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United States Department of Agriculture

Agricultural Research Service

Research Project: ANIMAL AND MANURE MANAGEMENT FOR SUSTAINABLE PRODUCTION AND REDUCED ENVIRONMENTAL IMPACT Title: Bacteroides isolated from four mammalian hosts lack host specific 16S rRNA gene phylogeny and carbon and nitrogen utilization patterns

Authors
item Atherly, Todd
item Ziemer, Cherie

Submitted to: MicrobiologyOpen
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 3, 2014
Publication Date: April 1, 2014
Repository URL: http://handle.nal.usda.gov/10113/58698
Citation: Atherly, T.A., Ziemer, C.J. 2014. Bacteroides isolated from four mammalian hosts lack host specific 16S rRNA gene phylogeny and carbon and nitrogen utilization patterns. MicrobiologyOpen. 3:225-238.

Interpretive Summary: The large intestine has trillions of microbes, primarily bacteria, which are able to use fiber which we and many mammals are not able to digest. One of the largest groups of bacteria are the Bacteroides species of which three species, Bacteroides ovatus, Bacteroides thetaiotaomicron, and Bacteroides xylanisolvens, are the primary species in the large intestine. These three species are thought to be primarily from the human large intestine, but were also isolated from cows, goats, and pigs. Molecular and carbon and nitrogen utilization methodology were used to determine if these Bacteroides from humans, cows, goats, and pigs were different. Some differences in the genomes were noted, but differences in the gene that determines the microbial identity or in what nitrogen and carbon sources these bacteria used was not noted. Bacteroides are not good nitrogen users and are thought to use ammonia and urea, but it was demonstrated that most of these Bacteroides species do not use ammonia or urea, and only a few nitrogen sources that most of these bacteria used were identified. All of these Bacteroides species were able to use a wide range of carbon sources. The data suggest that ability to use complex carbohydrates in the large intestine is important to humans and other mammals, such that these Bacteroides species are the same in all mammals.

Technical Abstract: Within the distal gut of mammals are trillions of microbes that utilize nutrients from diet, intestinal mucosa, and other gut microbes. One hundred three (103) isolates of B. ovatus, B. thetaiotaomicron, and B. xylanisolvens were recovered from cow, goat, human, and pig fecal enrichments with cellulose or xylan/pectin, representing the genetic diversity across the Bacteroides ovatus-thetaiotaomicron-xylanisolvens clade and host origin as assessed by 16S rRNA gene phylogeny and repetitive sequence based-PCR (rep-PCR). Isolates were compared using 16S rRNA gene sequencing, (rep-PCR), using BOX and ERIC rep-PCR primers, and phenotypic microarrays. Phylogenetic analysis of 16S rRNA gene sequences revealed high sequence homology in this Bacteroides clade, all within 97% similarity, except for three isolates; with distinct phylogenetic groupings by bacterial species but not host origin. Grouping the rep-PCR banding patterns of isolates at 90% similarity resulted in the majority of groups containing isolates from just one host. Phenotypic microarray analysis demonstrated that these Bacteroides species 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, with ammonia utilized only by two B. xylanisolvens. Guanine and xanthine, purine derivatives, were the most utilized nitrogen sources, followed by a few amino sugars and amino acids. Only rep-PCR analysis demonstrated host specific patterns, indicating that genomic changes due to co-evolution with host did not occur in the 16S rRNA or carbohydrate utilization genes for B. ovatus, B. thetaiotaomicron, and B. xylanisolvens bacteria isolated from four mammals with differing gut physiologies and diets. This is the first report to determine preferential utilization of purine derivatives and amino sugars as nitrogen sources, indicating that host associated genomic differences are outside of 16S rRNA and carbohydrate utilization genes, and suggest conservation of specific bacterial species with the same functionality across mammalian hosts for this Bacteroidetes clade.

Last Modified: 10/24/2014
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