Application of 16S rRNA gene-targetted fluorescence in situ hybridization and restriction fragment length polymorphism to study porcine microbiota along the gastrointestinal tract in response to different sources of dietary fibre

Castillo, M.; Skene, Gail; Roca, María J.; Anguita, Montserrat; Badiola, Ignacio; Duncan, Sylvia H.; Flint, Harry J.; Martín‐Orúe, S. M.

doi:10.1111/j.1574-6941.2006.00204.x

Cited by 60 publications

(39 citation statements)

References 38 publications

(36 reference statements)

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“…The predominant phyla present in the feces of both feeding groups of pigs at all time points were the Firmicutes and Bacteroidetes, similar to previous studies with both pig and human subjects (7,13,23), suggesting that the pig is a good animal model for studying the GI microbiome and the consequences of microbiota manipulation. The microbial populations were not statistically different between individuals at the start of the trial (day 1, no milk) at the phylum level, indicating that all pigs were starting with similar fecal microbiotas.…”

Section: Discussionsupporting

confidence: 85%

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Maga

Desai

Weimer

et al. 2012

Appl Environ Microbiol

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ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

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Section: Discussionsupporting

confidence: 85%

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Maga

Desai

Weimer

et al. 2012

Appl Environ Microbiol

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“…However, to maintain normal gut function, a minimum level of fibre has to be included in the diet (Wenk, 2001) and inclusion of dietary fibre can be a strategy to change the structure of the gut microbial communities (Castillo et al, 2007). The microbial ecosystem in the gastrointestinal (GI) tract is characterized by a high population density, wide diversity and complexity of hostmicrobe and microbe-microbe interactions (Zoetendal et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…The microbial ecosystem in the gastrointestinal (GI) tract is characterized by a high population density, wide diversity and complexity of hostmicrobe and microbe-microbe interactions (Zoetendal et al, 2004). However, the knowledge about the gut microbial diversity is still far from complete and the use of molecular techniques has revealed that many of the pig gut microbial communities have not previously been cultured (Leser et al, 2002;Castillo et al, 2007;Patterson et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Impact of chicory inclusion in a cereal-based diet on digestibility, organ size and faecal microbiota in growing pigs

Ivarsson

Liu

Dicksved

et al. 2012

Animal

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A total of 30 7-week-old pigs were used to evaluate the effects of chicory inclusion on digestibility, digestive organ size and faecal microbiota. Five diets were formulated: a cereal-based control diet and four diets with inclusion of 80 and 160 g/kg chicory forage (CF80 and CF160), 80 g/kg chicory root (CR80) and a mix of 80 g/kg forage and 80 g/kg chicory root (CFR). Generally, the pigs showed a high growth rate and feed intake, and no differences between the different diets were observed. The coefficients of total tract apparent digestibility (CTTAD) of energy, organic matter and CP did not differ between the control and CF80, whereas they were impaired in diet CF160. The CTTAD of non-starch polysaccharides and especially the uronic acids were higher (P , 0.05) with chicory inclusion, with highest (P , 0.05) values for diet CF160. Coliform counts were lower and lactobacilli : coliform ratio was higher (P , 0.05) in diet CFR than in the control. Global microbial composition was investigated by terminal restriction fragment length polymorphism combined with cloning and sequencing. Analysis of gut microbiota pattern revealed two major clusters where diet CF160 differed from the control and CR80 diet. Chicory forage diets were correlated with an increased relative abundance of one species related to Prevotella and decreased abundance of two other species related to Prevotella. For diet CFR, the relative abundance of Lactobacillus johnsonii was higher than in the other diets. This study shows that both chicory forage and root can be used as fibre sources in pig nutrition and that they modulate the composition of the gut microbiota differently.

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“…The porcine intestinal microbiota change in response to dietary carbohydrate composition due to specific substrate preferences of bacteria (6). Therefore, inclusion of specific nonstarch polysaccharides (NSP) in the diet of pigs allows manipulation of the composition of the intestinal microbiota.…”

mentioning

confidence: 99%

Nonstarch Polysaccharides Modulate Bacterial Microbiota, Pathways for Butyrate Production, and Abundance of Pathogenic Escherichia coli in the Pig Gastrointestinal Tract

Metzler‐Zebeli

Hooda

Pieper

et al. 2010

Appl Environ Microbiol

121

103

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The impact of nonstarch polysaccharides (NSP) differing in their functional properties on intestinal bacterial community composition, prevalence of butyrate production pathway genes, and occurrence of Escherichia coli virulence factors was studied for eight ileum-cannulated growing pigs by use of terminal restriction fragment length polymorphism (TRFLP) and quantitative PCR. A cornstarch-and casein-based diet was supplemented with low-viscosity, low-fermentability cellulose (CEL), with high-viscosity, low-fermentability carboxymethylcellulose (CMC), with low-viscosity, high-fermentability oat ␤-glucan (LG), and with highviscosity, high-fermentability oat ␤-glucan (HG). Only minor effects of NSP fractions on the ileal bacterial community were observed, but NSP clearly changed the digestion in the small intestine. Compared to what was observed for CMC, more fermentable substrate was transferred into the large intestine with CEL, LG, and HG, resulting in higher levels of postileal dry-matter disappearance. Linear discriminant analysis of NSP and TRFLP profiles and 16S rRNA gene copy numbers for major bacterial groups revealed that CMC resulted in a distinctive bacterial community in comparison to the other NSP, which was characterized by higher gene copy numbers for total bacteria, Bacteroides-Prevotella-Porphyromonas, Clostridium cluster XIVa, and Enterobacteriaceae and increased prevalences of E. coli virulence factors in feces. The numbers of butyryl-coenzyme A (CoA) CoA transferase gene copies were higher than those of butyrate kinase gene copies in feces, and these quantities were affected by NSP. The present results suggest that the NSP fractions clearly and distinctly affected the taxonomic composition and metabolic features of the fecal microbiota. However, the effects were more linked to the individual NSP and to their effect on nutrient flow into the large intestine than to their shared functional properties.

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Application of 16S rRNA gene-targetted fluorescence in situ hybridization and restriction fragment length polymorphism to study porcine microbiota along the gastrointestinal tract in response to different sources of dietary fibre

Cited by 60 publications

References 38 publications

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Impact of chicory inclusion in a cereal-based diet on digestibility, organ size and faecal microbiota in growing pigs

Nonstarch Polysaccharides Modulate Bacterial Microbiota, Pathways for Butyrate Production, and Abundance of Pathogenic Escherichia coli in the Pig Gastrointestinal Tract

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