Faecal microbiota and functional capacity associated with weaning weight in meat rabbits

Study on Changes in Gut Microbiota and Microbiability in Rabbits at Different Developmental Stages

This study used feces from 0-day-old (36 rabbits), 10-day-old (119 rabbits), and 60-day-old (119 rabbits) offspring rabbits and their corresponding female rabbits (36 rabbits) as experimental materials. Using 16s rRNA sequencing, the study analyzed the types and changes of gut microbiota in rabbits at different growth and development stages, as well as the correlation between gut microbiota composition and the weight of 60-day-old rabbits. All experimental rabbits were placed in the same rabbit shed. Juvenile rabbits were fed solid feed at 18 days of age and weaned at 35 days of age. In addition to identifying the dominant bacterial phyla of gut microbiota in rabbits at different age stages, it was found that the abundance of Clostridium tertium and Clostridium paraputrificum in all suckling rabbits (10-day-old) was significantly higher than that in rabbits fed with whole feed (60-day-old) (p < 0.05), while the abundance of Gram-negative bacterium cTPY13 was significantly lower (p < 0.05). In addition, Fast Expected Maximum Microbial Source Tracing (FEAST) analysis showed that the contribution of female rabbits' gut microbiota to the colonization of offspring rabbits' gut microbiota was significantly higher than that of unrelated rabbits' gut microbiota (p < 0.05). The contribution of female rabbits' gut microbiota to the colonization of gut microbiota in 0-day-old rabbits was significantly higher than that to the colonization of gut microbiota in the 10- and 60-day-old rabbits (p < 0.05). Finally, the correlation between gut microbiota composition and body weight of 60-day-old rabbits was analyzed based on a mixed linear model, and six ASVs significantly affecting body weight were screened. The above results provide important theoretical and practical guidance for maintaining gut health, improving growth and development performance, and feeding formulation in rabbits.

Lactic acid bacteria reduce bacterial diarrhea in rabbits via enhancing immune function and restoring intestinal microbiota homeostasis

BACKGROUND

Numerous previous reports have demonstrated the efficacy of Lactic acid bacteria (LAB) in promoting growth and preventing disease in animals. In this study, Enterococcus faecium ZJUIDS-R1 and Ligilactobaciiius animalis ZJUIDS-R2 were isolated from the feces of healthy rabbits, and both strains showed good probiotic properties in vitro. Two strains (108CFU/ml/kg/day) were fed to weaned rabbits for 21 days, after which specific bacterial infection was induced to investigate the effects of the strains on bacterial diarrhea in the rabbits.

RESULTS

Our data showed that Enterococcus faecium ZJUIDS-R1 and Ligilactobaciiius animalis ZJUIDS-R2 interventions reduced the incidence of diarrhea and systemic inflammatory response, alleviated intestinal damage and increased antibody levels in animals. In addition, Enterococcus faecium ZJUIDS-R1 restored the flora abundance of Ruminococcaceae1. Ligilactobaciiius animalis ZJUIDS-R2 up-regulated the flora abundance of Adlercreutzia and Candidatus Saccharimonas. Both down-regulated the flora abundance of Shuttleworthia and Barnesiella to restore intestinal flora balance, thereby increasing intestinal short-chain fatty acid content.

CONCLUSIONS

These findings suggest that Enterococcus faecium ZJUIDS-R1 and Ligilactobaciiius animalis ZJUIDS-R2 were able to improve intestinal immunity, produce organic acids and regulate the balance of intestinal flora to enhance disease resistance and alleviate diarrhea-related diseases in weanling rabbits.

