Abstract
Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.
Highlights
Bacteria that form the gut microbiota of warm-blooded animals belong to numerous phyla, but representatives of two phyla—Gram-negative Bacteroidetes and Gram-positive Firmicutes— commonly form over 90% of all microbiota in healthy adults [1,2,3,4,5,6]
B. dorei, B. clarus, B. uniformis, B. xylanisolvens, B. ovatus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. salanitronis, B. caecigallinarum, M. massiliensis, B. plebeius, B. coprocola, B. caecicola and B. mediterraneensis were specific for chickens
A certain degree of host adaptation could be expected as B. dorei, B. uniformis, B. xylanisolvens and B. ovatus were reported as common to human gut microbiota [8,9,25,26] and B. plebeius and B. caecigallinarum are common in chickens [27,28]
Summary
Bacteria that form the gut microbiota of warm-blooded animals belong to numerous phyla, but representatives of two phyla—Gram-negative Bacteroidetes and Gram-positive Firmicutes— commonly form over 90% of all microbiota in healthy adults [1,2,3,4,5,6]. Bacteroidetes have a higher potential to interact with their host and degrade complex polysaccharides [7,8,9], and their metabolism commonly produces acetate, propionate and succinate [10,11]. Firmicutes preferentially degrade oligosaccharides [7] or ferment metabolic byproducts such as lactate or acetate into butyrate [10,11]. Isolates belonging to phylum Bacteroidetes are classified mainly into families Rikenellaceae, Porphyromonadaceae, Prevotellaceae and Bacteroidaceae [12]. Out of these families, Bacteroidaceae with genera Bacteroides or Mediterranea represent one of the most frequent Gram-negative colonisers of the distal intestinal tract [3,4]
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