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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: Bacterial isolates from polysaccharide enrichments cluster by host origin for Firmicutes but not Bacteroidetes.

Author
item Ziemer, Cherie

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: July 31, 2014
Publication Date: N/A

Technical Abstract: The intestinal microbiota allows mammals to recover energy stored in plant biomass through fermentation of plant cell walls, primarily cellulose and hemicellulose. Bacteria were isolated from 8 week continuous culture enrichments with cellulose and xylan/pectin from cow (C, n=4), goat (G, n=4), human (H, n=4), and pig (P, n=6) feces. 16S rRNA genes were sequenced (ISU DNA Sequencing and Synthesis Facility) and analyzed using the Ribosomal Database Project (RDP) and Bionumerics software. 78% of isolates (1650 total) were from Firmicutes (743, 45%) and Bacteroidetes (544, 33%) phyla (by host origin: C 52% and 31%, G 43% and 34%, H 43% and 35%, P 42% and 32%, respectively). Using 98.5% similarity in 16S rRNA gene sequences to define bacterial species, about 95% of Bacteroidetes and 80% Firmicutes isolates did not match cultured bacterial species in the RDP. The Bacteroidaceae family predominated (~91% of total) the Bacteroidetes (487) in isolates from all host species with the other isolates placed in the Porphyromonadaceae (73) family. There was no host specificity in any bacterial species for isolate in the Bacteroidetes. By class, Clostridia (467) were the most abundant Firmicutes followed by Bacilli (186), Erysipelotricha (86), and Negativicutes (5). Lachnospiraceae was the predominant family of isolates from all 4 hosts averaging 16% of total, 36% of Firmicutes, and 58% of Clostridia isolates; 5 other families within the Clostridia were also represented in the isolates. There was some differentiation by host origin for bacterial species in the non-Clostridia Firmicutes. In Clostridia there was extensive differentiation by host origin for bacterial species. A total 105 species groupings were found in the Clostridia with 86 (82%) containing isolates from only one host. Only isolates that cluster at the species level with Tisserella praecuta and Clostridium clostridiformes included bacteria from all 4 hosts. It is not clear why Bacteroidetes did not differ by host origin but it may be related to their niche in the large intestine as polysaccharide fermenters; their genomes carry many glycoside hydrolase genes targeting a large range of carbohydrates. The predominance of Firmicutes and host origin associated speciation in bacteria isolated in these enrichments may drive previously observed differences observed among mammalian hosts by diet and gut physiology.

Last Modified: 11/25/2014
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