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New way to count microbes speeds research, cuts waste, could lead to new antibiotics

The new method is 35 times faster than conventional methods and uses 15 times less plastic.

University of Colorado Boulder researchers have developed a new way of counting microorganisms that works as much as 36 times faster than conventional methods, cuts plastic use more than 15-fold and substantially decreases the cost and carbon footprint of biomedical research.

The technique, described Oct. 30 in the journal Nature Microbiology , could revolutionize the way microbiology experiments are conducted around the world, allowing clinicians to diagnose and treat infections faster and researchers to test potential new antibiotics in a fraction of the time.

The invention comes as concern about antibiotic resistance grows worldwide, with drug-resistant bugs contributing to nearly 5 million deaths globally in 2019.

"We are in the middle of a silent pandemic of antimicrobial resistance and there is an urgent need to speed up the discovery of new antibiotics," said senior author Anushree Chatterjee, associate professor of chemical and biological engineering at CU Boulder. "We believe this new method can do that, and much more."

A new way to fill the pipeline

Since 1938, microbiologists have used a simple method, the colony forming unit (CFU) assay, for counting bacterial cells in a sample. They start by diluting the sample down into eight to 10 different concentrations, put drops from each into petri dishes filled with bacteria food, wait hours or days for individual colonies to form, and count them. If testing a new molecule to see how well it can kill bacteria, they add that in to see how many bacteria survive.

The process is notoriously laborious and wasteful, often taking hours to assess a small sample and producing mounds of discarded plastic.

Because it takes so long and costs so much, researchers must be choosy about which potential new drugs or combinations they test, so they're discouraged from taking chances, Chatterjee said.

This high-cost, low-profit equation has led pharmaceutical companies to steer away from developing new antibiotics.

"We are basically out of antibiotics," said Chatterjee, noting that many widely circulating pathogens -- including Staphylococcus aureas (staph) and Neisseria gonorrhoeae (Gonorrhea) -- are now resistant to most drugs designed to treat them.

"In order to have a sustainable pipeline of new options, we have to fundamentally change the way discovery is done," Chatterjee said.

Math instead of plastic

The new method, known as Geometric Viability Assay (GVA), replaces the arduous multi-step process of manual dilutions with a one-step process, informed by simple geometry and math.

"We are using the same kinds of math that can help students estimate the number of M&M's in a jar," said first author Christian Meyer, a postdoctoral fellow in the departments of Molecular, Cellular and Developmental Biology and Chemical and Biological Engineering. "Instead of counting all the M&M's individually, a clever student might count the bottom layer and then multiply by the height."

Similarly, instead of manually dividing the samples into numerous subsamples to make counting colonies easier, GVA counts colonies in one place, inside a portion of the cone of a single pipette tip, and then uses multiplication to calculate total concentration.

To do this, scientists embed the samples into a gel inside the cone, in which colonies form. When it's time to count, they can use various techniques -- including ones that involve taking a picture or using a paper ruler -- to accurately measure samples with anywhere from one to 1 billion microbes.

"It involves no mathematics that a high-school, calculus student couldn't perform," said Meyer. But it could have a big impact.

Faster, cheaper, greener

In laboratory tests measuring common bacteria like Escherichia coli (E. coli) and Salmonella enterica, the researchers found that while preparing 96 samples took three hours by classical methods, GVA took 5 minutes -- a 36-fold time savings. Even when compared to a more modern method involving robotics, GVA was still nine times faster and used one-tenth the plastic.

Using GVA, a single researcher could accurately measure the microbial concentration of 1,200 samples in a single day, the study found.

Ultimately, Chatterjee believes the method could also enable doctors to diagnose infection and find the right antibiotic for that infection faster.

"Instead of someone being in the hospital for three days while they figure out what that particular bug is sensitive to, we could potentially someday know overnight what the right antibiotic might be," she said, noting that more research is needed to advance to the clinical stage. Meyer invented the technique with Joel Kralj, a former assistant professor in the BioFrontiers Institute. The two are working with Venture Partners and have filed a provisional patent.

The research team has also created a website, and are now working to develop a smartphone version that scientists and the general public can use.

"Someone wise once said that the correct punctuation for a scientific advance is not an exclamation mark, but a semicolon," said Meyer. "In that spirit, while we are thrilled to be part of reinventing a core technique of microbiology, we are most excited for what will come next."

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Materials provided by University of Colorado at Boulder . Original written by Lisa Marshall. Note: Content may be edited for style and length.

Journal Reference :

  • Christian T. Meyer, Grace K. Lynch, Dana F. Stamo, Eugene J. Miller, Anushree Chatterjee, Joel M. Kralj. A high-throughput and low-waste viability assay for microbes . Nature Microbiology , 2023; DOI: 10.1038/s41564-023-01513-9

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Scientists develop faster, cheaper way to count microbes, discover new antibiotics

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IMAGE CAPTION: Christian Meyer demonstrates the Geometric Viability Assay (GVA), a new method for counting microbes that works 36 times faster than conventional methods.  Credit: Casey Cass/CU Boulder

University of Colorado Boulder researchers have developed a new way of counting microorganisms that works as much as 36 times faster than conventional methods, cuts plastic use more than 15-fold and substantially decreases the cost and carbon footprint of biomedical research.

Anushree Chaterjee with her students

Anushree Chatterjee, right works with research assistant Grace Lynch in the Chatterjee Lab. Credit: Casey A. Cass/CU Boulder

The technique, described Nov. 2 in the journal Nature Microbiology , could revolutionize the way microbiology experiments are conducted around the world, allowing clinicians to diagnose and treat infections faster and researchers to test potential new antibiotics in a fraction of the time.

The invention comes as concern about antibiotic resistance grows worldwide, with drug-resistant bugs contributing to nearly 5 million deaths globally in 2019 . 

“We are in the middle of a silent pandemic of antimicrobial resistance and there is an urgent need to speed up the discovery of new antibiotics,” said senior author Anushree Chatterjee, associate professor of chemical and biological engineering at CU Boulder. “We believe this new method can do that, and much more.”

A new way to fill the pipeline

Since 1938, microbiologists have used a simple method, the colony forming unit (CFU) assay, for counting bacterial cells in a sample. They start by diluting the sample down into eight to 10 different concentrations, put drops from each into petri dishes filled with bacteria food, wait hours or days for individual colonies to form, and count them.  If testing a new molecule to see how well it can kill bacteria, they add that in to see how many bacteria survive.

The process is notoriously laborious and wasteful, often taking hours to assess a small sample and producing mounds of discarded plastic.

Because it takes so long and costs so much, researchers must be choosy about which potential new drugs or combinations they test, so they’re discouraged from taking chances, Chatterjee said.

This high-cost, low-profit equation has led pharmaceutical companies to steer away from developing new antibiotics.

“We are basically out of antibiotics,” said Chatterjee, noting that many widely circulating pathogens — including Staphylococcus aureas (staph) and Neisseria gonorrhoeae (Gonorrhea)— are now resistant to most drugs designed to treat them.

“In order to have a sustainable pipeline of new options, we have to fundamentally change the way discovery is done,” Chatterjee said.

Math instead of plastic

The new method, known as Geometric Viability Assay (GVA), replaces the arduous multi-step process of manual dilutions with a one-step process, informed by simple geometry and math.

A cell phone takes a picture of microbes

Scientists can use a simple smart phone to count microbes quickly and efficiently. Credit: Casey Cass/CU Boulder

“We are using the same kinds of math that can help students estimate the number of M&M’s in a jar,” said first author Christian Meyer, a postdoctoral fellow in the departments of Molecular, Cellular and Developmental Biology and Chemical and Biological Engineering. “Instead of counting all the M&M’s individually, a clever student might count the bottom layer and then multiply by the height.”

Similarly, instead of manually dividing the samples into numerous subsamples to make counting colonies easier, GVA counts colonies in one place, inside a portion of the cone of a single pipette tip, and then uses multiplication to calculate total concentration. 

To do this, scientists embed the samples into a gel inside the cone, in which colonies form.

When it’s time to count, they can use various techniques— including ones that involve taking a picture or using a paper ruler— to accurately measure samples with anywhere from one to 1 billion microbes.

“It involves no mathematics that a high-school, calculus student couldn’t perform,” said Meyer.

But it could have a big impact.

Saving time, and the environment

In laboratory tests measuring common bacteria like Escherichia coli ( E. coli ) and Salmonella enterica , the researchers found that while preparing 96 samples took three hours by classical methods, GVA took 5 minutes — a 36-fold time savings. Even when compared to a more modern method involving robotics, GVA was still nine times faster and used one-tenth the plastic.

Using GVA, a single researcher could accurately measure the microbial concentration of 1,200 samples in a single day, the study found.

Ultimately, Chatterjee believes the method could also enable doctors to diagnose infection and find the right antibiotic for that infection faster.

“Instead of someone being in the hospital for three days while they figure out what that particular bug is sensitive to, we could potentially someday know overnight what the right antibiotic might be,” she said, noting that more research is needed to advance to the clinical stage.

The technology could also have applications for the food industry, and for studying the human microbiome.

Meyer invented the technique with Joel Kralj, a former assistant professor in the BioFrontiers Institute. The two are working with Venture Partners and have filed a provisional patent.

