Bacterial flora of fishes: A review

Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome

Habitual dietary changes have the potential to induce alterations in the host's gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.

Inclusion of Sorghum in Cyprinus carpio L. Diet: Effects on Growth, Flesh Quality, Microbiota, and Oxidative Status

This study investigates the impact of including sorghum in the diet of the common carp (Cyprinus carpio) on its growth, blood parameters, meat composition, intestinal microbiota, and oxidative stress. Experimental diets with varying sorghum content (0%-V0 or control, 10%-V1, 20%-V2, and 30%-V3) were administered to carp weighing 43 g initially. Notably, in the 30% variant, sorghum entirely replaced corn and barley in the diet. Chemical analysis of sorghum unveiled a protein content of 14% and a fat content of 3.9%. Sorghum inclusion led to a decline in final body weight and weight gain, particularly notable in the V3 group with 30% sorghum. However, other physiological parameters, such as feed conversion ratio, specific growth rate, and organ indices, remained unaffected. Protein and salt content in carp flesh increased with higher sorghum inclusion levels, while hematological parameters showed minimal variations. Analysis of the intestinal microbiota revealed increases in both aerobic and anaerobic bacterial populations with sorghum inclusion. Furthermore, sorghum concentration inversely correlated with glutathione levels and positively correlated with malondialdehyde content, indicating a disruption of antioxidant defense mechanisms and elevated oxidative stress.

Lysin and Lytic Phages Reduce Vibrio Counts in Live Feed and Fish Larvae

Vibrio species are naturally found in estuarine and marine ecosystems, but are also recognized as significant human enteropathogens, often linked to seafood-related illnesses. In aquaculture settings, Vibrio poses a substantial risk of infectious diseases, resulting in considerable stock losses and prompting the use of antimicrobials. However, this practice contributes to the proliferation of antimicrobial-resistant (AMR) bacteria and resistance genes. Our investigation aimed to explore the potential of biological agents such as bacteriophage CH20 and endolysin LysVPp1 in reducing Vibrio bacterial loads in both rotifer and fish larvae. LysVPp1's lytic activity was assessed by measuring absorbance reduction against various pathogenic Vibrio strains. Phage CH20 exhibited a limited host range, affecting only Vibrio alginolyticus GV09, a highly pathogenic strain. Both CH20 and LysVPp1 were evaluated for their effectiveness in reducing Vibrio load in rotifers or fish larvae through short-setting bioassays. Our results demonstrated the significant lytic effect of endolysin LysVPp1 on strains of Vibrio alginolyticus, Vibrio parahaemolyticus, and Vibrio splendidus. Furthermore, we have showcased the feasibility of reducing the load of pathogenic Vibrio in live feed and fish larvae by using a non-antibiotic-based approach, such as lytic phage and endolysin LysVPp1, thus contributing to the progress of a sustainable aquaculture from a One Health perspective.

Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes

The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.

Improvement of water quality with probiotics inclusion during simulated transport of Yellowfin Seabream Acanthopagrus latus larvae

OBJECTIVE

The expansion of marine aquaculture requires the shipment of early life stages from hatcheries to breeding centers. Thus, maintaining water quality parameters during transportation is crucial. This experiment investigated the effects of a commercial probiotic mixture (PM) (consisting of Bacillus licheniformis, Bacillus subtilis, Pediococcus acidilactici, and Lactobacillus acidophilus with a total count of 107  CFU/g) on water quality, bacterial population, and the survival of larvae of Yellowfin Seabream Acanthopagrus latus during a 24-h simulated transportation experiment.

METHODS

To simulate transportation, purified seawater was used as a control and purified seawater supplemented with 3 g of PM was used as the PM48 treatment. For the PM48 treatment, 3 g of PM was added to 1 L of purified seawater and mixed with 200 L of purified seawater 48 h prior to the main experiment.

RESULT

The use of probiotics resulted in an increase in larval survival up to 93.3% compared with 89.85% in the control group. Initial sampling showed a statistically significant difference inNO 2 - levels between the control and PM48 treatments. After transportation, the pH of the control treatment showed a significant decrease. The total number of bacteria and the total number of Vibrio spp. in water and fish larvae showed that within 48 h, the probiotics became the dominant population in the PM48 treatment. After 24 h, water samples and larvae from the control treatment showed a significant increase in bacterial load.

CONCLUSION

The results showed that probiotics can play a significant role in maintaining biotic and abiotic water quality parameters, leading to a better survival rate of larvae during transportation. These findings represent an important step in improving long-distance transport protocols.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Septicemic Outbreak in A Rainbow Trout Intensive Aquaculture System: Clinical Finds, Etiological Agents, and Predisposing Factors

On the 23rd of September 2022, a small intensive aquaculture unit populated with rainbow trout (Oncorhynchus mykiss) reported increased mortality in adults and juvenile fish. The unit comprised 12 enclosed concrete basins with a capacity of ten cubic meters of water, populated with 150 kg of fish each. Fish were subjected to a clinical examination on the site, after which whole fish were harvested for a bacteriological and histopathological examination. Water quality parameters were examined using classic biochemical methods and Fourier Transform Infrared Spectroscopy in order to find out whether the environment in which the fish live is also a predisposing factor that could facilitate different pathogens and induce a state of disease in the fish. Real-time PCR was performed on strains of Aeromonas spp. sampled from the fish to accurately identify the pathogen species. The goal was to accurately identify the problems and predisposing factors that lead to disease outbreaks.

Glutamine improves growth and intestinal health in juvenile hybrid groupers fed high-dose glycinin

Glutamine addition can improve immunity and intestinal development in fish. This study examined the protective roles of glutamine on growth suppression and enteritis induced by glycinin in juvenile hybrid groupers (female Epinephelus fuscoguttatus × male Epinephelus lanceolatus). The experiment set four isonitrogenous and isolipidic trial diets: a diet containing 10% glycinin (11S), 10% of 11S diet supplemented with 1% or 2% alanine-glutamine (1% or 2% Ala-Gln), and a diet containing neither 11S nor Ala-Gln (FM). A feeding trial was conducted in hybrid grouper for 8 weeks. Weight gain and specific growth rates in Groups 1% and 2% Ala-Gln were significantly higher than those of the 11S group but were similar to those of the FM group. The intestinal muscular layer thickness, plica height and width of the 2% Ala-Gln group were significantly higher than those of Group 11S. The enterocyte proliferation efficiency of the 11S group was significantly lower compared to other groups. Compared with the 11S group, Groups 1% and 2% Ala-Gln fish had increased intestinal lysozyme activities, complement 3 and immunoglobulin M as well as cathelicidin contents. The mRNA levels of tnf-α, il-1β, ifn-α, and hsp70 genes were more downregulated in Groups 1% and 2% Ala-Gln than in Group 11S. Compared with FM group, fish from the 11S group had significantly lower mRNA levels of myd88, ikkβ, and nf-κb p65 genes. These three values in the 2% Ala-Gln group were significantly lower than those in Group 11S but not significantly different from those of Group FM. The relative abundance of Vibrio in Group 11S was higher than that in Groups FM and 2% Ala-Gln. Intestinal glutamine, glutaminase, glutamic acid, α-ketoglutarate, malate dehydrogenase and ATP contents were higher in Groups 1% and 2% Ala-Gln than in Group 11S. These results suggest that glutamine is a useful feed additive to enhance growth and intestinal immunity, alleviate inflammation, and modulate gut microbiota in hybrid grouper fed high-dose glycinin.

