates lysozyme concentrations within the distal intestinal tissues.

Gut histology, immunology and the intestinal microbiota of rainbow trout, Oncorhynchus mykiss (Walbaum), fed process variants of soybean meal

The incorporation of PepSoyGen (PSG), a commercially produced fermented soybean meal product, was evaluated in a 205-d feeding trial. Three isonitrogenous and isocaloric experimental diets containing 0, 35, or 50% PSG and 40, 15, and 0% fish meal, respectively, were fed to Rainbow Trout Oncorhynchus mykiss. The diets containing either 0% or 35% PSG produced similar total tank weight gains, percent gains, and feed conversion ratios and were significantly different from the diets containing 50% PSG at the end of the trial. Mean individual fish lengths and weights were significantly greater in the fish receiving 35% PSG than either of the other two diets. Specific growth rate (SGR) was significantly lower in the 50% PSG treatment, but there was no significant difference in SGR between the other two diets. Viscerosomatic index was significantly lower in the fish fed 35% PSG. Hepatosomatic index was not significantly different among the diets, but fish receiving 50% PSG had a significantly poorer liver...

Rainbow Trout Rearing Performance, Intestinal Morphology, and Immune Response after Long-term Feeding of High Levels of Fermented Soybean Meal

Bacterial coldwater disease, caused by Flavobacterium psychrophilum, remains one of the most significant bacterial diseases of salmonids worldwide. A previously developed and reported live-attenuated immersion vaccine (F. psychrophilum; B.17-ILM) has been shown to confer significant protection to salmonids. To further characterize this vaccine, a series of experiments were carried out to determine the cross-protective efficacy of this B.17-ILM vaccine against 9 F. psychrophilum isolates (representing seven sequence types/three clonal complexes as determined by multilocus sequence typing) in comparison with a wild-type virulent strain, CSF-259-93. To assess protection, 28-day experimental challenges of rainbow trout (Oncorhynchus mykiss) fry were conducted following immersion vaccinations with the B.17-ILM vaccine. F. psychrophilum strains used in challenge trials were isolated from several fish species across the globe; however, all were found to be virulent in rainbow trout. The B.17-ILM vaccine provided significant protection against all strains, with relative percent survival values ranging from 51% to 72%. All vaccinated fish developed an adaptive immune response (as measured by F. psychrophilum-specific antibodies) that increased out to the time of challenge (8 weeks postimmunization). Previous studies have confirmed that antibody plays an important role in protection against F. psychrophilum challenge; therefore, specific antibodies to the B.17-ILM vaccine strain appear to contribute to the cross-protection observed to heterologous strain. The ability of such antibodies to bind to similar antigenic regions for all strains was confirmed by western blot analyses. Results presented here support the practical application of this live-attenuated vaccine, and suggest that it will be efficacious even in aquaculture operations affected by diverse strains of F. psychrophilum.

Assessment of cross-protection to heterologous strains of Flavobacterium psychrophilum following vaccination with a live-attenuated coldwater disease immersion vaccine.

Aquaculture is a rapidly growing global agriculture sector and the importance of fish health has become of upmost importance as production levels and stocking densities increase. Over the past few decades, there have been a large number of immunological investigations on commonly cultured finfish species. Further, new technologies and strategies that embody use of fish immunostimulants, probiotics, and vaccinology rely heavily upon a comprehensive understanding of teleost immune system mechanics. The teleost immune system works in concert to properly recognize, control, and clear aquatic pathogens. Recent findings have exemplified the cooperative efforts of the nonspecific and adaptive branches, and have put forth an emphasis on the importance of the mucosal immune response in all aspects of a mounted immune response. This review provides a generalized overview of the innate and adaptive arms of the fish immune system, and provides highlights of recently published work in the areas of signaling networks and mucosal immune interactions.

/pdf/a-review-of-immune-system-components-cytokines-and-4m2tzybqdr.pdf

Timothy J. Bruce

Papers

A Review of Fish Vaccine Development Strategies: Conventional Methods and Modern Biotechnological Approaches.

Gut histology, immunology and the intestinal microbiota of rainbow trout, Oncorhynchus mykiss (Walbaum), fed process variants of soybean meal

Rainbow Trout Rearing Performance, Intestinal Morphology, and Immune Response after Long-term Feeding of High Levels of Fermented Soybean Meal

Assessment of cross-protection to heterologous strains of Flavobacterium psychrophilum following vaccination with a live-attenuated coldwater disease immersion vaccine.

A Review of Immune System Components, Cytokines, and Immunostimulants in Cultured Finfish Species