Physiological and gut microbiome changes associated with low dietary protein level in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) determined by 16S rRNA sequence analysis

Effects of low protein feed on hepato-intestinal health and muscle quality of grass carp (Ctenopharyngodon idellus)

In this study, grass carp (33.28 ± 0.05 g) were fed three diets for 8 weeks: control (crude protein [CP] 30%, crude lipid [CL] 6%), low protein (LP; CP16%, CL6%), and low protein with high-fat (LPHF; CP16%, CL10%). The final body weight decreased in the LP and LPHF groups compared to the Control (P < 0.05). Liver triglycerides, total cholesterol, and nonesterified fatty acids were higher in the LP group than the Control, whereas these indexes in the LPHF group were higher than those in the LP group (P < 0.05). The LP group had intestinal barrier damage, while the LPHF group had a slight recovery. TNF-α, IL-8, and IL-1β content were lower in the LP group than in the Control (P < 0.05), and even higher in the LPHF group (P < 0.05). The expressions of endoplasmic reticulum stress-related genes Activating transcription factor 6 (ATF-6) and Glucose-regulated protein (GRP78) were higher in the LPHF group against the LP group (P < 0.05). The IL-1β and TNF-α content negatively correlated with intestinal Actinomycetes and Mycobacterium abundance (P < 0.05). The muscle fiber diameter was smaller in both the LP and LPHF groups than the control (P < 0.05), with the LP group showing metabolites related to protein digestion and absorption, and LPHF group exhibiting metabolites related to taste transmission. The results demonstrate reducing dietary protein affects growth, causing liver lipid accumulation, reduced enteritis response, and increased muscle tightness, while increasing fat content accelerates fat accumulation and inflammation.

Effect of dietary macronutrients and immune challenge on gut microbiota, physiology and feeding behaviour in zebra finches

Macronutrients play a vital role in host immunity and can influence host-pathogen dynamics, potentially through dietary effects on gut microbiota. To increase our understanding of how dietary macronutrients affect physiology and gut microbiota and investigate whether feeding behaviour is influenced by an immune threat, we conducted two experiments. First, we determined whether zebra finches (Taeniopygia guttata) exhibit shifts in physiology and gut microbiota when fed diets differing in macronutrient ratios. We found the type and amount of diet consumed affected gut microbiota alpha diversity, where microbial richness and Shannon diversity increased with caloric intake in birds fed a high-fat diet and decreased with caloric intake in birds fed a high protein diet. Diet macronutrient content did not affect physiological metrics, but lower caloric intake was associated with higher complement activity. In our second experiment, we simulated an infection in birds using the bacterial endotoxin lipopolysaccharide (LPS) and quantified feeding behaviour in immune challenged and control individuals, as well as birds housed near either a control pair (no immune threat), or birds housed near a pair given an immune challenge with LPS (social cue of heightened infection risk). We also examined whether social cues of infection alter physiological responses relevant to responding to an immune threat, an effect that could be mediated through shifts in feeding behaviour. LPS induced a reduction in caloric intake driven by a decrease in protein, but not fat consumption. No evidence was found for socially induced shifts in feeding behaviour, physiology or gut microbiota. Our findings carry implications for host health, as sickness-induced anorexia and diet-induced shifts in the microbiome could shape host-pathogen interactions.

Effects of different temperatures on Leiocassis longirostris gill structure and intestinal microbial composition

Fish are poikilothermic vertebrates and their physiological activities are affected by water temperature. In recent years, extreme weather has occurred frequently, and temperature changes have adversely affected the growth of farmed fish. To explore the changes in gill tissue structure caused by changing the water temperature and the relationship between the intestinal microbiota and the Leiocassis longirostris host adaptation mechanism, gill tissue sections and intestinal microbial 16S rRNA amplicon sequencing were conducted under different temperature stress (low temperature 4 °C, normal temperature 26 °C and high temperature 32 °C). The results showed that heat stress and cold stress caused injury and swelling, terminal congestion, cell vacuolation, and necrosis of the gill tissue of L. longirostris. For intestinal microbiota, the abundances of Pseudomonadota and Bacillota increased at the cold stress, while the abundances of Fusobacteriota and Bacteroidota increased at the heat stress. The number of opportunistic bacteria, mainly Aeromonas and Acinetobacter, was the highest under cold stress. In addition, the richness of the intestinal microbiota decreased significantly at heat and cold stresses, while evenness increased. Prediction of intestinal microbiota function showed that most common functions, such as metabolism of cofactors and vitamins, energy metabolism and replication and repair, were decreased significantly at heat stress and cold stress, and phylogenetic relationship analysis revealed significant differences among the groups. In conclusion, the change of temperature altered the gill tissue structure, and affected the structure and homeostasis of the intestinal microbiota, thus affecting the survival time of L. longirostris, and cold stress had a greater effect than heat stress.

