Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

“The resulting TC FASTA for each sample was then evaluated using BLASTn [77] against a custom database derived from the RDP-II database [78] and GenBank http://ncbi.”

“Results and Discussion Recent research related to host physiology (obesity) and the gastrointestinal bacterial populations have sparked a renewed interest in understanding the gut microbiome [26,27].”

“Results and Discussion Recent research related to host physiology (obesity) and the gastrointestinal bacterial populations have sparked a renewed interest in understanding the gut microbiome [26,27].”

“Information on microbial diversity within the gastrointestinal tract of humans has increased in recent years as a result of 16S rDNA-based analyses [9,10], yet similar data on the microbiomes of livestock is lacking [11,12].”

“The ace files generated by CAP3 were then processed to generate a secondary FASTA file containing the tentative consensus (TC) sequences of the assembly along with the number of reads integrated into each consensus.”

“Information on microbial diversity within the gastrointestinal tract of humans has increased in recent years as a result of 16S rDNA-based analyses [9,10], yet similar data on the microbiomes of livestock is lacking [11,12].”

“Although molecular approaches can also introduce their own forms of bias such as the ability to detect both viable and non-viable bacteria [18-20] they currently provide the most powerful tools available for elucidating the diversity of animal microbiomes [4,11,12,15].”

“The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”

“The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”

“may also be beneficial and improve digestion of complex organic matter such as cellulose and even act as beneficial probiotics [39-43].”

“These beneficial health effects relate to the ability of these intestinal bacterial populations to supply vital nutrients, convert metabolites and beneficially interact with host cells [6-8].”

“The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”

“Further studies have indicated that, in humans, intestinal microbial populations of clostridia could be responsible for the development of autism [28,29].”

“Although molecular approaches can also introduce their own forms of bias such as the ability to detect both viable and non-viable bacteria [18-20] they currently provide the most powerful tools available for elucidating the diversity of animal microbiomes [4,11,12,15].”

“The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”

“These beneficial health effects relate to the ability of these intestinal bacterial populations to supply vital nutrients, convert metabolites and beneficially interact with host cells [6-8].”

“coli serotype O157:H7 is commonly associated with the intestinal mucosa of cattle [67].”

“Culture-based methods are extremely time-consuming and to date we have only been able to culture approximately 1% of the bacteria in the gut [16].”

“Zoonotic pathogenic bacteria, such as Salmonella enterica and E. coli O157:H7 can live in the lower gut of cattle and cause human illnesses through carcass contamination, farm run-off, or crop contamination [ 57-60 ].”

“(tentative pectinoschiza) is another genus which has been poorly characterized in environments other than the rumen and has only been occasionally detected in the feces of pigs and humans [55,56].”

“4 million illnesses and over 500 deaths attributed to salmonellosis in the United States annually [63].”

“this bacteria as part of the intestinal community of chickens [ 48 ].”

“Results: Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the…”

“Such studies have raised a pertinent question: is there a microbiome profile in food animals that can increase production efficiency, product quality, and/or food safety? This question has been obliquely addressed through the use of probiotics, prebiotics and competitive exclusion products which seek to establish a he…”

“Further studies have indicated that, in humans, intestinal microbial populations of clostridia could be responsible for the development of autism [28,29].”

“The majority of these bacteria are vital to the maintenance of animal's health and it is expected that even minor perturbations in these populations may cause dramatic shifts that can affect livestock productivity [3-5].”

“A number of studies [11] have also evaluated powerful yet classical sequencing approaches, which involve PCR amplification, cloning and Sanger sequencing.”

“Results: Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the…”

“The majority of these bacteria are vital to the maintenance of animal's health and it is expected that even minor perturbations in these populations may cause dramatic shifts that can affect livestock productivity [3-5].”

“Consequently beef and dairy products are also well known sources of human Salmonellosis [59,64-66].”

“These effects are typically specifically associated with the individual Clostridium species involved [ 33 ,34].”

“Traditionally culture-based methods have been used to identify and enumerate commensal members of the ruminal and intestinal flora [13-15].”