The research team has also created a website , and are now working to develop a smartphone version that scientists and the general public can use.

“Someone wise once said that the correct punctuation for a scientific advance is not an exclamation mark, but a semicolon,” said Meyer.  “In that spirit, while we are thrilled to be part of reinventing a core technique of microbiology, we are most excited for what will come next.”

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The microbiome comprises trillions of microorganisms living on and inside each of us. Historically, researchers have only guessed at its role in human health, but in the last decade or so, genetic sequencing techniques have illuminated this galaxy of microorganisms enough to study in detail.

As researchers unravel the complex interplay between our bodies and microbiomes, they are beginning to appreciate the full scope of the field’s potential for treating disease and promoting health.

For instance, the growing list of conditions that correspond with changes in the microbes of our gut includes type 2 diabetes, inflammatory bowel disease, Alzheimer’s disease, and a variety of cancers.

“In almost every disease context that’s been investigated, we’ve found different types of microbial communities, divergent between healthy and sick patients,” says professor of biological engineering Eric Alm. “The promise [of these findings] is that some of those differences are going to be causal, and intervening to change the microbiome is going to help treat some of these diseases.”

Alm’s lab, in conjunction with collaborators at the Broad Institute of MIT and Harvard, did some of the early work characterizing the gut microbiome and showing its relationship to human health. Since then, microbiome research has exploded, pulling in researchers from far-flung fields and setting new discoveries in motion. Startups are now working to develop microbiome-based therapies, and nonprofit organizations have also sprouted up to ensure these basic scientific advances turn into treatments that benefit the maximum number of people.

 “The first chapter in this field, and our history, has been validating this modality,” says Mark Smith PhD ’14, a co-founder of OpenBiome, which processes stool donations for hospitals to conduct stool transplants for patients battling gut infection. Smith is also currently CEO of the startup Finch Therapeutics, which is developing microbiome-based treatments. “Until now, it’s been about the promise of the microbiome. Now I feel like we’ve delivered on the first promise. The next step is figuring out how big this gets.”

An interdisciplinary foundation

MIT’s prominent role in microbiome research came, in part, through its leadership in a field that may at first seem unrelated. For decades, MIT has made important contributions to microbial ecology, led by work in the Parsons Laboratory in the Department of Civil and Environmental Engineering and by scientists including Institute Professor Penny Chisholm.

Ecologists who use complex statistical techniques to study the relationships between organisms in different ecosystems are well-equipped to study the behavior of different bacterial strains in the microbiome.

Not that ecologists — or anyone else — initially had much to study involving the human microbiome, which was essentially a black box to researchers well into the 2000s. But the Human Genome Project led to faster, cheaper ways to sequence genes at scale, and a group of researchers including Alm and visiting professor Martin Polz began using those techniques to decode the genomes of environmental bacteria around 2008.

Those techniques were first pointed at the bacteria in the gut microbiome as part of the Human Microbiome Project, which began in 2007 and involved research groups from MIT and the Broad Institute.

Alm first got pulled into microbiome research by the late biological engineering professor David Schauer as part of a research project with Boston Children’s Hospital. It didn’t take much to get up to speed: Alm says the number of papers explicitly referencing the microbiome at the time could be read in an afternoon.

The collaboration, which included Ramnik Xavier, a core institute member of the Broad Institute, led to the first large-scale genome sequencing of the gut microbiome to diagnose inflammatory bowel disease. The research was funded, in part, by the Neil and Anna Rasmussen Family Foundation.

The study offered a glimpse into the microbiome’s diagnostic potential. It also underscored the need to bring together researchers from diverse fields to dig deeper.

Taking an interdisciplinary approach is important because, after next-generation sequencing techniques are applied to the microbiome, a large amount of computational biology and statistical methods are still needed to interpret the resulting data — the microbiome, after all, contains more genes than the human genome. One catalyst for early microbiome collaboration was the Microbiology Graduate PhD Program, which recruited microbiology students to MIT and introduced them to research groups across the Institute.

As microbiology collaborations increased among researchers from different department and labs, Neil Rasmussen, a longtime member of the MIT Corporation and a member of the visiting committees for a number of departments, realized there was still one more component needed to turn microbiome research into a force for human health.

“Neil had the idea to find all the clinical researchers in the [Boston] area studying diseases associated with the microbiome and pair them up with people like [biological engineers, mathematicians, and ecologists] at MIT who might not know anything about inflammatory bowel disease or microbiomes but had the expertise necessary to solve big problems in the field,” Alm says.

In 2014, that insight led the Rasmussen Foundation to support the creation of the Center for Microbiome Informatics and Therapeutics (CMIT), one of the first university-based microbiome research centers in the country. CMIT is based at the MIT Institute for Medical Engineering and Science (IMES).

Tami Lieberman, the Hermann L. F. von Helmholtz Career Development Professor at MIT, whose background is in ecology, says CMIT was a big reason she joined MIT’s faculty in 2018. Lieberman has developed new genomic approaches to study how bacteria mutate in healthy and sick individuals, with a particular focus on the skin microbiome.

Laura Kiessling, a chemist who has been recognized for contributions to our understanding of cell surface interactions, was also quick to join CMIT. Kiessling, the Novartis Professor of Chemistry, has made discoveries relating to microbial mechanisms that influence immune function. Both Lieberman and Kiessling are also members of the Broad Institute.

Today, CMIT, co-directed by Alm and Xavier, facilitates collaborations between researchers and clinicians from hospitals around the country in addition to supporting research groups in the area. That work has led to hundreds of ongoing clinical trials that promise to further elucidate the microbiome’s connection to a broad range of diseases.

Fulfilling the promise of the microbiome

Researchers don’t yet know what specific strains of bacteria can improve the health of people with microbiome-associated diseases. But they do know that fecal matter transplants, which carry the full spectrum of gut bacteria from a healthy donor, can help patients suffering from certain diseases.

The nonprofit organization OpenBiome, founded by a group from MIT including Smith and Alm, launched in 2012 to help expand access to fecal matter transplants by screening donors for stool collection then processing, storing, and shipping samples to hospitals. Today OpenBiome works with more than 1,000 hospitals, and its success in the early days of the field shows that basic microbiome research, when paired with clinical trials like those happening at CMIT, can quickly lead to new treatments.

“You start with a disease, and if there’s a microbiome association, you can start a small trial to see if fecal transplants can help patients right away,” Alm explains. “If that becomes an effective treatment, while you’re rolling it out you can be doing the genomics to figure out how to make it better. So you can translate therapeutics into patients more quickly than when you’re developing small-molecule drugs.”

Another nonprofit project launched out of MIT, the Global Microbiome Conservancy, is collecting stool samples from people living nonindustrialized lifestyles around the world, whose guts have much different bacterial makeups and thus hold potential for advancing our understanding of host-microbiome interactions.

A number of private companies founded by MIT alumni are also trying to harness individual microbes to create new treatments, including, among others, Finch Therapeutics founded by Mark Smith; Concerto Biosciences, co-founded by Jared Kehe PhD ’20 and Bernardo Cervantes PhD ’20; BiomX, founded by Associate Professor Tim Lu; and Synlogic, founded by Lu and Jim Collins, the Termeer Professor of Medical Engineering and Science at MIT.

“There’s an opportunity to more precisely change a microbiome,” explains CMIT’s Lieberman. “But there’s a lot of basic science to do to figure out how to tweak the microbiome in a targeted way. Once we figure out how to do that, the therapeutic potential of the microbiome is quite limitless.”

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Six Key Topics in Microbiology

This collection from the FEMS journals presents the latest high-quality research in six key areas of microbiology that have an impact across our world. All of the FEMS journals aim to serve the microbiology community with timely and authoritative research and reviews, and by investing back into the scientific community . The collection also features recordings from our FEMS Microbiology Webinars series , free presentations from microbiologists across the world.

Browse the latest collections below, with all papers free to read until the end of 2021 (or fully Open Access). If you would like to receive the latest updates from the FEMS journals make sure to sign up for our email alerts .

Antimicrobial Resistance

Environmental microbiology, pathogenicity and virulence, biotechnology and synthetic biology, microbiomes, food microbiology.

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FEMS Microbiology Ecology Webinar on the Environmental Dimension of Antibiotic Resitance

Webinar: Environmental Dimension of Antibiotic Resistance

Originally aired on 6th August 2020, this webinar from FEMS Microbiology Ecology covers the environmental dimension of antibiotic resistance and how the anthropogenic use of antibiotics in various ecosystems has implications for human health. Watch the webinar recording to learn more.

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FEMS Microbiology Ecology Webinar on Aquatic Microbial Ecology

FEMS Microbiology Ecology Webinar: Acquatic Microbial Ecology

Originally aired on 15th October 2020, this webinar from FEMS Microbiology Ecology covers aquatic microbial ecology. Aquatic habitats are rich environments for microbial life and have a global impact on the carbon and nitrogen cycles. The behaviour of microbes in response to changes in these environments can have a huge influence on ecology across the world. Watch the webinar recording to learn more. 

