Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi)

Effect of host breeds on gut microbiome and fecal metabolome in commercial pigs

BACKGROUND

Gut microbial composition and its metabolites are crucial for livestock production performance. Metabolite profiles from autopsied biospecimens provide vital information on the basic mechanisms that affect the overall health and production traits in livestock animals. However, the role of the host breed in the gut microbiome and fecal metabolome of commercial pigs remains unclear. In this work, differences in microbiota composition among three commercial pig breeds Duroc, Yorkshire, and Landrace were measured by 16S rRNA gene sequencing. Fecal metabolite compositions of the three pig breeds were detected using untargeted metabolomics.

RESULTS

There were significant differences in the gut microbiomes of the three species, indicating that host breed affects the diversity and structure of gut microbiota. Several breed-associated microorganisms were identified at different taxonomic levels. Notely, most microbial taxa were annotated as Lactobacillacea, Muribaculaceae, and Oscillospiraceae. Several bacteria, including Lactobacillus, Subdoligranulum, Faecalibacterium, Oscillospira, Oscillospiraceae_UCG-002, and Christensenellaceae_R-7_group, could be considered as biomarkers for improving the backfat thickness (BF) for commercial pigs. Additionally, KEGG analysis of gut microbiota further revealed that arginine biosynthesis, pyruvate metabolism, and fatty acid biosynthesis varied greatly among pig breeds. Multiple gut bacterial metabolites (e.g., spermidine, estradiol, and palmitic acid) were identified as breed-associated. Mediation analysis ultimately revealed the cross-talk among gut microbiota, metabolites, and BF thickness, proclaiming that the microbial and metabolic biomarkers identified in this study could be used as biomarkers for improving BF phenotype.

CONCLUSIONS

This work provides vital insights into breed effects on gut microbiota and metabolite compositions of commercial pigs and uncovers potential biomarkers that are significant for pig breed improvement.

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.

Fecal microbiota characterization of an Italian local horse breed

The Bardigiano horse is a traditional native Italian breed with a rich history and peculiar characteristics. Local breeds are proven to have unique genetic traits developed over generations to adapt to defined geographical regions and/or conditions. The specific microbial communities that coexist within these animals are unraveled by studying their microbiota, which permits a further step in the characterization of local heritage. This work aimed to characterize Bardigiano horse fecal microbiota composition. The data obtained were then compared with published data of a mix of athlete breeds to evaluate potential differences among local and specialized breeds. The study involved 11 Bardigiano mares between 3 and 4 years of age, from which stool was sampled for the study. Samples were processed for 16S rRNA sequencing. Data obtained were analyzed and plotted using R, RStudio, and FastTree software. The samples analyzed were similar to what literature has reported on horses of other breeds and attitudes at higher taxonomic levels (from phylum to genera). While at lower taxonomic levels, the difference was more marked highlighting specific families found in the Bardigiano breed only. Weight, province of origin, and breeding sites significantly affected microbiota composition (p-value ≤0.02, p-value ≤0.04, and p-value ≤0.05, respectively). The comparison with athlete breed showed a significant difference confirming that animal and environmental factors are crucial in determining fecal microbiota composition (p-value <0.001). Understanding the microbiota composition in local breeds like the Bardigiano horse is crucial for preserving biodiversity, managing animal health, and promoting sustainable farming practices.

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.

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.

Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus)

BACKGROUND

Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing.

RESULTS

The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity.

CONCLUSIONS

Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.

Effects of Dietary Supplementation of Lactobacillus acidophilus on Blood Parameters and Gut Health of Rabbits

This study aimed to evaluate the effects of Lactobacillus acidophilus D2/CSL (L-1 × 109 cfu/kg feed/day) on biochemical parameters, faecal score (FS), cecal pH, gut morphometry, microbiota and cecal short-chain fatty acid (SCFAs) in rabbits. Three zootechnical trials were performed and in each trial 30 rabbits were allotted to two groups; a probiotic group (L) and a control group (C). At slaughter (day 45), samples of blood, duodenum, jejunum, ileum, liver and spleen were collected and submitted to histomorphometric analyses. Blood biochemical analyses, cecal microbiota and SCFAs determination were also performed. In trial 1 and 3, L. acidophilus D2/CSL did not affect productive parameters (p > 0.05). However, L group of trial 1 showed a lower morbidity and mortality compared to the control. In trial 2, C group showed a higher daily feed intake (p = 0.018) and a positive statistical tendency for live weight and average daily gain (p = 0.068). On the contrary, albumin was higher and ALFA-1 globulin was lower in the C group compared to L (p < 0.05). In all the trials, FS, cecal pH, histomorphometry, microbiota and SCFAs were unaffected. In conclusion, L. acidophilus D2/CSL did not impair growth performances, gut and rabbit’s health, reducing morbidity and mortality.

