Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes

Abstract

Background Antimicrobial resistance poses super challenges in both human health and livestock production. Rumen microbiota is a large reservoir of antibiotic resistance genes (ARGs), which show significant varations in different host species and lifestyles. To compare the microbiome and resistome between dairy cows and dairy buffaloes, the microbial composition, functions and harbored ARGs of rumen microbiota were explored between 16 dairy cows (3.93 ± 1.34 years old) and 15 dairy buffaloes (4.80 ± 3.49 years old) using metagenomics. Results Dairy buffaloes showed significantly different bacterial species (LDA > 3.5 & P < 0.01), enriched KEGG pathways and CAZymes encoded genes (FDR < 0.01 & Fold Change > 2) in the rumen compared with dairy cows. Distinct resistive profiles were identified between dairy cows and dairy buffaloes. Among the total 505 ARGs discovered in the resistome of dairy cows and dairy buffaloes, 18 ARGs conferring resistance to 16 antibiotic classes were uniquely detected in dairy buffaloes. Gene tcmA (resistance to tetracenomycin C) presented high prevalence and age effect in dairy buffaloes, and was also highly positively correlated with 93 co-expressed ARGs in the rumen (R = 0.98 & P = 5E-11). In addition, 44 bacterial species under Lactobacillus genus were found to be associated with tcmA (R > 0.95 & P < 0.001). L. amylovorus and L. acidophilus showed greatest potential of harboring tcmA based on co-occurrence analysis and tcmA-containing contigs taxonomic alignment. Conclusions The current study revealed distinctive microbiome and unique ARGs in dairy buffaloes compared to dairy cattle. Our results provide novel understanding on the microbiome and resistome of dairy buffaloes, the unique ARGs and associated bacteria will help develop strategies to prevent the transmission of ARGs.

An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics

“…Those findings suggest that there exist some certain differences in the rumen’s degradation ability of carbohydrate substrates of dairy buffaloes of different ages. These results are in line with our previous research on dairy buffaloes [ 28 ]. On the basis of the aforementioned experimental results, we speculate that the reasons for the variation among different groups of those enzymes may be that genus Lactobacillus and Prevotella , which largely contributed to the pathways of starch and sucrose metabolism, carbon metabolism, and for their role of GHs production, are more abundant in the rumen of Y group’s dairy buffaloes, whereas the rumen environment of older age dairy buffaloes may not be suitable for the survival of the Lactobacillus and Prevotella [ 22 ].…”

“…Animals were obtained from the Buffalo Research Institute, Chinese Academy of Agricultural Sciences, and Guangxi Zhuang Nationality Autonomous Region (Nanning, China). The diet of dairy buffaloes was the same as in our previous study [ 28 ], which consisted of 60% corn silage, 20.8% corn, 7.4% wheat bran, 3.2% soybean meal, 6.0% cottonseed meal, and micronutrient supplement (96.0% DM, 13.8% CP, 39.1% DNF and 21.1% ADF). The studied buffaloes were reared on a dairy farm located in Nanning City, which belongs to the sub-tropical climate (22°48′ N, 108°22′ E) in China.…”

“…Using the raw data generated in our previous study comparing the rumen microbial resistome between dairy cows and dairy buffaloes [ 28 ], we further attempt to understand the establishment pattern of microbes and functions in relation to different ages of dairy buffaloes from juvenile (12 months old) to old age (>9 years old). The results will expand our understanding of the dynamic changes of rumen microbiota and provide novel insights into strategies for manipulating buffalo rumen microbes.…”

Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas

“…At the species level, Campedelli et al (2018) reported Lactobacillus amylovorus, Lactobacillus melliventris, Lactobacillus ultunensis, Lactobacillus vaginalis and Lactobacillus intestinalis of animal origin are all resistant to macrolide, penicillin and rifamycin, which is consistent with our research, indicated that these microbes in animals are common antibiotic-producing bacteria. Besides, Sun et al (2021) found that the resistance of dairy cows to tetracenomycin C shows a high prevalence rate, while Lactobacillus amylovorus has a strongest association with resistance to tetracenomycin C. Lactobacillus amylovorus is a beneficial microbiota present in the intestines of piglets (Kant et al, 2011), which can be used to treat diarrhea of piglets, respiratory diseases of dairy cows and enhance gastrointestinal immunity of animals (Roselli et al, 2007;Martinez et al, 2013;Amat et al, 2020). Our results showed that the resistance of Lactobacillus amylovorus to ten categories ARGs was positively correlated and its relative abundance was significantly higher in LA.…”

Citrus flavonoid extracts alter the profiling of rumen antibiotic resistance genes and virulence factors of dairy cows

“…The changes in these genes and factors are closely related to the composition of microbiota in the rumen (Ma et al, 2022). Recently, studies on rumen resistance, such as in dairy cows (Sun et al, 2021) and sheep (Yuan et al, 2022), have found that the abundance and distribution of resistome in the rumen are affected by the animals' diet (Auffret et al, 2017). For example, Auffret et al (2017) revealed that the dietary ratio of concentrate to forage significantly changed the ruminal ARG and VFG in beef cattle.…”