Exploring the Rumen Microbiota and Serum Metabolite Profile of Hainan Black Goats with Different Body Weights before Weaning

The critical role of the rumen microbiota in the growth performance of livestock is recognized, yet its significance in determining the body weight of goat kids before weaning remains less understood. To bridge this gap, our study delved into the rumen microbiota, serum metabolome, rumen fermentation, and rumen development in goat kids with contrasting body weights before weaning. We selected 10 goat kids from a cohort of 100, categorized into low body weight (LBW, 5.56 ± 0.98 kg) and high body weight (HBW, 9.51 ± 1.01 kg) groups. The study involved sampling rumen contents, tissues, and serum from these animals. Our findings showed that the HBW goat kids showed significant enrichment of VFA-producing bacteria, particularly microbiota taxa within the Prevotellaceae genera (UCG-001, UCG-003, and UCG-004) and the Prevotella genus. This enrichment correlated with elevated acetate and butyrate levels, positively influencing rumen papillae development. Additionally, it was associated with elevated serum levels of glucose, total cholesterol, and triglycerides. The serum metabonomic analysis revealed marked differences in fatty acid metabolism between the LBW and HBW groups, particularly in encompassing oleic acid and both long-chain saturated and polyunsaturated fatty acids. Further correlational analysis underscored a significant positive association between Prevotellaceae_UCG-001 and specific lipids, such as phosphatidylcholine (PC) (22:5/18:3) and PC (20:3/20:1) (r > 0.60, p < 0.05). In summary, this study underscores the pivotal role of the rumen microbiota in goat kids' weight and its correlation with specific serum metabolites. These insights could pave the way for innovative strategies aimed at improving animal body weight through targeted modulation of the rumen microbiota.

Temporal and spatial variations in body mass and thermogenic capacity associated with alterations in the gut microbiota and host transcriptome in mammalian herbivores

Most wild animals follow Bergmann's rule and grow in body size as cold stress increases. However, the underlying thermogenic strategies and their relationship with the gut microbiota have not been comprehensively elucidated. Herein, we used the plateau pikas as a model to investigate body mass, thermogenic capacity, host transcriptome, gut microbiota and metabolites collected from seven sites ranging from 3100 to 4700 m on the Qinghai-Tibetan Plateau (QTP) in summer and winter to test the seasonal thermogenesis strategy in small herbivorous mammals. The results showed that the increase in pika body mass with altitude followed Bergmann's rule in summer and an inverted parabolic shape was observed in winter. However, physiological parameters and transcriptome profiles indicated that the thermogenic capacity of pikas increased with altitude in summer and decreased with altitude in winter. The abundance of Firmicutes declined, whereas that of Bacteroidetes significantly increased with altitude in summer. Phenylalanine, tyrosine, and proline were enriched in summer, whereas carnitine and succinate were enriched in winter. Spearman's correlation analysis revealed significant positive correlations between Prevotella, Bacteroides, Ruminococcus, Alistipes and Akkermansia and metabolites of amino acids, pika physiological parameters, and transcriptome profiles. Moreover, metabolites of amino acids further showed significant positive correlations with pika physiological parameters and transcriptome profiles. Our study highlights that the changes in body mass and thermogenic capacity with altitude distinctly differentiate small herbivorous mammals between summer and winter on the QTP, and that the gut microbiota may regulate host thermogenesis through its metabolites.

Seasonal Variations in Production Performance, Health Status, and Gut Microbiota of Meat Rabbit Reared in Semi-Confined Conditions

In this study, we investigated the variations in production performance, health status, and gut microbiota of meat rabbits raised in the semi-confined barn during summer and winter. Compared to summer, rabbits reared in winter possessed significantly higher slaughter weight and carcass weight. Rabbits fed in the summer were more vulnerable to different stressors, which led to increased protein levels of HSP90, IL-1α, IL-1β, IL-2, and concentrations of MDA, but declined GSH and SOD activities. Additionally, significant differences in gut microbial communities were observed. Compared to the winter, rabbits fed in the summer had significantly lower and higher alpha and beta diversity. Both Firmicutes and Verrucomicrobiota were the dominant phyla, and they accounted for greater proportions in the winter than in the summer. At lower microbial taxa levels, several seasonal differentially enriched microbes were identified, such as Akkermansia muciniphila, the Oscillospiraceae NK4A214 group, the Christensenellaceae R-7 group, Alistipes, and Muribaculaceae. Functional capacities linked to microbial proliferation, nutrient metabolism, and environmental adaptive responses exhibited significantly different abundances between summer and winter. Moreover, strong interactions among different indicators were presented. Based on our findings, we not only proposed several potential strategies to ameliorate the undesirable effects of seasonal changes on the productivity and health of meat rabbits but also underscored the directions for future mechanistic studies of adaptation physiology.