FEMS Microbiology Ecology Webinar on Ecology of Soil Microorganisms

FEMS Microbiology Ecology Webinar on Ecology of Soil Microorganisms

Originally aired on 12th November 2020, this webinar from FEMS Microbiology Ecology covers the topic of ecology of soil microorganisms. Soil is alive, and soil microorganisms are the driving force of elemental biogeochemical cycling and the bridge linking above- and below-ground ecosystem interactions. The microbial ecology of soils has the potential to answer multiple questions that not only advance our basic understanding of ecological principles, but are also relevant for the present focal areas of the anthropogenic effects, ecosystem productivity and other applied subjects. Watch the webinar recording to learn more. 

FEMS Microbiology Ecology Webinar on Microbial Ecotoxicology

FEMS Microbiology Ecology Webinar on Microbial Ecotoxicology

Originally broadcast on 4th March 2021, this webinar from FEMS Microbiology Ecology covers the topic of microbial ecotoxicology. The term “microbial ecotoxicology” was coined to describe interdisciplinary investigations of the response of the microbial compartment in ecosystems subject to environmental contamination. Watch the webinar recording to learn more. 

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FEMS Webinar on Vaccines in the Time of COVID-19

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Originally broadcast on 10th March 2021, this webinar, chaired by Pathogens and Disease 's own Dr. Alfredo Garzino-Demo, covers the vitally important subject of vaccines in the time of COVID-19. Enjoy three insightful talks on vaccine development, followed by an in depth Q&A and discussion where the esteemed speakers answered questions from the audience. Watch the webinar recording to learn more. 

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FEMS Yeast Research Webinar on Advances in Synthetic Biology Tools to Engineer Yeast Cells for Biotechnology

Webinar: Advances in Synthetic Biology Tools to Engineer Yeast Cells for Biotechnology

Originally aired on 5th November 2020, this webinar from FEMS Yeast Research covers advances in synthetic biology tools to engineer yeast cells for biotechnology. Yeasts have long been used to produce alcoholic beverages and fuel ethanol. Its fast growth, well-developed genetics, robustness in large-scale fermentations and resistance to inhibitors and phages have made it the preferred microbial cell factories for production a broad range of valuable products such as biofuels, biochemicals, nutraceuticals and pharmaceuticals. Synthetic biology aims to build genetic circuits and synthetic cells to understand native biological systems and harness them for a wide range of applications. Watch the webinar recording to learn more. 

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FEMS Microbiology Ecology Webinar on the Sponge Microbiome

Webinar: Sponge Microbiome

Originally aired on 9th July 2020 to over 250 attendees, this webinar from FEMS Microbiology Ecology covers sponges, the oldest extant multicellular animals (i.e. more than 600 million years old). Marine sponges are ecologically important components of coral reef ecosystems where they provide habitat for a wide range of species and couple the benthic and pelagic zones through their high seawater filtration capability. Watch the webinar recording to learn more.

FEMS Microbiology Ecology Webinar on the Animal Microbiome

Webinar: Animal Microbiome

Originally aired on 24 September 2020, this webinar from FEMS Microbiology Ecology covers the fascinating topic of animal microbiomes. Microbial communities living on or in animals affect the physiology and behavior of their hosts. But what exactly is the interplay between these animal microbiomes and the animals themselves? Watch the webinar recording to learn more. 

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FEMS Microbiology Ecology Webinar on Sustainable Agriculture

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Originally broadcast on 20th May 2021, this webinar from FEMS Microbiology Ecology  explores sustainable agriculture by diving into the interactions between common crops and their microbiomes. Our speakers will demonstrate how modern sequencing techniques can reveal how plant microbiomes influence the postharvest pathogens and storability of crops, the root and soil rhizosphere, and plant performance. Watch the webinar recording to learn more. 


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ISSN: 1471-2180

10 things we learned about microbes in 2021

Mysterious microbes can be found all around us, and even inside our bodies.

A bacteriophage illustration.

Take a trip to the marvelous world of microbes, where bacteria breathe electricity, neon-yellow slime molds forage for snacks on the forest floor, and thousands of mysterious viruses hang out in your guts. This year, scientists made a slew of fascinating discoveries about the microscopic organisms living in and all around us — Here's a few of our favorite stories. 

Thousands of unknown viruses found in human gut

Researchers discovered more than 70,000 previously unknown viruses populating the human gut and infecting the bacteria that live there. They found these viruses using a method called metagenomics, which involves sampling genetic material from a large community of microbes and matching the sequences to specific species. After analyzing 28,000 gut microbiome samples taken from 28 countries, the team identified tens of thousands of newfound bacteriophages, or viruses that can infect bacteria . It's still unclear if and how these bacteriophages affect the body, but the vast majority likely aren't harmful to humans.

Read more: 70,000 never-before-seen viruses found in the human gut

Electric bacteria have an on-off switch 

Buried deep beneath the seabed, puny bacteria ( Geobacter ) exhale electricity through long, thin snorkels. And this year, in a study published Sept. 1 in the journal Nature , scientists discovered how to switch these electric microbes on and off. Within each bacterial cell, hair-like structures called pili sit just beneath the membrane, they found; these pili move like pistons in an engine, pumping up and down. As they pump, the pili push the microbes' snorkels out of the cell, allowing the bacteria to "breathe" a steady stream of electrons. But if you remove the pumping pili, the snorkels stay tucked inside the cell. Having found this on-off switch, the researchers say that the bacteria could someday inspire new technologies, like powerful microbe-powered batteries. 

Read more: Scientists discover on-off switch for bacteria that breathe electricity  

Rock-munching microbes live beneath Antarctic ice 

An ice-covered lake in Antarctica hosts a slew of microbes that survive by chowing down on crushed rocks. Researchers discovered this by studying sediment collected from Lake Whillans, a 23-square-mile (60 square kilometers) subglacial lake buried beneath 2,600 feet (800 meters) of ice. The lake undergoes periods of filling and draining, which in turn drive erosion. The team replicated this erosion in the lab and found that the lake sediments released various chemicals, such as hydrogen , methane and carbon dioxide, as well as gases and liquid that had been trapped within the sediment. For every chemical released from the rocks, the team found a group of microbes that have evolved to exploit it for energy.

Read more: Microbes that feast on crushed rocks thrive in Antarctica's ice-covered lakes  

Genes from viruses transform bacteria into superbugs 

Viruses that infect bacteria can slip their genes into their host's genome and offer them protection against antibiotics . 

In a study published July 16 in the journal Science Advances , researchers studied Pseudomonas aeruginosa , a type of bacteria that ranks among the leading causes of hospital-acquired infections. The team pitted six different strains of P. aeruginosa against one another in an animal model, to see which ones became dominant; they did this to figure out why some P. aeruginosa infections tend to be more difficult to treat than others. Two strains came out on top, and in the winners' DNA , the team found snippets of viral genetic material that seemed to help the bacteria form biofilms — clusters of bacterial cells that secrete a slimy shield and slow down their metabolisms. Biofilms protect bacteria from both the host immune system and antibiotic treatments, hinting that viruses may sometimes help transform bacteria into drug-resistant superbugs.

Read more: Genes from tiny viruses can turn bacteria into superbugs  

Ancient microfossil contains oldest known land fungus  

Scientists uncovered fossilized threadlike filaments in rocks from China 's Doushantuo Formation in Guizhou Province; these tiny tendrils, invisible to the naked eye, may be the world's oldest evidence of a fungus growing on land. The research team found these microfossils by taking 0.002-inch-thick (50 micrometers) slices of rock and placing them under a microscope; this revealed thin, branching filaments about 1/10 the width of a human hair and tiny spheres that could be interpreted as fungal spores. The fossil is about 635 million years old, meaning it would have formed during a frigid period known as "snowball Earth." The appearance of land fungi at that time may have helped reshape the planet's geochemistry and support the emergence of new ecosystems as Earth thawed out.

Read more: 635 million-year-old fossil is the oldest known land fungus

Ancient DNA shows common cold virus may predate Homo sapiens 

Scientists uncovered bits of viral DNA in two 31,000-year-old baby teeth and reconstructed the evolutionary history of the pathogens. Among their findings, they discovered that the human adenovirus C (HAdV-C), a species of virus that typically causes mild, cold-like illnesses in children, may have originated more than 700,000 years ago. Homo sapiens, meanwhile, are thought to have first emerged roughly 315,000 years ago, based on the oldest known fossil evidence. They based this conclusion off their analysis of two "nearly complete" HAdV-C genomes found in the baby teeth, which they compared to modern-day adenoviruses sampled between the 1950s and 2010s. 

Read more: Common cold virus may predate modern humans, ancient DNA hints

— Going viral: 6 new findings about viruses

— 6 superbugs to watch out for

— 5 ways gut bacteria affect your health  

Microbes from cow stomachs can break down plastic 

Bacteria drawn from cows' stomachs are capable of breaking down certain plastics, such as the polyethylene terephthalate (PET) used in soda bottles, food packaging and synthetic fabrics. 

Cows consume and digest a natural polyester produced by plants, called cutin, so scientists suspected that the microbes in animals' tummies may carry microbes that can also digest synthetic polyesters, like PET. They fished such microbes from the cow rumen, the largest compartment of the animal's stomach, and found that the bugs produced enzymes that could cut through PET, as well as two other plastics: polybutylene adipate terephthalate (PBAT), used in compostable plastic bags, and polyethylene furanoate (PEF), made from renewable, plant-derived materials. Scientists have discovered similar plastic-eating enzymes in the past, but not in cows.

