Gut colonization by a novel Clostridium species is associated with the onset of epizootic rabbit enteropathy

Genome-wide association studies for diarrhoea outcomes identified genomic regions affecting resistance to a severe enteropathy in suckling rabbits

Selection and breeding strategies to improve resistance to enteropathies are essential to reaching the sustainability of the rabbit production systems. However, disease heterogeneity (having only as major visible symptom diarrhoea) and low disease heritability are two barriers for the implementation of these strategies. Diarrhoea condition can affect rabbits at different life stages, starting from the suckling period, with large negative economic impacts. In this study, from a commercial population of suckling rabbits (derived from 133 litters) that experienced an outbreak of enteropathy, we first selected a few animals that died with severe symptoms of diarrhoea and characterized their microbiota, using 16S rRNA gene sequencing data. Clostridium genus was consistently present in all affected specimens. In addition, with the aim to identify genetic markers in the rabbit genome that could be used as selection tools, we performed genome-wide association studies for symptoms of diarrhoea in the same commercial rabbit population. These studies were also complemented with FST analyses between the same groups of rabbits. A total of 332 suckling rabbits (151 with severe symptoms of diarrhoea, 42 with mild symptoms and 129 without any symptoms till the weaning period), derived from 45 different litters (a subset of the 133 litters) were genotyped with the Affymetrix Axiom OrcunSNP Array. In both genomic approaches, rabbits within litters were paired to constitute two groups (susceptible and resistant, including the mildly affected in one or the other group) and run case and control genome-wide association analyses. Genomic heritability estimated in the designed experimental structure integrated in a commercial breeding scheme was 0.19-0.21 (s.e. 0.09-0.10). A total of eight genomic regions on rabbit chromosome 2 (OCU2), OCU3, OCU7, OCU12, OCU13, OCU16 and in an unassembled scaffold had significant single nucleotide polymorphisms (SNPs) and/or markers that trespassed the FST percentile distribution. Among these regions, three main peaks of SNPs were identified on OCU12, OCU13 and OCU16. The QTL region on OCU13 encompasses several genes that encode members of a family of immunoglobulin Fc receptors (FCER1G, FCRLA, FCRLB and FCGR2A) involved in the immune innate system, which might be important candidate genes for this pathogenic condition. The results obtained in this study demonstrated that resistance to an enteropathy occurring in suckling rabbits is in part genetically determined and can be dissected at the genomic level, providing DNA markers that could be used in breeding programmes to increase resistance to enteropathies in meat rabbits.

Akkermansia muciniphila and Parabacteroides distasonis synergistically protect from colitis by promoting ILC3 in the gut

Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the gastrointestinal tract. The etiology of IBD remains elusive, but the disease is suggested to arise from the interaction of environmental and genetic factors that trigger inadequate immune responses and inflammation in the intestine. The gut microbiome majorly contributes to disease as an environmental variable, and although some causative bacteria are identified, little is known about which specific members of the microbiome aid in the intestinal epithelial barrier function to protect from disease. While chemically inducing colitis in mice from two distinct animal facilities, we serendipitously found that mice in one facility showed remarkable resistance to disease development, which was associated with increased markers of epithelial barrier integrity. Importantly, we show that Akkermansia muciniphila and Parabacteroides distasonis were significantly increased in the microbiota of resistant mice. To causally connect these microbes to protection against disease, we colonized susceptible mice with the two bacterial species. Our results demonstrate that A. muciniphila and P. distasonis synergistically drive a protective effect in both acute and chronic models of colitis by boosting the frequency of type 3 innate lymphoid cells in the colon and by improving gut epithelial integrity. Altogether, our work reveals a combined effort of commensal microbes in offering protection against severe intestinal inflammation by shaping gut immunity and by enhancing intestinal epithelial barrier stability. Our study highlights the beneficial role of gut bacteria in dictating intestinal homeostasis, which is an important step toward employing microbiome-driven therapeutic approaches for IBD clinical management.

