ABSTRACT

Gastrointestinal Bacteroides play an important role in the health of their hosts. Do these Bacteroides perform the same functions in hosts that have different diets or gastrointestinal physiology? Do they show any co-evolution with the host environment? Within this study103 isolates of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using 16S rRNA gene sequencing, repetitive sequence based-PCR (rep-PCR), and phenotypic microarrays. Analysis of 16S rRNA gene sequences revealed high percent sequence identity in these Bacteroides; with distinct phylogenetic groupings by bacterial species, but not host origin. Phenotypic microarray analysis demonstrated these Bacteroides shared the ability to utilize many of the same carbon substrates, without differences due to species or host origin, indicative of their broad carbohydrate fermentation abilities. Limited nitrogen substrates were utilized; in addition to ammonia, guanine and xanthine, purine derivatives, were utilized by most isolates, followed by a few amino sugars. Only rep-PCR analysis demonstrated host specific patterns, indicating that genomic changes due to co-evolution with host did not occur by mutation in the 16S rRNA gene or by a gain or loss of carbohydrate utilization genes within these Bacteroides.

In the second part of the study 24 isolates, from the original 103, of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human and pig fecal enrichments with cellulose or xylan/pectin. Isolates were compared using whole genome sequencing to determine possible genotypic differences among Bacteroides species and among same species from different host origins. The GC% content and gene numbers of the isolates compared to their type strain were similar but variation in overall genome size was seen in isolates of the same species. A broad analysis of the Clusters of Orthologous groups (COGs) did not show host specificity. A closer look at 4 COG categories (amino acid, carbohydrate, cell wall, and signal transduction) was done. At this level of analysis some differences between species and isolates from differing hosts was evident. Polysaccharide utilization loci (PULs) were compared for homology against the type strains of the isolates. There was variation in the number of homologous and non-homologous PULs and total number of PULs in the isolates. Differences among glycoside hydrolase (GH) families of the isolates of different Bacteroides species were found; comparison of the Bacteroides xylanisolvens isolates demonstrated host related differences for pig isolates compared to other host origins. Differences among homologous capsular polysaccharide (CPS) loci were seen in the downstream gene content of some CPS loci in isolates from different hosts. The results suggest that many of the genetic functions of isolates in this Bacteroides clade are conserved but that there are some differences in genomes by Bacteroides species and mammalian host origin.