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Primeur weekly 2018-03-26

Quantum computing

Physicists reveal material for high-speed quantum internet ...

Focus on Europe

TUM junior scientist wins prestigious award for Computational Studies of Surface Catalytic Processes ...

Cosmologists create largest simulation of galaxy formation and break their own record ...

GigaSpaces triples annual revenue in France, building on strong global 2017 results ...

Atos and GENCI launch the Atos Joseph Fourier Award 2018 to accelerate research and innovation in numerical simulation, artificial intelligence and quantum computing ...

Middleware

Cavium Collaborates with Microsoft to demonstrate ThunderX2 platform compliant with Microsoft's Project Olympus specifications ...

Hardware

Pioneers of computer architecture receive ACM Turing Award ...

Mellanox's advanced Ethernet solutions selected to connect the Tel-Aviv Stock Exchange network infrastructure ...

GIGABYTE announces ThunderXStation: Industry's first Armv8 workstation based on Cavium's ThunderX2 processor ...

Cavium announces Packet Trakker: A programmable network telemetry suite ...

Applications

Los Alamos releases file index product to software community ...

NERSC supercomputers help researchers create reference catalogue for rumen microbiome ...

Major AI breakthrough by Optalysys demonstrating how its patented Optical Processing Technology performs deep learning at the speed of light ...

NVIDIA RTX technology realizes dream of real-time cinematic rendering ...

Batteries out of thin air ...

New method manages and stores data from millions of nerve cells - in real time ...

Groundbreaking research results in artificial intelligence ...

Taming chaos: Calculating probability in complex systems ...

Physicists made crystal lattice from polaritons ...

Golden touch: Next-gen optical disk to solve data storage challenge ...

COSMIC impact: Next-gen X-ray microscopy platform now operational ...

The Cloud

Mellanox simplifies hybrid Cloud connectivity between enterprises and Microsoft Azure ...

Cavium Technologies power end-to-end NVMe over Fabrics solutions ...

NERSC supercomputers help researchers create reference catalogue for rumen microbiome


Depiction of rumen microbiome. Credit: Ella Maru studio, www.scientific-illustrations.com.
19 Mar 2018 Berkeley - Using supercomputers at the National Energy Research Scientific Computing Center (NERSC), an international team led by William (Bill) Kelly, formerly at AgResearch New Zealand's Grasslands Research Centre, and including scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, generated a reference catalogue of rumen microbial genomes and isolates cultivated and sequenced from the Hungate1000 collection. One of the largest targeted cultivation and sequencing projects to date, the collection was produced through the coordinated efforts of rumen microbiology researchers worldwide.

At the beginning of the project, there were only reference genomes for 14 bacteria and one methanogen. The Hungate catalogue now contains a total of 501 genomes - 410 newly generated from this study, plus an additional 91 already publicly available from other studies. A paper highlighting this work was published in Nature Biotechnology .

The digestive tracts of ruminant (cud-chewing) animals such as cattle, sheep, and goats convert lignocellulosic plant matter to short-chain fatty acids used for nourishment with unparalleled efficiency, thanks to the activity of symbiotic microbes in the rumen. Rumen microbes play a vital role in allowing ruminant livestock to break down the food they eat, and produce milk, meat and wool which help support the livelihoods and food security of over a billion people worldwide. The process, however, is also the single largest human-influenced source of the greenhouse gas methane (CH4), with these animals releasing approximately 138 million U.S. short tons of CH4 into the atmosphere each year.

Understanding the diversity and function of the rumen microbiome is a critical step toward developing technologies and practices that support efficient global food production from ruminants while mitigating methane emissions. Additionally, there is considerable interest in identifying biotechnologically relevant enzymes for the conversion of plant feedstocks to biofuel and bioproducts.

"JGI is a world leader in conducting, enabling, and democratizing sequence­ based research - and one of the few places that does science at this large scale. Beyond the sequence generation, data processing, and big compute resources, we bring significant experience and expertise to help bridge the gap from sequence to biology", stated Rekha Seshadri, JGI computational biologist and co-first author of the paper.

The project was named in honour of the late Robert Hungate (1906-2004), a pioneering microbiologist who invented the widely-used method of cultivating strictly anaerobic bacteria that now bears his name.

The work, noted William Kelly, is the culmination of a JGI Community Science Programme (CSP) 2012 proposal that originated at a meeting of rumen microbiologists held in New Zealand in February 2011. Former JGI Director Eddy Rubin was one of the attendees at the meeting as the JGI had just published the first rumen metagenome study inScience, and his perspective on the scale of sequencing that was possible encouraged the development of an ambitious project.

William Kelly stated: "Our work to generate the Hungate genome catalogue provides the link between the classical microbiology that provided the cultivation basis for anaerobic (especially rumen) microbiology and the modern techniques that are independent of microbial cultivation. The combination of DNA and RNA sequence analysis and laboratory experiments with genome sequenced, characterized, cultivated strains can now be used to begin to reveal the intricacies of how the rumen microbial community functions."