The Diversity of Gut Microbiota at Weaning Is Altered in Prolactin Receptor-Null Mice

Maternal milk supports offspring development by providing microbiota, macronutrients, micronutrients, immune factors, and hormones. The hormone prolactin (PRL) is an important milk component with protective effects against metabolic diseases. Because maternal milk regulates microbiota composition and adequate microbiota protect against the development of metabolic diseases, we aimed to investigate whether PRL/PRL receptor signaling regulates gut microbiota composition in newborn mice at weaning. 16SrRNA sequencing of feces and bioinformatics analysis was performed to evaluate gut microbiota in PRL receptor-null mice (Prlr-KO) at weaning (postnatal day 21). The normalized colon and cecal weights were higher and lower, respectively, in the Prlr-KO mice relative to the wild-type mice (Prlr-WT). Relative abundances (Simpson Evenness Index), phylogenetic diversity, and bacterial concentrations were lower in the Prlr-KO mice. Eleven bacteria species out of 470 differed between the Prlr-KO and Prlr-WT mice, with two genera (Anaerotruncus and Lachnospiraceae) related to metabolic disease development being the most common in the Prlr-KO mice. A higher metabolism of terpenoids and polyketides was predicted in the Prlr-KO mice compared to the Prlr-WT mice, and these metabolites had antimicrobial properties and were present in microbe-associated pathogenicity. We concluded that the absence of the PRL receptor altered gut microbiota, resulting in lower abundance and richness, which could contribute to metabolic disease development.

Diversity and Co-Occurrence Pattern Analysis of Cecal and Jejunal Microbiota in Two Rabbit Breeds

This study aimed to evaluate the productive performance and microbiota variation in the jejunum and cecum of two rabbit breeds with different growth rates. This study was carried out on Native Middle-Egypt Breed (NMER) and Giant Flanders (GF) rabbits from 5 weeks to 12 weeks of age. Twenty NMER (NM) and GF male rabbits were slaughtered, and the jejunum and cecum tracts were collected to assay gut microbiota composition via 16S ribosomal RNA (rRNA) gene sequencing and histology examination. At 12 weeks of age, daily weight gain, villus height in the jejunum, total protein, and albumin were higher in GF rabbits than in NMER rabbits. Also, the jejunal villi of GF were well arranged in their dense borders. The microbiota between the jejunum and cecum was significantly different in terms of Beta-diversity. A significant correlation between Enterococcus (jejunum NM samples) and Lactobacillus (cecum GF samples) with body weight and weight gain was found (p < 0.05). Moreover, Escherichia-Shigella in the cecum of NM was significantly correlated with weight gain (p < 0.05). The most abundant genera identified in the jejunal and cecal contents of GF were generally beneficial microbiota. They may also play a role in reducing the pathogenic effects of Escherichia coli in these rabbits.

Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges

As one of the promising next-generation probiotics (NGPs), Akkermansia muciniphila, a well-known mucin-degrading bacterium, has been proven to be closely related to the metabolic diseases of its human host. However, the role of A. muciniphila in the host’s intestinal health remains ambiguous. Here, we comprehensively summarize and discuss the characteristics, the distribution, and the colonization of A. muciniphila in the human gastrointestinal tract (GIT). We propose that the application of A. muciniphila as a biomarker for longevity, for diagnostics and prognostics of intestinal diseases, or for intestinal health should be cautiously considered. Precise dietary regulation can mediate the treatment of intestinal diseases by altering the abundance of A. muciniphila. Although the beneficial role of A. muciniphila and its component in intestinal inflammation has been discovered, in gnotobiotic mice with specific gut microbiota, certain genotype, and colorectal cancer, or in animal models infected with a specific pathogen, A. muciniphila may be related to the occurrence and development of intestinal diseases. Genomic analysis, emphasizing the strain-level phylogenetic differences of A. muciniphila, indicates that a clear description and discussion of each strain is critical before its practical application. Our review provides much needed insight for the precise application of A. muciniphila.

