The composition and stability of the faecal microbiota of Merino sheep

Dynamics Changes of the Fecal Bacterial Community Fed Diets with Different Concentrate-to-Forage Ratios in Qinghai Yaks

(1) Background: This study aimed to investigate the effects of different dietary concentrate to roughage ratios on growth performance and fecal microbiota composition of yaks by 16S rRNA gene sequencing. (2) Methods: In the present study, three diets with different dietary forage-to-concentrate ratios (50:50, 65:35, and 80:20) were fed to 36 housed male yaks. (3) Results: The result shows that Final BW, TWG, and ADG were higher in the C65 group than in the C50 and C80 groups, but the difference was not significant (p > 0.05). DMI in the C65 group was significantly higher than in the other two groups (p < 0.05). The DMI/ADG of the C65 group was lower than that of the other two groups, but the difference was insignificant (p > 0.05). At the phylum level, Firmicutes were the most abundant in the C65 group, and the relative abundance of Bacteroidetes was lower in the C65 group than in the other two groups. At the genus level, the relative abundances of Ruminococcaceae_UCG_005, Romboutsia, and Christensenellaceae_R-7 were higher in the C56 group than in the C50 and C80 groups. The relative abundance of Lachnospiraceae_NK3A20 and Rikenellaceaewas_RC9_gut is lower in the C65 group, but the difference was insignificant (p > 0.05). At KEGG level 2, the relative abundance of lipid metabolism and energy metabolism were lowest in the C50 group, and both showed higher relative abundance in the C65 group. (4) Conclusions: In conclusion, the structure of fecal microbiota was affected by different concentrate-to-forage ratios. We found that feeding diets with a concentrate-to-forage ratio of 65:35 improved yaks’ growth and energy metabolism.

Identification, Superantigen Toxin Gene Profile and Antimicrobial Resistance of Staphylococci Isolated from Polish Primitive Sheep Breeds

The study aimed to analyze staphylococcal microbiota of the nasal cavity of the primitive sheep breeds Polish Świniarka and Wrzosówka kept on the same ecological farm. The research included the identification of staphylococcal species, evaluation of the prevalence of genes encoding enterotoxins, staphylococcal enterotoxin-like proteins, exfoliative toxins, toxic shock syndrome toxin 1, and detection of antimicrobial resistance. From 61 swab samples gathered from Świniarka (33) and Wrzosówka (28) healthy sheep, 127 coagulase-negative staphylococci (CoNS) were isolated. Based on PCR-RFLP analysis of the gap gene using AluI and HpyCH4V enzymes, the isolates were identified as: Staphylococcus xylosus (33.9%), S. equorum (29.1%), S. arlettae (15%), S. warneri (9.4%), S. lentus (7.9%), S. succinus (3.9%) and S. sciuri (0.8%). Three of these species, S. lentus, S. succinus, and S. sciuri, were detected only from the Świniarka breed. It was found that 77.2% of isolates harbored from 1 to 7 out of 21 analyzed genes for superantigenic toxins. The greatest diversity of toxin genes was recorded for S. equorum (16 different genes). The most prevalent gene was ser (40.2%). The incidence and number of resistances to antimicrobials were found to be bacterial species but not sheep breed dependent. The highest percentage of resistance was found for S. sciuri. The most frequent resistance was observed to clindamycin (45.7%). The findings of this study prove that toxigenic and antimicrobial resistant CoNS can colonize the nasal cavity of healthy sheep.

Characterization of fungal microbial diversity in Tibetan sheep, Tibetan gazelle and Tibetan antelope in the Qiangtang region of Tibet

Due to the high crude fiber content, straw of various crops is difficult to become a high quality forage resource. The degradation of cellulose in nature mainly depends on the cellulase secreted by microbes, which degrade cellulose into small molecular substances through chemical action, and the microbes that secrete cellulase mainly include some bacteria, fungi and actinomycetes, etc. The large and diverse microbial population contained in the mammalian gastrointestinal tract plays an important role in nutrient digestion. At present, many cellulose-degrading strains have been screened and obtained from animal digestive system and feces, such as Bacillus subtilis from the feces of Panda, Bacillus amyloliquefaciens from the cecum of goose. In this study, the fungal diversity was analysed in the fresh faeces of Tibetan sheep, Tibetan gazelle and Tibetan antelope in Qiangtang, Tibet. Results showed that the structure and species of gut fungi are different in three animals, which may be related to the different physiological functions among different animals, e.g., Tibetan antelope and Tibetan gazelle have stronger tolerance to rough feeding than Tibetan sheep. This study will lay a foundation for cellulose-degrading fungal development and provides technical support for improving rough feeding tolerance of Tibetan sheep.