Falcon gut microbiota is shaped by diet and enriched in Salmonella

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, avian gut microbiome studies commonly focus on birds of economic importance and the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 captive falcons-raptors of historic importance-in the context of avian evolution by sequencing the V4 region of the 16S rRNA gene. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and relative abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and contains Salmonella at appreciable levels. Salmonella presence was associated with altered functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut. Our results point to the necessity of screening for Salmonella and other human pathogens in captive birds to safeguard both the health of falcons and individuals who come in contact with these birds.

Feed Regime Slightly Modifies the Bacterial but Not the Fungal Communities in the Intestinal Mucosal Microbiota of Cobia Fish (Rachycentron canadum)

The bacterial community of the intestinal microbiota influences many host functions, and similar effects have been recently reported for the fungal community (mycobiota). Cobia is a tropical fish that has been studied for its potential in marine aquaculture. However, the study of its bacterial community has been underreported and the mycobiota has not been investigated. We analyzed the gut bacterial and fungal profile present in the intestinal mucosa of reared adult cobias fed two diets (frozen fish pieces (FFPs) and formulated feed (FF)) for 4 months by sequencing the 16S rRNA (V3-V4) and internal transcribed spacer-2 (ITS2) regions using Illumina NovaSeq 6000. No significant differences in the alpha diversity of the bacterial community were observed, which was dominated by the phyla Proteobacteria (~96%) and Firmicutes (~1%). Cobia fed FF showed higher abundance of 10 genera, mainly UCG-002 (Family Oscillospiraceae) and Faecalibacterium, compared to cobia fed FFPs, which showed higher abundance of 7 genera, mainly Methylobacterium-Methylorubrum and Cutibacterium. The inferred bacterial functions were related to metabolism, environmental information processing and cellular processes; and no differences were found between diets. In mycobiota, no differences were observed in the diversity and composition of cobia fed the two diets. The mycobiota was dominated by the phyla Ascomycota (~88%) and Basidiomycota (~11%). This is the first study to describe the gut bacterial and fungal communities in cobia reared under captive conditions and fed on different diets and to identify the genus Ascobulus as a new member of the core fish mycobiota.

Microbiome analysis reveals potential for modulation of gut microbiota through polysaccharide-based prebiotic feeding in Oreochromis niloticus (Linnaeus, 1758)

Characterization and functional profiling of the gut microbiota are essential for guiding nutritional interventions in fish and achieving favorable host-microbe interactions. Thus, we conducted a 30 days study to explore and document the gut microbial community of O. niloticus, as well as to evaluate the effects of a polysaccharide-based prebiotics with 0.5% and 0.75% Aloe vera extract on the gut microbiome through genomic analysis. The V3-V4 region of 16S rRNA was amplified and sequenced using Illumina HiSeq 2500, resulting in 1,000,199 reads for operational taxonomic unit (OTU) identification. Out of 8,894 OTUs, 1,181 were selected for further analysis. Our results revealed that Planctomycetes, Firmicutes, Proteobacteria, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in both control and treatment samples. Higher doses of prebiotics were found to improve Planctomycetes and Firmicutes while decreasing Proteobacteria and Verrucomicrobia. We observed increasing trends in the abundance of Bacilli, Bacillaceae, and Bacillus bacteria at the class, family, and genus levels, respectively, in a dose-dependent manner. These findings were consistent with the conventional colony count data, which showed a higher prevalence of Bacillus in prebiotic-supplemented groups. Moreover, predicted functional analysis using PICRUSt indicated a dose-dependent upregulation in glycolysis V, superpathway of glycol metabolism and degradation, glucose and xylose degradation, glycolysis II, and sulfoglycolysis pathways. Most of the energy, protein, and amino acid synthesis pathways were upregulated only at lower doses of prebiotic treatment. Our findings suggest that the gut microbiome of O. niloticus can be optimized through nutritional interventions with plant-based polysaccharides for improved growth performance in commercial fish.