Microbiomics Revealed the Disturbance of Intestinal Balance in Rabbits with Diarrhea Caused by Stopping the Use of an Antibiotic Diet

The harmful effects of diarrhea on the growth performance of rabbits have been well documented, but the details of the potential mechanism of intestinal diarrhea when antibiotics are stopped are still unclear. Here, PacBio sequencing technology was used to sequence the full length 16S rRNA gene of the microbiota of intestinal content samples, in order to characterize the bacterial communities in the small intestine (duodenum and jejunum) and large intestine (colon and cecum) in normal Hyplus rabbits and those with diarrhea. The histopathological examination showed that intestinal necrosis occurred in different degrees in the diarrhea group, and that the mucosal epithelium was shed and necrotic, forming erosion, and the clinical manifestation was necrosis. However, the intestinal tissue structure of the normal group was normal. The results revealed that there were significant differences in bacterial communities and structure between the diarrhea and normal groups of four intestinal segments (p < 0.05). In general, 16 bacterial phyla, 144 bacterial genera and 22 metabolic pathways were identified in the two groups. Tax4Fun functional prediction analysis showed that KEGG related to amino acid metabolism and energy metabolism was enriched in the large intestines of rabbits with diarrhea, whereas lipid metabolism was more abundant in the small intestine of rabbits with diarrhea. In conclusion, the change in the relative abundance of the identified dominant microbiota, which could deplete key anti-inflammatory metabolites and lead to bacterial imbalance and diarrhea, resulted in diarrhea in Hyplus rabbits that stopped using antibiotics.

Active or Autoclaved Akkermansia muciniphila Relieves TNF-α-Induced Inflammation in Intestinal Epithelial Cells Through Distinct Pathways

Intestinal inflammation is a major threat to the health and growth of young animals such as piglets. As a next-generation probiotics, limited studies have shown that Akkermansia muciniphila could alleviate inflammation of intestinal epithelial cells (IECs). In this study, a TNF-α-induced inflammatory model of IPEC-J2 cells, the intestinal porcine enterocytes, was built to evaluate the effects of active or inactive A. muciniphila on the inflammation of IECs. The viability of IPEC-J2 cells was the highest when treated with active (10⁸ copies/mL) or inactive (10⁹ copies/mL) A. muciniphila for 7.5 h (P < 0.01). Treated with 20 ng/mL of TNF-α and followed by a treatment of A. muciniphila, the mRNA level of proinflammatory cytokines (IL-8, IL-1β, IL-6 and TNF-α) was remarkably reduced (P < 0.05) along with the increased mRNA level of tight junction proteins (ZO-1 and Occludin, P < 0.05). Flow cytometry analysis showed that active or inactive A. muciniphila significantly suppressed the rate of the early and total apoptotic of the inflammatory IPEC-J2 cells (P < 0.05). According to results of transcriptome sequencing, active and inactive A. muciniphila may decline cell apoptosis by down-regulating the expression of key genes in calcium signaling pathway, or up-regulating the expression of key genes in cell cycle signaling pathway. And the bacterium may alleviate the inflammation of IECs by down-regulating the expression of PI3K upstream receptor genes. Our results indicate that A. muciniphila may be a promising NGP targeting intestinal inflammation.

