scholarly journals Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

2019 ◽  
Vol 37 (8) ◽  
pp. 953-961 ◽  
Author(s):  
Robert D. Stewart ◽  
Marc D. Auffret ◽  
Amanda Warr ◽  
Alan W. Walker ◽  
Rainer Roehe ◽  
...  
Keyword(s):  
Enzyme Discovery ◽  
Rumen Microbiome ◽  
Rumen Metagenome

scholarly journals Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism

2017 ◽  
Author(s):  
Robert Stewart ◽  
Marc D. Auffret ◽  
Amanda Warr ◽  
Tim Snelling ◽  
Richard Dewhurst ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Sequence Data ◽  
Good Match ◽  
Metagenomic Sequence ◽  
Microbial Genomes ◽  
Rumen Microbes ◽  
The Public ◽  
Enzyme Discovery ◽  
Rumen Microbiome ◽  
Metagenomic Sequence Data

AbstractThe cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome

scholarly journals A roadmap for metagenomic enzyme discovery

2021 ◽  
Author(s):  
Serina L. Robinson ◽  
Jörn Piel ◽  
Shinichi Sunagawa
Keyword(s):  
Biosynthetic Enzymes ◽  
Functional Metagenomics ◽  
Enzyme Discovery ◽  
Experimental Strategies

Shotgun metagenomic approaches to uncover new enzymes are underdeveloped relative to PCR- or activity-based functional metagenomics. Here we review computational and experimental strategies to discover biosynthetic enzymes from metagenomes.

scholarly journals PSXII-3 Rumen microbiome from beef steers undergoing grain adaptation with steam-flaked corn varying in bulk density

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 446-447
Author(s):  
Kaue Tonelli Nardi ◽  
Kaliu G Scaranto Silva ◽  
Igor Gomes Favero ◽  
Jordan K Hinds ◽  
Carly A Hoffmann ◽  
...  
Keyword(s):  
Bulk Density ◽  
Block Design ◽  
Order Effects ◽  
Beef Steers ◽  
Post Feeding ◽  
Rumen Microbiome ◽  
Randomized Complete Block Design ◽  
Ad Libitum ◽  
Microbiome Data ◽  
Adaptation Phase

Abstract The effects of steam-flaked corn bulk density during grain adaptation phase on ruminal microbiome were evaluated. Crossbred-Angus ruminally cannulated steers (n = 6; BW = 405 ± 42 kg) were assigned to a randomized complete block design (block = body weight) to 1 of 2 grain adaptation strategies: 1) steam-flaked corn (SFC) bulk density of 335 g/L; and 2) 412 g/L. Steers were ad libitum fed, individually, during 6-7d phases, consisting of: HAY, followed by the STEP-UP1 through STEP-UP4, diets, respectively, in which roughage was gradually replaced with grain until FINISHER diet was fed. Respective SFC bulk densities were fed throughout STEP-UP diets, while the FINISHER diet consisted of 335 g/L strategy only for both groups. Ruminal fluid samples (100 mL) were collected on d-5 of each step, at 6h post-feeding for DNA extraction. Microbiome data were sequenced by Illumnia® NovaSeq™ 6000 (16S rRNA). The SFC bulk density did not affect (P > 0.50) the relative abundance (RA) for any taxonomy classification. Regardless of SFC bulk density, inclusion of grain throughout adaptation phases affected domain (P ≤ 0.03) when initial phases were compared to FINISHER. Phylum RA were affected (P ≤ 0.05) for Actinobacteria (27%), Bacteroidetes (11%), and Euryarchaeota (2%). Within Class RA were affected (P ≤ 0.04) for Clostridia (46%), Actinobacteria (27%), and Bacilli (5%). Order effects on RA were observed (P ≤ 0.04) for Clostridiales (45%), Coriobacteriales (25%), and Lactobacillales (4%). Within Family RA was affected (P ≤ 0.03) for Coriobacteriaceae (25%), Lachnospiraceae (27%), Ruminococcaceae (6%), and Lactobacillaceae (4%), while a tendency (P = 0.09) was observed for Veillonellaceae (1%). In Genus, RA was affected (P ≤ 0.01) for Olsenela (22%), Pediococcus (3%), and Butyrivibrio (3%). As steers advance through subsequent grain adaptation phases until the FINISHER, more meaningful ruminal microbiome changes are observed than SFC density change.

