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Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

ABSTRACT: Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and large intestine (cecum and colon) plus feces, and characterized the effects of in-feed antibiotics (chlortetracycline, sulfamethazine and penicillin (ASP250)) on these communities. 16S rRNA gene sequence and metagenomic analyses of bacterial membership and functions revealed dramatic differences between small and large intestinal locations, including enrichment of Firmicutes and phage-encoding genes in the ileum. The large intestinal microbiota encoded numerous genes to degrade plant cell wall components, and these genes were lacking in the ileum. The mucosa-associated ileal microbiota harbored greater bacterial diversity than the lumen but similar membership to the mucosa of the large intestine, suggesting that most gut microbes can associate with the mucosa and might serve as an inoculum for the lumen. The collateral effects on the microbiota of antibiotic-fed animals caused divergence from that of control animals, with notable changes being increases in Escherichia coli populations in the ileum, Lachnobacterium spp. in all gut locations, and resistance genes to antibiotics not administered. Characterizing the differential metabolic capacities and response to perturbation at distinct intestinal locations will inform strategies to improve gut health and food safety.

SUBMITTER: Looft T

PROVIDER: S-EPMC4817603 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

Looft Torey T Allen Heather K HK Cantarel Brandi L BL Levine Uri Y UY Bayles Darrell O DO Alt David P DP Henrissat Bernard B Stanton Thaddeus B TB

The ISME journal 20140213 8

Disturbance of the beneficial gut microbial community is a potential collateral effect of antibiotics, which have many uses in animal agriculture (disease treatment or prevention and feed efficiency improvement). Understanding antibiotic effects on bacterial communities at different intestinal locations is essential to realize the full benefits and consequences of in-feed antibiotics. In this study, we defined the lumenal and mucosal bacterial communities from the small intestine (ileum) and lar ...[more]

PMID: 24522263

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Project description:Post-weaning diarrhea (PWD) in pigs has mainly an infectious basis and control strategies are centred on antibiotics added to the diet. Given concerns on the spread of multi-resistant bacteria, it is necessary to develop alternative prophylactic approaches to control PWD in piglets. The most promising alternative strategies are based on substances that act indirectly on the bacteria by stimulating the immune system or by improving gut health. The aim of this study was to evaluate the effect on the gut microbiota of feed supplemented with a mixture of essential oils (garlic and oregano) in weaning piglets, compared to traditional PWD management (in-feed antibiotics) and to a control group without any diet supplementation. The study involved 197 piglets from 18 litters in a single farm. The piglets were followed from birth to day 58 of age and were weaned at day 26. During the experimental period, the animals were monitored for weight and growth, average daily gain, morbidity and mortality. For the metataxonomics analysis, rectal samples were collected from 17 piglets from the three experimental groups at 4 different time-points (days 1, 12, 26 and 58). Results revealed that the gut microbiota in pre- and post-weaning piglets was dominated by the phyla Firmicutes (51%), Bacteroidetes (25%) and Proteobacteria (16%), which together make up for over 90% of the entire piglet core gut microbiota. The core microbiota comprised 10 taxa before weaning and 43 taxa after weaning, with 7 taxa overlapping between timepoints: two of them (Prevotella 9, p-value = 0.00095; Solobacterium p-value = 0.00821) were significantly more abundant after weaning. All alpha diversity indexes were significantly different between pre- and post-weaning, while only Shannon and Simpson diversity and equitability were significantly different between treatments. Based on the matrix of Bray-Curtis dissimilarities, samples showed clear clustering per timepoint (before and after weaning, p-value < 0.001) and between treatments by timepoint (p-value = 0.0086). The oil-diet group showed a consistently higher F:B ratio at all timepoints. These results show that the pig gut microbiota changes significantly with weaning, and suggest that the use of essential oils as feed supplementation to control PWD does not seem to alter sgnificantly the microbiota nor the growth parameters of piglets, however modifications of specific taxa may occur.

Project description:Microbial fermented feed is an important part of feed industry, while little research has focused on the solid-state fermentation of complete feed. Herein, the purpose of the present study was to investigate the effects of fermented complete feed (FCF) on the growth performance, biochemical profile, carcass traits, meat proximate composition, meat amino acid and fatty acid profile, and gut microbiome composition of finishing pigs, thereby providing references for the application of FCF in animal production. Twenty Duroc × Landrace × Yorkshire pigs with an average body weight (BW) of 48.74 ± 1.49 kg were divided randomly into control group (pigs received a basal diet, CN, n = 10) and FCF group (pigs fed with FCF, n = 10). The experiment lasted for 60 days. FCF improved the growth performance, which was indicated by a significantly increased final BW, average daily gain and average daily feed intake, and a significantly decreased feed-to-gain ratio. FCF improved biochemical profile, which was indicated by a higher alkaline phosphatase, glucose, immunoglobulin G, immunoglobulin M, superoxide dismutase, and total antioxidant capacity content. Pigs that received FCF had better carcass traits and meat quality than did pigs that received basal diet, which was indicated by a higher carcass length, crude protein content, lysine content, Glu content, C18:ln9c, C18:2n6c, C20:4n6, and unsaturated fatty acid content and a lower average back-fat thickness, C18:0, and saturated fatty acids. FCF significantly reduced the relative abundances of presumably pathogenic bacteria of phylum Proteobacteria and genus Escherichia-Shigella and enhanced the relative abundances of likely beneficial bacteria of phylum Firmicutes and genus Clostridium. In summary, FCF had a certain effect on the improvement of growth performance, serum biochemical profile, carcass traits, meat proximate composition, amino acid and fatty acid profile, and gut microbiome composition of finishing pigs.

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Dataset Information

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

Publications

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

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