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Nutrients 2015, 7(5), 3279-3299; doi:10.3390/nu7053279

Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure

1
Atlantic Food and Horticulture Research Station, Agriculture and Agri-Food Canada, Kentville, Nova Scotia B4N 1J5, Canada
2
Bureau of Food Surveillance and Science Integration, Food Directorate, Tunney's Pasture, Ottawa, Ontario K1A 0K9, Canada
3
Bureau of Nutrition, Food Directorate, Health Canada, Tunney's Pasture, Ottawa, Ontario K1A 0K9, Canada
*
Author to whom correspondence should be addressed.
Received: 3 February 2015 / Revised: 31 March 2015 / Accepted: 22 April 2015 / Published: 6 May 2015
(This article belongs to the Special Issue Microbiome and Human Health)
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Abstract

Fermentation differs between the proximal and distal gut but little is known regarding how the bacterial communities differ or how they are influenced by diet. In order to investigate this, we compared community diversity in the cecum and feces of rats by 16S rRNA gene content and DNA shot gun metagenomics after feeding purified diets containing different fermentable substrates. Gut community composition was dependent on the source of fermentable substrate included in the diet. Cecal communities were dominated by Firmicutes, and contained a higher abundance of Lachnospiraceae compared to feces. In feces, community structure was shifted by varying degrees depending on diet towards the Bacteroidetes, although this change was not always evident from 16S rRNA gene data. Multi-dimensional scaling analysis (PCoA) comparing cecal and fecal metagenomes grouped by location within the gut rather than by diet, suggesting that factors in addition to substrate were important for community change in the distal gut. Differentially abundant genes in each environment supported this shift away from the Firmicutes in the cecum (e.g., motility) towards the Bacteroidetes in feces (e.g., Bacteroidales transposons). We suggest that this phylum level change reflects a shift to ammonia as the primary source of nitrogen used to support continued microbial growth in the distal gut. View Full-Text
Keywords: cecum; feces; bacterial community; metagenome; diet cecum; feces; bacterial community; metagenome; diet
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Kalmokoff, M.; Franklin, J.; Petronella, N.; Green, J.; Brooks, S.P. Phylum Level Change in the Cecal and Fecal Gut Communities of Rats Fed Diets Containing Different Fermentable Substrates Supports a Role for Nitrogen as a Factor Contributing to Community Structure. Nutrients 2015, 7, 3279-3299.

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