Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564–566) and ceca (140–142, 218–220, 284–286, 312, and 482) across trials. OTU 564–566 was associated with lower performance, while OTUs 140–142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related toLactobacillusspp.,Ruminococcaceae,Clostridiales,Gammaproteobacteria,Bacteroidales,Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to theFirmicutes, withBacteroidetesandProteobacteriaalso identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius,Lactobacillus aviarius,Lactobacillus crispatus,Faecalibacterium prausnitzii,Escherichia coli,Gallibacterium anatis,Clostridium lactatifermentans,Ruminococcus torques,Bacteroides vulgatus, andAlistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health.

Grape marc (the skins, seeds, stalk, and stems remaining after grapes have been pressed to make wine) is currently a by-product used as a feed supplement by the dairy and beef industries. Grape marc contains condensed tannins and has high concentrations of crude fat; both these substances can reduce enteric methane (CH4) production when fed to ruminants. This experiment examined the effects of dietary supplementation with either dried, pelleted grape marc or ensiled grape marc on yield and composition of milk, enteric CH4 emissions, and ruminal microbiota in dairy cows. Thirty-two Holstein dairy cows in late lactation were offered 1 of 3 diets: a control (CON) diet; a diet containing dried, pelleted grape marc (DGM); and a diet containing ensiled grape marc (EGM). The diet offered to cows in the CON group contained 14.0kg of alfalfa hay dry matter (DM)/d and 4.3kg of concentrate mix DM/d. Diets offered to cows in the DGM and EGM groups contained 9.0kg of alfalfa hay DM/d, 4.3kg of concentrate mix DM/d, and 5.0kg of dried or ensiled grape marc DM/d, respectively. These diets were offered individually to cows for 18d. Individual cow feed intake and milk yield were measured daily and milk composition measured on 4d/wk. Individual cow CH4 emissions were measured by the SF6 tracer technique on 2d at the end of the experiment. Ruminal bacterial, archaeal, fungal, and protozoan communities were quantified on the last day of the experiment. Cows offered the CON, DGM, and EGM diets, ate 95, 98, and 96%, respectively, of the DM offered. The mean milk yield of cows fed the EGM diet was 12.8kg/cow per day and was less than that of cows fed either the CON diet (14.6kg/cow per day) or the DGM diet (15.4kg/cow per day). Feeding DGM and EGM diets was associated with decreased milk fat yields, lower concentrations of saturated fatty acids, and enhanced concentrations of mono- and polyunsaturated fatty acids, in particular cis-9,trans-11 linoleic acid. The mean CH4 emissions were 470, 375, and 389g of CH4/cow per day for cows fed the CON, DGM, and EGM diets, respectively. Methane yields were 26.1, 20.2, and 21.5g of CH4/kg of DMI for cows fed the CON, DGM, and EGM diets, respectively. The ruminal bacterial and archaeal communities were altered by dietary supplementation with grape marc, but ruminal fungal and protozoan communities were not. Decreases of approximately 20% in CH4 emissions and CH4 yield indicate that feeding DGM and EGM could play a role in CH4 abatement.

A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

The effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 ( Lachnospiraceae ), OTU 186/188 ( Lactobacillus johnsonii ), OTU 220 ( Lachnospiraceae ), OTUs 284 to 288 (unclassified bacterial spp. or Ruminococcaceae ), OTU 296/298 (unclassified bacterium or Clostridiales ), and OTU 480/482 ( Oxalobacteraceae ) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 ( Lactobacillus crispatus ), OTU 152 ( Lactobacillus reuteri or unclassified Clostridiales ), OTU 198/200 ( Subdoligranulum spp.), and OTU 490/492 (unclassified bacterium or Enterobacteriaceae ) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.

A chicken growth study was conducted to determine if litter type influenced gut microbiota and performance in broilers. Seven bedding materials were