Medium chain triglycerides improve the growth performance, immune and antioxidant functions, and intestinal health of weaned rabbits

The purpose is to study the effects of different doses of medium chain triglyceride (MCT) on growth performance, immune and oxidative functions, and intestinal health of weaned rabbits. A total of 600 weaned rabbits weighing about 993.26 g and at 35 d of age were randomly divided into five groups. The control group was fed a basal diet containing 2400 mg/kg soybean oil, and the experimental group was substituted with 600, 1200, 1800, and 2400 mg/kg MCT. The whole trial period lasted for 48 d. The results showed that treatment with 2400 mg/kg MCT significantly increased the weaning survival rate and crude fat digestibility (p < 0.05) and dramatically raised the levels of serum immunoglobulin (Ig)A, IgG, IgM, catalase, superoxide dismutase, and total antioxidant capability (p < 0.05). The villus height and crypt depth in 1800 mg/kg MCT group were observably enhanced (p < 0.05). The abundance of Bacteroidetes was significantly increased in 1800 and 2400 mg/kg MCT groups (p < 0.05). In conclusion, 1800 and 2400 mg/kg MCT substituting soybean oil in the diet of weaned rabbits can improve the growth performance and intestinal barrier function of weaned rabbits.

Gut microbiota alterations in response to sleep length among African-origin adults

Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.

Effects of ammonia on growth performance, lipid metabolism and cecal microbial community of rabbits

This study was designed to investigate the effect of ammonia on growth performance, lipid metabolism and intestinal flora of rabbits. A total of 150 female IRA rabbits (35-days-old) were randomly divided into three groups including 0 ppm (CG), 10 ppm (LAC) and 30 ppm ammonia (HAC) groups for a period of 28 days. The average daily weight gain (ADG) of rabbits was significantly reduced in LAC (-17.11%; p < 0.001) and HAC groups (-17.46%; p < 0.001) as compared with the CG. Serum concentration of high density lipoprotein (HDL) and glucose (Glu) were increased in LAC (+80.95%; +45.99; p < 0.05) and HAC groups (+219.05%; +45.89; p < 0.001), while apolipoprotein A1 (apoA1) was decreased in LAC (-58.49%; p < 0.001) and HAC groups (-36.92%; p < 0.001). The structural integrity of cecum was damaged, and the thickness of mucosa and serosa were significantly decreased in LAC and HAC. The acetate, butyrate and propionate level of cecal chyme were reduced in HAC group (-21.67%; -19.82%; -30.81%; p < 0.05). Microbial diversity and burden of Firmicutes were significantly decreased, while that of pathogenic bacteria, such as Bacteroidetes, Clostridium and Proteobacteria were increased in ammonia treated groups. Spearman's correlation confirmed that burden of Ruminococcaceae_NK4A214_group showed significantly negative correlation with acetic acid (r = -0.67; p < 0.001) while Barnesiellaceae_unclassified showed significantly positive correlation with propionic acid (r = 0.50; p < 0.001). In conclusion, ammonia treatment was responsible for an imbalance of intestinal flora, which affected lipid metabolism and damaged intestinal barrier of rabbits, resulting in low growth performance due to lipid metabolism dysfunction.

Enterococcus faecium PNC01 isolated from the intestinal mucosa of chicken as an alternative for antibiotics to reduce feed conversion rate in broiler chickens

Background

The development and utilization of probiotics had many environmental benefits for replacing antibiotics in animal production. Bacteria in the intestinal mucosa have better adhesion to the host intestinal epithelial cells compared to bacteria in the intestinal contents. In this study, lactic acid bacteria were isolated from the intestinal mucosa of broiler chickens and investigated as the substitution to antibiotic in broiler production.