Variation in Rumen Bacteria of Lacaune Dairy Ewes From One Week to the Next

Bacteria are the most abundant microorganisms in the rumen microbiota and play essential roles, mainly fermenting plant compounds that yield fatty acids. In this study, we aimed at assessing stability of both bacterial composition and of its associations with rumen and milk fatty acids phenotypes over a 1-week period. The study was performed using 118 Lacaune dairy ewes from the INRAE Experimental Unit of La Fage. Rumen and milk samples were obtained from the ewes twice, 1 week apart, and microbiota composition, volatile and long-chain fatty acid concentrations were analyzed. Bacterial composition was assessed using 16S rRNA gene sequencing, and microbiota and fatty acids were analyzed as compositional data. As we worked with relative abundances expressed in a constrained space, the centered log-ratio transformation enabled to transform data to work with multivariate analyses in the Euclidian space. Bacterial composition differed between the 2 weeks of sampling, characterized by different proportions of the two main phyla, Bacteroidetes and Firmicutes. The repeatability of the operational taxonomic units (OTUs) was low, although it varied significantly. However, 66 of them presented a repeatability of over 0.50 and were particularly associated with fatty acid phenotypes. Even though the OTUs from the same bacterial families presented similar correlations to fatty acids in both weeks, only a few OTUs were conserved over the 2 weeks. We proved with the help of sequencing data that there is significant change in microbial composition over a week in terms of abundance of different families of bacteria. Further studies are required to determine the impact of bacterial composition alterations over 1 week, and the specificities of the highly repeatable OTUs.

The Microbiota and Cytokines Correlation between the Jejunum and Colon in Altay Sheep

Simple Summary

Both the jejunum and the colon secrete unique immune factors that interact with the gut microbiota. Investigating the association of gut microbiota and the host immune system, we detected higher populations of Bacteroides, Fibrobacteres and Spirochetes in the colon than in the jejunum of Altay sheep, which is a unique breed in Xinjiang. Levels of IL-6 and IL-12 were lower in the colon than in the jejunum. IL-10 was positively correlated with Ruminococcus_2 in the jejunum. These results indicate a potential interaction between intestinal microbiota and the host immune system that may be considered for the prevention of sheep diseases and the screening of probiotics.

Abstract

Both the jejunum and colon release cytokines that interact with intestinal microbiota. However, it is largely unclear which cytokines and microbial populations are involved in the homeostasis of the intestinal ecosystem for sheep health. To address this, we collected contents for isolating microbiota and tissues for determining cytokines from the jejunum and colon of 7-month-old Altay sheep. We used the techniques of 16S rRNA sequencing and ELISA to detect microbial population and cytokine level, respectively. Correlations between microbial population and cytokines were analyzed by Spearman correlation coefficient. The correlation analysis revealed higher populations of Bacteroides, Fibrobacteres and Spirochetes in the colon than in the jejunum, and IL-6 and IL-12 levels were higher in the jejunum than in the colon. Association analysis further revealed a positive association between IL-10 level and both Ruminococcus_2 and norank_f_Bifidobacteriaceae population in the jejunum. The analysis also revealed positive associations between IL-6 level and Ruminococcaceae_UCG-014 and Ruminococcaceae_UCG-013 population, IL-10 and Prevotellaceae_UCG-004, as well as TNF-α and Prevotellaceae_UCG-003 in the colon. These results indicate a potential interaction between the intestinal microbiota and the host immune system that needs to be further clarified for considering dietary formulations to maintain animal health and disease prevention.

Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province

Background: The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai–Tibet Plateau (QTP). Results: Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak. Conclusions: In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.

