Integration of Gut Microbiota with Transcriptomic and Metabolomic Profiling Reveals Growth Differences in Male Giant River Prawns (Macrobrachium rosenbergii)

The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a tropical species cultured worldwide, has high market demand and economic value. Male GFP growth varies considerably; however, the mechanisms underlying these growth differences remain unclear. In this study, we collected gut and hemolymphatic samples of large (ML), medium (MM), and small (MS) male GFPs and used the 16S rRNA sequencing and liquid chromatography-mass spectrometry-based metabolomic methods to explore gut microbiota and metabolites associated with GFP growth. The dominant bacteria were Firmicutes and Proteobacteria; higher growth rates correlated with a higher Firmicutes/Bacteroides ratio. Serum metabolite levels significantly differed between the ML and MS groups. We also combined transcriptomics with integrative multiomic techniques to further elucidate systematic molecular mechanisms in the GFPs. The results revealed that Faecalibacterium and Roseburia may improve gut health in GFP through butyrate release, affecting physiological homeostasis and leading to metabolic variations related to GFP growth differences. Notably, our results provide novel, fundamental insights into the molecular networks connecting various genes, metabolites, microbes, and phenotypes in GFPs, facilitating the elucidation of differential growth mechanisms in GFPs.

Characterizing Growth-Retarded Japanese Eels (Anguilla japonica): Insights into Metabolic and Appetite Regulation

During field surveys and culture procedures, large growth disparities in Anguilla japonica have been observed. However, the potential causes are unknown. This study explored differences in digestive ability, metabolic levels, and transcriptomic profiles of appetite-related genes between growth-retarded eel (GRE) and normal-growing eel (NGE) under the same rearing conditions. The results showed that growth hormone (gh) mRNA expression in GREs was considerably lower than NGEs. The levels of total protein (TP), total cholesterol (T-CHO), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), blood ammonia (BA), blood urea nitrogen (BUN), and alkaline phosphatase (ALP) in GREs were significantly lower than in NGEs. Conversely, levels of glucose (GLU), alanine aminotransferase (ALT), and aspartate transaminase (AST) were higher in GREs. The activities of SOD, CAT, and T-AOC levels were also significantly lower in GREs, as were the activities of glucose-related enzymes including hexokinase (HK), pyruvate kinase (PK), phosphoenolpyruvate carboxykinase (PEPCK), and glucose-6-phosphatase (G6PASE). Additionally, orexigenic genes (npy and ghrelin) were dramatically downregulated, whereas anorexigenic genes (crh and pyy) were significantly upregulated in GREs. These findings suggested that variances in growth hormone, metabolic activities, and appetite level could be associated with the different growth rates of A. japonica. The present research not only revealed the characteristics of the growth, metabolism, and appetite of GREs but also offered new perspectives into the substantial growth discrepancies in A. japonica, providing novel ideas for enhancing fish growth.

Effects of dietary salidroside on intestinal health, immune parameters and intestinal microbiota in largemouth bass (Micropterus salmoides)

The largemouth bass has become one of the economically fish in China, according to the latest China Fishery Statistical Yearbook. The farming scale is constantly increasing. Salidroside has been found in past studies to have oxidative stress reducing and immune boosting properties. In this study, the addition of six different levels of salidroside supplements were 0、40、80、120、160 and 200 mg/kg. A 56-day feeding trial was conducted to investigate the effects of salidroside on the intestinal health, immune parameters and intestinal microbiota composition of largemouth bass. Dietary addition of salidroside significantly affected the Keap-1β/Nrf-2 pathway as well as significantly increased antioxidant enzyme activities resulting in a significant increase in antioxidant capacity of largemouth bass. Dietary SLR significantly reduced feed coefficients. The genes related to tight junction proteins (Occludin, ZO-1, Claudin-4, Claudin-5) were found to be significantly upregulated in the diet supplemented with salidroside, indicating that salidroside can improve the intestinal barrier function (p < 0.05). The dietary administration of salidroside was found to significantly reduce the transcription levels of intestinal tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) (p < 0.05). Furthermore, salidroside was observed to reduce the transcription levels of intestinal apoptosis factor Bcl-2 associated death promoter (BAD) and recombinant Tumor Protein p53 (P53) (p < 0.05). Concomitantly, the beneficial bacteria, Fusobacteriota and Cetobacterium, was significantly increased in the SLR12 group, while that of pathogenic bacteria, Proteobacteria, was significantly decreased (p < 0.05). In conclusion, the medium-sized largemouth bass optimal dosage of salidroside in the diet is 120mg/kg-1.

