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  • richardmitnick 10:08 am on February 16, 2014 Permalink | Reply
    Tags: , Microbes   

    From UC Berkeley: “Geographic variation of human gut microbes tied to obesity” 

    UC Berkeley

    February 14, 2014
    Robert Sanders

    People living in cold, northern latitudes have bacteria in their guts that may predispose them to obesity, according to a new study by researchers at the University of California, Berkeley, and the University of Arizona, Tucson.

    gut
    The types of microbes that live in the human gut vary with latitude. People in northern climes have more obesity-related bacteria than do people living farther south. iStock photo.

    The researchers’ analysis of the gut microbes of more than a thousand people from around the world showed that those living in northern latitudes had more gut bacteria that have been linked to obesity than did people living farther south.

    The meta-analysis of six earlier studies was published this month in the online journal Biology Letters by UC Berkeley graduate student Taichi Suzuki and evolutionary biology professor Michael Worobey of the University of Arizona.

    “People think obesity is a bad thing, but maybe in the past getting more fat and more energy from the diet might have been important to survival in cold places. Our gut microbes today might be influenced by our ancestors,” said Suzuki, noting that one theory is that obesity-linked bacteria are better at extracting energy from food. “This suggests that what we call ‘healthy microbiota’ may differ in different geographic regions.”

    “This observation is pretty cool, but it is not clear why we are seeing the relationship we do with latitude,” Worobey said. “There is something amazing and weird going on with microbiomes.”

    To Worobey, the results are fascinating from an evolutionary biology perspective. “Maybe changes to your gut community of bacteria are important for allowing populations to adapt to different environmental conditions in lots of animals, including humans,” he said.

    Body size increases with latitude

    Suzuki proposed the study while rotating through Worobey’s lab during his first year as a graduate student at the University of Arizona. Studies of gut microbes have become a hot research area among scientists because the proportion of different types of bacteria and Archaea in the gut seems to be correlated with diseases ranging from diabetes and obesity to cancer. In particular, the group of bacteria called Firmicutes seems to dominate in the intestines of obese people – and obese mice – while a group called Bacteroidetes dominates in slimmer people and mice.

    Suzuki reasoned that, since animals and humans in the north tend to be larger in size – an observation called Bergmann’s rule – then perhaps their gut microbiota would contain a greater proportion of Firmicutes than Bacteriodetes. While at the University of Arizona, and since moving to UC Berkeley, Suzuki has been studying how rodents adapt to living at different latitudes.

    “It was almost as a lark,” Woroby said. “Taichi thought that if Firmicutes and Bacteroidetes are linked to obesity, why not look at large scale trends in humans. When he came back with results that really showed there was something to it, it was quite a surprise.”

    map
    The researchers looked at data from more than 1,000 people from around the world. The blue represents the proportion of obesity-related bacteria in the gut, while red is the proportion of bacteria associated with slimness.

    Suzuki used data published in six previous studies, totaling 1,020 people from 23 populations in Africa, Europe, North and South America and Asia. The data on gut microbiomes were essentially censuses of the types and numbers of bacteria and Archaea in people’s intestinal track.

    He found that the proportion of Firmicutes increased with latitude and the proportion of Bacteriodetes decreased with latitude, regardless of sex, age, or detection methods. African Americans showed the same patterns as Europeans and North Americans, not the pattern of Africans living in tropical areas.

    “Bergmann’s rule – that body size increases with latitude for many animals – is a good one and presumed to be an adaptation for dealing with cold environments,” said Suzuki’s advisor Michael Nachman, professor of integrative biology and director of UC Berkeley’s Museum of Vertebrate Zoology. “Whether gut microbes also help explain Bergmann’s rule will require experimental tests, but Taichi’s discovery adds an intriguing and completely overlooked piece of the puzzle to this otherwise well-studied evolutionary pattern.”

    See the full article here.

    Founded in the wake of the gold rush by leaders of the newly established 31st state, the University of California’s flagship campus at Berkeley has become one of the preeminent universities in the world. Its early guiding lights, charged with providing education (both “practical” and “classical”) for the state’s people, gradually established a distinguished faculty (with 22 Nobel laureates to date), a stellar research library, and more than 350 academic programs.

    UC Berkeley Seal


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  • richardmitnick 1:18 pm on August 19, 2013 Permalink | Reply
    Tags: , , , , , Microbes   

    From Caltech: “A Home for the Microbiome” 

    Caltech Logo
    Caltech

    Caltech biologists identify, for the first time, a mechanism by which beneficial bacteria reside and thrive in the gastrointestinal tract

    08/18/2013
    Katie Neith

    “The human body is full of tiny microorganisms—hundreds to thousands of species of bacteria collectively called the microbiome, which are believed to contribute to a healthy existence. The gastrointestinal (GI) tract—and the colon in particular—is home to the largest concentration and highest diversity of bacterial species. But how do these organisms persist and thrive in a system that is constantly in flux due to foods and fluids moving through it? A team led by California Institute of Technology (Caltech) biologist Sarkis Mazmanian believes it has found the answer, at least in one common group of bacteria: a set of genes that promotes stable microbial colonization of the gut.

    gut
    A section of mouse colon is shown with gut bacteria (outlined in yellow) residing within the crypt channel.Credit: Caltech / Mazmanian Lab

    A study describing the researchers’ findings was published as an advance online publication of the journal Nature on August 18.

    ‘By understanding how these microbes colonize, we may someday be able to devise ways to correct for abnormal changes in bacterial communities—changes that are thought to be connected to disorders like obesity, inflammatory bowel disease and autism,’ says Mazmanian, a professor of biology at Caltech whose work explores the link between human gut bacteria and health.”

