Illumina Miseq platform analysis caecum bacterial communities of rex rabbits fed with different antibiotics

Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces

Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.

Extremely hair follicle density is associated with a significantly different cecal microbiota in rex rabbits

It has become increasingly clear that gut microbiota and skin are interconnected since the discovery of the 'gut-brain-skin' axis. Hair follicles (HFs) are skin microorganisms, but few studies have investigated their relationship to gut microbiota. Hence, we hypothesize that HFs have a close relationship with the gut, similarly to what was reported for the skin. Using rex rabbits as an animal model, one hundred healthy half-sibling rex rabbits were selected for the experiment, and 16 s rRNA gene sequencing was performed on the cecal microbiota of nine rabbits with the extremely high (HS) and low (LS) hair density (n = 9 per group) to determine differences between the composition and function of these communities. In comparison with the LS group, several alpha diversity index values were significantly lower in the HS group, although the higher variation in species composition in the HS group. Additionally, species diversity and abundance differed significantly in the cecum microbiota of HS and LS rabbits. Further, primary and secondary HF density was significantly correlated with the families Muribaculaceae and Bacteroidaceae, and genera Blautia, Bacteroides and Desulfovibrio. In particular, Muribaculaceae, Bacteroidaceae, Blautia and Bacteroides may support the development of HFs. Moreover, the expression of WNT4, WNT10a, WNT10b, CTNNB1 (β-catenin) and LEF1 in the skin was significantly higher in the HS group compared with the LS group. Altogether, the results of this study suggest that the extremely high density of HF in rabbits is associated with a significantly different microbiota diversity and community structure, and the Wnt/β-catenin signalling pathway was activated in the HS group. Thus, key bacteria may promote the development of HF.

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.

Antibiotic removal does not affect cecal microbiota balance and productive parameters in LP robust rabbit line

Antimicrobial resistance is an important threat to public health worldwide, being one of the main death causes in 2050. Moreover, global health is currently underpinned by the "One Health" concept, whereby livestock is strictly related to human and environmental health. However, in the case of the meat rabbit industry, antibiotic additives are still added to prevent gastrointestinal diseases. Current food and consumer awareness require the implementation of sustainable production systems, where robustness and resilience are increasingly important. Hence, the aim of this study was to evaluate the effect of antibiotic feed supplementation on microbiota, and productive performance during the rabbit growing period in a robust genetic line. For this purpose, a total of 432 weaned rabbits were randomly housed, cecum samples were taken on the weaning day and at the end of the growing period (28 and 61 days of age, respectively), and 16S rRNA sequencing analysis was performed. Results showed a higher microbiota complexity at the end of growing in both experimental groups. Firmicutes represented the dominant phylum of the cecal community, followed by Bacteroidota in both groups. Moreover, Victivallis and Escherichia-Shigella genera were only identified in the experimental group without antibiotic supplementation at the end of the growing period. In conclusion, antibiotic feed supplementation had no effect on microbiota composition and productive performance in the robust genetic line reared. These results evidence the importance of the development of rabbit robust genetic lines as an alternative tool to antibiotic administration in epizootic enteropathy control.

Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota

Background

The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota.

Results

Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects.

Conclusions

This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00738-2.

Comparison of Cecal Microbiota and Performance Indices Between Lean-Type and Fatty-Type Pekin Ducks

Fatty-type (FT) Pekin ducks exhibit higher lipid deposition than lean-type (LT) ducks. The gut microbiota plays an important role in modulating fat metabolism. We compared the growth performance, slaughter performance, and cecal microbiota of FT and LT Pekin ducks and analyzed the role of cecal microbiota in lipid deposition in Pekin ducks. A total of 140 1-day-old FT and LT Pekin ducks with similar body weights were randomly assigned to 10 cages, with 14 ducks in each replicate. All ducks were fed commercial diets from 28 to 42 days of age. Results showed that the average body weight and feed intake of FT ducks were higher than those of LT ducks. The breast muscle and eviscerated percentages of LT ducks were higher than those of FT ducks; the abdominal fat and sebum percentages of LT ducks were lower than those of FT ducks at 6 weeks of age (P < 0.01). 16S DNA sequencing of the cecal microbiota revealed that the bacterial abundance differed between FT and LT ducks at 4 and 6 weeks of age. The abundance of Firmicutes was higher, while that of Fusobacteria and Fusobacterium was lower in LT ducks than in FT ducks at 4 weeks of age. The abundance of Spirochaetes was higher, while that of Firmicutes and Bacteroides was lower in LT ducks than in FT ducks at 6 weeks of age. The abundance of Spirochaetes and Brachyspira in LT ducks was higher at 6 weeks than at 4 weeks of age. Interestingly, the abundance of Firmicutes and Bacteroides in FT ducks was higher at 6 weeks of age than at 4 weeks of age, while that of Fusobacteria and Fusobacterium was lower at 6 weeks than at 4 weeks of age. Linear discriminant analysis effect size analysis showed that Spirochaetes, Brachyspira, Alistipes, Campylobacter, Megamonas, Butyricicoccus, and Fusobacteria may be involved in the fat metabolism pathway as specific markers. We reveal the differences in microbial abundance in the cecal microbiota between FT and LT Pekin ducks and provide an insight into the role of cecal microbiota in lipid deposition in Pekin ducks.