IMPORTANCE

The contribution of the gut microbiome to the balance between homeostasis and inflammation is widely known. Nevertheless, the etiology of inflammatory bowel disease, which is known to be influenced by genetics, immune response, and environmental cues, remains unclear. Unlocking novel players involved in the dictation of a protective gut, namely, in the microbiota component, is therefore crucial to develop novel strategies to tackle IBD. Herein, we revealed a synergistic interaction between two commensal bacterial strains, Akkermansia muciniphila and Parabacteroides distasonis, which induce protection against both acute and chronic models of colitis induction, by enhancing epithelial barrier integrity and promoting group 3 innate lymphoid cells in the colonic mucosa. This study provides a novel insight on how commensal bacteria can beneficially act to promote intestinal homeostasis, which may open new avenues toward the use of microbiome-derived strategies to tackle IBD.

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.

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae

Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients.

Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients

Performance, health, bacterial metabolites and intestinal histomorphology in does and growing rabbits fed diets with increasing lignocellulose-to-cellulose proportions

Adequate levels of dietary fibre can reduce the risk of intestinal health disorders in rabbits after weaning. Therefore, it was the aim of the study to investigate the impact of different lignocellulose and cellulose addition to rabbits' diets on performance and intestinal traits in lactating does and weaned rabbits. A total of 60 rabbit does (4.41 ± 0.45 kg body weight) were fed isonitrogenous diets with lignocellulose and cellulose inclusion rates [%] of 0/8, 2/6, 4/4, 6/2 and 8/0, resulting in dietary lignin-to-cellulose ratios of 0.26, 0.30, 0.32, 0.34 and 0.40, respectively. The diets were fed from 4 d ante partum (a.p.) until day 28 post partum (p.p. weaning). After weaning, 40 young rabbits from each feeding group were fed the same diets for 12 d, when 10 rabbits per group were sacrificed. Body weight gain (BWG), feed intake and feed conversion ratio were obtained. Gastrointestinal content and gut tissue were obtained from the growing rabbits and pH, short-chain fatty acids (SCFA) concentration and gut morphology were investigated. Digestive disorders were scored, and the sanitary risk index was calculated. Does fed the highest lignocellulose addition increased their feed intake [g · kg BW^-1 · d^-1] in the first two weeks p.p. (p < 0.001) and increased BWG (p < 0.001) but without impact on their offsprings' performance. Weaned rabbits fed the highest lignocellulose inclusion showed a reduced feed intake and increased sanitary risk index. Additionally, a higher number of rabbits showed intestinal disorders for a short time (1-2 d, p < 0.001). In the colon content, a higher pH and a lower dry matter content were observed in this group. Caecal contents of 40-d old rabbits showed lower total SCFA, acetate and propionate and higher i-valerate and L-lactate concentrations after feeding diets with high lignocellulose contents. The diet did not influence the acetate-to-propionate ratio. No histomorphological changes were observed in the jejunum, while crypt depth and width were reduced in the caecum of weaned rabbits fed diets with lignocellulose addition. It can be concluded that different proportions of lignocellulose to cellulose addition to rabbits' diets have an impact on health and performance with differences between does and weaned rabbits. While a high lignocellulose inclusion proved beneficial for does, for weaned rabbits, a lower addition should be preferred.

Effect of Feeding Insoluble Fiber on the Microbiota and Metabolites of the Caecum and Feces of Rabbits Recovering from Epizootic Rabbit Enteropathy Relative to Non-Infected Rabbits