Read more: Microbes in cow stomachs can help recycle plastic

Bacteria that are invisible to the human immune system 

Scientists discovered bacteria in the central Pacific Ocean that are invisible to the human immune system. They found the bugs lurking about 1,650 miles (2,655 kilometers) southwest of Hawaii and 13,100 feet (4,000 meters) underwater, in a remote region that would have little contact with mammalian life. The team used a remote submarine to collect marine bacteria from samples of water, sponges, sea stars and sediments, and then cultured the bacteria back in the lab. They then exposed mouse and human immune cells to the bacteria, and strikingly, they found that 80% of the microbes, mostly belonging to the genus Moritella , escaped the cells' detection. This finding topples a long-held assumption that the human immune system evolved to detect any and all microbes, because this vigilance would help us quickly spot and fight off infectious bugs. 

Read more: Scientists find deep-sea bacteria that are invisible to the human immune system  

How brainless slime molds store memory 

Slime molds belong to the same taxonomic group as amoebas, and despite lacking a brain, the single-celled organisms have a simplistic form of memory. And in February, scientists uncovered a new clue as to how the brainless blobs pull off this feat. 

Slime molds can either exist as one tiny cell, with one nucleus, or as a gargantuan cell with many nuclei; these huge cells form tubular networks that move fluid, chemicals and nutrients around the whole organism. Scientists found that, in the neon-yellow slime mold Physarum polycephalum , the relative widths of these tubes can encode information. For instance, when the slime mold detects and engulfs a morsel of food, it leaves an "imprint" of thick tubes where the food once sat; this then influences which direction the blob can move next. 

Read more: This gooey, brainless blob can store memories  

Microbes lurking in lakes beneath Antarctic ice

More than 400 subglacial lakes lie beneath the Antarctic ice sheet, beyond the reach of sunshine. But thanks to geothermal heat flux — the flow of heat from the Earth's interior — scientists think that a teeming community of microbes may thrive in these pitch-black ecosystems. 

Although they're cut off from the sun's heat, heat from the planet's interior warms the underside of these lakes; this drives "vigorous" convection currents that stir up the water, liberating minerals from the sediment below while capturing oxygen and minerals from higher regions of the water column. The flow of oxygen- and mineral-rich water through the lakes should, theoretically, help fuel microbial growth, and the team plans to test this on a future expedition to a subglacial lake called Lake CECs, named after the Chilean scientific center Centro de Estudios Científicos.

Read more: Lakes beneath the Antarctic ice could be teeming with microbial life

Originally published on Live Science.  

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Nicoletta Lanese

Nicoletta Lanese is the health channel editor at Live Science and was previously a news editor and staff writer at the site. She holds a graduate certificate in science communication from UC Santa Cruz and degrees in neuroscience and dance from the University of Florida. Her work has appeared in The Scientist, Science News, the Mercury News, Mongabay and Stanford Medicine Magazine, among other outlets. Based in NYC, she also remains heavily involved in dance and performs in local choreographers' work.

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Department of Microbiology

A woman in a stream holds dirt in her hands.

Dam removals, restoration project on Klamath River expected to help salmon, researchers conclude

Julie Alexander on the Klamath River

The world’s largest dam removal and restoration project currently underway on the Klamath River in Oregon and California will aid salmon populations that have been devastated by disease and other factors. However, it will not fully alleviate challenges faced by the species, a team of researchers conclude in a just-published paper .

In the paper, published in Frontiers in Ecology and Evolution, Hallett and a team of researchers from Oregon State, Tribes in Oregon and California, and state and federal agencies outlined their predictions for salmon disease risk in the Klamath River following the removal of four hydroelectric dams. They also provide post-dam removal research and monitoring recommendations and insights to aid habitat restoration efforts.

Two faculty members in the Department of Microbiology, Jerri Bartholomew and Julie Alexander, focused on how the dam removals could impact pathogen exposure, such as parasites.

“There’s no question in my mind just the removal of these four dams will go a long way to knocking back that current infection zone by shifting things in terms of time and space where the hosts and parasites overlap,” said Alexander, an aquatic ecologist.

Michael Belchik, a fisheries biologist with the Yurok Tribe in California and co-author of the paper, said he thinks there will be noticeable gains for fish shortly after the dams are removed.

“I think you are going to see fish accessing new habitat right away, and that is going to be a cause for celebration,” said Belchik, who has worked for the Tribe since 1995.

One of the four dams was removed earlier this year, and the other three are slated to be taken down in early 2024. Removal of the dams will result in restoration of habitat originally altered more than 100 years ago with construction of the first dam.

Read more here .

Read more stories about: osu press releases , faculty and staff , microbiology , research

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Cover of Microbiology in the 21st Century: Where Are We and Where Are We Going?

Microbiology in the 21st Century: Where Are We and Where Are We Going?

  • Copyright and Permissions
  • The impact of microbes on the health of the planet and its inhabitants;
  • The fundamental significance of microbiology to the study of all life forms;
  • Research challenges faced by microbiologists and the barriers to meeting those challenges;
  • The need to integrate microbiology into school and university curricula; and
  • Public microbial literacy.

This is an exciting time for microbiology. We are becoming increasingly aware that microbes are the basis of the biosphere. They are the ancestors of all living things and the support system for all other forms of life. Paradoxically, certain microbes pose a threat to human health and to the health of plants and animals. As the foundation of the biosphere and major determinants of human health, microbes claim a primary, fundamental role in life on earth. Hence, the study of microbes is pivotal to the study of all living things, and microbiology is essential for the study and understanding of all life on this planet.

Microbiology research is changing rapidly. The field has been impacted by events that shape public perceptions of microbes, such as the emergence of globally significant diseases, threats of bioterrorism, increasing failure of formerly effective antibiotics and therapies to treat microbial diseases, and events that contaminate food on a large scale. Microbial research is taking advantage of the technological advancements that have opened new fields of inquiry, particularly in genomics. Basic areas of biological complexity, such as infectious diseases and the engineering of designer microbes for the benefit of society, are especially ripe areas for significant advancement. Overall, emphasis has increased in recent years on the evolution and ecology of microorganisms. Studies are focusing on the linkages between microbes and their phylogenetic origins and between microbes and their habitats. Increasingly, researchers are striving to join together the results of their work, moving to an integration of biological phenomena at all levels.

While many areas of the microbiological sciences are ripe for exploration, microbiology must overcome a number of technological hurdles before it can fully accomplish its potential. We are at a unique time when the confluence of technological advances and the explosion of knowledge of microbial diversity will enable significant advances in microbiology, and in biology in general, over the next decade. To make the best progress, microbiology must reach across traditional departmental boundaries and integrate the expertise of scientists in other disciplines. Microbiologists are becoming increasingly aware of the need to harness the vast computing power available and apply it to better advantage in research. Current methods for curating research materials and data should be rethought and revamped. Finally, new facilities should be developed to house powerful research equipment and make it available, on a regional basis, to scientists who might otherwise lack access to the expensive tools of modern biology.

It is not enough to accomplish cutting-edge research. We must also educate the children and college students of today, as they will be the researchers of tomorrow. Since microbiology provides exceptional teaching tools and is of pivotal importance to understanding biology, science education in schools should be refocused to include microbiology lessons and lab exercises. At the undergraduate level, a thorough knowledge of microbiology should be made a part of the core curriculum for life science majors.

Since issues that deal with microbes have a direct bearing on the human condition, it is critical that the public-at-large become better grounded in the basics of microbiology. Public literacy campaigns must identify the issues to be conveyed and the best avenues for communicating those messages. Decision-makers at federal, state, local, and community levels should be made more aware of the ways that microbiology impacts human life and the ways school curricula could be improved to include valuable lessons in microbial science.

  • Front Matter

The American Academy of Microbiology is the honorific leadership group of the American Society for Microbiology. The mission of the American Academy of Microbiology is to recognize scientific excellence and foster knowledge and understanding in the microbiological sciences.

The opinions expressed in this report are those solely of the colloquium participants and may not necessarily reflect the official position of the American Society for Microbiology.