Environmental enrichment changes rabbits' behavior, serum hormone level and further affects cecal microbiota

Many studies have shown that stress is associated with gut microbiota. Environmental enrichment (EE) could reduce stress in farm animals; however, limited information is available on the microbial community composition in rabbits raised with or without EE. This study aimed to identify EE influences on the behavior, serum hormonal levels, and cecal microbiota of rabbits. Two hundred Rex rabbits were segregated randomly within four cohorts (n = 50); reared for 76 d within standardized enclosures (non-enriched) or within cages containing a willow-stick (WS), rubber-duck (RD), or a can of beans (CB). The rabbits' ingestive, rest, locomotion, exploratory, grooming, and abnormal behavior were observed. The serum hormone levels for rabbits were measured, and cecal specimens were sequencedfrom the V3-V4 region using 16S rRNA amplicons. Environmental enrichment increased feeding and drinking time, promoted exploratory behavior, and reduced abnormal behavior in rabbits. Insulin-like growth factor 1(IGF-1) levels of the enriched cohorts were elevated in comparison to the control cohort. Serum cortisol level for CB cohort was markedly reduced in comparison to the control cohort (p < 0.05), while dopamine levels for CB cohort peaked. Further, we found that EE mainly affected the dominant microbiota. Several families, such as Erysipelotrichaceae, Tannerellaceae, Enterobacteriaceae, Burkholderiaceae, and Prevotellaceae were markedly reduced within the CB cohort. Bacteria such as Alloprevotella, Bifidobacterium, Enterobacteriaceae, Parabacteroides, and Erysipelatoclostridium were identified as having negative associations with the presence of serum cortisol. EE influenced rabbit behavior and serum hormonal levels, and CB enrichment was the most suitable for rabbits. Further, cecal microbiota composition and diversity were affected by CB enrichment. These findings suggested that CB could be considered for use in rabbit husbandry.

A new landscape of rabbit gut microbiota shaped by the infection of precocious parasites of Eimeria intestinalis

Rabbit intestinal coccidiosis is caused by one or several Eimeria species, which cause intestinal damage and secondary bacterial infection. However, the impact of Eimeria infection on gut microbiota is much unknown. To evaluate the influence, we detected the feces flora of SPF rabbits infected with the 1 × 10⁴ oocysts of E. intestinalis wild type (WT) and a precocious line (EIP8), a highly pathogenic species, by 16S rRNA sequencing. The microbiota of newly weaned rabbits post vaccination with low doses of EIP8 oocysts was also detected. In SPF rabbits, while Ruminococcaceae, Lachnospiraceae, and Bacteroidaceae were dominant families in all groups, EIP8 infection induced less changes in beta-diversity. In EIP8-infected rabbits, the intestinal flora whose abundance changed post infection accounted for less than 5.23 % of the entire flora. In comparison, it accounted for 27.18 % in WT group on d14 PI, while it was more than 20 % in diclazuril control group on d7 or d10 PI. The amount of fecal IgA and the abundance of IgA-production-related bacteria were similar in either EIP8 or WT infected rabbits. In the newly weaned rabbits, vaccination with EIP8 provided sufficient protection against challenge with WT parasites, as the body weight gain of vaccinated rabbits was similar to that of untreated animals, as well as more than 80 % reduction of oocyst output was detected when compared with unimmunized and challenged animals. Moreover, the vaccination had no significant impact on rabbit microbiota. Together, our findings suggested that the precocious line of E. intestinalis, compared with WT, induced a new fecal microbiota biodiversity in rabbits.

