7 ], after applying carvacrol at a low dose (2.2 mg/l) in a continuous culture system suggested that rumen microbes could adapt to carvacrol. (annexpublishers.co)
Metagenomic6
Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. (biomedcentral.com)
These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting. (biomedcentral.com)
MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. (biomedcentral.com)
Author of more than 300 journal papers, including in Nature Genetics, Nature Reviews Genetics, and Science, contributing to statistical methodology for genomic, microbiome and metagenomic profile predictions, quantitative genetics including knowledge of genetic mechanisms underlying complex traits, and development of bioinformatics pipelines for sequence analysis. (edu.au)
The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. (springeropen.com)
New gene-based technologies can now be employed to examine microbial diversity through the use of small sub-unit ribosomal DNA analysis (e.g. 16S rDNA) and to understand the function of complex microbial ecosystems in the rumen through metagenomic analysis. (nhbs.com)
Microbial12
While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. (nature.com)
Furthermore, while the level of adherence to the Green-MED diet and its specific green dietary components was associated with the magnitude of changes in microbiome composition, changes in gut microbial features appeared to mediate the association between adherence to the Green-MED and body weight and cardiometabolic risk reduction. (biomedcentral.com)
Although plant derivatives have shown promise in reducing enteric methane (CH 4 ) emissions from ruminants in short-term studies, investigation on possible rumen microbial adaptation to these compounds is still limited. (annexpublishers.co)
The objective of this study was to assess the possibility of mixed rumen microbial adaptation to antimethanogenic plant derivatives over relatively long-term in vitro incubation. (annexpublishers.co)
Indications of rumen microbial adaptation were observed in carvacrol and thymol as CH 4 significantly increased from almost complete inhibition at day 3 to almost 5 % of total gas at day 9. (annexpublishers.co)
This poses a challenge considering that rumen microbial adaptation to these plant-based products remains a possibility over longer periods of exposure [ 6 , 7 ]. (annexpublishers.co)
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattlerumen microbial community, and provide a comparison to short read-based methods. (biomedcentral.com)
Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. (biomedcentral.com)
We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community. (biomedcentral.com)
The bovine rumen is an organ that serves as the site of symbiosis between the cow and microbial species from all three taxonomic superkingdoms of life that are dedicated to the degradation of highly recalcitrant plant polymers [ 13 ]. (biomedcentral.com)
With efficiency unrivaled by most abiotic industrial processes, the protists, archaea, bacteria, and fungi that make up the rumen microbial community are able to process cellulose and other plant biopolymers into byproducts, such as volatile fatty acids (VFA), that can be utilized by the host. (biomedcentral.com)
Until recently, knowledge of ruminant gut microbiology was primarily obtained using classical culture based techniques, which probably only account for 10 to 20% of the rumen microbial population. (nhbs.com)
Fecal microbiome4
The objective of this study was to measure the effect of in-feed SCFP on the fecal microbiome of Holstein bull calves through 4 months of age. (biomedcentral.com)
Fecal samples were collected on d 0, 28, 56, 84, and 112 of the study to characterize the fecal microbiome community. (biomedcentral.com)
A random-forest regression method was implemented to more fully understand community succession in the calf fecal microbiome of the two treatment groups. (biomedcentral.com)
Twenty-two "age-discriminatory" ASVs (amplicon sequence variants) were identified in the fecal microbiome that were shared between the two treatment groups. (biomedcentral.com)
Microbiota1
The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV. (microbial-ecology.net)
To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea . (springer.com)
The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. (springer.com)
Volatile fatty acids (VFAs) are a group of common metabolites with a potential of universal infochemicals dedicated to transferring of information between higher organisms and bacteria either from microbiome or external environment. (preprints.org)
Genomes1
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
Amplicon1
We confirmed host phylogeny using the sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. (microbial-ecology.net)
Acetate1
The Tibetan sheep had higher rumen concentrations of total SCFA, acetate, butyrate and iso-acids but lower concentrations of propionate than small-tailed Han sheep. (cambridge.org)
Metagenomics2
Cow Rumen and the Early Days of Metagenomics Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities. (doe.gov)
Metagenomics approaches have facilitated the detection of complete microbiomes and viromes, including emerging pathogens or pathogens that cannot be easily cultured and isolated. (biomedcentral.com)
Diet5
Previous studies have linked the Mediterranean diet (MED) with improved cardiometabolic health, showing preliminary evidence for a mediating role of the gut microbiome. (biomedcentral.com)
Both MED diets induced substantial changes in the community structure of the gut microbiome, with the Green-MED diet leading to more prominent compositional changes, largely driven by the low abundant, "non-core," microorganisms. (biomedcentral.com)