Impact of Infection with Flavobacterium psychrophilum and Antimicrobial Treatment on the Intestinal Microbiota of Rainbow Trout

The diversity and composition of intestinal microbiota in rainbow trout have been studied using next-generation sequencing (NGS), although few studies have examined the effects of antimicrobials. We evaluated the effect of antibiotics florfenicol and erythromycin and infection with or without Flavobacterium psychrophilum on the intestinal microbiota in rainbow trout juveniles (30–40 g) using NGS. Prophylactic oral antibiotic treatments were administered for 10 days before groups of fish were injected intraperitoneally with virulent F. psychrophilum. Intestinal content (allochthonous bacteria) was collected at day −11, 0, 12, and 24 p.i., and the v3–v4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Before prophylactic treatment, Tenericutes and Proteobacteria were the most abundant phyla identified and Mycoplasma was the most abundant genus. Fish infected with F. psychrophilum had decreased alpha diversity and a high abundance of Mycoplasma. Fish administered florfenicol had increased alpha diversity compared to the control at day 24 p.i., although both florfenicol and erythromycin-treated fish had a higher abundance of potential pathogens, specifically Aeromonas, Pseudomonas, and Acinetobacter. Mycoplasma disappeared after treatment but appeared again after day 24. This study demonstrates that prophylactic oral treatment with antibiotics florfenicol and erythromycin as well as F. psychrophilum infection changed the composition of intestinal microbiota in rainbow trout juveniles that did not recover by day 24 p.i. and further long-term effects on the host need to be investigated.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Using the Gut Microbiome to Assess Stocking Efforts of the Endangered Pallid Sturgeon, Scaphirhynchus albus

The endangered Pallid Sturgeon, Scaphirhynchus albus, has been actively managed to prevent population declines, including stocking of hatchery-raised fish. The gut microbiome plays an innate role in an organism's absorption of nutrients by increasing nutrient availability and can provide new insights for Pallid Sturgeon management. In this study, the Pallid Sturgeon's microbiome is dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. It was also determined that the gut bacterial diversity in hatchery-raised Pallid Sturgeon was not significantly different from wild Pallid Sturgeon, supporting that hatchery-raised Pallid Sturgeon are transitioning effectively to wild diets. There is also a high degree of intraspecific variation in the bacterial and eukaryotic sequences amongst individual Pallid Sturgeon microbiomes, suggesting the Pallid Sturgeon may be omnivorous. This study demonstrated that genetic markers may be used to effectively describe the dietary requirements for wild Pallid Sturgeon and provides the first genetic evidence that Pallid Sturgeons are effectively transitioning from hatchery-raised environments to the wild.

Identification of New Amylolytic Enzymes from Marine Symbiotic Bacteria of Bacillus Species

α-amylases are one of the most common and important industrial enzymes widely used in various industries. The present study was conducted with the aim of isolating and identifying symbiotic α-amylase enzyme-producing bacteria in the intestine of Silago Sihama and Rasterliger Canagorta fish living in Qeshm Island, Hormozgan. The intestinal symbiotic bacteria of these species were isolated using nutrient agar culture medium; then, α-amylase producing bacteria were screened using a special culture medium containing starch and the Lugol’s solution test. The α-amylase enzyme activity of enzyme-producing bacteria was measured using the starch substrate. Finally, bacteria with the highest enzyme activity were selected and identified by the 16S rRNA gene sequence analysis. The results showed that out of 22 isolated bacteria, 10 were able to grow in a special culture medium, and 5 strains of these 10 bacteria had the ability to produce relatively stronger halos. The four bacterial strains belonging to the genus Bacillus that had the highest α-amylase enzyme activity were identified and registered in the NCBI gene database as B. subtilis strains HR13, HR14, HR15, and HR16. Among these four strains, two strains of B. subtilis, HR13 and HR16, displayed high enzyme activity and maximum activity at 60 °C at pH values of 5 and 7, respectively. α-Amylase enzymes isolated from marine symbiotic bacteria of Bacillus species can be considered potential candidates for application in various industries.

Isolation and identification of major bacteria from three Ethiopian rift valley lakes live and processed fish, and water samples: implications in sanitary system of fish products

Bacterial pathogens are a great threat to fish production. Gram-negative bacteria are among the major bacterial fish pathogens and are zoonotic with the potential to infect humans. This cross-sectional study was conducted to isolate and identify major gram-negative bacteria from live and processed fish, and water samples from Lakes Hawassa, Langanoo and Ziway. A total of 674 different types of samples: 630 tissue samples (210 samples for each intestine, Kkidney and liver collected from 210 live fish (Oreochromis niloticus, Cyprinus carpio and Clarias gariepinus), 20 processed fish samples from lake Ziway fish processing center and 24 lake water samples were included in the study from each lake. The mean values of pH, temperature, dissolved oxygen and nitrate in all water samples were within the normal range at which most freshwater fish species become non-stressed. Of a total of 674 samples included in the study, bacteria were isolated from 154(22.8%) samples with significant difference (P < 0.05) observed in some isolates with respect to sample origin. Of these 154 isolates, 103(66.8%) isolates were gram-negative bacteria consisting of 15 species based on morphology and a range of biochemical tests. From live fish samples, Escherichia coli was the dominant species with 15 isolates followed by Edwardsiella tarda (12), Salmonella Paratyphi (10), Salmonella Typhi (9),  Shigella dysenteriae (7), Shigella flexneri (7), Klebsiella pneumonia (7), Enterobacter aerogenes (6), Enterobacter cloacae (5), Pseudomonas aeruginosa (5), Vibrio parahemolyticus (5), Aeromonas sobria (4), Citrobacter freundii (4), Citrobacter koseri (4) and Plesiomonas shigelloides (3). The detection of the common fecal coliforms (E. coli, K. pneumoniae and E. aerogenes) and Salmonella spp. in processed fish indicates the potential danger of passage of pathogenic bacteria and/or their poisons to humans via infected and/or contaminated fish products. Human infection by pathogenic fish bacteria and food poisoning is possible through contamination of fish product in fish production chain due to inadequate handling, poor hygiene and contact with contaminated water. Therefore, producers, consumers and all other stakeholders need to be cautious during handling, processing and consumption of fish harvested from the study lakes.

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure

AIMS

We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides.

METHODS AND RESULTS

Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures.

CONCLUSIONS

Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.