This study aimed to investigate the effect of feeding insoluble fiber on the microbiota and metabolites of the caecum and feces of rabbits recovering from epizootic rabbit enteropathy relative to non-infected rabbits. Rabbits that had either recovered from epizootic rabbit enteropathy or ones that had never had epizootic rabbit enteropathy were fed on a diet of 32% or 36% neutral detergent fiber until they were 70 days of age. At this point, the short-chain fatty acid and ammonia levels were measured in caecotroph and fecal samples and compared using 2 × 2 ANOVA. The microbial composition of the samples was also analyzed using next-generation sequencing and compared by PERMANOVA. Caecotrophic samples from previously affected rabbits on lower fiber diets had higher short-chain fatty acid contents and higher species diversity index values for some indices (p < 0.05), although the fecal samples showed lower species diversity levels (p < 0.05). In addition, the PERMANOVA analyses demonstrated that differences were detected in the microbial composition of both fecal and caecotrophic samples, depending on the disease status at the outset of the experiment (p < 0.05). The results of this work show that, although there is some potential in the use of high-fiber diets for the treatment of rabbits that have had epizootic rabbit enteropathy, they are not able to produce the same digestive tract properties as those seen in rabbits that have never had the condition. This is true even after the rabbits have recovered from epizootic rabbit enteropathy.

An Investigation of the Relationship between Cyniclomyces guttulatus and Rabbit Diarrhoea

Cyniclomyces guttulatus is usually recognised as an inhabitant of the gastrointestinal (GI) tract in rabbits. However, large numbers of C. guttulatus are often detected in the faeces of diarrhoeic rabbits. The relationship of C. guttulatus with rabbit diarrhoea needs to be clearly identified. In this study, a C. guttulatus Zhejiang strain was isolated from a New Zealand White rabbit with severe diarrhoea and then inoculated into SPF New Zealand white rabbits alone or co-inoculated with Eimeriaintestinalis, another kind of pathogen in rabbits. Our results showed that the optimal culture medium pH and temperature for this yeast were pH 4.5 and 40-42 °C, respectively. The sequence lengths of the 18S and 26S ribosomal DNA fragments were 1559 bp and 632 bp, respectively, and showed 99.8% homology with the 18S ribosomal sequence of the NRRL Y-17561 isolate from dogs and 100% homology with the 26S ribosomal sequence of DPA-CGR1 and CGDPA-GP1 isolates from rabbits and guinea pigs, respectively. In animal experiments, the C. guttulatus Zhejiang strain was not pathogenic to healthy rabbits, even when 1 × 10⁸ vegetative cells were used per rabbit. Surprisingly, rabbits inoculated with yeast showed a slightly better body weight gain and higher food intake. However, SPF rabbits co-inoculated with C. guttulatus and E. intestinalis developed more severe coccidiosis than rabbits inoculated with C. guttulatus or E. intestinalis alone. In addition, we surveyed the prevalence of C. guttulatus in rabbits and found that the positive rate was 83% in Zhejiang Province. In summary, the results indicated that C. guttulatus alone is not pathogenic to healthy rabbits, although might be an opportunistic pathogen when the digestive tract is damaged by other pathogens, such as coccidia.

Nectarivorous Bird Emphysematous Ingluvitis (NBEI): A Novel Disease in Loriinae Birds Associated With Clostridium perfringens Infection

A retrospective study revealed ten cases of emphysematous ingluvitis in Loriinae birds from two zoological collections between 2009 and 2020. Common clinical features were sudden death with gas distention of the crop, subcutaneous cervical emphysema and poor body condition, but also included collapse, hypothermia and abandonment. Macroscopic examination revealed moderate crop enlargement, distention and thickening with minimal intraluminal content, and moderate to severe submucosal to transmural gas-filled cysts (emphysema). Histopathology identified widespread transmural multifocal to coalescing empty pseudo-cystic cavities with lytic necrosis, pyo-/granulomatous inflammatory infiltrates, epithelial ulceration, parakeratotic hyperkeratosis, epithelial ballooning degeneration, and occasional intralesional rod-shaped bacteria. The lesion may have impaired the birds' ability to ingest food, resulting in suboptimal body condition. Necrotizing to granulomatous aspiration pneumonia was also a feature in some cases. Anaerobic bacterial culture of four crops identified Clostridium perfringens with associated toxin genes for alpha and occasionally beta2 toxin (cpa and cpb2 genes respectively), by PCR analysis of bacterial isolates cultured from fresh or frozen tissue. C. perfringens was identified as the common etiological agent of emphysematous ingluvitis in crop and/or liver (six out of ten birds), and type A was confirmed in five birds. C. perfringens was not detected in the crop nor liver of two unaffected Loriinae birds. This is the first publication that characterizes nectarivorous bird emphysematous ingluvitis (NBEI), attributes C. perfringens as an etiological agent, and highlights this novel disease as an important cause of death in Loriinae birds, particularly in nestling and fledgling stage of development, but also in older lorikeets and lories.