Our findings support a mediating role of the gut microbiome in the beneficial effects of the Green-MED diet enriched with Mankai and green tea on cardiometabolic risk factors. (biomedcentral.com)
However, to the best of our knowledge, no study has tested the degree to which the MED diet exerts its beneficial effects on cardiometabolic health through modulation of the gut microbiome. (biomedcentral.com)
Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. (biomedcentral.com)
Systematic2
Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumenmetagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. (biomedcentral.com)
Small intestinal bacterial overgrowth and celiac disease: A systematic review with pooled-data analysis. (siboinfo.com)
Richness1
However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. (microbial-ecology.net)
Bacterial2
Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. (springer.com)
This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago. (springer.com)
Mutualistic1
Our results depict a new interesting mutualistic configuration of the enterocyte-associated microbiome in Hadza, stressing the importance of microbe-host interaction at the mucosal surface along the course of human evolution. (frontiersin.org)
Microorganisms2
Compared to Italians, the Hadza enterocyte-associated microbiome was characterized by a greater amount of adhesive microorganisms with pathogenic potential, such as Proteobacteria, Erysipelotrichaceae , Enterococcus , Clostridium and Sarcina . (frontiersin.org)
These technologies have the potential to revolutionize the understanding of rumen function and will overcome the limitations of classical based techniques, including isolation and taxonomic identification of strains important to efficient rumen function and better understanding of the roles of microorganisms in relation to achieving high productivity and decreasing environmental pollutants. (nhbs.com)
Methane1
The host's rumen microbiome plays a vital role in converting consumed feed into short chain fatty acids, which provide energy to the host but also produce methane as a by-product. (biomedcentral.com)
Sheep1
The aim of the present study was to gain insight into how the rumen epithelium of Tibetan sheep has adapted to the consumption of low-energy-level diets. (cambridge.org)
Carbon1
This indicates the potential use of the microbiome for achieving sustained changes in environmentally important traits through genetic selection, as well as its use as a management tool to identify animals likely to have a favorable or unfavorable carbon footprint. (biomedcentral.com)
Continuous1
The smaller part of the reticulorumen is the reticulum, which is fully continuous with the rumen, but differs from it with regard to the texture of its lining. (wikipedia.org)
Cattle2
The lining of the rumen wall is covered in small fingerlike projections called papillae, which are flattened, approximately 5mm in length and 3mm wide in cattle. (wikipedia.org)
Two groups of cattle were orally dosed twice weekly for 6 weeks with 3 × 109 CFU of a pool of three stx-negative LEE+E. coli O157:H7 strains (vaccine group) or three stx-negative LEE- non-O157:H7 E. coli strains (control group). (bvsalud.org)
Insight1
Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function. (nature.com)
Substantial1
Studies have obtained substantial compost microbiomes, yet the expressions and functions of these lignocellulolytic enzymes remains obscure. (researchsquare.com)
however, little is known of their effects on the hind-gut microbiome during the early life of calves. (biomedcentral.com)
nonetheless, very little is known about their intestinal microbiomes. (springer.com)
Protein1
Even though domestic cats and other carnivores evolved by eating low-carbohydrate diets rich in protein and fat, our results demonstrate that the feline microbiome and metabolite profiles are highly responsive to dietary change and in directions that are predictable. (biomedcentral.com)
Dietary2
It has been reported that adherence to MED dietary patterns is associated with a distinct gut microbiome profile [ 4 ]. (biomedcentral.com)
The presence of the above-mentioned phyla and their functions are known to differ among individuals depending on living environment, dietary habits, and other environmental exposures [ 3 ], but more research is needed to test how specific factors impact inter-individual GI microbiomes and how they influence host physiology. (biomedcentral.com)
Nutrition2
An important factor in the animal nutrition is the gut microbiome. (biomedcentral.com)
Based on a common roadmap for five years, the APL will enable INRAE and Lallemand Animal Nutrition to pool their material and human resources around a co-designed research and technology program. (lallemandanimalnutrition.com)
Effects1
Thus, our objective was to evaluate the effects of diets enriched in resistant starch or fibers on the fecal characteristics, microbiome, and metabolite profiles of cats. (biomedcentral.com)
Complex1
The presence of organisms from all major superkingdoms in varying degrees of abundance makes the rumen an excellent model for a complex, partially characterized metagenome system. (biomedcentral.com)
Higher1
For example, "pilot" project (small projects to "seed" your long-term research), student-specific, or "new investigator" grants may have a higher rate of success because their applicant pool is restricted by eligibility. (sueishaqlab.org)
Article1
Review article: the gut microbiome as a therapeutic target in the pathogenesis and treatment of chronic liver disease. (siboinfo.com)