Biotherapeutic microbial supplementation for ameliorating fish health: developing trends in probiotics, prebiotics, and synbiotics use in finfish aquaculture

Nutrition demands in aquaculture can be realized through quality aquafeeds as compounded diets that contribute to the growth and health of aquaculture species. Functional additives in feed, notably probiotics, prebiotics, and their admixture synbiotics, have been recently recognized for their biotherapeutic role as immunostimulants capable of conferring disease resistance, stress tolerance, and gastrointestinal health; counteracting the negative effects of anti-nutrients, pathogenic prevalence, and antimicrobials in finfish aquaculture. Formulated diets based on probiotics, prebiotics, and as a supplemental combination for synbiotics can significantly influence fish gut microbiomes, establishing the modalities of microbial dynamics to maximize host-associated benefits. These microbial functional-feed supplements are acclaimed to be biocompatible, biodegradable, and safe for dietary consumption as well as the environment. In fed fish aquaculture, prebiotic appended probiotic diet 'synbiotic' has propounded larger attention for its additional health and nutritional benefits. Synbiotic, prebiotic, and probiotic usage as functional feeds for finfish aquaculture thus provides promising prospects. Developing trends in their intended application are reviewed here forth.

Gut and Gill-Associated Microbiota of the Flatfish European Plaice (Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens

Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.

Gut Microbiome as a Potential Biomarker in Fish: Dietary Exposure to Petroleum Hydrocarbons and Metals, Metabolic Functions and Cytokine Expression in Juvenile Lates calcarifer

The gut microbiome of fish contains core taxa whose relative abundances are modulated in response to diet, environmental factors, and exposure to toxicogenic chemicals, influencing the health of the host fish. Recent advances in genomics and metabolomics have suggested the potential of microbiome analysis as a biomarker for exposure to toxicogenic compounds. In this 35-day laboratory study, 16S RNA sequencing and multivariate analysis were used to explore changes in the gut microbiome of juvenile Lates calcarifer exposed to dietary sub-lethal doses of three metals: vanadium (20 mg/kg), nickel (480 mg/kg), and iron (470 mg/kg), and to two oils: bunker C heavy fuel oil (HFO) (1% w/w) and Montara, a typical Australian medium crude oil (ACO) (1% w/w). Diversity of the gut microbiome was significantly reduced compared to negative controls in fish exposed to metals, but not petroleum hydrocarbons. The core taxa in the microbiome of negative control fish comprised phyla Proteobacteria (62%), Firmicutes (7%), Planctomycetes (3%), Actinobacteria (2%), Bacteroidetes (1%), and others (25%). Differences in the relative abundances of bacterial phyla of metal-exposed fish were pronounced, with the microbiome of Ni-, V-, and Fe-exposed fish dominated by Proteobacteria (81%), Firmicutes (68%), and Bacteroidetes (48%), respectively. The genus Photobacterium was enriched proportionally to the concentration of polycyclic aromatic hydrocarbons (PAHs) in oil-exposed fish. The probiotic lactic acid bacterium Lactobacillus was significantly reduced in the microbiota of fish exposed to metals. Transcription of cytokines IL-1, IL-10, and TNF-a was significantly upregulated in fish exposed to metals but unchanged in oil-exposed fish compared to negative controls. However, IL-7 was significantly downregulated in fish exposed to V, Ni, Fe, and HFOs. Fish gut microbiome exhibits distinctive changes in response to specific toxicants and shows potential for use as biomarkers of exposure to V, Ni, Fe, and to PAHs present in crude oil.

Soybean β-conglycinin and glycinin reduced growth performance and the intestinal immune defense and altered microbiome in juvenile pearl gentian groupers Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂

The utilization efficiency of soy protein is affected by its 2 anti-nutritional substances-the antigens β-conglycinin and glycinin. This study investigated their effects on the growth performance, intestinal immune defense, and microbiome in juvenile pearl gentian groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂). Three isonitrogenous and isolipidic diets were formulated containing fishmeal supplemented with 70 g/kg β-conglycinin or 100 g/kg glycinin, or no supplementation (control). Each experimental diet was fed to quadruplicate groups with 30 fish in each tank for 8 weeks. Dietary inclusion of either β-conglycinin or glycinin significantly reduced weight gain and specific growth rates, and cell proliferation of the distal intestine. Histological evaluation of the intestine tract revealed the inflammation signs, characterized by reducing of plica height and width as well as the number of the goblet cells, and widening of the lamina propria. The group fed the β-conglycinin diet had reduced lysozyme activity, contents of immunoglobulin M and complements 3 and 4. Increased activities of caspase-3 and -9 were observed in the group fed the β-conglycinin diet compared to the other 2 groups. In the intestinal microbiota, the relative abundances of the potentially pathogenic genera Photobacterium and Vibrio were significantly higher in the glycinin group than those in others. Therefore, the existence of soybean antigens (β-conglycinin or glycinin) could damage the structural integrity of the intestine, reduce immune defense, reshape the intestinal microbiome and, ultimately, impair growth in fish.

Gastrointestinal Microbiota of Spiny Lobster: A Review

The gastrointestinal (GI) microbiota is a group of complex and dynamic microorganisms present in the GI tract of an organism that live in symbiosis with the host and benefit the host with various biological functions. The communities of GI microbiota are formed by various aerobic, anaerobic, and facultatively anaerobic bacteria in aquatic species. In spiny lobsters, common GI microorganisms found in the GI tract are Vibrio, Pseudomonas, Bacillus, Micrococcus, and Flavobacterium, where the structure and abundance of these microbes are varied depending on the environment. GI microbiotas hold an important role and significantly affect the overall condition of spiny lobsters, such as secreting digestive enzymes (lipase, protease, and cellulase), helping in digesting food intake, providing nutrition and synthesising vitamins needed by the host system, and protecting the host against infection from pathogens and diseases by activating an immune mechanism in the GI tract. The microorganisms in the water column, sediment, and diet are primarily responsible for altering, manipulating, and shaping GI microbial structures and communities. This review also highlights the possibilities of isolating the indigenous GI microbiota as a potential probiotic strain and introducing it to spiny lobster juveniles and larvae for better health management.

Prevalence and Antimicrobial Resistance of Bacteria Isolated from Marine and Freshwater Fish in Tanzania

This study aimed to determine the prevalence and antimicrobial resistance of bacteria isolated from retail fish and shrimp in Tanzania. A total of 92 fish and 20 shrimp samples were analyzed. Fish samples consisted of 24 Nile tilapia, 24 Nile perch, and 24 red snapper. The isolates were identified by their morphological characteristics, conventional biochemical tests, and analytical profile index test kits. The antibiotic susceptibility of selected bacteria was determined by the disc diffusion method. Out of the 92 samples analyzed, 96.7% were contaminated with 7 different bacterial species. E. coli was the most prevalent bacteria (39%), followed by Klebsiella spp. (28%) and Salmonella spp. (16%). Other species isolated from this study were Staphylococcus spp. (8%), Citrobacter (4%), Shigella spp. (3%), and Pseudomonas spp. (1%). All samples were analyzed for Campylobacter spp.; however, none of the samples tested were positive for Campylobacter spp. Fish from the open-air market were contaminated by six bacterial species: E. coli (40%), Klebsiella spp. (26%), Salmonella spp. (24%), Shigella spp. (6.7%), Citrobacter spp. (6.5%), and Pseudomonas spp. (2%), while E. coli (37%), Klebsiella spp. (33%), Staphylococcus spp. (23%), and Shigella spp. (2%) were isolated in supermarket samples. According to the International Commission on Microbiological Specifications for Foods criteria, 54 (58.7%) and 38 (41.3%) samples were good and marginally acceptable, respectively. E. coli isolates were resistant to penicillin (PEN), erythromycin (ERY), gentamicin (GEN), azithromycin (AZM), and tetracycline (TET), while Salmonella spp. isolates exhibited resistance to gentamicin (CN), tetracycline (TET), penicillin (PEN), and erythromycin (ERY). These results suggest that the presence of these bacteria might cause a health risk/hazard to human beings and may cause disease to susceptible individuals, especially immune-compromised consumers.