Microbiome analysis reveals gut microbiota alteration in mice with the effect of matrine

Mounting evidence revealed the negative effects of abuse of antibiotic including the induction of decreased immunity and dysbacteriosis. Matrine displayed multiple beneficial effects such as anti-inflammatory, antiviral and antibacterial, but studies of its influence on gut microbiota are still insufficient to report. Here, the present study was conducted to investigate the influence of matrine on the gut microbiota of mice and amoxicillin was used as a positive control. A total of 21 cecal samples were obtained from seven groups for high-throughput sequencing analysis based on V3-V4 variable region of 16S rRNA genes. Results revealed that the diversity and abundance of gut microbiota in mice gradually decreased with the increase of the concentration of amoxicillin, whereas matrine administration did not effect the intestinal microbial community structure. Additionally, amoxicillin and matrine supplementation also caused significant changes in the relative abundance of some intestinal bacteria. Specifically, the ratio of Klebsiella and Corynebacterium_1, Bacteroides and Parasutterella in the amoxicillin treated-group were increased as compared to the control group, whereas Muribaculaceae_unclassified, Alistipes and Lactobacillus were significantly decreased. Conversely, matrine administration significantly increased the proportion of beneficial bacteria such as Ruminiclostridium_9, Lachnospiraceae_NK4A136_group and Ruminococcaceae_unclassified. In conclusion, amoxicillin administration could change the microbial community composition and structure by increasing the proportion of pathogenic to beneficial bacteria, whereas matrine could increase the number of beneficial bacteria. Moreover, this study provides a theoretical basis for finding alternatives to antibiotics to decrease bacterial resistance and intestinal flora imbalance.

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.

Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

Background

The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.

Results

Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.

Conclusions

This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

Transcriptome Analysis of the Effects of Fasting Caecotrophy on Hepatic Lipid Metabolism in New Zealand Rabbits

Simple Summary

Caecotrophy in small herbivores, including rabbits, is the instinctive behavior of eating soft feces. Little is known about the impact of caecotrophy on growth and metabolism. In the present study, we used an Elizabeth circle to prevent rabbits from eating soft feces and measured changes in feed intake, body weight, internal organ weight, serum biochemical indices and liver lipid droplet accumulation. Liver tissue was also used for transcriptome sequencing. Results indicated that fasting caecotrophy decreased rabbit growth and lipid synthesis in the liver.

Abstract

In order to investigate the effects of fasting caecotrophy on hepatic lipid metabolism in rabbits, 12 weaned female New Zealand white rabbits were randomly divided into (n = 6/group) a control and fasting caecotrophy group. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their own soft feces for a 60-day period. Growth and blood biochemical indices, transcriptome sequencing and histology analysis of the liver were performed. Compared with the control group, final weight, weight gain, liver weight, growth rate and feed conversion ratio, all decreased in the experimental group (p < 0.05). RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads (approximately 45.06 Gb of high-quality clean data) that were mapped to the rabbit genome. After a five-step filtering process, 14,964 genes were identified, including 444 differentially expressed genes (p < 0.05, foldchange ≥ 1). A number of differently expressed genes linked to lipid metabolism were further analyzed including CYP7A1, SREBP, ABCA1, GPAM, CYP3A1, RBP4 and RDH5. The KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation of the differentially expressed genes indicated that main pathways affected were pentose and glucuronide interactions, starch and sucrose metabolism, retinol metabolism and PPAR signaling. Overall, the present study revealed that preventing caecotrophy reduced growth and altered lipid metabolism, both of which will help guide the development of new approaches for rabbits’ feeding and production. These data also provide a reference for studying the effects of soft feces in other small herbivores.

Influence of dietary supplementation with Bacillus velezensis on intestinal microbial diversity of mice

Yaks are an aboriginal breed of the Qinghai-Tibet plateau (3000 m), which are highly adaptable to cold and hypoxic environments. It is noticed that hypoxia and hypothermia can induce changes in intestinal microbial structure in animals. Increasing evidences suggested that probiotics supplementation can improve the balance of gut microbiota of animals. However, so far, very few studies have emphasized on the probiotics isolated from yaks in the Qinghai-Tibet Plateau. Therefore, a potential probiotic strain Bacillus velezensis was isolated from yaks. In the present study, a total of 18 Kunming mice (15-18 g) were equally distributed into two groups; control and probiotic treated groups (1 × 10⁹ CFU/day). During the experimental period, all the mice from both groups were given standard normal diet ad libitum. At the end of the experiment, mice were euthanized and the intestines (duodenum, jejunum, ileum, and cecum) were removed for high-throughput sequencing. The results demonstrated that Bacillus velezensis supplementation showed beneficial effects on the gut microbiota of mice. Specifically, Bacillus velezensis supplementation increased the population of Lactobacillus and Ruminococcus in the duodenum, and Candidatus Arthromitus in the jejunum. Additionally, Acinetobacter in the duodenum and Helicobacter in the cecum were decreased after feeding Bacillus velezensis. Altogether, these findings suggested that Bacillus velezensis isolated from Tibetan yaks can improve gut microbiota of mice.

