Taxonomic and functional profiling of cow rumen metagenomes

MAGNI, C; MANNO, MARIANO TORRES; BLANCATO, VS; ESPARIZ, M

Buenos Aires

Congreso; LVI Reunión Anual de SAIB; 2020

Sociedad Argentina de Investigación Bioquímica y Biología Molecular

Ruminants can transform the energy stored in plants into food products that can be used by Humans. The rumen microbiota is composed of protozoa, bacteria, fungi, and archaea, which are responsible for plant material degradation. In this work, rumen samples of young (Y, less than one year old) or adult (A, 2.5 years) regional cows, feed with grass (P) or alfalfa plus balanced rations (R) were analyzed. DNA was extracted and sequenced by WGS, reads were quality filtered for taxonomic analysis and assembly into contigs for protein prediction. The two major phyla detected were Bacteroidetes and Firmicutes, Proteobacteria was highly represented followed by Actinobacteria, being all of them involved in carbohydrate digestion. Bacteroidetes were dominant in samples AP-4, AR-5, and YP-1 showing >48% frequency and in YR-2 only 35.8%. Firmicutes represented 43.4% of counts in YR-2 whereas in the rest was less than 30%. Proteobacteria represented 11.7% of counts in YP-1, in the remaining samples it was less than 9%. The higher frequencies of Fibrobacteres (involved in cellulose degradation) were found in YP-1 and AP-4 samples (1.4%, 1.1%); whereas in AR-5 and YR-2 were 0.7 and 0.8%. The more abundant phylum of rumen Archaea in the samples was Euryarchaeota. Prevotella and Bacteroides were the most abundant genera in the samples, followed by Clostridium. The cellulolytic genera Ruminococcus, Fibrobacter, Eubacterium, and Butyrivibrio, were less represented. Eight of the ten most prevalent archaeal genera belonged to the methanogens group, Methanobrevibacter and Methanosarcina were found as the more abundant. To infer the metabolic capacity of the metagenomes the KEGG module completion ratios (MCR) were calculated. MCR indicated that the metagenomes had complete or almost complete central carbohydrate metabolisms. Pectin degradation was not feasible in sample YR-2. Three methanogenesis reported pathways were biologically feasible in the samples. Among the pathways that lead to Volatile Fatty Acids in rumen bacteria, only the conversion from acetylCoA to acetate was found. Among the Xenobiotics biodegradation pathways, only catechol ortho-cleavage was found in the AP-4 sample. Pertussis pathogenicity signature was found in all the samples suggesting the presence of the pathogen in the rumen of the cows. The assembled metagenomes were searched against the SARG v2.0 database to predict the antibiotic resistance gene pattern. On average 0.12% of the samples predicted proteins were found in the database. Among the 7400 resistance genes found per sample the frequency of vancomycin, multidrug, macrolides, polymyxin, fosfidomycin, bacitracin resistance genes was between 5 to 15%. Beta-lactam, rifamycin, and tetracycline resistances were found barely above 1%. This study provides a snapshot of the structure and functional characteristics of the rumen microbiome and resistome of young and adult cows adapted to two regional feed strategies.