Results

In addition to acid resistance, high temperature resistance, antimicrobial sensitivity tests, and intestinal epithelial cell adhesion, Enterococcus faecium PNC01 (E. faecium PNC01) was showed to be non-cytotoxic to epithelial cells. Draft genome sequence of E. faecium PNC01 predicted that it synthesized bacteriocin to perform probiotic functions and bacteriocin activity assay showed it inhibited Salmonella typhimurium from invading intestinal epithelial cells. Diet supplemented with E. faecium PNC01 increased the ileal villus height and crypt depth in broiler chickens, reduced the relative length of the cecum at day 21, and reduced the relative length of jejunum and ileum at day 42. Diet supplemented with E. faecium PNC01 increased the relative abundance of Firmicutes and Lactobacillus, decreased the relative abundance of Bacteroides in the cecal microbiota.

Conclusion

E. faecium PNC01 replaced antibiotics to reduce the feed conversion rate. Furthermore, E. faecium PNC01 improved intestinal morphology and altered the composition of microbiota in the cecum to reduce feed conversion rate. Thus, it can be used as an alternative for antibiotics in broiler production to avoid the adverse impact of antibiotics by altering the gut microbiota.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01609-z.

Identification of the relationship between the gut microbiome and feed efficiency in a commercial pig cohort

Feed efficiency (FE) is an economically important trait in pig production. Gut microbiota plays an important role in energy harvest, nutrient metabolism, and fermentation of dietary indigestible components. Whether and which gut microbes affect FE in pigs are largely unknown. Here, a total of 208 healthy Duroc pigs were used as experimental materials. Feces and serum samples were collected at the age of 140 d. We first performed 16S rRNA gene and metagenomic sequencing analysis to investigate the relationship between the gut microbiome and porcine residual feed intake (RFI). 16S rRNA gene sequencing analysis detected 21 operational taxonomic units showing the tendency to correlation with the RFI (P < 0.01). Metagenomic sequencing further identified that the members of Clostridiales, e.g., Ruminococcus flavefaoiens, Lachnospiraceae bacterium 28-4, and Lachnospiraceae phytofermentans, were enriched in pigs with low RFI (high-FE), while 11 bacterial species including 5 Prevotella spp., especially, the Prevotella copri, had higher abundance in pigs with high RFI. Functional capacity analysis suggested that the gut microbiome of low RFI pigs had a high abundance of the pathways related to amino acid metabolism and biosynthesis, but a low abundance of the pathways associated with monosaccharide metabolism and lipopolysaccharide biosynthesis. Serum metabolome and fecal short-chain fatty acids were determined by UPLC-QTOF/MS and gas chromatography, respectively. Propionic acid in feces and the serum metabolites related to amino acid metabolism were negatively correlated with the RFI. The results from this study may provide potential gut microbial biomarkers that could be used for improving FE in pig production industry.

Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

The microbiota is extremely important for the animal's health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species, while the highest variability was found in the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.

Yeast cell wall product enhanced intestinal IgA response and changed cecum microflora species after oral vaccination in chickens

The study was designed to explore the effect of a commercial yeast cell wall product (YP) on chicken intestinal IgA response and cecum microbiome after oral vaccination. Chickens were fed with YP during the experiments and orally immunized with live Newcastle disease virus (NDV) vaccine at 2 wk of age. Then, the animals were sacrificed, and samples were collected to measure the indicators of hemagglutination inhibition (HI), IgA response, IgA + cells, and cecum microbiome populations. The results showed that supplement of YP significantly enhanced serum NDV HI titer, intestinal NDV-specific secretory IgA, and intestinal IgA + cells. The sequencing results revealed that obviously increased relative abundance of Ruminococcaceae and decreased population of Bacteroidaceae in cecum were found in YP group. In summary, YP supplementation in diet enhanced intestinal IgA response to NDV vaccination by oral route and modulated the cecum microbiota to the advantage of the host in chickens.