Board of Governors, American Academy of Microbiology

Eugene W. Nester, Ph.D. (Chair) University of Washington

Kenneth I. Berns, M.D., Ph.D. University of Florida Genetics Institute

James E. Dahlberg, Ph.D. University of Wisconsin, Madison

Arnold L. Demain, Ph.D. Drew University

E. Peter Greenberg, Ph.D. University of Iowa

J. Michael Miller, Ph.D. Centers for Disease Control and Prevention

Stephen A. Morse, Ph.D. Centers for Disease Control and Prevention

Harriet L. Robinson, Ph.D. Emory University

Abraham L. Sonenshein, Ph.D. Tufts University Medical Center

David A. Stahl, Ph.D. University of Washington

Judy D. Wall, Ph.D. University of Missouri

Colloquium Steering Committee

Roberto G. Kolter, Ph.D. Harvard Medical School (Co-Chair)

Moselio Schaechter, Ph.D. San Diego State University (Co-Chair)

Stanley R. Maloy, Ph.D. San Diego State University

David A. Relman, M.D. Stanford University School of Medicine

Margaret A. Riley, Ph.D. Yale University

Carol A. Colgan, Director American Academy of Microbiology

Colloquium Participants

Victor de Lorenzo, Ph.D. Centro Nacional de Biotecnologia, Madrid, Spain

William E. Goldman, Ph.D. Washington University of Medicine, St. Louis

Peter M. Hecht, Ph.D. Microbia, Inc., Cambridge, Massachusetts

Laura A. Katz, Ph.D. Smith College

Roberto G. Kolter, Ph.D. Harvard Medical School

Mary E. Lidstrom, Ph.D. University of Washington

William W. Metcalf, Ph.D. University of Illinois

Eugene W. Nester, Ph.D. University of Washington

Gary J. Olsen, Ph.D. University of Illinois

Moselio Schaechter, Ph.D. San Diego State University

Gisela Storz, Ph.D. National Institutes of Health

Saeed Tavazoie, Ph.D. Princeton University

Jennifer J. Wernegreen, Ph.D. Marine Biology Laboratory, Woods Hole, Massachusetts

Merry Buckley, Ph.D. Freelance Science Writer, Ithaca, New York

  • Executive Summary
  • Introduction

Microbiology has never been more exciting or important than it is today. Powerful new technologies, including novel imaging techniques, genomics, proteomics, nanotechnology, rapid DNA sequencing, and massive computational capabilities have converged to make it possible for scientists to delve into inquiries that many thought would never be approachable. As a result, hardly a day goes by without another discovery that points to the central importance microbial life has in carrying out the cycles of gases and nutrients that sustain all life and affect conditions on this planet. The increasing human population, combined with increases in global travel, has apparently created a sharp rise in the emergence and re-emergence of infectious diseases, alarming the public and frustrating public health officials.

Issues of microbial contamination are also more pressing now than ever. The microbial quality of our food and water in a crowded, complex world must be vigorously addressed to maintain health and a high quality of life for the all citizens of the world. Finally, a bioterrorism event involving spores of Bacillis anthracis occurred in the United States in 2001, and continuing investigations worldwide reveal that bioterrorism is a genuine threat from ill-intentioned groups and individuals using other microbes and toxins.

As microbiology is faced with this tumult of advancements, opportunities, problems, and threats, the science stands at the threshold of a new era. But in what direction is microbial science going? What is really important and what is merely distraction? What will best improve people's lives and the health of our shared planet? In short, what new directions should microbiology take in the 21 st century?

Microbiologists want to know how microbial science is changing in the wake of advancements in technology and growing human pressures on the world's resources. They want to know what topics deserve exploration and where the obstacles to exploring those areas lie. As we stand at the convergence of genomics, public concerns about bioterrorism, global outbreaks of infectious diseases, unprecedented computational power, and the possibility of large-scale ecological disasters, where do the greatest opportunities lie in microbiology and what obstacles must be overcome for these opportunities to be realized?

It is clear to microbiologists that microbes are the basis of the biosphere; they are the support system for life on earth and the wellspring from which all other life has arisen through billions of years of evolution. Since microbes are fundamental to life and microbial science is in the headlines now more than ever before, it follows that educating young people in microbial science is critical. But where does microbiology fit into existing school curricula? How can college biology coursework be updated to reflect more accurately the pivotal place of microbial science in understanding our world? How can the public-at-large be made aware of microbes, the role of microbes in sustaining life, and the danger posed by modern infectious diseases? And how should public outreach campaigns be conducted? What are the important messages to deliver? How can the importance of microbes and microbiology be conveyed to people in power, the decision-makers?

To answer such questions, the American Academy of Microbiology convened a colloquium in Charleston, South Carolina on September 5–7, 2003. Experts in the fields of bacteriology, virology, eukaryotic microbiology, medicine, biotechnology, molecular biology, and education met to discuss the central role of microbes in maintaining life on earth, the current research challenges that face the field, the pivotal role of microbiology education to training in all life sciences, and methods for encouraging public literacy of microbial science.

  • The Central Role of Microbes and Microbiology

Microbes affect all life and the physical and chemical make-up of our planet. They have done so since the origin of life. No other group of organisms can make such a claim. Life without all other creatures is possible, but life without microbes is not. Consequently, we believe that one cannot carry out in-depth studies of any branch of biology or geology without taking into account the activities of microbes. Microbes are the masters of the biosphere, and ours indeed is a planet of the microbes.

Microorganisms are also determinants of human health and the source of critical materials for medical and industrial use. Microbiology, therefore, is as central to the study of life as biochemistry, genetics, evolution, or molecular biology. The informed biologist must treat microbiology as core and not as a particular branch of biology.

Microbes As the Basis of Life

The root of the tree of life.

Microbes were the progenitors of all the complex and varied biological forms that now exist on Earth. Plants and animals emerged within a microbial world and have retained intimate connections with, and dependency upon, microorganisms. As the root of the tree of life, microbes were the original templates from which all life was formed and to which all life has an intimate familiarity. In order to understand the evolution of organisms we see today at the tips of the branches of the tree of life, it is necessary to study how they are related to their ancestors and what those ancestors were like.

By studying the microorganisms living today that echo the properties of the first life forms, microbiologists seek to understand the forces and processes that created our global ecosystem. Moreover, microorganisms are the preeminent systems to use in experimental evolution, as they offer the researcher fast generation times, genetic flexibility, unequaled experimental scale, and manageable study systems. Studies using microbes have led to groundbreaking insights into the evolution of all species. For example, investigations of the interrelatedness of microbes first brought to light the current model of the evolutionary relatedness of all life on earth, the tree of life (See Box 1 – the Tree of Life).

The Tree of Life Before and After Molecular Microbiology.


Life not only began with microorganisms, the continued existence of life on earth totally relies on the inconspicuous microbe. It has been estimated that a staggering 5×10 31 (50,000,000,000,000,000,000,000,000,000,000—weighing more than 50 quadrillion metric tons) microbial cells exist on this planet, and it is difficult to overstate their importance to the biosphere. Microbes are responsible for cycling the critical elements for life, including carbon, nitrogen, sulfur, hydrogen, and oxygen. By cycling these elements in soils, microbes regulate the availability of plant nutrients, thereby governing soil fertility and enabling the efficient plant growth that sustains human and animal life. Microbes also play a big role in cycling atmospheric gases, including the compounds responsible for the “greenhouse effect,” which, paradoxically, sustains life on our planet, but through global warming, poses a threat to all living things. More photosynthesis is carried out by microbes than by green plants. It turns out that, excluding cellulose, microbes constitute approximately 90% of the biomass of the whole biosphere (more than 60% if cellulose is considered).

Since microbes can take up nutrients and other elements that larger organisms often cannot exploit, microorganisms are positioned at the base of many food chains, where they siphon previously inert, inorganic materials into the biosphere. Microbes are also master recycling experts; they degrade biological wastes and release the critical elements for use by other organisms.

Scientists have only begun to understand the ways that microorganisms are tuned into their environments, how they respond to changes, and how they communicate with other members of microbial communities to carry out the functions that sustain the biosphere. Understanding these phenomena will lead to a more complete knowledge of our global ecosystem and may allow scientists to correct human damage to ecosystems, large and small. Humans are latecomers to this planet, and a great deal may be learned from microbes about the maintenance of essential planetary processes.


Humans have an intimate relationship with microorganisms. Despite their overwhelmingly beneficial impact on the environment, a small notorious set of bacteria, fungi, parasites, and viruses may cause disease. In the struggle against disease, our bodies attempt to establish a delicate balance between the microorganisms and viruses that are beneficial to our health and those that exploit the human host to the body's detriment. More than 90% of the cells in our bodies are microorganisms; bacteria and fungi populate our skin, mouth, and other orifices. Microbes enable efficient digestion in our guts, synthesize essential nutrients, and maintain benign or even beneficial relationships with the body's organs. The presence of these organisms influences our physical and mental health. In experiments, it has been found that sterile animals are markedly less healthy than animals that have been naturally colonized by microorganisms.

How do microorganisms cause disease? Pathogenic microorganisms and viruses have an individual ecological strategy that determines where they strike and what impacts they have on the host. One root of the problem is that pathogens colonize areas within the human body that our immune system sees as “privileged.” In the process of gaining access to these locations or in maintaining their colonies, microorganisms and viruses may cause damage to human tissues, creating signs and symptoms of disease. Disease may also begin when the immune system detects a microbial cell or virus. The body's immune system responds with an attack on the foreign organism that may cause harm to the body itself. In some cases, the damage caused by pathogens in human tissues or the immune response to them can promote the transmission of the pathogen to a new host. Hence, causing disease is just another ecological strategy for certain microorganisms—one in which the human body is used as a habitat for multiplication, persistence, and transmission.

Disease emergence—the situation where a new disease-causing microbe or virus is identified or an old one causes a new disease—is a hot-button topic today. From the E. coli strain O157 to SARS, new diseases and new pathogens are identified every year, frightening the public and confounding public health officials responsible for stemming the tide of outbreaks. Many circumstances likely play a role in the increased rate of disease emergence, including a variety of host, environmental, and social factors.


Industry and medicine are increasingly reliant on microorganisms to generate chemicals, antibiotics, and enzymes that improve our world and save lives. Microbes are being domesticated with the tools of molecular biology for production of biodegradable plastics and all types of new materials. Biotechnology, which will soon be a pillar of the industrial base in the U.S., employs microorganisms and viruses in a number of ways, including such divergent applications as the genetic engineering of crops and gene therapy. Microbiology research has enabled these successful technologies, and future advancements in using microbes in industry and medicine rely on conducting effective research today.