Influence of selected factors on the Firmicutes, Bacteroidetes phyla and the Lactobacillaceae family in the digestive tract of sheep

In this study, we used 10 healthy sheep, which gave birth to healthy twins. Stool samples were collected from mothers and their offspring 3 times during the study (0, 28 and 56 day postpartum). Milk samples were taken from the mothers at the same time. RT PCR analysis of faeces and milk was performed in order to assess the level of bacteria from the Firmicutes and Bacteroidetes phyla including the family Lactobacillaceae (phylum Firmicutes). The composition of mother's milk was also analyzed and their BCS. The data were compiled statistically. The obtained results showed that the level of the studied groups of bacteria may change due to the change of diet. Additionally, there were significant differences between lambs and mothers in the levels of the studied groups of bacteria. Analysis also shown that in the digestive system of mothers was a smaller disproportion in the level of the studied bacterial phyla than in lambs. The results also indicated the occurrence of differences in the bacterial composition at the individual level, both in ewes and their offspring. Additionally, in the conducted experiment, there were differences in the level of Firmicutes and Bacteroidetes groups depending on the sex.

Bioaugmentation of animal feces as a mean to mitigate environmental contamination with anthelmintic benzimidazoles

Anthelmintics are used to control infestations of ruminants by gastrointestinal nematodes. The limited metabolism of anthelmintics in animals result in their excretion in feces. These could be piled up in the floor of livestock farms, constituting a point source of environmental contamination, or used as manures in agricultural soils where they persist or move to water bodies. Hence the removal of anthelmintics from feces could mitigate environmental contamination. We hypothesized that a thiabendazole-degrading bacterial consortium would also degrade other benzimidazole anthelmintics like albendazole, fenbendazole, ricobendazole, mebendazole and flubendazole. In liquid culture tests the consortium was more effective in degrading compounds with smaller benzimidazole substituents (thiabendazole, albendazole, ricobendazole), rather than benzimidazoles with bulky substituents (fenbendazole, flubendazole, mebendazole). We then explored the bioaugmentation capacity of the consortium in sheep feces fortified with 5 and 50 mg kg^-1 of thiabendazole, albendazole and fenbendazole. Bioaugmentation enhanced the degradation of all compounds and its efficiency was accelerated upon fumigation of feces, in the absence of the indigenous fecal microbial community. The latter contributes to anthelmintics degradation as suggested by the significantly lower DT₅₀ values in fumigated vs non-fumigated, non-bioaugmented feces. Overall, bioaugmentation could be an efficient means to reduce environmental exposure to recalcitrant anthelmintic benzimidazoles.

The Impact of Host Genotype, Intestinal Sites and Probiotics Supplementation on the Gut Microbiota Composition and Diversity in Sheep

Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Levels of Main Bacterial Phyla in the Gastrointestinal Tract of Sheep Depending on Parity and Age

Simple Summary

The ruminant microbiome is considered a specific ecosystem found within the gastrointestinal tract. A balanced intestinal microbiota is important not only for maintaining gut homeostasis, but also for regulating immune function and has a direct impact on the gut–brain axis. Factors, such as pregnancy, age, or genetics, can influence the microbial composition of the digestive system. The results of the study suggest that the parity, as well as the age of the animals, may affect the level of microorganisms in the digestive system.

Abstract

During pregnancy and parturition, the homeostasis of the body is disturbed, and the immune system is undermined, which is associated with hormonal changes within the body. Recently, it has also been suggested that physiological and hormonal changes associated with pregnancy may affect the composition of the gastrointestinal microbiome. Therefore, the aim of this study was to determine the composition of the microbiome in the third month of pregnancy in sheep in their first and second parity. Eighteen females in total were selected for the experiment, and they were divided into two groups: primiparous (aged 1 year) and multiparous ones (aged 2 years). The animals were fed the same fodder, and did not show any disease symptoms. Fecal samples were collected individually from each female (n = 20), and then bacterial DNA isolation and real-time PCR were performed for the main bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) and families (Lactobacillaceae and Clostridia). The obtained results showed the differentiation in the microbiome between the primiparous and multiparous ewes with respect to the following groups: Bacteroidetes, Proteobacteria, and Actinobacteria—the level was higher in the case of the primiparas. These results suggest that the parity and age of the females may affect the gastrointestinal microbiome, but further studies are recommended.

Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

Background

The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability.

Results

The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups.

Conclusion

The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

Smallholder Farmers' Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Simple Summary

Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity.

Abstract

Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.

Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

Evaluation of Changes in the Levels of Firmicutes and Bacteroidetes Phyla of Sheep Feces Depending on the Breed

Simple Summary

The microbiome plays an important role in the digestive system of ruminants. It affects the health status of animals and their development and production rates. However, its composition may be influenced by factors such as diet, age, gender, and health condition. The study was conducted on three breeds of sheep that were kept in one environment and fed with the same feed. The microbiological analysis showed that the animal microbiome is also influenced by breed.

Abstract

Studies carried out so far have indicated the effect of the microbiome on the composition of ruminant products. Recent studies have shown that not only diet, but also genetic factors can affect the microbiological composition of the digestive system. The aim of the study was to determine the differences in the levels of selected bacterial phyla in terms of breed differences. Three sheep breeds, i.e., Olkuska, Romanov, and old-type Polish Merino, differing in their use (meat–wool, meat, prolificacy) and country of breed origin were included in the study. Sheep at the same age and of the same sex were kept for a period of 3 months in the same environmental conditions and fed the same feed in the same proportions. The study included real-time PCR (polymerase chain reaction) analysis of feces collected before the slaughter and measurements of body weight and chilled carcasses. The obtained results showed significant differences between the breeds in the levels of bacterial populations tested. There were also differences in body weight between the breeds during the first weight measurements, however, the final results did not show any differences—after three months of maintenance all of them reached similar body weights, despite differences in fecal microbiological composition. The study suggests that in addition to diet and environmental conditions, the microbiology can also be influenced by breed.

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics

How complex communities assemble through the animal's life, and how predictable the process is remains unexplored. Here, we investigate the forces that drive the assembly of rumen microbiomes throughout a cow's life, with emphasis on the balance between stochastic and deterministic processes. We analyse the development of the rumen microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data and find that the animals shared a group of core successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifest as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Overall, our findings show that together with strong deterministic constrains imposed by diet and age, stochastic colonization in early life has long-lasting impacts on the development of animal microbiomes.

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

Background

One of the greatest impediments to global small ruminant production is infection with the gastrointestinal parasite, Haemonchus contortus. In recent years there has been considerable interest in the gut microbiota and its impact on health. Relatively little is known about interactions between the gut microbiota and gastrointestinal tract pathogens in sheep. Thus, this study was undertaken to investigate the link between the faecal microbiota of sheep, as a sample representing the gastrointestinal microbiota, and infection with H. contortus.

Results

Sheep (n = 28) were experimentally inoculated with 14,000 H. contortus infective larvae. Faecal samples were collected 4 weeks prior to and 4 weeks after infection. Microbial analyses were conducted using automated ribosomal intergenic spacer analysis (ARISA) and 16S rRNA gene sequencing. A comparison of pre-infection microbiota to post-infection microbiota was conducted. A high parasite burden associated with a relatively large change in community composition, including significant (p ≤ 0.001) differences in the relative abundances of Firmicutes and Bacteroidetes following infection. In comparison, low parasite burden associated with a smaller change in community composition, with the relative abundances of the most abundant phyla remaining stable. Interestingly, differences were observed in pre-infection faecal microbiota in sheep that went on to develop a high burden of H. contortus infection (n = 5) to sheep that developed a low burden of infection (n = 5). Differences observed at the community level and also at the taxa level, where significant (p ≤ 0.001) in relative abundance of Bacteroidetes (higher in high parasite burden sheep) and Firmicutes (lower in high parasite burden sheep).

Conclusions

This study reveals associations between faecal microbiota and high or low H. contortus infection in sheep. Further investigation is warranted to investigate causality and the impact of microbiome manipulation.

Microbiota in viral infection and disease in humans and farm animals

The influence of the microbiota on viral infection susceptibility and disease outcome is undisputable although varies among viruses. The purpose of understanding the interactions between microbiota, virus, and host is to identify practical, effective, and safe approaches that target microbiota for the prevention and treatment of viral diseases in humans and animals, as currently there are few effective and reliable antiviral therapies available. The initial step for achieving this goal is to gather clinical evidences, focusing on the viral pathogens-from human and animal studies-that have already been shown to interact with microbiota. The subsequent step is to identify mechanisms, through experimental evidences, to support the development of translational applications that target microbiota. In this chapter, we review evidences of virus infections altering microbiota and of microbiota enhancing or suppressing infectivity, altering host susceptibility to certain viral diseases, and influencing vaccine immunogenicity in humans and farm animals.