Metataxonomic and Histopathological Study of Rabbit Epizootic Enteropathy in Mexico

Simple Summary

Epizootic rabbit enteropathy (ERE) is a worldwide-distributed dysbiotic syndrome that affects young rabbits. In Mexico, ERE represents 32% of the enteropathies that occur in rabbit production farms. The etiology of this syndrome has not been clarified yet; however, it has been associated with nutritional, environmental, and microbial factors. A metataxonomic and histopathology study of ERE was carried out to compare the lesions and gastrointestinal microbiota of healthy and positive-ERE rabbits. The results revealed a difference in the diversity and abundance of the gastrointestinal microbiota in rabbits with ERE. The genus Clostridium and the species. Cloacibacillus porcorum and Akkermansia muciniphila were associated with the presentation of ERE. Histopathologic analysis showed smaller crypt sizes in the colon of ERE rabbits.

Abstract

Epizootic rabbit enteropathy (ERE) affects young rabbits and represents 32% of the enteropathies in rabbit production farms in Mexico. The etiology of this syndrome has not been clarified yet. A metataxonomic and histopathology study of ERE was carried out to compare the gastrointestinal microbiota and histopathological lesions of healthy and positive-ERE rabbits. The metataxonomic study was done using an Illumina MiSeq (MiSeq^® system, Illumina, San Diego California, USA) massive segmentation platform, and a Divisive Amplicon Denoising Algorithm 2 (DADA2 algorithm) was used to obtain Shannon and Simpson diversity indices as well as the relative abundance of the identified communities. For the histopathological study, paraffin sections of the cecum, ileo-cecal valve, and colon were stained with eosin and hematoxylin. AxioVision 4.9 software (Carl Zeiss MicroImaging GmbH, Jena, Germany) was used to measure the crypt depths. Statistical analysis was done using PERMANOVA analysis for the metataxonomic study and ANOVA for the histopathology study. Histopathologic analysis showed smaller sizes of crypts in the colon of ERE rabbits. Differences were observed in the diversity and abundance of the gastrointestinal microbiota between the analyzed groups. The genus Clostridium and the species Cloacibacillus porcorum and Akkermansia muciniphila were associated with ERE. The results obtained from this study can provide information for future clarification of the etiology and proposals of effective treatments.

Rabbit Enteropathies on Commercial Farms in the Iberian Peninsula: Etiological Agents Identified in 2018-2019

Simple Summary

Digestive disorders are the main cause of economic damage in rabbit farms and, usually, antibiotic treatment is the first choice to control them. Nevertheless, a broad range of infectious agents can be involved in such disorders, as we have observed in our diagnosis work as a veterinary diagnostic laboratory. In this study, a global and updated overview of the frequency of detection of those etiological agents is provided. We have seen differences depending on the age of the affected rabbits, with young rabbits (<15 days old) being the most affected by enteropathogenic Escherichia coli strains, while in preweaning and growing rabbits, a coinfection of two or three pathogens is the most prevalent situation. Clostridium spiroforme and E. coli are the main bacterial agents detected in preweaning rabbits, but enterotoxigenic Bacteroides fragilis has just appeared as a new possible emergent pathogen. Coinfections between bacteria (C. spiroforme and E. coli), parasites (Eimeria spp.), and viruses (rotavirus) are much more frequent than simple infections in growing rabbits; for this reason, complete laboratory studies are required to establish on-farm disease control measures.

