Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Apr 16;3:16.
doi: 10.1186/s40168-015-0078-5. eCollection 2015.

Resistant Starch Diet Induces Change in the Swine Microbiome and a Predominance of Beneficial Bacterial Populations

Affiliations
Free PMC article

Resistant Starch Diet Induces Change in the Swine Microbiome and a Predominance of Beneficial Bacterial Populations

Özgün C O Umu et al. Microbiome. .
Free PMC article

Abstract

Background: Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host's gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However, few studies have focused on how they influence the gut microbiome and how these interactions influence host health. The aim of this study is to investigate how the gut microbiome of growing pigs responds to diets containing gel-forming alginate and fermentable resistant starch and to predict important interactions and functional changes within the microbiota.

Results: Nine growing pigs (3-month-old), divided into three groups, were fed with either a control, alginate-, or resistant starch-containing diet (CON, ALG, or RS), and fecal samples were collected over a 12-week period. SSU (small subunit) rDNA amplicon sequencing data was annotated to assess the gut microbiome, whereas comprehensive microarray polymer profiling (CoMPP) of digested material was employed to evaluate feed degradation. Gut microbiome structure variation was greatest in pigs fed with resistant starch, where notable changes included the decrease in alpha diversity and increase in relative abundance of Lachnospiraceae- and Ruminococcus-affiliated phylotypes. Imputed function was predicted to vary significantly in pigs fed with resistant starch and to a much lesser extent with alginate; however, the key pathways involving degradation of starch and other plant polysaccharides were predicted to be unaffected. The change in relative abundance levels of basal dietary components (plant cell wall polysaccharides and proteins) over time was also consistent irrespective of diet; however, correlations between the dietary components and phylotypes varied considerably in the different diets.

Conclusions: Resistant starch-containing diet exhibited the strongest structural variation compared to the alginate-containing diet. This variation gave rise to a microbiome that contains phylotypes affiliated with metabolically reputable taxonomic lineages. Despite the significant microbiome structural shifts that occurred from resistant starch-containing diet, functional redundancy is seemingly apparent with respect to the microbiome's capacity to degrade starch and other dietary polysaccharides, one of the key stages in digestion.

Keywords: 16S rRNA gene; Alginate; Bacterial community; Growing pigs; Gut microbiota; Resistant starch.

Figures

Figure 1
Figure 1
Comprehensive microarray polymer profiling (CoMPP) of plant cell wall components (PCWCs) and principle component analysis (PCA). Heatmap (A) shows the relative abundances of PCWCs in each sample. Color intensity is proportional to mean spot signal. T1 to T7 refer to the time-points when samples were collected. PCA plot (B) shows the comparison of PCWC composition between diets. Labels contain name of diet type (CON, ALG, RS), pig number for the specific diet with numbers between 1 and 3 and time-point numbers between 1 and 7 in the order (starting from T1 as first time-point). HG, homogalacturonan; AGP, arabinogalactan protein; GlcA, glucuronic acid.
Figure 2
Figure 2
Community diversity represented by Shannon index at an OTU level for samples from each diet. Shannon indexes were calculated based on the average of ten iterations at equal subsampling size of 1,781 for each sample. Each bar represents the samples from the pigs fed with different diets; alginate-containing diet (ALG) blue, control diet (CON) green, and resistant starch-containing diet (RS) red.
Figure 3
Figure 3
Comparison of the gut community composition. (A) Principle coordinate analysis (PCoA) plot generated based on the calculated distances in an unweighted UniFrac matrix. Samples were grouped by color and shape in terms of diet group they belong to; alginate-containing diet (ALG) red (circle), control diet (CON) blue (square), and resistant starch-containing diet (RS) orange (triangle). Labels contain name of diet type (CON, ALG, RS), pig number for the specific diet with numbers between 1 and 3, and time-point numbers between 1 and 7 in the order (starting from T1 as first time-point). (B) The statistical significances of differences in unweighted UniFrac distances between diets. Significance degree (calculated using Student’s t-test with 1,000 Monte Carlo simulations) is represented as no significance (P > 0.05) with NS; P < 0.05 with one star (*); P < 0.005 with two stars (**).
Figure 4
Figure 4
Significantly different bacterial genera in relative abundance between different diets. Genera that have different relative abundances in ALG or RS pigs compared to CON pigs were determined by ANCOVA. The shown mean relative abundance percentages of the taxa were calculated using all samples taken over time within each diet. Significance degree is represented with stars; P < 0.05 with one star (*); P < 0.01 with two stars (**); P < 0.001 with three stars (***). The significance was stated next to the bar together with the abbreviations of compared diets (ALG, CON, and RS) when the bar does not appear for at least one of the diets due to a very low relative abundance percentage.
Figure 5
Figure 5
The relative abundances of bacterial families for each fecal sample over time. The size of each square represents the mean relative abundance of bacterial families (%) for the indicated time-point and was determined from fecal samples of three pigs that were fed with the same diet. Samples were ordered in terms of time within each diet and labeled beginning with diet type (ALG, CON, and RS) and time-point from T1 to T7 (T1: day −7, T2: day 1, T3: day 3, T4: day 7, T5: week 3, T6: week 7 and T7: week 12).
Figure 6
Figure 6
Imputed metagenomic differences between ALG and RS pigs compared to CON pigs. The relative abundance of metabolic pathways encoded in each imputed sample metagenome was analyzed using STAMP [63]. Extended error bars show significantly different KEGG pathway maps in RS (A) and ALG (B) pigs compared to CON pigs (P < 0.05, confidence intervals = 95%).
Figure 7
Figure 7
Correlation networks of OTUs and PCWCs in each diet. OTUs were grouped at 97% SSU rRNA gene identity and the networks were plotted based on eLSA with significant local similarity scores (p < 0.001). (A), (B), and (C) networks represent CON, ALG, and RS, respectively. The numbers on nodes are OTU numbers, and PCWCs are labeled with their targeting monoclonal antibodies. All PCWCs are shown by one color (green) while OTUs belonging to different families are represented by different colors (see legend). The size of each node is proportional to the value of relative abundances. Solid edges (black) are positively associated while dashed edges (red) are negatively associated. Edges without any tip show co-occurrence without time delay; while one, two, and three time-point delays are indicated on the affected feature with an arrow, circle, or diamond tip, respectively. HG, homogalacturonan; AGP, arabinogalactan protein; GlcA, glucuronic acid.

Similar articles

See all similar articles

Cited by 41 articles

See all "Cited by" articles

References

    1. Ray K. Gut microbiota: married to our gut microbiota. Nat Rev Gastroenterol Hepatol. 2012;9:555. doi: 10.1038/nrgastro.2012.165. - DOI - PubMed
    1. Robles Alonso V, Guarner F. Linking the gut microbiota to human health. Br J Nutr. 2013;109:S21–6. doi: 10.1017/S0007114512005235. - DOI - PubMed
    1. Delzenne NM, Neyrinck AM, Cani PD. Gut microbiota and metabolic disorders: how prebiotic can work? Br J Nutr. 2013;109:S81–5. doi: 10.1017/S0007114512004047. - DOI - PubMed
    1. Zijlstra RT, Jha R, Woodward AD, Fouhse J, Kempen TATG V. Starch and fiber properties affect their kinetics of digestion and thereby digestive physiology in pigs. 2013; 49–58. - PubMed
    1. Landon S, Salman H. The resistant starch report - Food Australia Supplement. 2012.

LinkOut - more resources

Feedback