Isolation and identification of proteolytic lactic-acid bacteria of the common carp (Cyprinus carpio) by spontaneous fermentation to obtain functional peptides

High proteolytic activity and several biological functions (antimicrobial, antioxidant, antihypertensive, among others) have been attributed to lactic-acid bacteria (LAB) isolated from fish and peptides obtained from proteolysis. Therefore, the objective of this research was isolating, characterizing, and identifying LAB with proteolytic activity by spontaneous fermentation from common carp (Cyprinus carpio) reared in ponds and wild ones obtained from Lago de Chapala, Jalisco, Mexico. Spontaneous fermentation from complete carp specimens was observed, considering two sampling points (skin and intestines) at 15 °C at 5 and 10 days. Isolated LAB-from both reared and wild specimens-were identified and morphologically characterized; identification was performed by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Proteolytic activity was assessed by the presence of the proteolytic halo. A total of five genera and eight different LAB proteolytic species were isolated from all the carp samples. At 10 days, greater proteolytic LAB diversity was obtained from the intestine (Tukey's, p < 0.05); the proteolytic halo with the greatest diameter was recorded in wild carp skin with Lactiplantibacillus plantarum S5P2 (2.8 cm) at 5 days of fermentation, followed by Leuconostoc mesenteroides S5I1 (2.73 cm) and Leuconostoc pseudomesenteroides S5P2 (2.66 cm) (p < 0.05). In conclusion, proteolytic capability of LAB isolated from carp (Cyprimus carpio)-both wild and reared-is influenced by the ecosystem where they develop. These proteolytic LAB may be used in biotechnological industries to obtain bioactive peptides by fermenting substrates rich in proteins.

Environmental Water and Sediment Microbial Communities Shape Intestine Microbiota for Host Health: The Central Dogma in an Anthropogenic Aquaculture Ecosystem

From increasing evidence has emerged a tight link among the environment, intestine microbiota, and host health status; moreover, the microbial interaction in different habitats is crucial for ecosystems. However, how the environmental microbial community assembly governs the intestinal microbiota and microbial communities of multiple habitats contribute to the metacommunity remain elusive. Here, we designed two delicate experiments from temporal and spatial scales in a shrimp culture pond ecosystem (SCPE). Of the SCPE metacommunity, the microbial diversity was mainly contributed to by the diversity of^–β_{IntraHabitats} and β_{InterHabitats}, and water and sediment communities had a large contribution to the shrimp intestine community as shown by SourceTracker and Sloan neutral community model analyses. Also, phylogenetic bin-based null model results show that microbial assembly of three habitats in the SCPE appeared to be largely driven by stochastic processes. These results enrich our understanding of the environment–intestinal microbiota–host health closely linked relationship, making it possible to be the central dogma for an anthropogenic aquaculture ecosystem. Our findings enhance the mechanistic understanding of microbial assembly in the SCPE for further analyzing metacommunities, which has important implications for microbial ecology and animal health.

Identification of Chemicals Associated Gambusia affinis (Cyprinodontiformes: Poeciliidae), and Their Effect on Oviposition Behavior of Culex tarsalis (Diptera: Culicidae) in the Laboratory

The western mosquitofish, Gambusia affinis (Baird & Girard), has been used worldwide for the control of larval mosquitoes for more than 100 yr. We found that the western encephalitis mosquito, Culex tarsalis Coquillett (Diptera: Culicidae), can detect the presence of G. affinis in oviposition sites based on associated chemicals, leading to a decrease in the number of egg rafts laid. Three volatile chemical compounds were identified in the headspace above the water where G. affinis had been held for 24 h. Oviposition bioassays conducted using standards of the volatile compounds identified (dimethyl disulfide [DMDS], dimethyl trisulfide [DMTS], and S-methyl methanethiosulphonate) found that females reduced oviposition only when low concentrations of DMTS were present, but this response was not consistent across all trials and concentrations tested. DMDS, DMTS, and S-methyl methanethiosulphonate are known bacterial metabolic waste products and may be the source of the compounds. Two nonvolatile compounds of interest were found to be present in the Gambusia-exudate water. After tasting Cx. tarsalis were deterred from ovipositing onto Gambusia-treated water from which the bacteria had been removed by filtration, indicating that the kairomone may consist of nonvolatile compound(s). One of the nonvolatile compounds isolated from the Gambusia-treated water has a benzene ring structure similar to that of cholesterol but the structure of the two nonvolatile deterrents remains to be fully characterized. Our research shows that three volatile compounds and two nonvolatile compounds are present in water associated with G. affinis (Poeciliidae: Gambusia) and affect the oviposition behavior of Cx. tarsalis in laboratory bioassays.

Aeromonas sobria regulates proinflammatory immune response in mouse macrophages via activating the MAPK, AKT, and NF-κB pathways

Aeromonas sobria, a Gram-negative bacterium that can colonize both humans and animals, is found in a variety of environments, including water, seafood, meat, and vegetables (Cahill, 1990; Galindo et al., 2004; Song et al., 2019). Aeromonas spp. are conditionally pathogenic bacteria in aquaculture, which can rapidly proliferate, causing disease and even death in fish, especially when the environment is degraded (Neamat-Allah et al., 2020, 2021a, 2021b). In developing countries, Aeromonas spp. have been associated with a wide spectrum of infections in humans, including gastroenteritis, wound infections, septicemia, and lung infections (San Joaquin and Pickett, 1988; Wang et al., 2009; Su et al., 2013). Infections caused by Aeromonas spp. are usually more severe in immunocompromised individuals (Miyamoto et al., 2017). The presence of a plasmid encoding a β‍-lactamase in A. sobria that confers resistance to β-lactam antibiotics poses a huge challenge to the treatment of diseases caused by this microorganism (Lim and Hong, 2020). Consequently, an in-depth understanding of the interaction between A. sobria and its hosts is urgently required to enable the development of effective strategies for the treatment of A. sobria infections.