Preparation of valine-curcumin conjugate and its in vitro antibacterial and antitumor activity and in vivo biological effects on American eels (Anguilla rostrata)

Curcumin (Cur) exhibits diverse natural pharmacological activities, despite its limited water solubility (hydrophobicity) and low bioavailability. In this investigation, a valine-curcumin conjugate (Val-Cur) was synthesized through amino acid side chain modification, and its solubility increased to 1.78 mg/mL. In vitro experimental findings demonstrated that the antibacterial activity of Val-Cur against Escherichia coli, Staphylococcus aureus, Aeromonas hydrophila, and Vibrio parahaemolyticus was significantly superior to that of Cur. The inhibition rate of Val-Cur against HepG2 (human hepatocellular carcinoma) cells was higher than that of Cur at low concentrations (below 25 μmol/L), although the IC50 value of Val-Cur did not differ significantly from that of Cur. In vivo biological effects of Val-Cur were assessed by adding it into the feed (150 mg/kg) of American eels (Anguilla rostrata). Val-Cur significantly improved the growth performance (↑weight gain rate, ↑specific growth rate, and ↓feed conversion rate) and activities of intestinal digestive enzymes (amylase and lipase) and antioxidant enzymes (superoxide dismutase) in American eels. Additionally, Val-Cur significantly improved serum biochemical indices (↑high-density lipoprotein cholesterol, ↓low-density lipoprotein cholesterol, ↓aspartate and alanine aminotransferases). Furthermore, Val-Cur increased intestinal microbial diversity, reduced the abundance of potentially pathogenic bacteria (Spiroplasma, Clostridium, and Pseudomonas), and elevated the abundance of beneficial digestion-promoting bacteria (Romboutsia, Phyllobacterium, Romboutsia sedimentorum, and Clostridium butyricum) conducive to glucose metabolism (P < 0.05). To the best of our knowledge, this study is the first to explore water-soluble curcumin in aquaculture, and the findings will lay the groundwork for the potential application of water-soluble curcumin in the field of aquaculture.

Quantitative characterization and dynamics of bacterial communities in ready-to-eat chicken using high-throughput sequencing combined with internal standard-based absolute quantification

Ready-to-eat (RTE) chicken products are prone to bacterial contamination, posing foodborne illness risks. High-throughput sequencing (HTS) has been widely used to study the distribution of pathogenic and spoilage bacteria in RTE chicken products but lacks quantitative data on taxa abundances. In this study, we employed a method combining HTS with absolute quantification, using Edwardsiella tarda as an internal standard strain, to achieve the relative and absolute abundances of microbiota in RTE chicken products stored at 4 and 25 °C. The results showed that the addition of appropriate concentration of internal standard strains exhibited no significant impact on the structure composition, relative abundance, and absolute abundance of bacterial communities in chicken meat, achieving comprehensive absolute quantification in RTE chicken products. Furthermore, the absolute abundance of bacterial genera at the end of storage followed a log-normal distribution, with most genera having an absolute abundance between 103 and 105 CFU/g. This study provides insights into the quantification of bacterial communities in RTE chicken products, laying a foundation for the development of strategies to extend the shelf life of RTE products.