Probiotic Properties of Lactobacillus paracasei subsp. paracasei L1 and Its Growth Performance-Promotion in Chicken by Improving the Intestinal Microflora

Lactobacillus paracasei subsp. paracasei L1 was previously isolated from sweet potato sour liquid. This bacterial species specifically binds onto starch granular surfaces, triggering the enzymatic hydrolysis of raw starch. We investigated the functional and safety properties of strain L1 in vitro to establish its probiotic potential, and analyzed its effect on growth performance and intestinal microflora of chicken in feeding experiments. The optimal growth conditions of strain L1 included low pH and high concentrations of bile salts and NaCl. Its 1-, 2-, and 24-h autoaggregation values were 15.8 ± 1.2%, 20.4 ± 2.3%, and 47.2 ± 0.8%, respectively, with the surface hydrophobicity value at 560 nm of 38.1 ± 2.7%. Further, its adhesion rate to Caco-2 cells was 22.37 ± 1.44%. Strain L1 was resistant to erythromycin and azithromycin, but sensitive to other antibiotics tested. For the feeding experiments, 240 chickens with similar weights were randomly divided into a control (C) group and strain L1 (L) group and fed for 8 weeks. Strain L1 promoted the weight gain of chickens in L group. A significant increase in the population size of the two phyla and 23 genera in the small intestine was observed in the presence of strain L1 (P < 0.05), with 0 phyla and 4 genera showing significant increase in the cecum (P < 0.05). In the small intestine, the abundance of six functional genes at Kyoto Encyclopedia of Genes and Genomes (KEGG) level 2 and 49 genes at KEGG level 3 was significantly increased in group L (P < 0.05), with lesser changes noted in the cecum. An increase in the metabolic pathway functions, including enzyme families and the digestive system, was observed in the intestinal microbiota in the L group compared to the C group. However, the other metabolic pathway functions, including metabolism of fatty acid biosynthesis, as well as metabolism of glycerolipids and propanoate, increased in the cecal microbiota of the L group relative to the C group. These changes are most likely related to the changes in the gut microbiota composition. Collectively, strain L1 supplementation may promote growth performance and improve the intestinal microflora in chicken although further studies are needed to confirm this.

Probiotics isolated from yaks improves the growth performance, antioxidant activity, and cytokines related to immunity and inflammation in mice

BACKGROUND

Yaks living in the high-altitude hypoxic environment of Tibetan plateau (3600 m) have special gut microbes. However, it is still little research on yak probiotics until now. Therefore, the purpose of our study was to evaluate the growth promoting effect, antioxidant capability, immune effect, and anti-inflammatory ability of Bacillus subtilis and Bacillus velezensis isolated from Tibetan yaks in mice model.

RESULTS

The results showed that the isolated strains supplementation not only improve the growth performance but also increased the length of villus in the small intestine and intestinal digestive enzyme activity. Importantly, we observed that the T-AOC, SOD, and GSH-PX levels were increased and the MDA content was reduced in probiotic-treated mice, which implied that probiotics supplementation can ameliorate the antioxidative activity of mice. The levels of AST and ALT correlated with the hepatic injury were reduced and the levels of AKP, TP, GLB, ALB, Ca, and P were markedly higher than those in the control group. Additionally, mice treated with probiotics exhibited higher serum IgG, IgM and IgA, which can reflect the immune status to some extent. At the same time, the major pro-inflammatory factor TNF-α, IL-6, and IL-8 were down-regulated and the anti-inflammatory factor IL-10 was up-regulated compared with the control groups.

CONCLUSIONS

In conclusion, these results demonstrated that Bacillus subtilis and Bacillus velezensis supplementation can increase overall growth performance and ameliorate the blood parameters related to inflammation and immunity of mice.

