Variation in gut bacterial composition is associated with Haemonchus contortus parasite infection of sheep

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

BACKGROUND

The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control.

METHODS

Eggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content.

RESULTS

The heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep.

CONCLUSIONS

The present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep.

Bacteria associated with ovine gut parasites Trichuris ovis and Haemonchus contortus

An associated microbiome of any host helps it in different metabolic processes ranging from the decomposition of food to the maturation of gametes. Organisms with a parasitic mode of life, though present at nutritious sites inside their host, maintain their own microbiome. Nevertheless, the comprehensive characterization and functionality of microbiome in parasitic organisms remain understudied. We selected two nematode parasites of Kashmir Merino sheep viz;Haemonchus contortus and Trichuris ovis based on their higher prevalence, difference in mode of nutrition, habitation site and effect on host. The objective of the study was to explore the bacteria associated with these parasitic nematodes of sheep. We adopted a 16S rRNA metagenomic sequencing approach to estimate and compare the bacterial communities present in these two nematode species. Nematode parasites from Kashmir Merino sheep were identified morphologically and confirmed with DNA characterization. H. contortus was dominated by phylum Proteobacteria (57%), Firmicutes (25%), Bacteroidota (15%) and Actinobacteriota (3%). Conversely, T. ovis showed Proteobacteria (78%) followed by Firmicutes (8%), Bacteroidota (8%), Actinobacteriota (1%), Fusobacteriota (1%) and other phyla (4%). This study provides a comprehensive account of the microbiome composition of H. contortus and T. ovis, both of which are highly prevalent among Kashmir Merino sheep. Additionally, T. ovis exhibited a greater bacterial diversity compared to H. contortus. Notably, these nematodes were found to harbor certain pathogenic bacteria. This study can further be carried forward in gaining insights into the complex relationship between the microbiota of a parasite and its pathogenicity, reproductive potential and host microbiome modification.

Amino acid profiles, amino acid sensors and transporters expression and intestinal microbiota are differentially altered in goats infected with Haemonchus contortus

Infection with the nematode Haemonchus contortus causes host malnutrition and gastrointestinal injuries. The objective of this study was to investigate the effects of H. contortus infection on gastrointestinal contents of free amino acids (AA), the expression of AA transporters and microbiota with a focus on amino acid metabolism. Twenty-four Xiangdong black goats (13 ± 1.5 kg, 6 months old) were randomly assigned into the control group (n = 8) and the infected group (n = 16). The results showed that H. contortus infection increased (P < 0.05) the free AA contents in jejunum and ileum digesta. The concentrations of blood threonine, phenylalanine and tyrosine were lower (P < 0.05) in the infected group as compared to the control group. In the jejunum and ileum epithelium, H. contortus infection significantly (P < 0.05) down-regulated the expression of AA transporter b^0,+AT/rBAT and B0AT1, but up-regulated (P < 0.05) the expression of transporter CAT2 and xCT. Furthermore, microbiota in both jejunum (Bifidobacteriaceae, Lachnospiraceae, Bacteroidaceae, Enterobacteriaceae, and Micrococcaceae) and ileum (Acidaminococcaceae, Desulfovibrionaceae, Bacteroidaceae, and Peptostreptococcaceae) were also altered at the family level by H. contortus infection. The  commensal bacteria of jejunum showed a close correlation with amino acids, AA transporters, and amino acid metabolism, especially cystine. In conclusion, H. contortus infection affected the intestinal AA contents and the expression of intestinal AA transporters, suggesting altered AA metabolism and absorption, which were accompanied by changes in the relative abundances of gut bacteria that mediate amino acid metabolism.

Microbial community in resistant and susceptible Churra sheep infected by Teladorsagia circumcincta

Gastrointestinal nematodes (GIN) are a major threat to health and welfare in small ruminants worldwide. Teladorsagia circumcincta is a nematode that inhabits the abomasum of sheep, especially in temperate regions, causing important economic losses. Given that T. circumcincta and microbiome share the same niche, interactions between them and the host are expected. Although it is known that within a sheep breed there are animals that are more resistant than others to infection by GIN, it is not known if the microbiome influences the phenotype of these animals. Under this condition, 12 sheep were classified according to their cumulative faecal egg count (cFEC) at the end of a first experimental infection, 6 as resistant group (RG) and 6 as susceptible group (SG) to T. circumcincta infection. Then, all sheep were experimentally infected with 70,000 L3 of T. circumcincta and at day 7 days post-infection were euthanized. At necropsy, gastric mucosa and gastric content from abomasum were collected to extract bacterial DNA and sequence V3-V4 region from 16S rRNA gene using Ilumina technology. After bioanalysis performed, results showed that α-diversity and β-diversity remained similar in both groups. However, resistant phenotype sheep showed a higher number of bacteria butyrate-fermenting species as Clostridium sensu stricto 1 (abundance in RG: 1.29% and in SG: 0.069%; p = 0.05), and Turicibacter (abundance in RG: 0.31% and in SG: 0.027%; p = 0.07) in gastric content but also Serratia spp in gastric mucosa (abundance in RG: 0.12% and in SG: 0.041%; p = 0.07). A trend towards a significant negative correlation between cFEC and Clostridium sensu stricto 1 abundance in gastric content was detected (r = - 0.537; p = 0.08). These data suggest that microbiome composition could be another factor associated with the development of the resistant phenotype modifying the interaction with the host and the in last instance affecting the individual risk of infection.

Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus

The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.

Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep

Background

Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in host-helminth interactions in ruminants has been extensively examined and the present study added to this body of knowledge by assessing the effects of resistance and susceptibility to helminth infection in the gastro-intestinal tract (GIT). Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 highly helminth-susceptible (High-FEC) and 10 highly helminth-resistant (Low-FEC) sheep. FEC status was confirmed during the experiment. Using samples from the faeces and the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon, DNA was extracted and used for 16 rRNA gene amplicon sequencing.

Results

The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum displaying major differences between the High-FEC and Low-FEC animals in values for alpha and beta diversity. After taking all samples into account and adjusting for GIT segment, the High-FEC and Low-FEC sheep differed significantly for four genera Butyrivibrio, Mycoplasma, Lachnoclostridium and Succiniclasticum. In the duodenum, the abundances of Aminipila, Lachnoclostridium and Mogibacterium differed significantly between the High-FEC and Low-FEC sheep. In the ileum, on the other hand, the genus Mycoplasma was significantly depleted in the Low-FEC group.

Conclusions

The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to support a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The microbial populations were most rich and diverse in the duodenum of helminth-resistant sheep, comprising bacterial genera that generally ferment carbohydrates. This observation suggests that helminth-resistant sheep can reorganize the duodenal microbiome taxa which may restrict the development of parasites.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00172-1.

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

Background

Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3–V4 region of the 16S rRNA gene using Illumina MiSeq.

Results

We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones.

Conclusions

Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00141-0.

Describing the intestinal microbiota of Holstein Fasciola-positive and -negative cattle from a hyperendemic area of fascioliasis in central Colombia

The ability to identify compositional changes in the intestinal microbiota of parasitized hosts is important for understanding the physiological processes that may affect animal productivity. Within the field of host–parasite interactions, many studies have suggested that helminths can influence the microbial composition of their hosts via their immunomodulatory effects. Bovine fascioliasis is a helminthiasis widely studied by immunologists, but with little information available regarding gut microbial communities. Thus, we aimed to describe the composition of the intestinal microbiota of Holstein Fasciola-positive and -negative cattle using parasitological methods and ELISA (enzyme-linked immunosorbent assay). Bovine fecal samples (n = 65) were obtained from livestock slaughter plants in the Cundi-Boyacense Colombian highlands (a hyperendemic region for bovine fascioliasis) and studied by amplicon-based next-generation 16S-rRNA and 18S-rRNA gene sequencing. From these samples, 35 were Fasciola hepatica-negative and, 30 were F. hepatica-positive in our detection analysis. Our results showed a reduction in the relative abundance of Bacteroidetes and Ascomycota in the Fasciola-positive samples, along with decreased relative abundances of the commensal taxa previously associated with fermentation and digestion processes. However, metabolomic approaches and functional analyzes of the intestinal microbiota are necessary to support these hypothesis. These findings are a small first step in the development of research aimed at understanding how microbial populations in bovines are modulated in liver helminth infections.

Fasciola hepatica, a liver parasite, infects a wide variety of hosts, mostly ruminants. Ruminant infections with this parasite cause economic losses worldwide, mainly in livestock. Given its importance, much research has been carried out on this parasite, a lot of which has focused on its ability to alter the immune responses of its host. However, little is known about the numerous other interactions it has with the host and how they might affect the host’s intestinal microbiota. Here, we observed a reduction in the abundance of microorganisms associated with the fermentation and digestion of vegetable fiber, two important processes in animal health and productivity. Therefore, it is possible that F. hepatica, in addition to the previously documented liver alterations, also generates changes in the intestinal microbiota that may impact its bovine host. These findings are a small first step in the research of microbial populations in cattle infected with liver helminths which open the door to further research aimed at identifying alternative treatments for parasites such as F. hepatica.