Effects of replacing wheat bran with palm kernel cake or fermented palm kernel cake on the growth performance, intestinal microbiota and intestinal health of tilapia (GIFT, Oreochromis niloticus)

A nine-week feeding trial was conducted to evaluate the effects of replacing wheat bran (WB) with palm kernel cake (PKC) or fermented palm kernel cake (FPKC) on the growth performance, intestinal microbiota and intestinal health of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) (initial weight 7.00 ± 0.01 g). Eleven isonitrogenous and isolipidic experimental diets were formulated by replacing 0, 20, 40, 60, 80, and 100% of dietary WB with PKC or FPKC. Replacement of WB with PKC concentrations up to 80% had no significant effect on the growth rate of tilapia or feed utilisation (p > 0.05). FPKC improved the growth performance of tilapia, with optimum growth achieved at 40% replacement level (p < 0.05). Complete replacement with PKC significantly decreased the activity of lipase and trypsin, and reduced the height of muscularis and the height of villus (p < 0.05). However, FPKC significantly increased amylase activity and villus height (p < 0.05). The apparent digestibility of dry matter and energy decreased linearly with increasing levels of PKC substitution, while FPKC showed the opposite trend (p < 0.05). PKC replacement of WB by 20% significantly reduced serum diamine oxidase activity and endothelin levels and increased intestinal tight junctions (p < 0.05). However, FPKC significantly decreased diamine oxidase activity and increased intestinal tight junctions (p < 0.05). PKC completely replaced WB, up-regulating the expression of pro-inflammatory factors (il-1β) (p < 0.05). When 40% of WB was replaced with FPKC, the expression of pro-inflammatory factors (il-1β and il-6) was decreased significantly (p < 0.05). Completely replacement of WB with PKC reduced the abundance of Firmicutes and Chloroflexi, while FPKC reduced the abundance of Fusobacteriota and increased the levels of Actinobacteriota. WB can be replaced with PKC up to 80% in tilapia feeds. However, the high percentage of gluten induced intestinal inflammation, impaired gut health, and reduced dietary nutrient utilisation and growth performance. Complete replacement of WB with FPKC promoted intestinal immunity. It also improved dietary nutrient utilisation and growth performance. However, the optimal growth was achieved at a 40% replacement level.

Potential mechanisms of different methylation degrees of pectin driving intestinal microbiota and their metabolites to modulate intestinal health of Micropterus salmoides

Four diets containing 8 % cellulose, low methyl-esterified pectin (LMP), high methyl-esterified pectin (HMP) and MMP (half LMP and half HMP) were designed to evaluate the potential mechanisms by which different esterification degrees of pectin drive intestinal microbiota and their metabolites modulating the intestinal health of Micropterus salmoides. The results showed that both dietary LMP and HMP consistently upregulated intestinal zonula occludens protein 1 (Zo-1), Caludin-1, and Caludin-4, and downregulated intestinal tumor necrosis factor-alpha (TNF-α), interleukin-8 (IL-8), and interleukin-1 beta (IL-1β) gene expression (P < 0.05). Dietary HMP separately upregulated intestinal Occludin, nuclear factor erythroid2-related factor 2 (Nrf2), B-cell lymphoma-2 (Bcl-2), and Bcl-2 associated agonist of cell death (BAD) gene expression, as well as the digesta propionate content, OTUs, Sobs, Shannon, Chao, and ACE indices (P < 0.05), whereas dietary LMP decreased digesta arginine, 4-aminobutyric, L-tyrosine, and phenylalanine contents (P < 0.05). Moreover, dietary HMP decreased plasma lipopolysaccharide and d-lactic acid contents and increased intestinal superoxide dismutase and glutathione peroxidase activities and immunoglobulin (Ig) receptor and IgM levels (P < 0.05). Collectively, dietary HMP improves intestinal health by increasing intestinal flora α-diversity and enhancing intestinal mechanical barrier, anti-inflammatory, antioxidant, and immune functions. On the contrary, the interference of dietary LMP with butyrate, tyrosine, arginine, and 4-aminobutyric acid metabolism is the main reason for its detrimental effects on intestinal health.