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.

Managing the Health of Captive Herds of Exotic Companion Mammals

Common medical problems diagnosed and treated in individual companion exotic mammals are relevant in a herd-health setting. Many of these problems are often associated with poor husbandry and/or inappropriate nutrition. Rabbits, ferrets, chinchillas, and rodents have been domesticated alongside humans and an understanding of their ethology gives veterinarians a base knowledge in making recommendations for animals in their care. This article briefly reviews the ethology and husbandry in such species, but detailed needs are beyond the scope of this article.

Characterization of faecal and caecal microbiota of free-ranging black-tailed prairie dogs (Cynomys ludovicianus) using high-throughput sequencing of the V4 region of the 16S rRNA gene

Black-tailed prairie dogs (Cynomys ludovicianus) are keystone species within their grassland ecosystems; their population stability affects a multitude of other species. The goals of this study were to explore, describe and compare the bacterial communities in caecal and hard faecal samples from free-ranging black-tailed prairie dogs (n = 36) from KS, USA, using high-throughput sequencing of the V4 region of the 16S rRNA gene and to compare sex and geographic locations. A total of 22 paired faecal and caecal samples were collected post-mortem from free-ranging black-tailed prairie dogs from 5 different geographical locations. The results revealed that the microbiota of both faecal and caecal samples were dominated by the phylum Firmicutes (genera belonging to the Clostridiales order). There was significantly greater richness in faecal compared with caecal samples. There were significant differences between the 5 different geographic regions (P < 0.001), specifically in the relative abundances of genera. There were differences in rare members of the microbiome between faecal samples from male and female prairie dogs but with no significant impact on overall community structure. This study provides novel data and expands our knowledge about the gastrointestinal microbiome composition of free-ranging black-tailed prairie dogs, which has potential to inform conservation efforts and improve their captive management.

The effect of dietary supplementation with silkworm pupae meal on gastrointestinal function, nitrogen retention and blood biochemical parameters in rabbits

BACKGROUND

The aim of this study was to determine the effect of dietary inclusion of silkworm pupae meal (SPM) on nutrient digestibility, nitrogen utilization, gastrointestinal physiology and blood biochemical parameters in rabbits. Thirty Termond White rabbits were divided into three groups: SBM - fed a diet containing 10% soybean meal (SBM), SPM5 - fed a diet containing 5% SBM and 5% SPM, and SPM10 - fed a diet containing 10% SPM.

RESULTS

Nutrient digestibility and nitrogen retention decreased with increasing SPM inclusion levels in rabbit diets. The dietary inclusion of SPM caused a significant increase in the stomach pH. Group SPM10 rabbits were characterized by the highest cecal tissue and digesta weights. The lowest cecal pH was noted in group SPM5. The relative weights of colonic tissue and digesta tended to increase with increasing levels of SPM. The total and intracellular activity of bacterial α-galactosidase decreased significantly in both SPM groups. The replacement of SBM with SPM led to a decrease in the activity of bacterial β-glucuronidase in the cecal digesta. The intracellular activity of bacterial α-arabinofuranosidase increased, and its release rate decreased in the cecum of rabbits in SPM groups. The extracellular activity of bacterial β-xylosidase in the cecal digesta tended to decrease in group SPM10. The highest extracellular and intracellular activity of bacterial β-cellobiosidase in the cecal digesta was noted in the SPM5 treatment. The lowest and the highest activity of bacterial N-acetyl-β-D-glucosaminidase (NAGase) was observed in groups SBM and SPM10. The SPM10 treatment contributed to a decrease in the cecal concentrations of butyric, iso-valeric and valeric acids. The lowest total concentration of putrefactive short-chain fatty acids (PSCFAs) was observed in group SPM10. The cecal concentration of propionic acid tended to increase in group SPM5, whereas the cecal concentration of iso-butyric acid tended to decrease in group SPM10. The colonic concentration of iso-valeric acid was lowest in group SPM5. SPM treatments resulted in a significant increase in plasma albumin concentration. Plasma urea concentration was significantly higher in group SPM10 than in SBM and SPM5.

