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


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Article Info

DATE

2021-07-01

AUTHORS

Hui-Zeng Sun, Ke-Lan Peng, Ming-Yuan Xue, Jian-Xin Liu

ABSTRACT

BackgroundAntimicrobial 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.ResultsDairy 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.ConclusionsThe 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. More... »

PAGES

44

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    http://scigraph.springernature.com/pub.10.1186/s42523-021-00103-6

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    28 schema:description BackgroundAntimicrobial 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.ResultsDairy 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.ConclusionsThe 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.
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    34 schema:keywords BackgroundAntimicrobial resistance
    35 ConclusionsThe current study
    36 KEGG pathways
    37 L. acidophilus
    38 L. amylovorus
    39 Lactobacillus genus
    40 TCMA
    41 acidophilus
    42 addition
    43 age effects
    44 alignment
    45 amylovorus
    46 analysis
    47 antibiotic classes
    48 antibiotic resistance genes
    49 bacteria
    50 bacterial species
    51 buffaloes
    52 cattle
    53 challenges
    54 class
    55 co-occurrence analysis
    56 composition
    57 cows
    58 current study
    59 dairy buffaloes
    60 dairy cattle
    61 dairy cows
    62 different bacterial species
    63 different host species
    64 distinctive microbiome
    65 effect
    66 function
    67 genes
    68 genus
    69 great potential
    70 health
    71 high prevalence
    72 host species
    73 human health
    74 large reservoir
    75 lifestyle
    76 livestock production
    77 metagenomic analysis
    78 metagenomics
    79 microbial composition
    80 microbiome
    81 microbiota
    82 novel understanding
    83 pathway
    84 potential
    85 prevalence
    86 production
    87 profile
    88 reservoir
    89 resistance
    90 resistance genes
    91 resistive profile
    92 resistome
    93 results
    94 rumen
    95 rumen microbiota
    96 ruminal microbiome
    97 species
    98 strategies
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    101 transmission of ARGs
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    105 schema:name Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes
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