The Effects of Different Feeding Regimes on Body Composition, Gut Microbial Population, and Susceptibility to Pathogenic Infection in Largemouth Bass

This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = 50,025 in triplicate, PI, n = 7), and a combination of both (n = 50,025 in triplicate, PFI, n = 8) on different metabolic parameters of the largemouth bass, Micropterus salmoides (0.67 ± 0.09 g, culture period from June 2017 to July 2018). Throughout the experimental period, different areas of water (including input water of the front, middle of the pond, and from the drain off at the back) and their mixed samples were simultaneously analyzed to find the source of the main infectious bacteria. Various feeding strategies may differentially affect body composition and shape the gut microbiota, but the mode of action has not been determined. Results showed that no significant differences were found in the growth performance except for the product yield using a different culture mode (PFI vs. WF). For muscle composition, the higher ∑SFA, ∑MUFA, ∑n-6PUFA, and 18:3n-3/18:2n-6 levels were detected in largemouth bass fed with iced fish, while enrichment in ∑n-3PUFA and ∑HUFA was detected in largemouth bass fed with commercial feed. For the gut microbiota, Fusobacteria, Proteobacteria, and Firmicutes were the most dominant phyla among all the gut samples. The abundance of Firmicutes and Tenericutes significantly decreased and later increased with iced fish feeding. The relative abundance of species from the Clostridia, Mollicutes, Mycoplasmatales, and families (Clostridiaceae and Mycoplasmataceae) significantly increased in the feed plus iced fish (PFI) group relative to that in the iced fish (PI) group. Pathways of carbohydrate metabolism and the digestive system were enriched in the commercial feed group, whereas infectious bacterial disease resistance-related pathways were enriched in the iced fish group, corresponding to the higher rate of death, fatty liver disease, and frequency and duration of cyanobacteria outbreaks. Feeding with iced fish resulted in more activities in the digestive system and energy metabolism, more efficient fatty acid metabolism, had higher ∑MUFA, and simultaneously had the potential for protection against infectious bacteria from the environment through a change in intestinal microbiota in the pond of largemouth bass culturing. Finally, the difference in feed related to the digestive system may contribute to the significant microbiota branch in the fish gut, and the input and outflow of water affects the intestinal flora in the surrounding water and in the gut, which in turn affects growth and disease resistance.

Effects of salinity on growth, physiology, biochemistry and gut microbiota of juvenile grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is among the most important freshwater fish species in China. However, it remained unclear how salinity could affect grass carp. Two experiments were performed. The first experiment was a 4-day acute salt tolerance experiment with six salinities (0, 4, 8, 12, 16, and 20 ppt). The second experiment was an 8-week chronic salt stress experiment with three salinities (0, 2 and 6 ppt). To investigate the intestinal bacterial community of grass carp from three salinities (0, 2, and 6 ppt), the 16S rDNA sequencing was performed. The results showed that grass carp exhibited great adaptability to low salinity (2 ppt), with no significant difference in growth and maintained stable physiological and immune status. However, exposed to high salinity (6 ppt) caused significant deleterious effects on grass carp, including growth inhibition as well as physiological and immune-related changes. The gut microbiota in grass carp changed with salinity. With the increase of salinity, the proportion of beneficial bacteria in the gut of grass carp gradually decreased, while some harmful bacteria gradually occupied the dominant position. Changes in gut microbial composition ultimately affected the growth of grass carp. This study helps further clarify the effects of salinity on grass carp.

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.

Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla)

In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.