Omics analysis revealed the possible mechanism of streptococcus disease outbreak in tilapia under high temperature

High temperature is a main cause to result in the outbreak of tilapia streptococcal disease. However, the underlying mechanisms are not well understood. In this study, we first confirmed that tilapia infected with Streptococcus agalactiae (S. agalactiae) had a higher mortality at high temperature (35 °C) than that at normal temperature (28 °C). Subsequently, the effects of high temperature on gene expression pattern of S. agalactiae and intestinal microbiota of tilapia were respectively detected by RNA-seq and 16S rDNA sequencing. RNA-seq identified 357 differentially expressed genes (DEGs) in S. agalactiae cultured at 28 °C and 35 °C. GO and KEGG analysis showed that these DEGs were highly involved in metabolic processes, including glucose, lipid and amino acid metabolisms, which indicates that S. agalactiae have stronger vitality and are likely to be more infectious under high temperature. Microbiota analysis revealed that high temperature could influence the bacterial community composition of tilapia intestine, accompanied by changes in intestinal structure. Compared to feed at 28 °C, the total bacterial species as well as pathogens, such as norank_f__Rhizobiales_Incertae_Sedis, Pseudorhodoplanes, Ancylobacter, in tilapia intestine were significantly increased at 35 °C, which may weaken the immune resistance of tilapia. Taken together, our results suggest that high temperature evoked tilapia susceptible to S. agalactiae should be the combined effect of enhanced S. agalactiae metabolism and dysregulated tilapia intestinal microbiota.

Effects of different protein and lipid levels on the growth performance and intestinal microflora of loach (Paramisgurnus dabryanus)

The aim of this study was to examine the effects of dietary protein and lipid levels on the growth performance and homeostasis of the intestinal flora in Paramisgurnus dabryanus. An 8-wk 3 × 3 two-factorial experiment was conducted to investigate the interaction between dietary crude protein (CP: 30%, 35%, 40%) and ether extract (EE: 6%, 10%, 14%) on the growth rate and the intestinal microflora of P. dabryanus. A total of 2,160 fish (5.19 ± 0.01 g) were randomly allotted to 36 aquariums each with 60 fish. Fish were fed the experimental diet twice daily. Results revealed that weight gain rate (WGR), specific growth rate (SGR), protein efficiency ratio and net protein utilization significantly increased when increasing protein levels from 30% to 40% (P < 0.05). Both WGR and SGR enhanced first but reduced thereafter with maximum value at 10% lipid level as dietary lipid increased from 6% to 14% (P < 0.05). Significant interactions between protein and lipid were found with feed conversion rate, lipid efficiency ratio and net lipid utilization (P < 0.05). At the phylum level, Proteobacteria and Actinobacteria were the dominant bacteria; at the genus level, Burkholderia-Caballeronia-Paraburkholderia was the dominant bacteria. Fish fed the diet containing 10% lipid had a higher abundance of Proteobacteria and unclassified_f_Eenterobacteriaceae than those fed the 14% lipid diet, and a higher abundance of Rhodobacter than those fed the 6% lipid diet (P < 0.05). Analysis of the predicted functions showed that metabolism in the intestine of fish in the CP40EE10 group was more active than that in CP30EE14 group. Polynomial regression analysis found that a diet containing 40.87% protein and 9.88% lipid can be considered optimal for P. dabryanus.

Transport Stress Induces Oxidative Stress and Immune Response in Juvenile Largemouth Bass (Micropterus salmoides): Analysis of Oxidative and Immunological Parameters and the Gut Microbiome

Transport is essential in cross-regional culturing of juvenile fish. Largemouth bass (Micropterus salmoides) often exhibit decreased vitality and are susceptible to disease after transportation. To study the effects of transport stress on juvenile largemouth bass, juveniles (average length: 8.42 ± 0.44 cm, average weight 10.26 ± 0.32 g) were subjected to a 12 h simulated transport, then subsequently, allowed to recover for 5 d. Liver and intestinal tissues were collected at 0, 6 and 12 h after transport stress and after 5 d of recovery. Oxidative and immunological parameters and the gut microbiome were analyzed. Hepatocytic vacuolization and shortened intestinal villi in the bass indicated liver and intestinal damage due to transport stress. Superoxide dismutase, lysozyme and complement C3 activities were significantly increased during transport stress (p < 0.05), indicating that transport stress resulted in oxidative stress and altered innate immune responses in the bass. With the transport stress, the malondialdehyde content first increased, then significantly decreased (p < 0.05) and showed an increasing trend in the recovery group. 16S rDNA analysis revealed that transport stress strongly affected the gut microbial compositions, mainly among Proteobacteria, Firmicutes, Cyanobacteria and Spirochaetes. The Proteobacteria abundance increased significantly after transport. The Kyoto Encyclopedia of Genes and Genomes functional analysis revealed that most gut microbes played roles in membrane transport, cell replication and repair. Correlation analyses demonstrated that the dominant genera varied significantly and participated in the measured physiological parameter changes. With 5 days of recovery after 12 h of transport stress, the physiological parameters and gut microbiome differed significantly between the experimental and control groups. These results provide a reference and basis for studying transport-stress-induced oxidative and immune mechanisms in juvenile largemouth bass to help optimize juvenile largemouth bass transportation.