Highly nutritious diet resists Salmonella Typhimurium infections by improving intestinal microbiota and morphology in broiler chickens

Salmonella Typhimurium (S. Typhimurium) infection in broiler chickens threatens public health and livestock production. In this study, we explored the effects of highly nutritious (crude protein 21.8%, metabolizable energy 3.16 Mcal/kg) and lowly nutritious (crude protein 18.1%, metabolizable energy 2.98 Mcal/kg) diets on S. Typhimurium infection by altering the intestinal morphology and environment in broiler chickens. The highly nutritious diet significantly increased the body weight gain and reduced feed conversion ratio on day 1 to 21 (P < 0.01). The highly nutritious diets promoted the intestinal villus height, crypt depth, and their ratio to improve the intestinal epithelial maturation (P < 0.05). Highly nutritious diets significantly increased the expression of claudin-1, occludin, and NF-κB genes in the intestinal epithelium on the days of 14 and 21 (P < 0.05). S. Typhimurium activated the expression of TLR4, MyD88, and NF-κB genes to cause an inflammatory response. The S. Typhimurium can increase the activity of myeloperoxidase, which cause an inflammatory response. The S. Typhimurium significantly reduced the diversity indexes of the ileal microbiota (P < 0.05), increased the abundance of Cyanobacteria which can synthesize toxins. The highly nutritious diet group challenged with S. Typhimurium can increase the abundance of Lactobacillus in the ileum, which lead to improved intestinal health (P < 0.05). It is concluded that increasing the nutritional level of dietary is beneficial to improve the resistance to S. Typhimurium infection by altering the intestinal bacterial community.

Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits

Understanding how the gut microbiome and short-chain fatty acids (SCFAs) affect finishing weight is beneficial to improve meat production in the meat rabbit industry. In this study, we identified 15 OTUs and 23 microbial species associated with finishing weight using 16S rRNA gene and metagenomic sequencing analysis, respectively. Among these, butyrate-producing bacteria of the family Ruminococcaceae were positively associated with finishing weight, whereas the microbial taxa related to intestinal damage and inflammation showed opposite effects. Furthermore, interactions of these microbial taxa were firstly found to be associated with finishing weight. Gut microbial functional capacity analysis revealed that CAZymes, such as galactosidase, xylanase, and glucosidase, could significantly affect finishing weight, given their roles in regulating nutrient digestibility. GOs related to the metabolism of several carbohydrates and amino acids also showed important effects on finishing weight. Additionally, both KOs and KEGG pathways related to the membrane transportation system and involved in aminoacyl-tRNA biosynthesis and butanoate metabolism could act as key factors in modulating finishing weight. Importantly, gut microbiome explained nearly 11% of the variation in finishing weight, and our findings revealed that a subset of metagenomic species could act as predictors of finishing weight. SCFAs levels, especially butyrate level, had critical impacts on finishing weight, and several finishing weight-associated species were potentially contributed to the shift in butyrate level. Thus, our results should give deep insights into how gut microbiome and SCFAs influence finishing weight of meat rabbits and provide essential knowledge for improving finishing weight by manipulating gut microbiome.

Antimicrobial Effects of Black Soldier Fly and Yellow Mealworm Fats and Their Impact on Gut Microbiota of Growing Rabbits

This study aimed to evaluate the in vitro antimicrobial activities of two types of insect fats extracted from black soldier fly larvae (HI, Hermetia illucens L.) and yellow mealworm larvae (TM, Tenebrio molitor L.) and their effects as dietary replacement of soybean oil (S) on cecal fermentation pattern, and fecal and cecal microbiota in rabbits. A total of 120 weaned rabbits were randomly allotted to three dietary treatments (40 rabbits/group) -a control diet (C diet) containing 1.5% of S and two experimental diets (HI diet (HID) and TM diet (TMD)), where S was totally substituted by HI or TM fats during the whole trial that lasted 41 days. Regarding the in vitro antimicrobial activities, HI and TM fats did not show any effects on Salmonella growth. Yersinia enterocolitica showed significantly lower growth when challenged with HI fats than the controls. The insect fat supplementation in rabbit diets increased the contents of the cecal volatile fatty acids when compared to the control group. A metataxonomic approach was adopted to investigate the shift in the microbial composition as a function of the dietary insect fat supplementation. The microbiota did not show a clear separation as a function of the inclusion, even if a specific microbial signature was observed. Indeed, HI and TM fat supplementation enriched the presence of Akkermansia that was found to be correlated with NH3-N concentration. An increase in Ruminococcus, which can improve the immune response of the host, was also observed. This study confirms the potential of HI and TM fats as antibacterial feed ingredients with a positive influence on the rabbit cecal microbiota, thus supporting the possibility of including HI and TM fats in rabbit diets.