Aeromonas sobria Induces Proinflammatory Cytokines Production in Mouse Macrophages via Activating NLRP3 Inflammasome Signaling Pathways

Aeromonas sobria, a common conditional pathogenic bacteria, is widely distributed in the environment and causes gastroenteritis in humans or septicemia in fish. Of all Aeromonas species, A. sobria is the most frequently isolated from human infections especially in immunocompromised subjects. Innate immunity is the first protection system of organism to resist non-specific pathogens invasion; however, the immune response process of hosts against A. sobria infection re\mains unexplored. The present study established an A. sobria infection model using primary mouse peritoneal macrophages (PMφs). The adherence and cytotoxicity of A. sobria on PMφs were determined by May-Grünwald Giemsa staining and LDH release measurement. Pro-inflammatory cytokine expression levels were measured using qPCR, western blotting, and ELISA methods. We also investigated the levels of ASC oligomerization and determined the roles of active caspase-1 in IL-1β secretion through inhibition assays and explored the activated pattern recognition receptors through immunofluorescence. We further elucidated the roles of activated inflammasome in regulating the host's inflammatory response through inhibition combined with ELISA assays. Our results showed that A. sobria induced lytic cell death and LDH release, whereas it had no adhesive properties on PMφs. A. sobria triggered various proinflammatory cytokine transcription level upregulation, and IL-1β occupied the highest levels. The pro-IL-1β protein expression levels increased in a dose-dependent manner with MOI ranging from 1 to 100. This process was regulated by ASC-dependent inflammasome, which cleavage pro-IL-1β into active IL-1β p17 with activated caspase-1 p20. Meanwhile, the expression levels of NLRP3 receptor significantly increased, location analysis revealed puncta-like surrounding nuclear, and inhibition of NLRP3 inflammasome downregulated caspase-1 activation and IL-1β secretion. Blocking of NLRP3 inflammasome activation through K⁺ efflux and cathepsin B or caspase approaches downregulated A. sobria-induced proinflammatory cytokine production. Overall, these data indicated that A. sobria induced proinflammatory cytokine production in PMφs through activating NLRP3 inflammasome signaling pathways.

A Slimy Business: the Future of Fish Skin Microbiome Studies

Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.

Taxonomic and Functional Characteristics of the Gill and Gastrointestinal Microbiota and Its Correlation with Intestinal Metabolites in NEW GIFT Strain of Farmed Adult Nile Tilapia (Oreochromis niloticus)

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

Characterization of the microbiota of commercially traded finfish fillets

The profile of human gut microbiota is known to be affected by diet and is linked to human health. Seafood is a highly consumed food and it accounts for a large proportion of food-borne illness. The objective of this study is to characterise the microbiota of fish fillets of various species sold in the Canadian market. We test 19 fish fillet samples from nine species in five fish families, ten of which were previously determined to be mislabeled as different species. The microbiota profiles were characterized using 16S rRNA gene high-throughput sequencing. Despite the complexities of the supply chain to produce these fillets, the major microbial groups were fairly consistent across samples. Significant differences in microbial taxa were observed between species, families, and based on labelling accuracy. Several putative spoilage and putative pathogenic taxa were identified. Studying food-associated microbiota can provide comprehensive information on food safety, authenticity, and traceability.

Bacterial biomechanics-From individual behaviors to biofilm and the gut flora

Bacteria inhabit a variety of locations and play important roles in the environment and health. Our understanding of bacterial biomechanics has improved markedly in the last decade and has revealed that biomechanics play a significant role in microbial biology. The obtained knowledge has enabled investigation of complex phenomena, such as biofilm formation and the dynamics of the gut flora. A bottom-up strategy, i.e., from the cellular to the macroscale, facilitates understanding of macroscopic bacterial phenomena. In this Review, we first cover the biomechanics of individual bacteria in the bulk liquid and on surfaces as the base of complex phenomena. The collective behaviors of bacteria in simple environments are next introduced. We then introduce recent advances in biofilm biomechanics, in which adhesion force and the flow environment play crucial roles. We also review transport phenomena in the intestine and the dynamics of the gut flora, focusing on that in zebrafish. Finally, we provide an overview of the future prospects for the field.

Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health

Background

Tor putitora, the largest freshwater fish of the Indian subcontinent, is an endangered species. Several factors have been attributed towards its continuous population decrease, but very little is known about the gut microbiome of this fish. Also, the fish gut microbiome serves as a reservoir of virulence factors and antibiotic resistance determinants. Therefore, the shotgun metagenomic approach was employed to investigate the taxonomic composition and functional potential of microbial communities present in the gut of Tor putitora, as well as the detection of virulence and antibiotic resistance genes in the microbiome.

Results

The analysis of bacterial diversity showed that Proteobacteria was predominant phylum, followed by Chloroflexi, Bacteroidetes, and Actinobacteria. Within Proteobacteria, Aeromonas and Caulobacter were chiefly present; also, Klebsiella, Escherichia, and plant symbionts were noticeably detected. Functional characterization of gut microbes endowed the virulence determinants, while surveillance of antibiotic resistance genes showed the dominance of β-lactamase variants. The antibiotic-resistant Klebsiella pneumoniae and Escherichia coli pathovars were also detected. Microbial genome reconstruction and comparative genomics confirmed the presence of Aeromonads, the predominant fish pathogens.

Conclusions

Gut microbiome of endangered Tor putitora consisted of both commensals and opportunistic pathogens, implying that factors adversely affecting the non-pathogenic population would allow colonization and proliferation of pathogens causing diseased state in asymptomatic Tor putitora. The presence of virulence factors and antibiotic resistance genes suggested the potential risk of dissemination to other bacteria due to horizontal gene transfer, thereby posing a threat to fish and human health. The preservation of healthy gut microflora and limited use of antibiotics are some of the prerequisites for the conservation of this imperilled species.

A non-invasive method to monitor marine pollution from bacterial DNA present in fish skin mucus

Marine coastal contamination caused by human activity is a major issue worldwide. The implementation of effective pollution monitoring programs, especially in coastal areas, is important and urgent. The use of biological, physiological, or biochemical measurements to monitor the impacts of pollution has garnered increasing interest, particularly for the development of new non-invasive tools to assess water pollution. Fish skin mucus is in direct contact with the marine environment, making it a favourable microenvironment for the formation of biofilm bacterial communities. In this study, we developed a non-invasive technique, sampling fish skin mucus to determine and analyse bacterial community composition using next-generation sequencing. We hypothesised that bacterial communities associated with the skin mucus of a common harbour benthic blennioid triplefin fish, Forsterygion capito, would reflect conditions of different marine environments. We detected clear differences in bacterial community alpha-diversity between contaminated and reference sites. Beta-diversity analysis also revealed differences in the bacterial community structure of the skin mucus of fish inhabiting different geographical areas. The relative abundance of different bacterial orders varied among sites, as determined by linear discriminant analysis (LDA) and effect size (LEfSe) analyses. The observed variation in bacterial community compositions correlated more strongly with variation in hydrocarbons than to various metal concentrations. Using advanced DNA sequencing technologies, we have developed a novel non-invasive, low-cost and effective tool to monitor the impacts of pollution through analysis of the bacterial communities associated with fish skin mucus.

