ABSTRACT
The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are poorly understood. Here, we provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese. We characterize the microbial communities in samples taken from five different locations across the Parmesan cheese production chain, confirming that the final product contains microorganisms derived from cattle gut, milk, and the nearby environment. In addition, we carry out a human pilot study showing that Bifidobacterium mongoliense strains from cheese can transiently colonize the human gut, a process that can be enhanced by cow milk consumption.
Subject(s)
Cheese/microbiology , DNA, Bacterial/genetics , Gastrointestinal Microbiome/genetics , Milk/microbiology , Phylogeny , Animals , Bifidobacterium/classification , Bifidobacterium/genetics , Bifidobacterium/isolation & purification , Cattle , Corynebacterium/classification , Corynebacterium/genetics , Corynebacterium/isolation & purification , DNA Barcoding, Taxonomic , Feces/microbiology , Humans , Lactobacillus delbrueckii/classification , Lactobacillus delbrueckii/genetics , Lactobacillus delbrueckii/isolation & purification , Pilot Projects , Prevotella ruminicola/classification , Prevotella ruminicola/genetics , Prevotella ruminicola/isolation & purification , RNA, Ribosomal, 16S/genetics , Streptococcus thermophilus/classification , Streptococcus thermophilus/genetics , Streptococcus thermophilus/isolation & purificationABSTRACT
AIM: To reassemble Prevotella ruminicola genome from rumen metagenomic data of cattle and buffalo and compare with the published reference genome. METHOD: Rumen microbial communities from Mehsani buffaloes (n = 8) and Kankrej cattle (n = 8), each adapted to different proportions of a dry or green roughage diet, were subjected to metagenomic sequencing by Ion Torrent PGM, and subsequent reads were analyzed by MG-RAST. Using reference-guided assembly of the sequences against the published P. ruminicola strain 23, draft genomes of 2.56 and 2.46 Mb were reconstructed from Mehsani buffalo and Kankrej cows, respectively. The genomes were annotated using the RAST Server and carbohydrate active enzyme (CAZyme) analysis. RESULTS: Taxonomic analysis by MG-RAST revealed P. ruminicola to be the most abundant species present among the rumen microflora. Functional annotation of reconstructed genomes using the RAST Server depicted the maximum assignment of coding sequences involved in the subsystems amino acid and derivatives and carbohydrate metabolism. CAZyme profiling revealed the glycoside hydrolases (GH) family to be the most abundant. GH family subclassification revealed that the extracted genomes had more sequence hits for GH2, GH3, GH92 and GH97 as compared to the reference. CONCLUSION: The results reflect the metabolic significance of rumen-adapted P. ruminicola in utilizing a coarse diet for animals based on acquisition of novel genetic elements.
Subject(s)
Prevotella ruminicola/genetics , Rumen/microbiology , Animals , Bacteria/classification , Bacteria/enzymology , Bacteria/genetics , Bacteria/isolation & purification , Bacterial Proteins/genetics , Buffaloes , Cattle , Gastrointestinal Microbiome , Genome, Bacterial , Metagenomics , Open Reading Frames , Phylogeny , Prevotella ruminicola/classification , Prevotella ruminicola/enzymology , Prevotella ruminicola/isolation & purificationABSTRACT
The Prevotellas comprise a diverse group of bacteria that has received surprisingly limited attention at the whole genome-sequencing level. In this communication, we present the comparative analysis of the genomes of Prevotella ruminicola 23 (GenBank: CP002006) and Prevotella bryantii B(1)4 (GenBank: ADWO00000000), two gastrointestinal isolates. Both P. ruminicola and P. bryantii have acquired an extensive repertoire of glycoside hydrolases that are targeted towards non-cellulosic polysaccharides, especially GH43 bifunctional enzymes. Our analysis demonstrates the diversity of this genus. The results from these analyses highlight their role in the gastrointestinal tract, and provide a template for additional work on genetic characterization of these species.
Subject(s)
Genome, Bacterial , Prevotella ruminicola/genetics , Prevotella/genetics , Animals , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Molecular Sequence Data , Phylogeny , Prevotella/classification , Prevotella/enzymology , Prevotella/isolation & purification , Prevotella ruminicola/classification , Prevotella ruminicola/enzymology , Prevotella ruminicola/isolation & purification , Rumen/microbiologyABSTRACT
Two representative strains of Gram-negative rumen bacteria from the genus Prevotella were used as model organisms in order to evaluate the effect of cinnamaldehyde (the secondary metabolite found in extracts of the Cinnamomum family) vs. sodium monensin on growth, cell size and cell protein production. Prevotella bryantii B(1)4 was found to be remarkably more resistant to the action of both compounds than Prevotella ruminicola 23. The approximate IC(50) concentrations of sodium monensin influenced the increase in cell size of both strains during growth, which was much more pronounced in the case of the B(1)4 strain. A similar effect was observed in strain B(1)4 when 1.438 mmol/L cinnamaldehyde was added to the growth medium, indicating a possible interference with cell division. The action of cinnamaldehyde on P. bryantii B(1)4 was concentration-dependent, in contrast to the effect observed on P. ruminicola 23.