  • Microbiology as the Foundation of Biology

In light of the critical functions microbes carry out to the benefit and detriment of life on earth, the study of microbiology must be treated as a core subject. Moreover, microbes are ideal experimental systems for investigating many of the otherwise confounding key questions in biology.

Microbiology directly provides important tools for experimental science. Because of their relative simplicity, microbes are ideal systems for sorting out basic questions about the origin of sex, speciation, adaptation, cellular function, genetics, biochemistry, and physical properties of all other living organisms. Of particular significance is the ability, using single-celled microorganisms, to match a gene with a characteristic of the organism, otherwise known as linking genotype with phenotype. Microbial cells in culture are not the only available microbial tools. Microbial communities can be put to good use in exploring ecological principles and identifying the metabolic properties, interactions, and communications at work in a relatively simple ecosystem.

The “virtual microbial cell” (a complete computer simulation of the minimal set of genes and functions at work in one live bacterium or yeast) also may be highly instructive, allowing researchers to build models of complete metabolic pathways, cell circuits, and other phenomena to create a virtual network that describes a cell. Such a virtual status may, in fact, soon turn into a physical reality, as the emerging field of Synthetic Biology (building up bacteria from scratch endowed with desired properties) develops and comes to fruition.

Current Issues and Research Challenges

  • “Calm urged over mystery virus; a flu-like illness has downed at least 50 staff in two days at the Prince of Wales Hospital,” South China Morning Post (Hong Kong), March 13, 2003.
  • “Probe Begins Trip to Mars In Quest for Water, and Life,” The New York Times, June 11, 2003.
  • “3rd Death in Hepatitis Outbreak; Pa. probe focuses on handling of produce,” Newsday, November 15, 2003.
  • “Engineered corn found to kill butterflies,” Milwaukee Journal Sentinel, August 22, 2000.
  • “Infections eyed as cause of cancer, heart disease,” The Boston Herald, April 18, 1999.

Today, microbiology is in the headlines more than ever before, and research behind the headlines, and behind other critical issues of which the public is largely unaware, is changing rapidly.


The public is now more aware of microorganisms and viruses than at any other time in history. Unfortunately, that public awareness is usually laced with anxiety and dread. Events of the last ten years and the tone of the media coverage of those events have served to feed the public's fear and create the perception of an increased risk from the microbial world. Such “microbiophobia” has resulted in surges in the popularity of disinfectants, antimicrobial soaps, and other products that purport to keep disease at bay. Bioterrorism and the distinct possibility that anthrax or another infectious microbe could be used as a weapon against innocent civilians, crops, or livestock have frightened people across the globe. An apparent increase in the emergence of novel infectious diseases, including SARS, West Nile disease, and others, has also brought microbes into the public eye. Recently, conventional health therapies to combat certain infectious diseases, including AIDS and tuberculosis, have failed due to the ongoing evolution of these pathogens, heightening public doubts about the ability of scientists and physicians to protect the public even from familiar diseases. A few chronic diseases that were once thought to be due to factors like genetic susceptibility or chance have instead been shown to be the work of bacteria or viruses. And in the U.S. and other developed nations, large-scale food contamination events are on the rise, often sickening tens or hundreds of people before public health officials can identify the sources of infection and restrict the public's exposure.

Advancements in microbiology over the last ten years are frequently overlooked in the wake of public concerns about biowarfare, infectious disease, and foodborne illness. Yet, the progress of the last decade is undeniable. Pharmaceutical research now relies heavily on microbes and microbiology for drug discovery and production. Green chemistry, in which microorganisms are employed to carry out industrial processes, is an increasingly effective strategy for tackling issues of safety and sustainability in chemical-related industries. Biotechnology, too, relies on microbial technologies and microbial genes for carrying out modifications that improve crops, breeds of livestock, and synthetic feed-stocks. In agriculture, microbes and microbial products are now used in probiotic therapies, antibiotics, and pest control measures. Advancements in food microbiology have improved the safety of the food we buy in our supermarkets and restaurants, doubtlessly saving lives every single day. At hazardous waste sites, microbes have been put to work digesting noxious chemicals—metabolizing them into harmless materials, thereby preventing further contamination of soil and water. Bioterrorism and disease are frightening, but progress in microbiology and advancements in applying microbes to solve seemingly intractable human problems should be kept in mind.

How Research Is Changing

Not only has the public's perception of microbiology changed in the last decade, the practice of microbiology research has been altered as well. The past ten years of microbiology have been dynamic and exciting, and new discoveries have been built upon the remarkable work of the past.


Microbiology once focused almost solely on individual microorganisms grown in isolation under artificial conditions, attempting to extrapolate an understanding of disease or the environment from minute observations recorded in the laboratory. Today, however, much of the science is moving away from reductionist approaches and into the realm of synthesis—weaving together a fabric of measurements and observations of the microorganism, its environment, and the influence of other organisms at many scales to create an integrative picture of microbial activities. Once unfamiliar, the concept that cells consist of a network of interacting proteins now permeates the science. A greater emphasis is now being placed on systems-level research, in which microbes in their habitats are being treated as a series of interrelated compartments, processes, and feedbacks. Placing a synthetic or systems lens on microbiology can be highly instructive and has several advantages over strict reductionism. It is hoped that in the future, integrative approaches will enable microbiologists to predict microbiological outcomes, allowing them to pinpoint the consequences of a perturbation of human health or of a given ecosystem.


In the past ten years, microbiologists have increasingly recognized the importance of ecology and evolution. Studies in experimental ecology and evolution have provided evidence on the principles that apply not only to microbes, but possibly to larger organisms as well. Ecological thinking has become dominant, and microbiology is no longer the test tube science of the past. An example is the realization that the way microbes cause disease is, in fact, an ecological problem requiring understanding of both the microbe and its environment—the host in the case of disease.

A change has also taken place in the investigative style of research in microbiology. Previously, many lines of inquiry were closed due to technological limitations or a lack of expertise in fields tangential to microbiology, like soil science, geology, or medicine. In these cases, the problem under investigation was often re-defined to suit the techniques at hand and the academic experience of the principal investigator. Today, these lines of inquiry are often explored head-on by applying the technology advancements of the last ten years and, more importantly, recruiting expertise and resources from other disciplines, often through collaborations.


Technological progress has reformed the landscape of microbiology research, making long-standing questions about microbes finally amenable to study. Chief among the significant advancements of the last ten years is the development of technologies that make genomics possible, including increased computational power, more rapid DNA sequencing, and other laboratory techniques. Genomics employs all or part of the genome, the full genetic complement of a cell, to answer questions about an organism. Although genomics has impacted most of the life sciences and enabled new insights into the functions and processes of all life forms, its most significant impact has been on microbiology, a development that has opened new insights into the ecology and evolution of microorganisms. Other large-scale research, such as proteomics or transcriptomics (the pattern of gene expression), has also had a great impact on the practice of microbiology research. Improvements in information technology have increased interactions between researchers of all fields, enabling a continuing dialogue on the commonalties between microbiology and other disciplines. Nanotechnology and related approaches should allow researchers to experiment with single cells, answering long-standing questions about microbial physiology. Finally, high-end imaging techniques such as nuclear magnetic resonance imaging (NMR), ESR, and others have allowed detailed analyses of microbial cell structure and the structure of microbial communities.

With the advent of molecular microbiology, traditional approaches for defining microbial causation of disease, such as Koch's postulates, have been found insufficient, as they oftentimes lead to “false negative” conclusions. Researchers have struggled with creating robust standards for identifying microbial causation that go beyond Koch's postulates and make use of technological advancements to identify causative links even for microbes that cannot be cultivated in the lab.

  • Hot Research Topics

A number of areas of microbiology research are particularly topical in the wake of technological advancements and discoveries that have brought to light previously unexplored aspects of microbial life. Topics including genomics, biocomplexity, infectious disease, the origins of life, and the application of microbes to improve quality of life are at the forefront of the list of previously unattainable research areas that are being actively pursued today.


Bacteria and archaea tend to have smaller genomes than eukarytic cells, which makes them more amenable to sequencing. The study of genomics has had a huge impact on microbiology. Lines of inquiry related to the factors that govern microbial genome organization, dynamics, and stability are highly approachable using these genomic techniques. But, despite the vast tracts of sequence data that are available, more rapid and accurate methods of annotation attributing a function to a gene are sorely needed. Scientists can now explore questions related to the extents of diversity within naturally occurring microbial communities and to the functional significance of that diversity. Metagenomic technologies are being used to examine the DNA of nonculturable bacteria and microbial consortia without any sub-culturing, thereby allowing us to understand the interplay of genes and functions in an ecosystem, regardless of the specific microbial hosts. We can now ask how the genes of all members of a community relate to the functions carried out by that particular community.

Many other critical questions about microbial life may now be addressed using genomics. Interested readers are referred to the American Academy of Microbiology's colloquia reports “The Global Genome Question: Microbes as the Key to Understanding Evolution and Ecology” and “Microbial Ecology and Genomics: A Crossroads of Opportunity” (see ).