High Dietary Histamine Induces Digestive Tract Oxidative Damage in Juvenile Striped Catfish (Pangasianodon hypophthalmus)

A 56-day feeding trial investigated the effects of dietary histamine on the antioxidant capacity, gastric and intestinal barrier functions, and growth performance of striped catfish (Pangasianodon hypophthalmus). Seven isonitrogenous (34.0% crude protein) and isolipidic (10.5% crude lipid) diets were formulated with supplemental 0, 15, 30, 60, 120, 240, and 480 mg/kg of histamine, named H0, H15, H30, H60, H120, H240, and H480 group, respectively. Results showed that the weight gain rate, specific growth rate, relative intestinal length in the H240 and H480 groups, and the condition factors in the H480 group were significantly lower than those in the H0 group. Intestinal total antioxidant capacity, peroxidase, catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase activities in the H480 group were significantly lower than those in the H0 group, whereas intestinal malondialdehyde content exhibited the opposite trend. Intestinal complement 3, complement 4, immunoglobulin M, and Recombinant Mucin 2 in the H480 group were significantly lower than those in the H0 group, in contrast to intestinal lipopolysaccharide content. Intestinal IL-10 gene expression in the H480 group was significantly lower than that in the H0 group, whereas the TNF-α, IL-1, IL-6, and IL-8 gene expression exhibited opposite results. Scanning and transmission electron microscopic observation of the gastrointestinal tract revealed severe damage to the gastric mucosa and intestinal epithelium in the H480 group. The abundance of Treponema in the histamine groups was significantly higher than that in the H0 group. These results indicated that high dietary histamine decreases intestinal immunity and antioxidant capacity, inducing digestive tract oxidative damage and ultimately decreasing the growth of striped catfish.

Intestinal flora and immunity response to different viscous diets in juvenile largemouth bass, Micropterus salmoides

An 8-weeks feeding trial was conducted to estimate the effects of different viscous cellulose on the intestinal flora and health in juvenile largemouth bass (Micropterus salmoides). Four isoproteic and isolipidic experimental diets were formulated (crude protein 42.50%, crude lipid 13.70%) to contain 8% cellulose (control group; 5.14 mPa s), 8% low viscous carboxymethyl cellulose (CMC) with 800 mPa s (Lvs-CMC group; 182.15 mPa s), 8% middle viscous CMC with 2000 mPa s (Mvs-CMC group; 320.48 mPa s) and 8% high viscous CMC with 5000 mPa s (Hvs-CMC group; 440.65 mPa s), respectively. The weight gain rate, specific growth rate, protein efficiency ratio, protein and lipid deposition rate in the CMC groups were dramatically lower than those in the control group, while feed conversion rate showed an opposite result. Plasma diamine oxidase activity, endothelin-1 and lipopolysaccharide concentrations in the Mvs-CMC and Hvs-CMC groups were significantly higher than in the control group, accompanied by a significant down-regulation of Occludin, Caludin-1 and Caludin-4. Intestinal glutathione concentration, superoxide dismutase and catalase activities in the CMC groups were significantly lower than in the control group, accompanied by a significant up-regulation of Keap1 and down-regulation of Nrf2. Moreover, CMC diets dramatically down-regulated the expression levels of IL-10 and TGF-β1. Digesta total short chain fatty acid and acetate concentrations in the CMC groups were dramatically higher than in the control group, while butyrate concentration showed an opposite result. The OTU, Sobs, Shannon and Simpson indices of intestinal flora in the CMC groups were dramatically lower than in the control group. Notably, structural analysis showed that dietary CMC dramatically increased the abundance of C. somerae and P. shigelloides, but reduced the abundance of C. colicanis and C. perfringens. In summary, increasing dietary viscosity adversely affects the intestinal flora structure and diversity, increases acetate/butyrate-producing bacterial ratio and the abundance of pathogenic microorganisms, disrupting intestinal flora homeostasis, impairs mucosa barrier function, induces intestinal inflammation and epithelial cell apoptosis in juvenile largemouth bass. Our findings demonstrate that soluble cellulose is more detrimental to intestinal health and growth in juvenile largemouth bass compared to insoluble cellulose, and the adverse effects of soluble cellulose are mainly caused by its viscosity. Importantly, this study demonstrate that viscosity is the main characteristic of non-starch polysaccharides that are detrimental to the intestinal health of fish.

Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals

Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities.

