While feed efficiency (FE) is a trait of great economic importance to the pig industry, the influence of the intestinal microbiome in determining FE is not well understood. The objective of this experiment was to determine the relative influence of FE and farm of birth on the pig colonic microbiome. Animals divergent in residual feed intake (RFI) were sourced from two geographically distinct locations (farms A + B) in Ireland. The 8 most efficient (low RFI (LRFI)) and 8 least efficient (high RFI, (HRFI)) pigs from farm A and 12 LRFI and 12 HRFI pigs from farm B were sacrificed. Colonic digesta was collected for microbial analysis using 16S ribosomal RNA gene sequencing and also for volatile fatty acid analysis. The α-diversity differed between the farms in this study, with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05), with no difference identified in either Chao1 or observed measures of diversity (P > 0.05). In the analysis of β-diversity, pigs clustered based on farm of birth rather than RFI. Variation in the management of piglets, weight of the piglets, season of the year, sanitary status and dam dietary influence could potentially be causative factors in this large variation between farms. However, despite significant variation in the microbial profile between farms, consistent taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of BS11 (P < 0.05) and a tendency toward increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had increased abundance of Colinsella (P < 0.05), a tendency toward increased Bacteroides and CF231 (P < 0.10). At species level, Ruminococcus flavefaciens had increased abundance in the LRFI compared to the HRFI animals. In conclusion, while farm of birth has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of FE status was apparent.

Coffee is a relatively rich source of chlorogenic acids (CGA), which, as other polyphenols, have been postulated to exert preventive effects against CVD and type 2 diabetes. As a considerable proportion of ingested CGA reaches the large intestine, CGA may be capable of exerting beneficial effects in the large gut. Here, we utilise a stirred, anaerobic, pH-controlled, batch culture fermentation model of the distal region of the colon in order to investigate the impact of coffee and CGA on the growth of the human faecal microbiota. Incubation of coffee samples with the human faecal microbiota led to the rapid metabolism of CGA (4 h) and the production of dihydrocaffeic acid and dihydroferulic acid, while caffeine remained unmetabolised. The coffee with the highest levels of CGA (P< 0·05, relative to the other coffees) induced a significant increase in the growth of Bifidobacterium spp. relative to the control vessel at 10 h after exposure (P< 0·05). Similarly, an equivalent quantity of CGA (80·8 mg, matched with that in high-CGA coffee) induced a significant increase in the growth of Bifidobacterium spp. (P< 0·05). CGA alone also induced a significant increase in the growth of the Clostridium coccoides–Eubacteriumrectale group (P< 0·05). This selective metabolism and subsequent amplification of specific bacterial populations could be beneficial to host health.

Many epidemiological and experimental studies have suggested an important role for dietary fibre (DF) of cereals in the prevention of colon cancer. The objective of the present study was to explain the effects of the DF of barley Rihane (BR) on azoxymethane (AOM)-induced aberrant crypt foci (ACF) and colonic bacterial diversity in rats. Following an acclimatisation period, rats were divided into four groups and fed a control (C) diet or experimental diet containing 30 % of BR. DF content in the experimental diet was twice that of the C diet (total DF was 8·69 % in the C diet and 15·24 % in the BR diet). At 7 and 8 weeks of age, rats received two successive subcutaneous injections of AOM at 20 mg/kg body weight. At 12 weeks after the first injection, ten animals from each group were killed. The BR diet decreased colonic pH (P < 0·05) compared with the C diet. The total number of ACF observed decreased considerably in the BR/AOM group compared with the C/AOM group (P < 0·05). Comparison of similarity coefficients showed variability of colonic microbiota species between the different groups. In addition, we showed inter-individual variability within the same group. This similarity was affected by BR and AOM. The present results show that bifidobacteria numbers were lower in rats fed the BR diet compared with those fed the C diet. However, the number of enterobacteria in colonic content was increased (P < 0·05) in the BR group compared with the C group. The results from the present study show that the DF of BR reduced the incidence of AOM-induced ACF and increased microbiota biodiversity.