Multi-kingdom microbiota and functions changes associated with culture mode in genetically improved farmed tilapia (Oreochromis niloticus)

Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are intensively farmed in China, where most of the yield derives from the pond culture system (PCS). The in-pond raceway system (IPRS) is a new type of highly efficient aquaculture mode, and has been recommended as a novel system for GIFT farming. To determine the effects of these culture modes on the gut microbiome of GIFT, we conducted a 90-days experiment in IPRS and PCS units. A 16S rRNA gene profile analysis showed that the composition of gut microbiota in GIFT under IPRS and PCS conditions gradually separated as rearing progressed, with divergent responses by the midgut and hindgut bacteria. The α-diversity in hindgut decreased significantly by day 90, as compared with on day 7 (p < 0.05), with a significantly greater decrease in PCS-reared fish than in IPRS fish (p < 0.05). The α-diversity of microbiota in midgut remained stable (p > 0.05). The overall dominant gut bacteria were Bacteroidetes, Proteobacteria, and Firmicutes. Rearing mode affected the taxonomic profile of the gut bacteria; in midgut, IPRS samples had more Firmicutes and Fusobacteria compared with PCS samples, but less Proteobacteria, Verrucomicrobia, and Actinobacteria. Firmicutes was enriched in IPRS hindgut, and Fusobacteria was enriched in PCS hindgut. Using random-forest models and LEfSe, we also screened core taxa that could discriminate between the gut microbial communities under IPRS and PCS conditions. The genus Cetobacterium (of family Fusobacteriaceae) was significantly enriched in midgut in IPRS fish, and enriched in hindgut in PCS fish. The genus Clostridium sensu stricto (of family Clostridiaceae 1) was significantly enriched in both IPRS midgut and hindgut. Analysis with PICRUSt2 software revealed that the culture modes were similar in their effects on the gut microbial metabolic functions. The predicted pathways were significantly enriched in the metabolism class (level 1). Further, the relative abundance of functions related to amino acid metabolic, carbohydrate metabolic, energy metabolic, and metabolic of cofactors and vitamins were high at hierarchy level 2, as the metabolic activity of intestinal bacteria is especially active. Overall, this study enhances our understanding of the characteristics of gut microbiota in GIFT under IPRS and PCS culture modes. Moreover, our findings provide insights into the microecological balance in IPRS units, and a theoretical reference for further development of this culture system.

Low Protein Diets Supplemented With Alpha-Ketoglutarate Enhance the Growth Performance, Immune Response, and Intestinal Health in Common Carp (Cyprinus carpio)

To investigate the effects of alpha-ketoglutarate (AKG) supplementation in a low protein (LP) diet on the growth performance, immune response, and intestinal health of common carp (Cyprinus carpio), 600 carp were randomly divided into five dietary groups: a normal protein (NP) diet containing 32% crude protein, an LP diet formulated with 28% crude protein, and LP with AKG at 0.4%, 0.8%, and 1.2% (dry matter). After an 8-week trial period, the results demonstrated that an LP diet led to a decrease in performance, immune response, and intestinal barrier function. Compared with the LP group, the final body weight and weight gain rate in the LP+0.4% AKG group were significantly higher, the feed conversion ratio was significantly decreased with the addition of 0.4% and 0.8% AKG. The supplementation with 0.4% and 0.8% AKG markedly increased the activities of T-SOD and GSH-Px, as well as the expression levels of GPX1a and GPX1b relative to the LP group, whereas the MDA content was significantly decreased in the LP+0.4% AKG group. In addition, the expression levels of tight junctions including claudin-3, claudin-7, ZO-1, and MLCK were significantly up-regulated in the LP+0.4% AKG group, and the relative expression levels of the pro-inflammatory factors IL-1β and IL-6α were significantly lower with the addition of 0.4%, 0.8%, and 1.2% AKG. Moreover, the abundance of Proteobacteria in the LP+0.4% AKG group was lower than that in the LP group, and the abundance of Firmicutes and Fusobacteria was higher at the phylum level. The abundance of Citrobacter in the LP+0.4% AKG group was decreased compared to the LP group, while the abundance of Aeromonas was increased at the genus level. In short, the effects of AKG on the intestinal health of the common carp were systematically and comprehensively evaluated from the perspectives of intestinal physical barrier, chemical barrier, biological barrier, and immune barrier. We found that an LP diet supplemented with 0.4% AKG was beneficial to the growth performance and intestinal health of common carp.