"This project is a great example of how science can progress rapidly if we do things together", added study co-first author Sinead Leahy, now with the New Zealand Agricultural Greenhouse Gas Research Centre. "The project helps further fill the gap in our knowledge of anaerobic microorganisms as it specifically targets the specialized anaerobic rumen environment and reports genome sequences from strains that have yet to be taxonomically assigned or phenotypically characterized but which are among the most abundant rumen micro-organisms."

The Hungate catalogue encompasses 75% of genus-level taxa reported from the rumen. The researchers were able to assign individual microbes to the major metabolic pathways involved in rumen function. They reported that in total, the catalogue of genomes encode nearly 33,000 degradative Carbohydrate-Active Enzymes which can break down plant cell walls. Other metabolic highlights and evolutionary vignettes of the rumen microbiome are presented in the manuscript. They noted an interesting instance of evolution by gene loss of the universally conserved enolase, the penultimate enzyme in glycolysis, the metabolic pathway that converts glucose to pyruvate. Rumen-specific adaptations such as de novo synthesis of B12 and potential vertical inheritance of the rumen microbiome are discussed.

To test the value of the Hungate collection as a resource that underpins metagenomic analysis, 1.4 million coding sequences (CDS) from the reference genomes were searched against ~1.9 billion CDS from over 8,000 varied metagenomic samples, stored in the Integrated Microbial Genomes & Microbiomes (IMG/M) database. The IMG/M system supports annotation, analysis, and distribution of microbial genomes and microbiomes.

The majority of Hungate genomes were indeed present in available rumen metagenomes. "However, there was significant overlap with the human microbiome - almost a third of the species were detected in human digestive system samples, inadvertently increasing the reference set for the study of the human microbiome as well. IMG is a comprehensive resource of sequence data integrated with environmental metadata (which is key), without which, these observations would not have been made", stated Rekha Seshadri. The importance of integrating microbiome data across all habitat types to enable novel correlations and discovery, is one of the main pillars of the recently proposed National Microbiome Data Collaborative (NMDC) in which JGI is playing a leadership role.

"This publication marks a significant contribution to rumen microbiology and the genome sequences, coupled with their corresponding cultures, will make the Hungate Collection an outstanding resource for rumen microbiology groups around the world to link microbial genomes to rumen function and shedding light on what has been described as the world’s largest commercial fermentation process", stated William Kelly, Sinead Leahy and Graeme Attwood of AgResearch in a joint statement.

The Hungate Collection was conceived as a community resource. Access to bacterial cultures can be requested from AgResearch New Zealand. All available genomic data and annotations are available through the JGI Integrated Microbial Genomes & Microbiomes (IMG/M) portal. Additionally, all 410 genomes sequenced in the study can be downloaded via a dedicated portal .

The Hungate1000 project was funded by the New Zealand Government in support of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases. The genome sequencing and analysis component of the project was supported by the JGI through the Community Science Programme, and used resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the Office of Science of the U.S. Department of Energy.

Seshadri R et al. have authored the paper titled "Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection". The paper was published inNature Biotechnology- 2018 March 19 - doi:10.1038/nbt.4110.
Source: National Energy Research Scientific Computing Center - NERSC

Back to Table of contents

Primeur weekly 2018-03-26

Quantum computing

Physicists reveal material for high-speed quantum internet ...

Focus on Europe

TUM junior scientist wins prestigious award for Computational Studies of Surface Catalytic Processes ...

Cosmologists create largest simulation of galaxy formation and break their own record ...

GigaSpaces triples annual revenue in France, building on strong global 2017 results ...

Atos and GENCI launch the Atos Joseph Fourier Award 2018 to accelerate research and innovation in numerical simulation, artificial intelligence and quantum computing ...

Middleware

Cavium Collaborates with Microsoft to demonstrate ThunderX2 platform compliant with Microsoft's Project Olympus specifications ...

Hardware

Pioneers of computer architecture receive ACM Turing Award ...

Mellanox's advanced Ethernet solutions selected to connect the Tel-Aviv Stock Exchange network infrastructure ...

GIGABYTE announces ThunderXStation: Industry's first Armv8 workstation based on Cavium's ThunderX2 processor ...

Cavium announces Packet Trakker: A programmable network telemetry suite ...

Applications

Los Alamos releases file index product to software community ...

NERSC supercomputers help researchers create reference catalogue for rumen microbiome ...

Major AI breakthrough by Optalysys demonstrating how its patented Optical Processing Technology performs deep learning at the speed of light ...

NVIDIA RTX technology realizes dream of real-time cinematic rendering ...

Batteries out of thin air ...

New method manages and stores data from millions of nerve cells - in real time ...

Groundbreaking research results in artificial intelligence ...

Taming chaos: Calculating probability in complex systems ...

Physicists made crystal lattice from polaritons ...

Golden touch: Next-gen optical disk to solve data storage challenge ...

COSMIC impact: Next-gen X-ray microscopy platform now operational ...

The Cloud

Mellanox simplifies hybrid Cloud connectivity between enterprises and Microsoft Azure ...

Cavium Technologies power end-to-end NVMe over Fabrics solutions ...