“Such studies have raised a pertinent question: is there a microbiome profile in food animals that can increase production efficiency, product quality, and/or food safety? This question has been obliquely addressed through the use of probiotics, prebiotics and competitive exclusion products which seek to establish a he…”

“The new method of bTEFAP is not limited to detecting organisms via culture methods, and can be used to define what constitutes a "healthy" or an "unhealthy" microbiome profile by correlating populations of bacterial species with dietary energy and protein utilization, host growth rate and efficiency, host gene express…”

“Other than this original description there are only a handful of reports of Alistipes as a member of the intestinal population, including one study which identified this organism as being isolated from the ceca of turkeys [51].”

“Consequently beef and dairy products are also well known sources of human Salmonellosis [59, 64-66 ].”

“difficile [35-37] and can also cause significant productivity problems including reducing the protein availability in fresh forage diets [38].”

“The new method of bTEFAP is not limited to detecting organisms via culture methods, and can be used to define what constitutes a "healthy" or an "unhealthy" microbiome profile by correlating populations of bacterial species with dietary energy and protein utilization, host growth rate and efficiency, host gene express…”

“Traditionally culture-based methods have been used to identify and enumerate commensal members of the ruminal and intestinal flora [13-15].”

“difficile [35-37] and can also cause significant productivity problems including reducing the protein availability in fresh forage diets [38].”

“These beneficial health effects relate to the ability of these intestinal bacterial populations to supply vital nutrients, convert metabolites and beneficially interact with host cells [6-8].”

“These effects are typically specifically associated with the individual Clostridium species involved [33,34].”

“Such studies have raised a pertinent question: is there a microbiome profile in food animals that can increase production efficiency, product quality, and/or food safety? This question has been obliquely addressed through the use of probiotics, prebiotics and competitive exclusion products which seek to establish a he…”

“may also be beneficial and improve digestion of complex organic matter such as cellulose and even act as beneficial probiotics [ 39-43 ].”

“Investigators such as Robert Hungate and Marvin Bryant characterized some ruminal and intestinal microbial populations, and related the biochemistry of these microorganisms to their roles in animal nutrition [1,71]; however they were limited to the use of culture-based methodologies.”

“difficile [35-37] and can also cause significant productivity problems including reducing the protein availability in fresh forage diets [38].”

“Bacteroides are also noted to participate in natural genetic transfer of antimicrobial resistance genes [45].”

“Most of the existing studies seeking to evaluate microbial diversity in the intestinal tract utilize fingerprinting methodologies such as denaturing gradient gel electrophoresis (DGGE) [68].”

“coli O157:H7 can live in the lower gut of cattle and cause human illnesses through carcass contamination, farm run-off, or crop contamination [57-60].”

“Traditionally culture-based methods have been used to identify and enumerate commensal members of the ruminal and intestinal flora [13-15].”

“The new method of bTEFAP is not limited to detecting organisms via culture methods, and can be used to define what constitutes a "healthy" or an "unhealthy" microbiome profile by correlating populations of bacterial species with dietary energy and protein utilization, host growth rate and efficiency, host gene express…”

“Prevotella spp (tentative oralis, ruminicola and albensis) is a well known genus associated with the rumen of cattle [49,52-54] and is associated with ruminal carbohydrate and protein fermentation.”

“Prevotella spp (tentative oralis, ruminicola and albensis) is a well known genus associated with the rumen of cattle [49,52-54] and is associated with ruminal carbohydrate and protein fermentation.”

“Prevotella spp (tentative oralis, ruminicola and albensis) is a well known genus associated with the rumen of cattle [49,52-54] and is associated with ruminal carbohydrate and protein fermentation.”

“coli O157:H7 can live in the lower gut of cattle and cause human illnesses through carcass contamination, farm run-off, or crop contamination [57-60].”

“may also be beneficial and improve digestion of complex organic matter such as cellulose and even act as beneficial probiotics [39-43].”

“The new method of bTEFAP is not limited to detecting organisms via culture methods, and can be used to define what constitutes a "healthy" or an "unhealthy" microbiome profile by correlating populations of bacterial species with dietary energy and protein utilization, host growth rate and efficiency, host gene express…”

“may also be beneficial and improve digestion of complex organic matter such as cellulose and even act as beneficial probiotics [39-43].”

“NET and C# analysis pipeline the resulting BLASTn outputs were compiled, validated using taxonomic distance methods, and data reduction analysis performed as described previously (Dowd et al., 2008b).”