In addition to genomics-related topics, questions related to biocomplexity are at the forefront of microbiology research. Biocomplexity in microbiology encompasses the interactions among microbes and between microbes and their environment. The emphasis in biocomplexity research is on the whole ecosystem, rather than its parts, seeking to identify the emergent properties that cannot be found in studies of individual components. Interdisciplinary collaboration is inherent in this kind of research since it often calls for the expertise of environmental engineers, biologists who study larger organisms, soil scientists, hydrologists, marine biologists, and other related professionals. Research in biocomplexity should progress rapidly in the coming years. Questions on the shape of microbial biocomplexity, its temporal and spatial variability, will doubtless be investigated. Other questions related to microbial biocomplexity are the definition of a microbial “species,” how species are created, and at what rate.


Grappling with topics related to infectious disease is certainly not new for microbiologists, but the discoveries and advancements of the past ten years have revealed new horizons in the field, presenting exciting opportunities to improve the quality of human life. The ability to predict the emergence of disease is a particularly critical topic. Research into the environmental factors that trigger the emergence of pathogens, the factors that drive disease migration, and seasonal patterns in disease frequency may shed light on the factors that affect how new and old diseases emerge and persist in populations. These observations will enable us to design better therapeutic strategies for new and existing pathogens.

Recent discoveries that have linked human diseases (e.g., stomach ulcers and cervical cancer) to bacterial or viral causes highlight the possibility that other chronic illnesses with mysterious etiologies may also be microbially mediated. Candidates include inflammatory bowel disease, diabetes, rheumatoid arthritis, sarcoidosis, systemic lupus erythematosus, and coronary artery disease. Research into the causes of these diseases and others will shed more light on these diseases and their diagnosis, prevention, and treatment.


Science now has better tools at its disposal to explore the origins of life, and microbes are well suited to experimental approaches for understanding these first organisms. The evolutionary origins of sex may also be explored using microbial systems. Analysis of the distribution of sex (here referring to the fusion of gametes) on the emerging tree of life indicates that this process arose very early in the evolution of eukaryotic cells. Research will also focus on assembling the complete tree of life, a comprehensive phylogenetic framework that includes all life forms on earth.


To an ever-greater extent, microbes can be put to use to improve the human condition. Methods of detecting and identifying novel microbial products are likely to be scrutinized and improved upon, expanding the ability to exploit the metabolic versatility of microbes in providing powerful antibiotics, therapeutics, and other materials. It is also likely that microbes can be put to work in energy recovery and utilization. In this respect, microbial production of H 2 is bound to be one of the keys for addressing the unavoidable shortage of energy in the future and for mitigating the greenhouse effect of fuel combustion.

Other Hot Topics in Microbiology.

  • Meeting Future Research Challenges

The future is bright for microbiology. Advancements in the study of infectious disease, microbial ecology, plant and animal pathology, and biotechnology promise to improve human life and the well being of the environment, and new opportunities have come about through social and scientific changes. Progress on these synthetic activities will be hastened through improvements in technology and through changes in education and training.

Technological Hurdles

Several technological hurdles stand before today's microbiology researchers. To make progress, science should not accept the limitations placed on discovery by traditional methods, conventional approaches, or existing infrastructure. Particular attention should be focused on the technologies that enable genomics, single-cell analyses, microbial cultivation, and establishment and maintenance of microbiological databases.

Although progress in microbial genomics is being made at a fantastic rate, availability of appropriate tools still places limits on research. It would be ideal to have the complete genomes of many thousands of species and strains of microbes, but this is currently not possible, given the limits on the speed of sequencing and computational capacity for data manipulation, which both translate into limitations in funds available for such an endeavor. Accelerated and inexpensive sequencing capabilities are needed to conduct sequencing on this scale. In order to interpret microbial genome sequence data in a meaningful way, more tools and approaches beyond those that solely rely on gene homology for inferring gene function are sorely needed. Annotation of genomes is currently a major hurdle for the field, and standards and methods are needed that can accelerate the process and provide consistent high quality results.


The ability to analyze single cells has eluded microbiologists in the past. In order to better understand the activities of microbes in their natural settings, technologies and assays that would allow the monitoring of single cells in a variety of conditions, including in situ , are necessary. Specific capabilities should include genome sequencing, gene expression analysis, and the ability to measure intracellular pools of small molecules. Ideally, these analyses should be amenable to high-throughput approaches.


Improved technologies for cultivating diverse microbes are badly needed. It is never far from a microbiologist's mind that more than 99% of microbes have never been cultivated in the laboratory. The fact that the vast majority of microbial life cannot be scrutinized with respect to growth, metabolism, and reproduction comprises a massive gap in our understanding of the microbial world.

Currently, a need exists for quantitative digital formatting of microbiological data in a portable and standardized fashion. To better integrate microbiological data from multiple studies and from multiple laboratories, an effort should be made to standardize data collection and annotation.

Scientific Needs

  • Researchers must integrate their work with that of scientists in related fields.
  • Computational scientists should become more familiar with and integral to microbiology.
  • Microbiology materials and data must be more carefully curated.
  • Powerful, but expensive, modern equipment should be housed in community facilities, open to researchers who might not otherwise have access to these technologies.


The issues surrounding microbiology touch on so many other disciplines that meeting the grand challenges in microbiology requires integrating the expertise of professionals in many fields. The response to public concerns about bioterrorism, for example, presents a formidable task that requires the contributions of micro-biologists, physicians, pathologists, forensic scientists, and others.

In light of the opportunities and challenges in microbiology today, a number of fields of expertise are especially ripe for integration. Pathogenic microbiologists should see themselves as microbial ecologists who should study both the microbe and the host with analogous intensity. Enhancing the linkages between organic chemistry and microbiology would prove helpful to a number of areas of inquiry, including bioremediation and green chemistry. Microbiology should borrow expertise from systems engineering in efforts to create networks of metabolic pathways. Other interdisciplinary opportunities include collaborations with professionals in imaging sciences, statistics, nanotechnology, biosystematics, mathematics, biochemistry, ecology, and structural chemistry. Moreover, some relatively neglected fields within microbiology should be revived and facilitated by integrating with these related disciplines, including microbial physiology and the biology of eukaryotic microbes (fungi, protists). Collaborations between micro-biologists who work with prokaryotic or eukaryotic microbes and virologists should also be encouraged.

Some successful integrations have already taken place. The fields of geology and microbiology have already been joined on a number of levels to cope with questions surrounding the significance of microorganisms in global geological processes, and molecular biology has met up with information science to provide bioinformatics, which is used to manage genetic and protein sequence data.

A number of routes could be developed to foster these integrations. Visiting fellowships could be established to bring professionals with expertise in statistics, biochemistry, or ecology, for example, into microbiology labs and vice versa, placing microbiologists into statistics, biochemistry, or ecology labs. Microbiologists and professionals in related disciplines could also assemble into working communities across departmental boundaries to cooperate on subjects best addressed through multidisciplinary collaborations. Other integrations could be encouraged by funding agencies.


There is a need to bring computational science into closer contact with the daily work of microbiology. The basic skills involved in computer science, including programming, for instance, should be acquired, or at least be highly familiar, to the average microbiologist.


A great need exists to improve the current modes of curation, entry, storage, and distribution of materials and data related to microbiology. The procedures surrounding culture collections, in particular, need to be revamped. Distribution of cultures has to be conducted in a way that both respects the need for national security and recognizes the ability of these materials, in the hands of researchers, to further the science that directly benefits society. If the international microbiological community does not confront the need for thoughtful review of potentially problematic materials and data, then mechanisms governing release and distribution of data will be imposed by others.

Progress in microbiology has always been enabled by the technology available, a fact that is still true today. However, many researchers are stymied by a lack of access to the expensive instruments that would enable them to make the greatest strides. Facilities for housing and making these technologies available to microbiology researchers would allow investigators in moderately funded and underfunded labs to achieve their full potential. In these technology centers, investigators could come to conduct work, using techniques like NMR, spectroscopy, and other imaging methods, under the guidance of trained staff. Regional centers could even promote technology development and could play a part in advancing training, education, and out-reach among participating educational institutions.

  • Key Opportunities for Microbial Biologists

There are more opportunities available for microbiologists today than at any time in the history of the field. Although the microbiological advancements of the last two centuries have been profound, a great deal of biology remains to be discovered and described through study of the microbial world. Microbiology can be used to push back the frontiers of biology, opening up new ways to harness the power of biology to improve human health and the environment. Microbiologists must participate in this effort.


Career opportunities for microbiologists abound in the wake of new technologies that have changed the face of biology. Biotechnology, in particular, is intimately connected with microbiology and calls for the skills of microbiologists to execute the work that holds the potential to improve the quality of human life. Without a profound grasp of microbiology, much of biotechnology is not possible. As a future pillar of the industrial base in the United States, biotechnology offers many chances for microbiologists to contribute in substantive ways to the future of the world.

Antibiotic discovery is also closely tied to the skills of microbiologists. The importance of this field cannot be overstated, since most individuals in developed countries have experienced first-hand the life-saving power of antibiotic therapies. However, the threat of microbial resistance to antibiotics looms large.