Abstract

Digestive disorders are the main cause of economic damage to rabbit farms. This article provides a global and updated overview of the diverse etiological agents causing them, since 757 clinical cases were analyzed during 2018 and 2019—Ninety-five from young rabbits (<15 days old), 117 from preweaning rabbits (15–35 days old), and 545 from growing rabbits. Etiological diagnosis was carried out by bacteriological culture and a set of real time polymerase chain reaction (qPCR) tests for the detection of enteropathogenic Escherichia coli (EPEC), Clostridium spiroforme, C. perfringens, rotavirus A, Bacteroides fragilis, and Eimeria spp. Also, 40 EPEC and 38 non EPEC isolates were investigated for the presence of other colonization factors (afr2, ral, liftA, and paa) by qPCR. EPEC is the most prevalent agent in young rabbits, and although different virulence profiles have been found among EPEC isolates, the liftA+, ral+, and paa+ profile is the most prevalent. C. spiroforme and EPEC are the more frequently detected pathogens in preweaning rabbits, but B. fragilis appears to be a new possible emergent pathogen. In growing rabbits, diverse co-infections between C. spiroforme, Eimeria spp., EPEC, and rotavirus are much more frequent than infections due to only one of them. Other pathogens detected in very few cases are Salmonella spp. and Enterococcus hirae.

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

Weaning weight is an important economic trait in the meat rabbit industry. Evidence has linked the gut microbiota to health and production performance in rabbits. However, the effect of gut microbiota on meat rabbit weaning weight remains unclear. In this study, we performed 16S rRNA gene sequencing analysis of 135 faecal samples from commercial Ira rabbits. We detected 50 OTUs significantly associated with weaning weight. OTUs that showed positive associations with weaning weight were mostly members of the family Ruminococcaceae which are important in degrading dietary fibres and producing butyrate. On the contrary, OTUs annotated to genera Blautia, Lachnoclostridium and Butyricicoccus correlated with fat deposition were negatively associated with weaning weight. Predicted functional capacity analysis revealed that 91 KOs and 26 KEGG pathways exhibited potential correlations with weaning weight. We found that gut microbiota involved in the metabolism of amino acids, butanoate, energy and monosaccharides affected weaning weight. Additionally, cross-validation analysis indicated that 16.16% of the variation in weaning weight was explained by the gut microbiome. Our findings provide important information to improve weaning weight of meat rabbits by modulating their gut microbiome.

Myxomatosis and Rabbit Haemorrhagic Disease: A 30-Year Study of the Occurrence on Commercial Farms in Spain

In this retrospective study, we describe the relative occurrence of clinical myxomatosis, and rabbit haemorrhagic disease (RHD), on 1714 commercial farms visited in Spain, between 1988 and 2018. We determined the annual prevalence based on 817 visits to 394 farms affected by myxomatosis. Myxomatosis was more prevalent from August to March, being lowest in June (3%) and highest in September (8.9%). With regard to RHD, we assessed 253 visits to 156 affected farms. We analyzed mean annual and monthly incidence. Two important RHD epidemics occurred; the first in 1988-1989 due to RHDV GI.1 (also known as RHDV), and the second from 2011 to 2013 due to RHDV GI.2 (RHDV2 or RHDVb). These epidemics occurred at times when effective vaccination had not been carried out. Relative monthly incidence in 2011-2018 was higher from April to August (p < 0.001). The results we obtained from 1404 necropsies on 102 farms did not clearly relate serosanguinous nasal discharge in rabbits with disease caused by GI.2 infection. We also assessed vaccination schedules used on 200 doe farms visited from the end of 2014 to 2018; 95.5% vaccinated against myxomatosis and 97.5% against RHD. Both diseases remain prevalent; however, effective vaccination has produced a steady decline in myxomatosis and RHDV GI.1 and GI.2 on-farm detection. The maintenance of high hygienic standards will be needed to continue and improve this control. However, further studies are required to investigate the causes of sustained virus presence and vaccine breaks.