Dietary supplementation with Bacillus subtilis and xylo-oligosaccharides improves growth performance and intestinal morphology and alters intestinal microbiota and metabolites in weaned piglets

The present study was conducted to investigate the effects of dietary supplementation with Bacillus subtilis (BS) and xylo-oligosaccharides (XOS) on growth performance, intestinal morphology, intestinal microbial community, and metabolites of weaned piglets. One hundred and twenty-eight piglets were randomly allocated to one of four groups, including a control group (basal diet), BS group (basal diet + 500 g t-1 BS), XOS group (basal diet + 250 g t-1 XOS), and BS + XOS group (basal diet + 500 g t-1 BS + 250 g t-1 XOS). Dietary BS and XOS were mixed with the basal diet. All groups had eight replicates with four piglets per replicate. The experiment lasted for 42 days. The results showed that dietary XOS supplementation increased the ADFI and ADG, while decreasing the F/G. Dietary BS or XOS supplementation improved the intestinal morphology of weaned piglets by increasing the villus height and the ratio of villus height to crypt depth in the ileum. In addition, dietary XOS supplementation increased the concentrations of butyrate in the ileum and tryptamine and spermidine in the colon, while decreasing the concentration of indole in the colon compared with the control group. Dietary BS supplementation increased the colonic concentrations of butyrate, tryptamine, and cadaverine, while decreasing the concentration of skatole compared with the control group. The LEfSe analysis identified 16 biomarkers in the ileum of the BS group. The intestinal microbiota alterations of weaned piglets indicated that dietary BS or XOS supplementation could improve intestinal health by increasing the gut microbial diversity and altering the relative abundances of different bacterial species. Moreover, Spearman's correlation analysis revealed the potential link between gut microbiota alterations and metabolite changes of weaned piglets. These findings suggest that dietary XOS supplementation could alone improve the growth performance, while dietary BS or XOS and BS with XOS supplementation could influence intestinal health by altering the intestinal morphology, microbial community, and metabolites of weaned piglets. Meanwhile, there were interactions between BS and XOS in intestinal metabolites.

Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes

Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.

Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)

This study aimed to analyze the intestinal flora of male versus female swamp eels, which have the unique characteristic of sex reversal. Same-aged swamp eels from the same parents, kept under the same conditions in terms of environment, diet, etc., were used as the study materials. After breeding for 1 year, 18 healthy swamp eels (nine males and nine females), weighing 39.4 ± 2.3 g, were selected. The intestinal contents of three swamp eels of the same sex were combined and labeled as follows: FM1-FM3 (n = 3) for females and MM1-MM3 (n = 3) for males. High-throughput sequencing was used to research the v3-v4 region of 16S rDNA in the intestinal flora. The results suggested significant differences in the structure, composition, and diversity of the intestinal flora of male versus female swamp eels. The relative abundances of Actinobacteria and Spirochaetes in female swamp eels were significantly higher (p < 0.05) than in male swamp eels at the phylum level. The relative abundances of Mycobacterium, Bacillus, and Vagococcus in female swamp eels were considerably higher (p < 0.05) than in male swamp eels at the genus level. The Alpha diversity of females was higher than that of males, and the Shannon index of females was also significantly higher (p < 0.05, Tukey’s HSD) than that in males. Investigations of Beta diversity, including NMDS ordination, UPGMA cluster analysis, and PLS-DA analysis, showed that female and male swamp eels could be clearly distinguished based on significant differences in intestinal flora between the FM group and the MM group. LEfSe analysis showed that the dominant bacteria were Cetobacterium in male swamp eels and Clostridium_sp_ND2, Mycobacterium, Alphaproteobacteria, and Bacilli in female swamp eels. The results showed dramatic differences in the intestinal flora between the sexes, which indicates the need for a more in-depth study on sex reversal in the future.

