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Genes, Early Environment Sculpt the Gut Microbiome

Mice raised in built environments with different relative abundances of diverse microbes (left and right) have a correspondingly diverse gut microbiome. These signature characteristics remained even when the mice were moved to a new facility, and they persisted into the next generation. (Credit: Zosia Rostomian/Berkeley Lab)

Scientists from Berkeley Lab and PNNL have found that genes and early environment play big roles in shaping the gut microbiome. The microbes retained a clear “signature” formed where the mice were first raised, and the characteristics carried over to the next generation. The findings could potentially be used to develop designer diets optimized to an individual’s microbiome.

New Bacteria Groups, and Stunning Diversity, Discovered Underground


One of the most detailed genomic studies of any ecosystem to date has revealed an underground world of stunning microbial diversity, and added dozens of new branches to the tree of life.

Berkeley Lab Participates in New National Microbiome Initiative

ThepotentialimpactofaunifiedMicrobiomeinitiativetounderstandandresponsiblyharnesstheactivitiesofmicrobial communities. (Credit: Diana Swantek, Berkeley Lab)

The initiative will advance the understanding of microbiome behavior and enable the protection of healthy microbiomes, which are communities of microorganisms that live on and in people, plants, soil, oceans, and the atmosphere. Microbiomes maintain the healthy function of diverse ecosystems, and they influence human health, climate change, and food security.

Scientists Take Key Step Toward Custom-made Nanoscale Chemical Factories

The shell of a bacterial microcompartment (or BMC) is mainly composed of hexagonal proteins, with pentagonal proteins capping the vertices, similar to a soccer ball (left). Scientists have engineered one of these hexagonal proteins, normally devoid of any metal center, to bind an iron-sulfur cluster (orange and yellow sticks, upper right). This cluster can serve as an electron relay to transfer electrons across the shell. Introducing this new functionality in the shell of a BMC greatly expands their possibilities as custom-made bio-nanoreactors. (Credit: Clément Aussignargues/MSU, Cheryl Kerfeld and Markus Sutter/Berkeley Lab)

Scientists have for the first time reengineered a building block of a geometric nanocompartment that occurs naturally in bacteria. The new design provides an entirely new functionality that greatly expands the potential for these compartments to serve as custom-made chemical factories.

CinderBio Harnesses Extreme Microbes for Greener Industry

(from left) Steve Yannone, Jill Fuss and Adam Barnebey (Photo: Roy Kaltschmidt/Berkeley Lab)

It’s no secret that extremophiles, or microbes that live in places like polar glaciers and toxic waste pools, may hold treasures worth billions. Now basic biology research has led to the formation of CinderBio, a startup co-founded by Berkeley Lab scientists Steve Yannone and Jill Fuss that produces heat- and acid-stable enzymes.

Scientists Call for National Effort to Understand and Harness Earth’s Microbes for Health, Energy, Agriculture, and Environment

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To understand and harness the capabilities of Earth’s microbial ecosystems, nearly fifty scientists from Department of Energy national laboratories, universities, and research institutions propose a national effort called the Unified Microbiome Initiative.

It Takes a Thief

The overall architecture of Cas1–Cas2 bound to protospacer DNA with line segments that indicate DNA lengths spanning a total of 33 nucleotides.

The discovery by Berkeley Lab researchers of the structural basis by which bacteria are able to capture genetic information from viruses and other foreign invaders for use in their own immunological system holds promise for studying or correcting problems in human genomes.

Dirty, Crusty Meals Fit for (Long-Dormant) Microbes

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Biocrust’s microbes lie dormant for long periods until precipitation (such as a sudden downpour) awakens them. Understanding more about the interactions between the microbial communities—also called “microbiomes”—in the biocrusts and their adaptations to their harsh environments could provide important clues to help shed light on the roles of soil microbes in the global carbon cycle.

Gut Microbes Enable Coffee Pest to Withstand Extremely Toxic Concentrations of Caffeine

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Scientists discovered that coffee berry borers worldwide share 14 bacterial species in their digestive tracts that degrade and detoxify caffeine. They also found the most prevalent of these bacteria has a gene that helps break down caffeine. Their research sheds light on the ecology of the destructive bug and could lead to new ways to fight it.

Unlocking the Key to Immunological Memory in Bacteria

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Berkeley Lab researchers have revealed how bacteria “steal” genetic information from foreign invaders for use in their own immunological memory system.