Mucosa-associated microbiota from different regions of the gastrointestinal (GI) tract of adult broilers was studied by analysis of 16S rRNA gene sequences. The microbiota mainly comprised Gram-positive bacteria along the GI tract. Fifty-one operational taxonomic units (OTUs) (from 98 clones) were detected in the ceca, as compared with 13 OTUs (from 49 clones) in the crops, 11 OTUs (from 51 clones) in the gizzard, 14 OTUs (from 52 clones) in the duodenum, 12 OTUs (from 50 clones) in the jejunum and nine OTUs (from 50 clones) in the ileum. Ceca were dominantly occupied by clostridia-related sequences (40%) with other abundant sequences being related to Faecalibacterium prausnitzii (14%), Escherichia coli (11%), lactobacilli (7%) and Ruminococcus (6%). Lactobacilli were predominant in the upper GI tract and had the highest diversity in the crop. Both Lactobacillus aviarius and Lactobacillus salivarius were the predominant species among lactobacilli. Candidatus division Arthromitus was also abundant in the jejunum and ileum.

Aims:  To assess the potential of essential oils and structurally related synthetic food additives in reducing bacterial pathogens in swine intestinal tract. Methods and Results:  The antimicrobial activity of essential oils/compounds was measured by determining the inhibition of bacterial growth. Among 66 essential oils/compounds that exhibited ≥80% inhibition towards Salmonellatyphimurium DT104 and Escherichia coli O157:H7, nine were further studied. Most of the oils/compounds demonstrated high efficacy against S. typhimurium DT104, E. coli O157:H7, and E. coli with K88 pili with little inhibition towards lactobacilli and bifidobacteria. They were also tolerant to the low pH. When mixed with pig cecal digesta, these oils/compounds retained their efficacy against E. coli O157:H7. In addition, they significantly inhibited E. coli and coliform bacteria in the digesta, but had little effect on the total number of lactobacilli and anaerobic bacteria. Conclusions:  Some essential oils/compounds demonstrated good potential, including efficacy, tolerance to low pH, and selectivity towards bacterial pathogens, in reducing human and animal bacterial pathogens in swine intestinal tract. Significance and Impact of the Study:  This study has identified candidates of essential oils/compounds for in vivo studies to develop antibiotic substitutes for the reduction of human and animal bacterial pathogens in swine intestinal tract.

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Aims: To determine the effect of pig diets in vitro on the antimicrobial activity of carvacrol, thymol and cinnamaldehyde, and to identify an emulsifier/stabilizer that can stabilize the essential oil (EO) components in aqueous solution and retain their antimicrobial activity in the presence of the diets. Methods and Results: Emulsification of essential oil components with hydrocolloid solution was achieved by blending with a Polytron. Antimicrobial activity was measured through in vitro assays to determine the inhibition of bacterial growth by measuring the optical density at 600 nm or plating on nutrition agar after incubation of the mixtures of an EO component with the culture of Salmonella serotype Typhimurium DT104 in the presence or absence of pig diets. The results generated through the in vitro assays indicated that pig diets were able to abolish the antimicrobial activity of EOs. Xanthan, fenugreek and yellow mustard gums were the best in forming stable emulsions of five different EO components among ten different plant polysaccharides and surfactants examined. Emulsification of all the EO components in the fenugreek gum solution did not alter their antimicrobial activity. However, the antimicrobial activity of geraniol was significantly reduced when emulsified with other polysaccharides and surfactants. Both fenugreek and xanthan gum solutions were unable to protect the antimicrobial activity of carvacrol and thymol when mixed with the diets. Although cinnamaldehyde required no emulsification, but a high concentration (equivalent to at least three times of minimum bactericidal concentration for cinnamon oil) to inhibit Salmonella growth significantly in the presence of the diets, emulsification in fenugreek gum appeared to be essential for cinnamaldehyde solution to retain its antimicrobial activity during storage. Conclusions: The diets for newly weaned pigs were a significant factor limiting the antimicrobial activity of EOs and their components. Cinnamaldehyde required a high concentration to retain its antimicrobial activity in the diets, in addition to its requirement for emulsification to stabilize its activity during the storage. Significance and Impact of the Study: The assay with the diets used in this study for measuring the antimicrobial activity can be used in vitro for rapid and effective screening of potential antimicrobials for swine production. This study has identified polysaccharides that are able to stabilize EO component solutions. It has also identified cinnamaldehyde for further in vivo studies that may have potential in future application in controlling Salmonella and possibly other enteric pathogens in swine production.

Aims:  To assess the potential of essential oils and structurally related synthetic food additives in inhibiting the growth of Clostridium perfringens for the control of necrotic enteritis in chickens. Methods and Results:  The antimicrobial activity of essential oils/compounds was measured by determining the inhibition of bacterial growth. Thirty‐three of 66 oils/compounds exhibited ≥80% inhibition. Seven with the highest potency were further studied. The oils/compounds had MIC95 values between 167 and 425 μg ml−1. Most of them were tolerant to low pH (2·0) and exhibited minor or no inhibition of Lactobacillus isolates from the chicken intestine. When mixed with chicken ileal digesta, the oils/compounds retained their efficacy against C. perfringens, but had little effect on the total number of lactobacilli and anaerobic bacteria in the digesta. Conclusions:  Some essential oils/compounds demonstrated good potential in controlling C. perfringens. Significance and Impact of the Study:  This study has identified candidates of essential oils/compounds for in vivo studies for the control of necrotic enteritis in chickens.