scholarly journals Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Bo He ◽  
Shuwen Jin ◽  
Jiawen Cao ◽  
Lan Mi ◽  
Jiakun Wang
Keyword(s):  
Rumen Microbiome ◽  
Sheep Rumen ◽  
Hu Sheep

scholarly journals Garlic skin induces shifts in the rumen microbiome and metabolome of fattening lambs

animal ◽  
2021 ◽  
Vol 15 (5) ◽  
pp. 100216
Author(s):  
W. Zhu ◽  
Z. Su ◽  
W. Xu ◽  
H.X. Sun ◽  
J.F. Gao ◽  
...  
Keyword(s):  
Rumen Microbiome

scholarly journals PSVI-22 Rumen microbiome of beef cattle is modulated by backgrounding systems

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 220-220
Author(s):  
Bobwealth O Omontese ◽  
Ashok K Sharma ◽  
Jason Langlie ◽  
Joe Armstrong ◽  
Alfredo DiCostanzo ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Developmental Stages ◽  
Production Systems ◽  
Rumen Fluid ◽  
Illumina Miseq ◽  
High Energy ◽  
Shannon Index ◽  
Bacterial Gene ◽  
Beef Calves ◽  
Rumen Microbiome

Abstract Backgrounding (BKG) segment in beef production systems is characterized by utilization of different forages which affect growth performance and carcass characteristics. However, it is unclear how BKG systems impact rumen microbiome. We investigated rumen microbiome dynamics of beef calves under different BKG systems. At weaning, Angus and Angus x Simmental beef calves (n = 38) were stratified by age, weight, and sex in a completely randomized design into 1 of 3 BKG treatments for 55 d: 1) perennial pasture (PP; quackgrass, orchardgrass; smooth bromegrass, red clover, and alfalfa); 2) summer annual cover crop (CC; cereal oats, purple top turnips, hunter forage brassica, and graza forage radish); and 3) dry lot (DL; haylage, corn, and DDGS). After BKG, all calves were assigned to a high energy ration in a feedlot. Rumen sample was collected via esophageal tubing at weaning, BKG and feedlot. A total of 190 rumen fluid samples were used to sequence the hypervariable V4 region of the 16S rRNA bacterial gene on an Illumina MiSeq platform. The results showed that BKG systems largely influenced rumen bacterial communities. Specifically, microbiome composition and diversity were not different at weaning, diverged significantly during BKG (Shannon index, Bray Curtis distance metrics; P < 0.001) and homogenized during feedlot. During the BKG segment, the bacterial genera Agrobacterium, Coprococcus, and Ruminococcus were dominant in CC whereas Fibrobacteraceae and Mycoplasmataceae was most dominant in DL. Moreover, rumen microbiome patterns of CC and DL calves showed increased plasticity in early stages of development but not during feedlot with PP showing fewer changes over time. These results indicate that BKG systems significantly modulate the rumen microbiome of beef cattle and, underscore the importance of early developmental stages as potential targets for feeding interventions that can impact the animal microbiome to enhance animal performance.

scholarly journals Selected Alternative Feed Additives Used to Manipulate the Rumen Microbiome

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1542
Author(s):  
Marta Michalak ◽  
Konrad Wojnarowski ◽  
Paulina Cholewińska ◽  
Natalia Szeligowska ◽  
Marcel Bawej ◽  
...  
Keyword(s):  
Digestive System ◽  
Animal Husbandry ◽  
Review Article ◽  
Feed Additives ◽  
Microbial Fermentation ◽  
Plant Origin ◽  
Gelidium Amansii ◽  
Alternative Feed ◽  
Rumen Microbiome ◽  
General Recognition

In recent years, a boost in the ruminant population has been observed, and consequently, an increase in the animals’ demand for nutrients and methane emissions. Methane emission is generated during the microbial fermentation of feed in the rumen, and a percentage even up to 12% of the energy obtained by this process can be wasted. In addition, the use of antibiotics in animal husbandry is being increasingly restricted. restricted. As a result, there is a continuous search for innovative feed additives that can serve as alternatives to antibiotics, and will also be safe for both people and the environment. In the present review article, additives were selected on basis that, according to studies conducted so far, may positively affect the microbiome of the digestive system by improving indicators and/or reducing methane production. Among them, probiotics, prebiotics or their combination—synbiotics are at the forefront of research. However, additives in the form of algae or plant origin are also gaining ground in popularity, such as essential oils, fermented wheat straw or Gelidium amansii, due to their general recognition as safe (GRAS) for both humans and environment.

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