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus

Coilia nasus is influenced by various external pressures during spawning migration and these anadromous transitions can lead to specific gut microbiome characteristics that affecting the host biological process. Therefore, the purpose of this study was to determine the variations of components and functions in the gut prokaryotic microbiome during spawning migration as well as the key factors that triggered the changes. The gut microbiome in C. nasus was mainly consisted of Proteobacteria, Bacteroidetes, Firmicutes, Deinococcus-Thermus and Fusobacteria via 16S rRNA Gene Amplicon Sequencing. The relative abundance of Acinetobacter and Clostridium increased, while Corynebacterium, Actinomyces, Bacillus, Klebsiella and Ochrobactrum decreased after entering freshwater, indicated the preference of C. nasus gut microbial members transferred from seawater to freshwater. Additionally, the proportion of Firmicutes significantly decreased and then increased, as well as the arise of some soil bacteria in gut, corresponding to the phenomenon that C. nasus are fasting during the upstream process and refeeding after entering the spawning grounds. The function prediction of gut microbiome was also consistent with the above results. The present study generally demonstrated the gut microbiome dynamics and the significant correlation between the gut microbiome and salinity and feeding behavior in the spawning migration of C. nasus.

Specific pathogens and microbial abundance within liver and kidney tissues of wild marine fish from the Eastern Mediterranean Sea

This study is an initial description and discussion of the kidney and liver microbial communities of five common fish species sampled from four sites along the Eastern Mediterranean Sea shoreline. The goals of the present study were to establish a baseline dataset of microbial communities associated with the tissues of wild marine fish, in order to examine species-specific microbial characteristics and to screen for candidate pathogens. This issue is especially relevant due to the development of mariculture farms and the possible transmission of pathogens from wild to farmed fish and vice versa. Although fish were apparently healthy, 16S rRNA NGS screening identified three potential fish bacterial pathogens: Photobacterium damselae, Vibrio harveyi and Streptococcus iniae. Based on the distribution patterns and relative abundance, 16 samples were classified as potential pathogenic bacteria-infected samples (PPBIS). Hence, PPBIS prevalence was significantly higher in kidneys than in liver samples and variation was found between the fish species. Significant differences were observed between fish species, organs and sites, indicating the importance of the environmental conditions on the fish microbiome. We applied a consistent sampling and analytical method for monitoring in long-term surveys which may be incorporated within other marine fish pathogens surveys around the world.

Innate Immune Responses of Skin Mucosa in Common Carp (Cyprinus Carpio) Fed a Diet Supplemented with Galactooligosaccharides

Galactooligosaccharides (GOS) are well-known immunomodulatory prebiotics. We hypothesize that GOS supplemented in feed modulates innate immune responses in the skin-associated lymphoid tissue (SALT) of common carp. The aim of this study was to determine the impact of GOS on mRNA expression of the immune-related genes in skin mucosa. During the feeding trial, the juvenile fish (bodyweight 180 ± 5 g) were fed two types of diet for 50 days: control and supplemented with 2% GOS. At the end of the trial, a subset of fish was euthanized (n = 8). Skin mucosa was collected, and RNA was extracted. Gene expression analysis was performed with RT-qPCR to determine the mRNA abundance of the genes associated with innate immune responses in SALT, i.e., acute-phase protein (CRP), antimicrobial proteins (His2Av and GGGT5L), cytokines (IL1β, IL4, IL8, IL10, and IFNγ), lectin (CLEC4M), lyzosymes (LyzC and LyzG), mucin (M5ACL), peroxidase (MPO), proteases (CTSB and CTSD), and oxidoreductase (TXNL). The geometric mean of 40s s11 and ACTB was used to normalize the data. Relative quantification of the gene expression was calculated with ∆∆Ct. GOS upregulated INFγ (p ≤ 0.05) and LyzG (p ≤ 0.05), and downregulated CRP (p ≤ 0.01). We conclude that GOS modulates innate immune responses in the skin mucosa of common carp.

Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

BACKGROUND

Increased inclusion of plant proteins in aquafeeds has become a common practice due to the high cost and limited supply of fish meal but generally leads to inferior growth performance and health problems of fish. Effective method is needed to improve the plant proteins utilization and eliminate their negative effects on fish. This study took a unique approach to improve the utilization of soybean meal (SBM) by fish through autochthonous plant-degrading microbe isolation and subsequent fermentation.

RESULTS

A strain of Shewanella sp. MR-7 was isolated and identified as the leading microbe that could utilize SBM in the intestine of turbot. It was further optimized for SBM fermentation and able to improve the protein availability and degrade multiple anti-nutritional factors of SBM. The fishmeal was able to be replaced up to 45% by Shewanella sp. MR-7 fermented SBM compared to only up to 30% by SBM in experimental diets without adverse effects on growth and feed utilization of turbot after feeding trials. Further analyses showed that Shewanella sp. MR-7 fermentation significantly counteracted the SBM-induced adverse effects by increasing digestive enzymes activities, suppressing inflammatory responses, and alleviating microbiota dysbiosis in the intestine of turbot.

CONCLUSIONS

This study demonstrated that plant protein utilization by fish could be significantly improved through pre-digestion with isolated plant-degrading host microbes. Further exploitation of autochthonous bacterial activities should be valuable for better performances of plant-based diets in aquaculture.

Using poly(β-hydroxybutyrate-β-hydroxyvalerate) as carbon source in biofloc-systems: Nitrogen dynamics and shift of Oreochromis niloticus gut microbiota

Inorganic‑nitrogen removal is essential for the sustainable operation of aquaculture industry and also influences the health of aquatic animals, which may be accomplished by utilizing biofloc technology. In this paper, we studied the use of three different carbon sources 1) longan seed powder (LP), 2) Poly(β-hydroxybutyrate-β-hydroxyvalerate) (PHBV) and 3) synthesized PHBV and LP (PHBVL) in biofloc systems for 90days to investigate the nitrogen dynamics and gut microbiota of Nile tilapia (Oreochromis niloticus). The PHBVL and PHBV groups had higher total inorganic‑nitrogen removal efficiencies (70.99±19.45% and 63.54±19.44%) than the LP group (35.02±11.21%), which had an accumulation of nitrate. Meanwhile, the biofloc in PHBVL and PHBV group generally had a higher amino acid composition, particularly for methionine and lysine, but was not reflected in the tilapia muscle. High-throughput sequencing indicated that the different carbohydrates shaped different bacterial community compositions in the fish gut after exposure in the three environments for 90-day. These differences, which resulted in different gut digestive enzyme activities (amylase, lipase and trypsin), and growth performance, which the food conversion ratio in the PHBVL group was lower than LP and PHBV group, the final body weight in PHBVL group was average 4.33% and 3.65% bigger than in LP and PHBV group. Network analysis revealed that the keystone taxa (90.33%) were Proteobacteria, Chloroflexi, Actinobacteria, Planctomycetes, Verrucomicrobia and Bacteroidetes, which relative abundance varied in the fish gut in the three groups. The experiment verified the feasibility and advantage to use biodegradable polymers (BDPs) as carbohydrates for biofloc systems.

Influence of chitosan nanoparticles and fennel essential oils (Foeniculum vulgare) on the shelf life of Huso huso fish fillets during the storage

Fish and fishery products are important parts of the human diet, but the microbial, chemical, and physical deteriorations limit their shelf life. Using the modified atmospheric packaging system and edible coatings is one of the main procedures to improve the shelf life of fish. In this research, the effect of chitosan nanoparticles (CNPs) loaded with fennel essential oils along with modified atmosphere packaging (MAP) system on chemical, microbial, and sensorial properties of Huso huso fish fillets during storage at fridge were evaluated. The results showed that coating fish fillets with CNPs and fennel EO significantly reduced the peroxide value, total volatile nitrogen, and thiobarbituric acid value compared with the control samples. Microbial analyses showed a lower number of mesophilic, psychotropic, pseudomonas, and lactic acid bacteria in coated fillets compared with control and MAP packaging. Fish fillets coated with CNPs and EO showed high acceptability in all sensorial attribute through the storage. It can be concluded that using CNPs and fennel EO along with MAP packaging can enhance the shelf life for H. huso fillets up to 18 days in the fridge.