Transcriptome analysis revealed ameliorative effect of probiotic Lactobacillus johnsonii BS15 against subclinical necrotic enteritis induced hepatic inflammation in broilers

Subclinical necrotic enteritis (SNE) broadly occurs in boilers, which reduces the growth performance by causing serious economic and social problems. The following study was conducted to better understand the molecular mechanism of the SNE on liver inflammation and to examine the innovative prevention of Lactobacillus johnsonii BS15 upon SNE. The research was based on the regulatory molecular mechanism of Lactobacillus johnsonii BS15, and its effect on liver inflammatory pathways in the broiler with SNE infection. Day old one hundred and eighty (Cobb 500) broiler chickens were distributed into 3 groups (control, SNE and BS15 group) and reared for 28 days. RNA sequencing was used for the analysis of gene expression extracted from liver samples. Gene expression was detected with the help of quantitative real-time PCR (qRT-PCR). RNA-Seq analysis revealed altered expressions of genes involved in liver inflammatory pathway. A total number of 385 genes were found as differentially expressed (DEGs) in the liver samples that belonged to SNE group as compared with the control liver samples (p < 0.05). Out of those 385 genes, 117 were down-regulated and 268 were up-regulated. The DEGs related to liver inflammation between control group and SNE group or SNE and BS15 groups, included cluster of differentiation 80 (CD80), Interleukin 1 beta (IL1B), Phosphoinositide 3- Kinase regulatory subunit 5 (PIK3R5), Toll-like receptor 4 (TLR4), Toll-like receptor 2 A (TLR2A), and proto-oncogene protein (FOS). The RNA-Seq analysis provided DEGs expression and this result was validated by qRT-PCR. Results confirmed that these genes are essential in the regulation of liver inflammation in the SNE infected chickens. Findings of current research indicated that the hepatic inflammation could be induced by SNE in broilers. Simultaneously, effects of SNE infection on liver could be subsided by improved TLRs signaling pathway with the naturally present prophylactic strategy as BS15.

Zearalenone Changes the Diversity and Composition of Caecum Microbiota in Weaned Rabbit

Mycotoxins exhibit several severe effects on intestinal health, but few studies have assessed mycotoxins effect on the intestinal microflora and its repercussions to humans and animals. In this study, we evaluated the effect of zearalenone (ZEA), one of the most harmful mycotoxins on the structure of caecal microbiota in rabbits. Twenty-eight male weaned rabbits were randomly divided into four groups and orally given different concentrations of ZEA (400, 800, and 1600 μg/kg.b.w). Microbial communities in caecum samples of rabbits were analyzed for 16S rRNA by Illumina sequencing through Illumina Miseq platform after being fed for 28 days. The results showed that increasing ZEA doses increased the species richness but did not significantly increased the species diversity of the caecum microbiota in the rabbits. In addition, the caecum microbiota from the samples in different ZEA-treated groups was clustered according to their dosing regimens. At the phylum level, ZEA decreased the abundance of Actinobacteria and significantly increased the abundance of Cyanobacteria, Synergistetes, and Proteobacteria. At the genus level, there were declines in the abundance of Adlercreutzia, Blautia, Desulfitobacter, Lactobacillus, Oxalobacter, and p-75-a5. The decrease of abundance in Lactobacillus, Desulfitobacter, and p-75-a5 was particularly noticeable. In conclusion, zearalenone could increase α-diversity but significantly decrease the abundance of some bacteria with the important metabolic functions. These findings suggested that ZEA could modify the caecum microbiota.

Rabbit Microbiota Changes Throughout the Intestinal Tract

To gain insight into the importance of carefully selecting the sampling area for intestinal microbiota studies, cecal and fecal microbial communities of Caldes meat rabbit were characterized. The animals involved in the study were divided in two groups according to the feed intake level they received during the fattening period; ad libitum (n = 10) or restricted to 75% of ad libitum intake (n = 11). Cecum and internal hard feces were sampled from sacrificed animals. Assessment of bacterial and archaeal populations was performed by means of Illumina sequencing of 16S rRNA gene amplicons in a MiSeq platform. A total of 596 operational taxonomic units (OTUs) were detected using QIIME software. Taxonomic assignment revealed that microbial diversity was dominated by phyla Firmicutes (76.42%), Tenericutes (7.83%), and Bacteroidetes (7.42%); kingdom Archaea was presented at low percentage (0.61%). No significant differences were detected between sampling origins in microbial diversity or richness assessed using two alpha-diversity indexes: Shannon and the observed number of OTUs. However, the analysis of variance at genus level revealed a higher presence of genera Clostridium, Anaerofustis, Blautia, Akkermansia, rc4-4, and Bacteroides in cecal samples. By contrast, genera Oscillospira and Coprococcus were found to be overrepresented in feces, suggesting that bacterial species of these genera would act as fermenters at the end of feed digestion process. At the lowest taxonomic level, 83 and 97 OTUs in feces and cecum, respectively, were differentially represented. Multivariate statistical assessment revealed that sparse partial least squares discriminant analysis (sPLS-DA) was the best approach for this purpose. Interestingly, the majority of the most discriminative OTUs selected by sPLS-DA were found to be differentially represented between sampling origins in univariate analysis. Our study provides evidence that the choice of intestinal sampling area is relevant due to important differences in some taxa's relative abundance that have been revealed between rabbits' cecal and fecal microbiota. An appropriate sampling intestinal area should be chosen in each microbiota assessment.

Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age

Gut microbial diversity and the core microbiota of the Jinhua pig, which is a traditional, slow-growing Chinese breed with a high body-fat content, were examined from a total of 105 fecal samples collected from 6 groups of pigs at 3 weaning ages that originated from 2 strains and were raised on 3 different pig farms. The bacterial community was analyzed following high-throughput pyrosequencing of 16S rRNA genes, and the fecal concentrations of short-chain fatty acids (SCFAs) were measured by gas chromatograph. Our results showed that Firmicutes and Bacteroidetes were the dominant phyla, and Lactobacillus, Streptococcus, Clostridium, SMB53, and Bifidobacterium were the most abundant genera. Fifteen predominant genera present in every Jinhua pig sample constituted a phylogenetic core microbiota and included the probiotics Lactobacillus and Bifidobacterium, and the SCFA-producing bacteria Clostridium, Prevotella, Bacteroides, Coprococcus, Roseburia, Ruminococcus, Blautia, and Butyricicoccus. Comparisons of the microbiota compositions and SCFA concentrations across the 6 groups of pigs demonstrated that genetic background and weaning age affected the structure of the gut microbiota more significantly than the farm. The relative abundance of the core genera in the pigs, including Lactobacillus, Clostridium, Prevotella, Bacteroides, Roseburia, Ruminococcus, Blautia, and Butyricicoccus varied dramatically in pigs among the 2 origins and 3 weaning ages, while Oscillospira, Megasphaera, Parabacteroides, and Corynebacterium differed among pigs from different farms. Interestingly, there was a more significant influence of strain and weaning age than of rearing farm on the SCFA concentrations. Therefore, strain and weaning age appear to be the more important factors shaping the intestinal microbiome of pigs.

Probiotic Lactobacillus johnsonii BS15 Improves Blood Parameters Related to Immunity in Broilers Experimentally Infected with Subclinical Necrotic Enteritis

The probiotic strain Lactobacillus johnsonii BS15 could exert beneficial effects on growth performance, lipid metabolism, and intestinal microflora in healthy broilers and those afflicted with subclinical necrotic enteritis (SNE). In particular, BS15 prevents SNE by enhancing intestinal immunity. To further understand the immune regulatory mechanism of BS15, we evaluated its effects on the overall immunity of broilers by determining blood parameters in healthy and SNE broilers. In this study, two experiments were conducted. Experiment 1 involved a 42-day experimental period and used 450 1-day-old male chicks. The chicks were randomly divided into three groups and fed with a basal diet with or without 1 × 10⁵ or 10⁶ colony-forming units (cfu) BS15/g as feed. Experiment 2 involved a 28-day experimental period and used 180 1-day-old male chicks. The chicks were randomly allotted into three groups and given with or without 1 × 10⁶ cfu BS15/g BS15 as feed. SNE infection was treated in all broilers, except in those in the normal diet group. Antioxidant abilities, immunoglobulins, and cytokines in the serum were assessed. T-lymphocyte subsets in peripheral blood were also determined. The first experiment demonstrated that BS15 enhanced the antioxidant abilities; the serum levels of immunoglobulins, interleukin-2, and interferon-gamma; and CD3⁺CD4⁺ T-lymphocyte percentage in peripheral blood on day 21. However, limited significant changes were observed on day 42. The second experiment revealed that BS15 supplementation positively influenced the antioxidant abilities and increased the serum levels of immunoglobulins and cytokines that were affected by SNE. BS15 also positively affected T-lymphocyte subsets in peripheral blood during SNE infection. These findings suggest that BS15 supplementation may prevent SNE in broilers by improving blood parameters related to immunity and enhancing intestinal immunity. Furthermore, BS15 supplementation can improve blood parameters in healthy broilers, especially at the starter phase.