Dietary Administration of the Bacillus subtilis Enhances Immune Responses and Disease Resistance in Chickens

Bacillus subtilis (B. subtilis) has a variety of proposed beneficial effects for chickens, including growth promotion and disease prevention. In this study, chickens were fed a diet containing B. subtilis for 21 days and growth performance, intestinal morphology, intestinal microbiota, immune responses, and disease resistance were investigated. After 21 days of feeding, chickens fed a diet containing B. subtilis had higher body weights. The concentrations of serum immunoglobulins IgA and IgM were significantly increased by B. subtilis in the diet. Moreover, chickens fed with B. subtilis had greater villus height (VH), shallower crypt depth (CD), and a higher VH/CD ratio in the jejunum than chickens fed a standard control diet. Diet with B. subtilis can balance intestinal microbiota, facilitate an increase in beneficial bacteria, and inhibit the pathogenic bacteria after 21 days of feeding. After an Escherichia coli (E. coli) challenge, the survival rate of chickens fed with B. subtilis was 66.67%, which was significantly higher than the controls. The E. coli contents in spleens and lungs from chickens fed a diet with B. subtilis were lower than those in controls. In addition, B. subtilis can trigger the toll-like receptor 4 and cause induction of proinflammatory cytokine (Il1β, Il6, and Il8) production to develop innate immune responses in chickens. In conclusion, diets containing B. subtilis can improve growth performance, serum immunoglobulin levels, the intestinal villus-crypt system, intestinal homeostasis, immune responses, and disease resistance against E. coli in chickens.

Bacillus licheniformis-Fermented Products Reduce Diarrhea Incidence and Alter the Fecal Microbiota Community in Weaning Piglets

Prophylactic use of antibiotics in-feed has been effective in decreasing the incidence of diarrhea in weaning piglets. However, the overuse of antibiotics as prophylactic or therapeutic agents in animal feed leads to the evolution of drug-resistant bacteria and antibiotic residues in pigs. This study investigated the effects of Bacillus licheniformis-fermented products on diarrhea incidence and the fecal microbial community in weaning piglets. A total of 120 crossbred piglets with an average initial body weight of 9.87 ± 1.43 kg were randomly allotted to four dietary treatments consisting of three replicate stalls with 10 piglets in each. The dietary treatments comprised a basal diet as control, control plus 1 g/kg or 4.5 g/kg of B. licheniformis-fermented products, and control plus 30 mg/kg antibiotics (bacitracin methylene disalicylate). Results showed that 4.5 g/kg of B. licheniformis-fermented product supplementation significantly reduced diarrhea incidence in weaning piglets. Principal coordinate analysis and a heatmap of species abundance indicated distinct clusters between the groups treated with antibiotics and B. licheniformis-fermented products. The bacterial richness and evenness in the feces decreased in weaning piglets fed 1 g/kg of B. licheniformis-fermented products and antibiotics. The abundance of the genera [Ruminococcus] gauvreauii group, Ruminococcaceae UCG-005, and Ruminococcaceae UCG-008 in the feces decreased in weaning piglets fed B. licheniformis-fermented products or antibiotics. The average abundance of the genus Prevotella 9 in the feces was positively correlated with the concentration of B. licheniformis-fermented products and negatively correlated with the diarrhea incidence in weaning piglets. Furthermore, the average abundance of the genus Prevotella 9 in the feces was positively correlated with the growth performance of weaning piglets. These results demonstrate that B. licheniformis-fermented products can improve diarrhea incidence and fecal microflora composition in weaning piglets.