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 to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also 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, and Alistipes 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.Because feed constitutes approximately 70% of the cost of raising broiler chickens (1), the most common measures of bird performance have been linked to weight gain and feed efficiency. Broiler performance is closely linked to the genetics, diet, age, and rearing environment of the bird (1,23,32,54). Genetic selection has largely driven the vast improvements observed in weight gain and feed efficiency in meat chickens over the last 50 years, although a small proportion of these improvements have been attributed to nutrition and other management practices (32). The genetic changes associated with improved weight gain and feed efficiency have also resulted in changes to the gut physiology and gut microbial community composition of birds (44). Diet, age, and environmental factors have also been reported to influence the gut microbiota (43,71,72). Therefore, there appears to be a clear link between bird performance and gut microbiota composition.In medicine, much interest has already focused on the influence of the gut microbiota in human health (35,78) and energy metabolism (73,74,83).
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.
A chicken growth study was conducted to determine if litter type influenced gut microbiota and performance in broilers. Seven bedding materials were investigated and included soft and hardwood sawdust, softwood shavings, shredded paper, chopped straw, rice hulls, and reused softwood shavings. Microbial profiling was done to investigate changes in cecal bacterial communities associated with litter material and age. Cecal microbiota were investigated at 14 and 28 d of age (n = 12 birds/litter material). At both ages, the cecal microbiota of chickens raised on reused litter was significantly (P < 0.05) different from that of chickens raised on any of the other litter materials, except softwood shavings at d 28. Cecal microbiota was also significantly different between birds raised on shredded paper and rice hulls at both ages. Age had a significant influence on cecal microbiota composition regardless of litter material. Similarity in cecal microbial communities among birds raised on the same litter treatment was greater at 28 d of age (29 to 40%) than at 14 d of age (25 to 32%). Bird performance on the different litter materials was measured by feed conversion ratio, live weight, and feed intake. Significant (P < 0.05) differences were detected in live weight at 14 d of age and feed intake at 14 and 28 d of age among birds (n = 160/treatment) raised on some of the different litter materials. However, no significant (P > 0.05) differences were observed in feed conversion ratio among birds raised on any of the 7 different litter materials at either 14 or 28 d of age. The type of litter material can influence colonization and development of cecal microbiota in chickens. Litter-induced changes in the gut microbiota may be partially responsible for some of the significant differences observed in early rates of growth; therefore, litter choice may have an important role in poultry gut health particularly in the absence of in-feed antibiotics.
In a survey of soil and wheat or maize rhizoplane bacteria isolated using a medium containing azelaic acid and tryptamine as sole carbon and nitrogen sources, respectively, a large proportion of Burkholderia-l i ke bacteria were found. Among them, a homogeneous group of strains was identifiable based on phenotypic properties, fatty acid composition, DNA-DNA hybridizations and 16s rDNA sequences. According to molecular data, this group belongs to the genus Burkholderia but its weak similarity to previously described species suggests that it belongs to a novel species. Closest 16s rDNA phylogenetic neighbours of this species are Burkholderia caryophylli and two previously named Pseudomonas species which clearly appear to be part of the Burkholderia genus and were thus named Burkholderia glathei comb. nov. ), where wheat is grown either continuously or in rotation with a lupin-based pasture; the soil is an alphisol. Walpeup is an experimental wheat-growing station, situated in Victoria (Australia), on a very poor sandy soil, in a fixed sand dune system. Soil samples of the two Australian stations have been collected and used for growing wheat (cv. Spear) in pots under glasshouse conditions (three plants per pot containing 1.5 kg soil). After 3-4 weeks, wheat plants were harvested and used to isolate bacteria from their rhizoplane, as above. A few strains were isolated directly on PCAT medium from salt-affected and hydrophobic soils near Adelaide. Also included in Table 1 are 18 reference strains of Burkholderia, Pseudomonas, Ralstonia and Alcaligenes. Among the eleven type strains of Burkholderia species, only type strains of B. mallei and B. pseudomallei were not grown in this laboratory.Biochemical characterization. All tests were performed at 28 "C. The Biolog GN system was used as recommended by the manufacturer to test the oxidation of 95 carbon substrates. Results were read automatically with a spectrophotometer after 24 or 48 h incubation at 28 "C. To test the reproducibility of the method, eight isolates were run in duplicate. Numerical analysis of the results was made using the G N Microlog 2N software which calculates Microlog distances derived from the number of differences between strains. This software also permits clustering analysis using the UPGMA (unweighted mean pair group method) algorithm of Sneath & Sokal(44).Carbon substrate assimilation tests were performed using auxanographic API 50CH strips (bioMCrieux) as recommended by the manufacturer. Nine isolates were tested in duplicate. Numerical analysis was performed on data obtained after 7 d incubation. Interstrain distances were calculated using the coefficient of Dice and a phenogram was built using UPGMA.The API 20NE microtube system (bioMCrieux) was used as a standardized method to test oxidase activity, nitrate reduction, gelatin and aesculin hydrolysis, glucose fermentation, arginine dihydrolase activity and production of indole, P-galactosidase and urease.MIDI-FAME. The MIDI-FAME technique is based on the conversion of fatty acids to met...
Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression.
Molecular techniques present a new opportunity to study roots and their interactions in soil. Extraction and quantification of species-specific DNA directly from soil allows direct identification of roots in mixed swards reducing the need for labour-intensive methods to recover and identify individual roots. DNA was extracted directly from up to 0.5 kg of soil and the presence of individual species quantified using speciesspecific probes with quantitative real-time PCR. A range of plant and soil factors influenced the DNA content measured in roots and it was necessary to account for these influences when converting DNA amount to root mass. The utility of the method for quantitative root studies was demonstrated in an experiment to investigate the effect of lime on root growth of acid-soil resistant and sensitive perennial grasses grown together in an aluminium-toxic soil. The root mass of an acid-soil resistant species was unaffected by lime application, whereas that of an acid-soil sensitive species was restricted by soil acidity. Molecular techniques present a promising tool for quantification of root mass directly in soil and have applications for field studies involving mixed species of plants.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.