The Farmed Atlantic Salmon (Salmo salar) Skin-Mucus Proteome and Its Nutrient Potential for the Resident Bacterial Community

Norway is the largest producer and exporter of farmed Atlantic salmon (Salmo salar) worldwide. Skin disorders correlated with bacterial infections represent an important challenge for fish farmers due to the economic losses caused. Little is known about this topic, thus studying the skin-mucus of Salmo salar and its bacterial community depict a step forward in understanding fish welfare in aquaculture. In this study, we used label free quantitative mass spectrometry to investigate the skin-mucus proteins associated with both Atlantic salmon and bacteria. In particular, the microbial temporal proteome dynamics during nine days of mucus incubation with sterilized seawater was investigated, in order to evaluate their capacity to utilize mucus components for growth in this environment. At the start of the incubation period, the largest proportion of proteins (~99%) belonged to the salmon and many of these proteins were assigned to protecting functions, confirming the defensive role of mucus. On the contrary, after nine days of incubation, most of the proteins detected were assigned to bacteria, mainly to the genera Vibrio and Pseudoalteromonas. Most of the predicted secreted proteins were affiliated with transport and metabolic processes. In particular, a large abundance and variety of bacterial proteases were observed, highlighting the capacity of bacteria to degrade the skin-mucus proteins of Atlantic salmon.

Trivalent Phosphorus and Phosphines as Components of Biochemistry in Anoxic Environments

Phosphorus is an essential element for all life on Earth, yet trivalent phosphorus (e.g., in phosphines) appears to be almost completely absent from biology. Instead phosphorus is utilized by life almost exclusively as phosphate, apart from a small contingent of other pentavalent phosphorus compounds containing structurally similar chemical groups. In this work, we address four previously stated arguments as to why life does not explore trivalent phosphorus: (1) precedent (lack of confirmed instances of trivalent phosphorus in biochemicals suggests that life does not have the means to exploit this chemistry), (2) thermodynamic limitations (synthesizing trivalent phosphorus compounds is too energetically costly), (3) stability (phosphines are too reactive and readily oxidize in an oxygen (O₂)-rich atmosphere), and (4) toxicity (the trivalent phosphorus compounds are broadly toxic). We argue that the first two of these arguments are invalid, and the third and fourth arguments only apply to the O₂-rich environment of modern Earth. Specifically, both the reactivity and toxicity of phosphines are specific to aerobic life and strictly dependent on O₂-rich environment. We postulate that anaerobic life persisting in anoxic (O₂-free) environments may exploit trivalent phosphorus chemistry much more extensively. We review the production of trivalent phosphorus compounds by anaerobic organisms, including phosphine gas and an alkyl phosphine, phospholane. We suggest that the failure to find more such compounds in modern terrestrial life may be a result of the strong bias of the search for natural products toward aerobic organisms. We postulate that a more thorough identification of metabolites of the anaerobic biosphere could reveal many more trivalent phosphorus compounds. We conclude with a discussion of the implications of our work for the origin and early evolution of life, and suggest that trivalent phosphorus compounds could be valuable markers for both extraterrestrial life and the Shadow Biosphere on Earth.

Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

AIMS

The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss).

METHODS AND RESULTS

From July to September 2015, 29 specimens of 3-year-old (an average weight from 240·9 ± 37·7 to 850·7 ± 70·1 g) rainbow trout O. mykiss were studied. Next-generation high-throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout O. mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities test revealed the significant dissimilarity between the microbiota of stomach and intestine (P ≤ 0·05).

CONCLUSIONS

A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co-infections and can be useful for the development of new strategies for disease control programs.

An evaluation of microalgae as a recombinant protein oral delivery platform for fish using green fluorescent protein (GFP)

Recombinant proteins produced by biological systems such as bacteria, yeasts, mammalian and insect cell cultures are widely used for clinical or industrial purposes. Most therapeutic protein drugs require purification, cold chain, and injection, which make them prohibitively expensive and hinders their widespread use. Here, we describe a new economical oral vaccination platform using algae and evaluated its potential for the delivery of recombinant drugs using GFP expressed in the chloroplast of algal cells. The transplastomic algae expressing recombinant GFPs were freeze-dried for long-term storage at ambient temperature and for easy handling in feeding. GFPs bioencapsulated by lyophilized Chlamydomonas reinhardtii were found intact without degradation for several months at ambient temperature. The expression level of GFP in the lyophilized algae was estimated at 0.47 μg/mg dry weight. The GFPs bioencapsulated and orally delivered to Danio rerio were immunostained and observed in the intestinal tissues using a confocal microscope. Furthermore, the uptaken GFPs in the intestine were detected in the blood using ELISA and the detected level was 5.4 ng of GFP/μl of serum. These results demonstrate that microalgae can be a viable protein production and oral delivery system to vaccinate fish. The results give greater justification to continue exploring the concept of microalgal-based oral vaccines. The potential of the technology would greatly benefit aquaculture farmers by providing them with affordable, environmentally sustainable, and user-friendly vaccines.

Microcapillary sampling of Baltic Sea copepod gut microbiomes indicates high variability among individuals and the potential for methane production

The paradox of methane oversaturation in oxygenated surface water has been described in many pelagic systems and still raises the question of the source. Temora sp. and Acartia sp. commonly dominate the surface and subsurface waters of the central Baltic Sea. It is hypothesised that their gut microbiome at least partly contributes to the methane anomaly in this ecosystem. However, the potential pathway for this methane production remains unclear. Using a microcapillary technique, we successfully overcame the challenge of sampling the gut microbiome of copepods <1 mm. 16S rRNA gene amplicon sequencing revealed differences among the dominant bacterial communities associated with Temora sp. (Actinobacteria, Betaproteobacteria and Flavobacteriia) and Acartia sp. (Actinobacteria, Alphaproteobacteria and Betaproteobacteria) and the surrounding water (Proteobacteria, Cyanobacteria and Verrucomicrobia), but also intraspecific variability. In both copepods, gut-specific prokaryotic taxa and indicative species for methane production pathways (methanogenesis, dimethylsulfoniopropionate or methylphosphonate) were present. The relative abundance of archaea and methanogens was investigated using droplet digital polymerase chain reaction and showed a high variability among copepod individuals, underlining intra- and interspecific differences in copepod-associated prokaryotic communities. Overall, this work highlights that the guts of Temora sp. and Acartia sp. have the potential for methane production but are probably no hotspot.