CONCLUSIONS

The results of this study suggest that rabbit diets can be supplemented with SPM at up to 5%.

Fecal Bacterial Microbiota of Healthy Free-Ranging, Healthy Corralled, and Chronic Diarrheic Corralled Rhesus Macaques (Macaca mulatta)

A clinical challenge to nearly every primate facility in North America is chronic idiopathic diarrhea (CID), the pathogenesis of which has yet to be fully elucidated. However, wild macaques appear resistant to CID, a trend that we observed in the free-ranging population of the Caribbean Primate Research Center. The gastrointestinal microbiota has been shown to have a significant role in the pathogenesis of disease and in maintaining normal health and development of the gut. In humans, chronic diarrhea is associated with alteration of the gut microbiota, which has lower bacterial diversity than does the microbiota of healthy humans. The current study was designed to describe and compare the fecal bacterial microbiota of healthy corralled, CID corralled, and healthy, free-ranging macaques. Fresh fecal samples were collected from healthy corralled (HC; n = 30) and CID (n = 27) rhesus macaques and from healthy macaques from our free-ranging colony (HF; n = 43). We excluded macaques that had received antibiotics during the preceding 60 d (90 d for healthy animals). Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced and compared with known databases. The relative abundance of Proteobacteria was higher in CID animals than HC animals, but otherwise few differences were found between these 2 groups. HF macaques were differentially enriched with Christensenellaceae and Helicobacter, which are highly associated with a 'healthy' gut in humans, as compared to corralled animals, whereas CID animals were enriched with Proteobacteria, which are associated with dysbiosis in other species. These results indicate that environment has a greater influence than health status on the gut microbiota. Furthermore, the current data provided targets for future studies on potential clinical interventions, such as probiotics and fecal transplants.

Effect of Fermented Rapeseed Meal on the Gastrointestinal Microbiota and Immune Status of Rabbit (Oryctolagus cuniculus)

Simple Summary

The unique digestive properties of rabbits consist of highly specialised communities of intestinal microbes that, unfortunately, make them susceptible to metabolic diseases. This is why breeders, to improve the functions of the digestive tract, often use special feed additives, i.e., probiotics, prebiotics or synbiotics. The need to become independent from soybean meal (SBM), which is currently the basic source of protein in animal nutrition, and the need to stimulate the gastrointestinal tract (GIT), has increased interest in fermented components that have a positive effect on the intestinal microbiota and are a source of valuable protein. In this study, the impact of the diversified proportion of fermented rapeseed meal (FRSM) in the diet of rabbits on the immune parameters and the microbiota of the digestive tract was assessed. The reducing effect of the tested feed component against coliform bacteria and Escherichia coli within the small intestine and colon of animals and the anaerobic biota of Clostridium perfringens in the duodenum and cecum of animals was observed while in the duodenum—an increase in the beneficial biota of lactic acid bacteria. The conducted analysis also showed many complex correlations between the number of intestinal microbiota groups and the level of immunoglobulins. The results of the conducted research indicate that FRSM, in addition to valuable nutritional values, may play an important probiotic role in the GIT of rabbits. Research of this type is especially important in terms of reducing the use of antibiotics for therapeutic purposes through nutritional prevention of animals.

Abstract

The present study was conducted to determine the effect of the use of varying amounts of fermented rapeseed meal in diets for rabbits on the immune status and microbiota of segments of the GIT. Forty 35 day old rabbits used in the experiment were assigned to four groups: the control group (group C) were fed a standard diet and the experimental received 4%, 8% or 12% fermented rapeseed meal (included in place of standard soybean meal). Class A, G and M immunoglobulins were determined in the blood plasma. In the food content collected after slaughter, microbiological parameters were determined for individual sections of the digestive tract. Rabbits from the groups receiving a diet with an increased proportion of fermented rapeseed meal (8% or 12%) had lower concentrations of anaerobic bacteria and Escherichia coli in the intestinal contents. Research has shown that the increase in intake of fermented rapeseed meal was correlated with an increase in the correlations between the immunoglobulin level and the size of the microbial population in the GIT. In light of the presented results fermented rapeseed meal, by supplying valuable bioactive substances, appears to be a good component in the diet of rabbits, enhancing immune system development and helping to prevent disturbances of the gut microbiota.

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

BACKGROUND

Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS).

RESULTS

Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome.

CONCLUSIONS

Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.

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.

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

Background

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors.

Methods

We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms.

Results

We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.

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.