Studies of the mechanism of fatty liver formation in Takifugu fasciatus following copper exposure

Fatty liver is widely observed during Takifugu fasciatus production, but the mechanisms underlying fatty liver formation remain unknown. The present study was conducted to determine the potential effects of copper (Cu) on hepatic lipid deposition and metabolism in T. fasciatus after 21 days of exposure to Cu (levels: 0, 20 and 100 μg/L). Copper exposure decreased the weight gain rate (WG) in T. fasciatus, but increased the values of the viscerosomatic index (VSI) and hepatosomatic index (HSI) compared with the control. The time-dependent Cu accumulation in tissues increased as the Cu concentration increased. The order of Cu accumulation was liver > intestine > muscle. The lipid content, triglyceride (TG) content and lipoprotein lipase (LPL) activity increased after Cu exposure compared with the control. In addition, more lipid droplets and greater vacuolization were observed in the liver after exposure to 20 μg/L Cu than after 100 μg/L Cu. The expression of genes involved in lipogenesis (g6pd, 6pgd, lpl, fas and acc), lipolysis (hsl and cpt 1) and transcription (ppar α and ppar ^©) was dependent on Cu. An analysis of the intestinal microbiome community showed that the highest values of the Chao 1 index, ACE, Shannon index and Simpson index were obtained in fish exposed to 20 μg/L Cu, whereas the lowest values were obtained after the 100 μg/L Cu treatment. The Principal Coordinates Analysis (PCoA) plots of the data revealed structural differences in the groups treated with Cu compared with the control group. At the phylum level, the intestinal microbiota in the Cu-treated and control fish were dominated by Proteobacteria and Bacteroidetes. The higher Firmicutes to Bacteroidetes ratio was observed in fish treated with 20 μg/L Cu compared with other groups, while the lowest ratio was observed in fish exposed to 100 μg/L Cu. Our study revealed the mechanisms by which Cu exposure altered (i) lipid deposition in the body and (ii) the intestinal microbiome, which may contribute to maintain the health status of T. fasciatus for the aquaculture.

Comparative analysis of the composition and function of fecal-gut bacteria in captive juvenile Crocodylus siamensis between healthy and anorexic individuals

The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.

Gut microbiota of newborn piglets with intrauterine growth restriction have lower diversity and different taxonomic abundances

Aim

Intrauterine growth retardation (IUGR) is a prevalent problem in mammals. The present study was conducted to unveil the alterations in intestinal microbiota in IUGR piglets.

Methods and Results

We identified the alterations of small intestinal microbiota in IUGR piglets on 7, 21 and 28 days of age using 16S rRNA sequencing. The results showed that IUGR piglets had a decreased alpha diversity of jejunum microbiota at 7 and 21 days of age; had lower abundances of Bacteroidetes and Bacteroides in the jejunum at 7, 21 and 28 days of age, Oscillibacter in the jejunum at 21 days of age, and Firmicutes in the ileum at 21 days of age; whereas they had higher abundances of Proteobacteria and Pasteurella in the ileum at 21 days of age and Escherichia–Shigella in the jejunum at 28 days of age. Correlation analysis showed that Bacteroides, Oscillibacter and Ruminococcaceae_UCG‐002 compositions were positively associated with the body weight (BW) of IUGR piglets, nevertheless Proteobacteria and Escherichia–Shigella relative abundances were negatively correlated with the BW of IUGR piglets. Gene function prediction analysis indicated that microbiota‐associated carbohydrate metabolism, lipid metabolism, glycan biosynthesis and metabolism, amino acid metabolism, and xenobiotics biodegradation and metabolism were downregulated in the IUGR piglets compared to control piglets.

Conclusions

The present study profiled the intestinal microbiota of newborn piglets with IUGR and the newborn IUGR piglets have lower diversity and different taxonomic abundances. Alterations in the abundances of Bacteroidetes, Bacteroides, Proteobacteria Escherichia–Shigella and Pasteurella may be involved in nutrient digestion and absorption, as well as the potential mechanisms connecting to the growth and development of IUGR in mammals.

Significance and Impact of the Study

The small intestinal microbiota were highly shaped in the IUGR piglets, which might further mediate the growth and development of IUGR piglets; and the gut microbiota could serve as a potential target for IUGR treatment.