Comparative Analysis of the Gut Microbiota of Mandarin Fish (Siniperca chuatsi) Feeding on Compound Diets and Live Baits

Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.

The Effect of a Total Fishmeal Replacement by Arthrospira platensis on the Microbiome of African Catfish (Clarias gariepinus)

An increasing number of fishmeal supplements are becoming the focus of aquaculture research, with a special emphasis on microalgae/cyanobacteria such as spirulina being considered as sustainable alternatives. New feed ingredients can have a far-reaching impact on the intestinal microbiome and therefore play an important role in the development and the health of fish. However, the influence of these alternatives on the microbiome is largely unknown. We undertook a 10 weeks feeding experiment on 120 African catfish with an initial body weight of 50.1 ± 2.95 g. To understand the effect of the spirulina supplementation, two isoenergetic experimental diets were formulated, containing either fishmeal or spirulina as a protein source. The 16S rRNA sequencing was used to analyze the intestinal bacteria microbiota. Results show that the observed richness indicated no significant statistical difference, but Chao1, ACE, Shannon, and Simpson indices indicate a possible increase in bacterial richness for the spirulina diet. The most abundant bacteria in both experimental groups were Fusobacteriia with the only taxa from the genus Cetobacterium. The bacterium from genus Romboutsia was more likely to be found in the microbiome of fish fed the fishmeal diet. In spirulina-fed fish, the genera Plesiomonas and Bacteroides were the most dominant microbes observed. Even though some genera were more abundant in the spirulina group, the overall microbial community structure was not affected by diets.

Effects of Dietary Protein Level on the Gut Microbiome and Nutrient Metabolism in Tilapia (Oreochromis niloticus)

Simple Summary

Dietary protein is an important factor affecting aquaculture. In this study, the homeostasis of the gut microbiome and metabolic profile of the liver and serum of tilapia were analyzed, comparing those fed with different diets to evaluate the effect of diet on protein levels. As a result, there was no significant difference found in the diversity and richness of the gut microbiome but had differences in the microbial composition of the gut among different groups. As for the liver metabolome of the tilapia, the glucose content increased along with increased protein levels. As for serum metabolome, the levels of tyrosine, guanosine, and inosine were significantly different. In summary, diets with different protein levels can affect the composition of gut microbiota and glycolysis and amino acid metabolism in tilapia. These results may also help to improve the conditions of tilapia cultivation.

Abstract

Dietary protein is one of the most important nutritional factors in aquaculture. The aim of this study was to examine the effects of dietary protein levels on the gut microbiome and the liver and serum levels of metabolites in tilapia. Tilapia were fed a diet with a low (20%), moderate (30%), or high (40%) content of crude protein, and the homeostasis of the gut microbiome and metabolic profile of the liver and serum were analyzed. The results showed no significant differences in the diversity and richness of the gut microbiome among the groups; however, there were differences in the microbial composition of the gut. The metabolome analysis of liver samples revealed a difference in the glucose level among the groups, with the highest glucose level in fish fed a high protein diet. In addition, there were significant differences in the levels of tyrosine, guanosine, and inosine among the metabolome analysis of serum samples of these groups. In summary, diets with different protein levels could affect the composition of gut microbiota and the dynamic balance of microbial communities. Dietary protein content can also affect glycolysis and amino acid metabolism in tilapia.

Physiological and gut microbiome changes associated with low dietary protein level in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) determined by 16S rRNA sequence analysis

The aim of this study was to determine the effects of different dietary protein levels on the growth, physiological parameters, and gut microbiome of genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Two pellet feed diets with low (25%, LPD) and normal (35%, NPD) protein levels were fed to GIFT in aquaria at 28°C for 8 weeks. The LPD reduced trypsin activity and inhibited the growth of GIFT. The serum alanine amino transferase and aspartate transaminase activities, hepatic malondialdehyde content, and superoxide dismutase, glutathione peroxidase, and catalase activities were significantly higher in LPD GIFT than in NPD GIFT (p < .05). The LPD led to decreased lysozyme activity and increased levels of C3 (p < .05). A 16S rRNA gene profiling analysis showed that the LPD significantly affected the gut microbial composition. Compared with the NPD, the LPD significantly decreased intestinal microbial diversity (p < .05). The macronutrient distribution affected the taxonomic profile of gut bacteria, mainly the phyla Bacteroidetes, Proteobacteria, and Firmicutes. The LPD favored growth of the genus Bacteroides. The NPD appeared to increase the abundance of the genera Lawsonia, Romboutsia, and Sphingomonas. Our results showed that, compared with NPD GIFT, the LPD GIFT had weakened nonspecific immune function, altered microbial community structure, and decreased gut microbial diversity.