New environmental model for thermodynamic ecology of biological phosphine production

We present a new model for the biological production of phosphine (PH₃). Phosphine is found globally, in trace amounts, in the Earth's atmosphere. It has been suggested as a key molecule in the phosphorus cycle, linking atmospheric, lithospheric and biological phosphorus chemistry. Phosphine's production is strongly associated with marshes, swamps and other sites of anaerobic biology. However the mechanism of phosphine's biological production has remained controversial, because it has been believed that reduction of phosphate to phosphine is endergonic. In this paper we show through thermodynamic calculations that, in specific environments, the combined action of phosphate reducing and phosphite disproportionating bacteria can produce phosphine. Phosphate-reducing bacteria can capture energy from the reduction of phosphate to phosphite through coupling phosphate reduction to NADH oxidation. Our hypothesis describes how the phosphate chemistry in an environmental niche is coupled to phosphite generation in ground water, which in turn is coupled to the phosphine production in water and atmosphere, driven by a specific microbial ecology. Our hypothesis provides clear predictions on specific complex environments where biological phosphine production could be widespread. We propose tests of our hypothesis in fieldwork.

Natural Products Containing 'Rare' Organophosphorus Functional Groups

Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.

Microbiota Landscape of Gut System of Guppy Fish (Poecilia reticulata) Plays an Outstanding Role in Adaptation Mechanisms

Microbial consortium that is present in fish gut systems works together to achieve unknown specific roles. Here, we collected guppy fish from hydrocarbon- and trace metal-contaminated wastewater to assess the relationships between gut microbiota and host fish adaptation. Targeted genes and 16S rRNA amplicon sequencing have been used to identify gut bacteria of guppies. Mineral-conditioned medium contributes to identify bacteria with the ability to grow and/or to tolerate hydrocarbon and trace metals. Additionally, trace metals' tolerance minimum inhibitory concentration (MIC) of microbiota was evaluated. We first isolated bacteria from the gut system, and we showed that Bacillus spp., Staphylococcus spp., Shigella spp., Salmonella spp, Pseudomonas spp., Citrobacter spp., Salmonella enterica ssp.arizonae sp., Enterobacter spp, and Acinetobacter spp. are part of guppy gut microbiota. Some representative species are able to degrade and/or tolerate gasoline and/or diesel fuel hydrocarbons. Tolerance to trace metals was observed in Gram-positive and Gram-negative bacteria. We showed that minimal inhibitory concentration (MIC) of some microbiota isolated from gut systems has been found including for mercury (Hg) between 2 and 4‰, cobalt (Co) Co (2 and 5‰), zinc (Zn) (9 and 18‰), and plomb (Pb) (22 and 27‰). Zn and Pb were the trace metals for which the rate of tolerance was significantly higher. Finally, we showed that cytochrome c oxidase is not interfering in presence of trace metals. The working consortium showed that bacteria should work together to achieve their best.

In Vitro Selection and Identification of Potential Probiotics Isolated from the Gastrointestinal Tract of Nile Tilapia, Oreochromis niloticus

Fish gut bacteria can be used as probiotics for aquaculture. The aim of this study is to screen and identify beneficial probiotic bacteria from the gut of Nile tilapia, Oreochromis niloticus. Nine out of one hundred thirty-five isolates were non-pathogenic through intraperitoneal injection and had antibacterial activities with at least a strain from the five isolated fish pathogens, Aeromonas sobria, Aeromonas hydrophila, Pseudomonas aeruginosa, Pseudomonas putida, and Staphylococcus aureus. Further tests showed that such isolates can survive in the presence of high bile concentration (10%) and at different acidic pH values. A strains (14HT) was sensitive to all selected antibiotics, two strains were (9HT and 11HT) resistant to streptomycin and three strains (9HT, 11HT and 38HT) had resistance to two antibiotics. Four isolates (11HT, 33HT, 38HT and 41HT) had an amylase and a protease activities and one strain (47HT) showed only amylase activity. Based on 16S rRNA gene analysis, the isolated strains were identified as follows: Lactococcus lactis (8HT, 9HT, 11HT and 33HT); Enterococcus faecalis (14HT), Lysinibacillus sp. (38HT) and Citrobacter freundii (39HT, 41HT and 47HT).

The accumulation, histopathology, and intestinal microorganism effects of waterborne cadmium on Carassius auratus gibelio

Cadmium (Cd) is known to be a potentially toxic heavy metals to the fish health and growth. Carassius auratus gibelio (C. a. gibelio) specimens were exposed to waterborne Cd (0, 0.05, 0.10, 0.15, and 0.20 mg/L CdCl₂) for 14 days. Cd accumulation, liver and intestine histopathology, and intestinal microorganism were investigated in the present study. The results indicated that Cd accumulation in the gill, liver, intestine, and muscle gradually decreased as Cd concentration increased. The gill accumulated higher amounts of Cd than other tissues. The histopathology of liver and intestine underwent changes with different Cd concentrations, including hepatocyte hypertrophy, aggregation of blood cells, sinusoids, lipidosis, necrosis of hepatic tissues, the erosion of villi, necrosis in the mucosal layer, the appearance of vacuoles in the lamina propria, hyperplasia, and swelling of goblet cells. Moreover, the core gut microbiota existed in the intestinal microorganism and did not change as Cd concentration increased. However, the diversity of intestinal microorganism was significantly reduced compared with that of the control sample. The present results indicated that C. a. gibelio exposed to Cd suffered toxicity, and Cd could affect the biodiversity of the intestinal microbiota of C. a. gibelio.

K-Selection as Microbial Community Management Strategy: A Method for Improved Viability of Larvae in Aquaculture

Aquaculture has the potential to become a major food supplier in a world with an increasing human population, and increased consumption of fish will likely have positive health implications. For marine aquaculture, the production of high quality juveniles is a bottleneck. Survival until the juvenile stage is typically as low as 10–15% for many species, which indicates suboptimal rearing conditions. Substantial evidence indicates that the poor performance and viability of larvae is largely due to detrimental larvae-microbiota interactions. This emphasises the need for microbial management strategies in the cultivation of marine fish larvae. Disinfection and probiotics are the most studied microbial management methods so far. However, most studies on these methods overlooked the role of mutualistic relationships between microbes and hosts, and have not proposed or examined methods steering toward such relationships. Based on ecological theory and a number of experiments, we find support for the hypothesis that current practise in aquaculture generally selects for r-strategic, opportunistic microbes, which results in detrimental host–microbiota interactions. Thus, the challenge is to develop technology and methods for microbial management at the ecosystem level that creates a K-selected microbial community, and by this mean select against r-strategic opportunists. Here we summarise experiments done during 25 years and with marine larvae of five different species showing that: (1) K-selection strategies result in different water microbiota with less opportunists, (2) this influences the microbiota of the fish larvae, and (3) the larvae cultivated in water inhabited by a K-selected microbiota perform better. Improved performance of larvae includes improved appetite, earlier onset of and faster growth, increased survival, and increased robustness to stress. K-selection as a method for management of the microbial community is a robust approach that allows steering of host–microbiota interactions in larviculture toward mutualism. It could also be applicable for young stages of other domesticated animals. Our review illustrates that a change from a “beat-them” to a “join-them” strategy for microbial management in larval rearing can lead to a more sustainable aquaculture industry.