    See the full article here.

    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
    Caltech buildings


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  • richardmitnick 11:59 am on March 18, 2013 Permalink | Reply
    Tags: , , Microbes,   

    From PNNL: “Seeing the Messages Microbes Send” 

    Novel chemical imaging instrument shows how bacteria support diverse, nearby colonies

    March 2013
    Suraiya Farukhi
    Christine Sharp

    Results: With a novel technique that noninvasively analyzes microbes, scientists at Pacific Northwest National Laboratory profiled, for the first time, the chemicals that a cyanobacterium makes available to others. Over 4 days, Synechococcus sp. PCC 7002 steadily secretes two molecules that could be used as resources by other bacteria that are nearby. The technique that chemically profiles the microbial communities in both space and time is Nanospray Desorption Ionization Electrospray Mass Spectrometry, or nano-DESI. This instrument was built by Dr. Julia Laskin and her team at Pacific Northwest National Laboratory. This research graced the cover of Analyst.

    nano
    Scientists at Pacific Northwest National Laboratory used the nano-DESI to show how bacteria support other colonies. No image credit.

    ‘This is a tool that will help microbiologists identify molecules that promote or inhibit growth of microbial communities,’ said Lab Fellow Laskin. ‘It also gives us much better control for studying interactions between microbial communities.’

    Why It Matters: Understanding microbial ecology — how bacteria, algae and other microbes influence each other — could provide basic answers needed to advance sustainable energy. For example, Synechococcus sp. PCC 7002 uses carbon dioxide and sunlight to produce sugars that fuel the colony. Knowing how to best grow and modify these bacteria to mass-produce fuels could increase our nation’s energy independence. Here, nano-DESI provides key data for sustainable energy, but the opportunities stretch much farther.

    ‘Any place where there are microbes and you have a format where nano-DESI could be applied, you can study that ecology,’ said Dr. Allan Konopka, a biologist and Lab Fellow at PNNL who worked on the study. ‘This opens doors to a host of applications, such as understanding how bacteria associated with plant roots affect a plant.'”

    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

    i1


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  • richardmitnick 1:46 pm on January 4, 2012 Permalink | Reply
    Tags: , , , Microbes   

    An INL Fact Sheet: “Microbial Metabolic Systems” 

    Description
    The Microbial Metabolic Systems focus at INL is a systems biology approach to more effectively understanding and controlling microbial processes. An enhanced understanding of key microbial processes is being gained by coupling existing genomics, transcriptomics, and proteomics efforts with new metabolomic techniques and data. We use hypothesis-driven research to investigate the impacts of environment, perturbations and manipulations on microbial systems for the purpose of controlling the products and applications of those systems.

    Our focus is on developing and using advanced metabolomic techniques to study C-1 prokaryotes. Our definition of “C-1” includes a variety of prokaryotic metabolic systems that involve the transformation of single-carbon compounds. We have targeted specific C-1 metabolic processes of interest to the Department of Energy (DOE):

    Methanogenesis – methane production by methanogenic bacteria
    Methanotrophy – methane/methanol utilization by methanotrophic bacteria
    Bioleaching – carbon fixation in chemoautolithotrophic bacteria and
archaea (e.g., Acidithiobacillus ferrooxidans, Acidianus spp., etc.)
    Calcite Precipitation – subsurface calcite precipitationt by urea hydrolyzing bacteria
    Bicarbonate Transport – photoautotrophic carbon fixation by cyanobacteria
    Hydrogenase Systems – hydrogen production by Carboxydothermus hydrogenoformans.

    i1
    Our focus is on developing and using advanced metabolomic techniques to study C-1 prokaryotes. Our definition of “C-1” includes a variety of prokaryotic metabolic systems that involve the transformation of single-carbon compounds. We have targeted specific C-1 metabolic processes of interest to the Department of Energy (DOE)

    INL is leveraging existing research programs and expertise in C-1 microbial metabolic systems to develop a recognized capability that will be more broadly applied to other microbial systems relevant to DOE missions.”

    See the full Fact Sheet here. There is a lot more information.

     
  • richardmitnick 4:11 pm on November 9, 2011 Permalink | Reply
    Tags: , , , , Microbes   

    From Berkeley Lab: “Berkeley Lab Researchers Create First of Its Kind Gene Map of Sulfate-reducing Bacterium:” 


    Berkeley Lab

    Work Holds Implications for Future Bioremediation Efforts

    Lynn Yarris
    November 09, 2011

    Critical genetic secrets of a bacterium that holds potential for removing toxic and radioactive waste from the environment have been revealed in a study by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). The researchers have provided the first ever map of the genes that determine how these bacteria interact with their surrounding environment.

    ‘Knowing how bacteria respond to environmental changes is crucial to our understanding of how their physiology tracks with consequences that are both good, such as bioremediation, and bad, such as biofouling,’ says Aindrila Mukhopadhyay, a chemist with Berkeley Lab’s Physical Biosciences Division, who led this research. ‘We have reported the first systematic mapping of the genes in a sulfate-reducing bacterium – Desulfovibrio vulgaris – that regulate the mechanisms by which the bacteria perceive and respond to environmental signals.'”

    i1
    Desulfovibrio vulgaris is an anaerobic sulfate-eating microbe that can also consume toxic and radioactive waste, making it a prime candidate for bioremediation of contaminated environments. (Photo courtesy of Berkeley Lab)

    i3
    A first-of-its-kind gene map of the Desulfovibrio vulgaris bacterium could play an important role in future clean-ups of a wide range of contaminated environments. (Image courtesy of Berkeley Lab)

    See the full very important article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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