Scientific discoveries can be put into action more rapidly through greater collaborations between academia and industry. By cooperating to develop concepts and inquiries, microbiologists and industrial decision-makers can bring technologies to market or apply microbial solutions to persistent manufacturing problems. Efforts should be made to overcome regulatory and cultural obstacles that stand in the way of such collaborations.

Finally, increased emphasis on systems-level and quantitative research in microbiology has opened new doors for microbiologists working in interdisciplinary research teams or who have backgrounds in other disciplines. Individuals with experience in physics, mathematics, engineering, or computer sciences are in high demand in microbiology today, and this will likely continue for the foreseeable future.


As planet resources become more scarce, and environmental awareness is translated into a widespread social demand, industry is bound to reformulate many of its traditional chemically-catalyzed processes into more environmentally-friendly alternatives and products. Every prospective study (for instance the OECD reports “Biotechnology for a Clean Environment” and “The Application of Biotechnology to Industrial Sustainability”) predicts the booming of a new multi-billion dollar market around processes and goods originating in biocatalysis, both for biosynthesis of added-value molecules or for biodegradation and pollutant removal.

The emerging interfaces between chemical engineering and microbial genetics/metabolism will create countless job opportunities for those who seize the right training early enough in the process. The fields of large-scale mining and metallurgy, so far limited to hard-core engineering, will soon benefit from ongoing advances in geomicrobiology, and experts in this field soon will be in great demand. The relatively new field of green chemistry will, thus, offer employment perspectives for microbiologists and present a chance for scientists to work at the forefront of developing sustainable technologies.


Growing concern about biological security promises to create a number of employment and research opportunities for microbiologists. Bioterrorism has defined a need, in this country and elsewhere, for new and improved infrastructures to address issues related to national security. Microbial science is key to proper execution of these new security measures. The opportunities are diverse; establishment of research centers related to bioterrorism, development of secure culture collections, vaccine development, database development, and other activities will all require the contributions of microbiologists. It is important to note that, with respect to biological security, global preparation requires global knowledge. It is critical for science to protect the freedom to exchange information on the biological agents of disease.

  • Training to Meet the Needs and Challenges of the Future

The training of tomorrow's microbiologists is taking place in fourth grade classrooms, in high school biology labs, and in the lecture halls of universities all over the world. Although the educational systems of past and present have produced the great minds of microbiology, improvements need to be made if microbiology is to fulfill its potential in the new century.

Given the central importance of microbial science to biology in general, teaching of microbiology should be thoroughly integrated into school curricula. At the undergraduate level, emphasis needs to be placed on textbook revision and on integrating microbial sciences into the basic coursework for biology.

Microbiology Education in Schools

As both the root of the tree of life and the matrix that supports the biosphere, microbes should take center stage in science curricula at the elementary, middle, and high school levels. If we are to achieve a well-educated public, versed in the fundamentals of biology and capable of tackling the demands of the new century, the importance of microbiology must be acknowledged by teachers and policy-makers and translated into meaningful school lessons. In practice, this means that microbiology should be integrated into all phases of biology education, not segregated as separate coursework or, as is often the case, as a few sessions at the beginning of a biology course. Achieving integration of microbiology in school curricula will require that educational decision-makers understand and acknowledge the magnitude of microbial contributions to life on earth.

Reorienting school curricula begins with changes in biology textbooks. General biology texts should be organized around a microbiology core. In this way, studying micro-biology can enrich the study of plants, insects, and animals. For example, explaining the importance of microbial gut flora to termites would lend depth and greater applicability to the simple lesson that “termites eat wood.” The food chain in the ocean does not start out by small fish being eaten by big fish, but by microbial populations providing the bulk of the organic material required to set the chain in motion. The oxygen we breathe is not made just by plant photosynthesis, but, to an even greater extent, by the activities of microbes.

More specialized books can also be developed to address the “Grand Challenge” questions, those issues that continue to inspire and confound biologists. Such texts can serve to illustrate the latest discoveries, technologies, and the future of inquiry in microbiology.

Changing the textbooks that schools use has, in the past, proven to be an arduous, protracted process. But, educating the public, beginning with young people, about the importance of microbiology in day-to-day life and in the future of industry is more than a worthy goal—it is an imperative.

Games could also be used for injecting microbiology into curricula. Through creative games or video games based on microbial themes like natural selection, teachers can bring the lessons and fascination of microbiology to students in a friendly, hands-on way. Biology education can be made more engaging with microbial demonstrations and hands-on microbiology lab exercises, which are inexpensive and accessible to a wide range of classroom budgets. Centering lab experiments around simple illustrations of microbial phenomena like decomposition or growth would circumvent both the tedium associated with rote memorization of science lessons and the “gross-out factor” involved, e.g., with frog dissection. Placing a microscope and a sleeve of Petri dishes in every classroom would go a long way toward engaging students in microbiology and in the scientific exploration of the world around them. Some of these activities have already been developed, and more should be created.

Better visual aids are also needed in science classrooms; children would find micrographs of elegant and grotesque microbes appealing, for example. One successful demonstration of the power of microbial illustrations in education can be found on the website for the Marine Biological Laboratory at . A powerful resource for teachers is , sponsored, in part, by the American Society for Microbiology.

In high school biology, in particular, microbiology needs to be taught in an appealing, captivating manner. Many current teachers need to be retrained in the technology and theory associated with the modern microbial science.

Training at the Undergraduate Level

At the undergraduate level, microbiology education takes on two different aspects: training future microbiologists and training biologists in other fields. With respect to training the microbiologists of tomorrow, efforts need to be directed toward revising textbooks to reflect new knowledge on the global importance of microbes and toward overcoming the emphasis on memorization that may still plague some microbiology coursework.

It is clear that all life scientists should receive microbiology training as part of their core curriculum. The topics of microbial physiology, evolution, biochemistry, and genetics should all be worked into the curriculum of undergraduate life sciences students. Luckily, there are many opportunities to introduce appropriate microbiology coursework into the curricula of other disciplines. Organic chemistry courses, for example, which are required for almost all biology students, would benefit from examples taken from microbiology and green chemistry to demonstrate the synthesis of complex compounds from simple precursors. Even students in fields outside of the life sciences would benefit from lessons in microbiology, perhaps presented in biology exploration courses for non-majors as a “microbes and you” segment.

In addition to changes in curricula, improvements are needed at the departmental and college levels as well. In many universities, microbiology is treated strictly as a field of specialization, not as a core subject. Given the fundamental significance of microbial sciences, there should be recognition of the importance of a having a critical mass of microbial sciences faculty. Such faculty need not necessarily be housed in microbiology departments. Appointments of microbiologists are highly desirable in departments of geology, chemistry, clinical medicine, engineering, and even history. These faculty can cross traditional departmental barriers to interact across many fields, effectively educating and training the next generation of scientists.

Promoting Microbial Literacy

Review the facts: microbes were the first life forms, they are important determinants of human health, and they carry out the processes that ensure clean drinking water and fertile soil. They are the most genetically and biochemically diverse forms of life and are the most rapidly evolving organisms on the planet. Microbes govern environmental cycling of the world's nutrients and the substances necessary for life. In every crevice and on every surface, from the deep earth's crust to steaming sulfurous plumes, to the gut of every insect on the planet, microbes are there. They are a key component of all biological systems. In light of these truths, it is readily apparent that microbiologists must make an effort to educate both the public and policy-makers. However, it is less obvious which messages should be conveyed and how best to communicate these facts.

Public Literacy

There is a serious gulf between the excitement experienced by those working in microbiology and the level of awareness in the general public. However, there is evidence to indicate that increased levels of support for public literacy on major public health issues like HIV-AIDS, West Nile disease, and SARS, influences college student choices of majors and research projects. In other words, increased public literacy may help guide students into fields where their energies are most needed. Moreover, public opinion can be guided by an increased awareness of the unsolved problems in microbiology and thus influence leaders to dedicate resources to areas of need. Hence, training programs that are designed to address the grand problems of microbiology should include outreach programs that foster public and governmental awareness.

What is the best way to educate the public about micro-biology? Mechanisms for informing the public about successes in microbiology and about pressing public health issues are sorely needed.


In conveying information about microbiology to the public, it is critical first to define the target audiences and the type of information that is appropriate to convey to each audience. Potential target audiences for microbio-logical outreach comprise a long list, including business leaders, students and teachers at all levels, public officials, health professionals (who may not be sufficiently familiar with microbiology), farmers, restaurant personnel, decision-makers at federal agencies, and others.

In order to achieve the most effective outreach programs, the process of educating the public should have well-defined goals. Specific outreach programs should be conceived with specific educational goals in mind that can be implemented over a designated time period. This approach would allow targeted assessments to determine whether outreach programs were effective in communicating microbiology to the public. For example, it could be the goal of one program to educate the public on a particular microbiology topic within five to ten years, and surveys or other metrics could be used to measure the level of knowledge of the target audience.

  • The intimate connections between microbial ecology and evolution, infectious disease, and the failure of standard antimicrobial therapies.
  • Microbial diversity as one of the last uncharted frontiers with tremendous potential for fundamental new discoveries.
  • Microbes as the foundation of the biosphere.
  • The concept that the human body is nine parts microbe and one part human—for every nine microbial cells there is just one human cell.
  • The tree of life and the relative placements of plants, animals, and microbes.
  • The development and use of microbes as factories.


What are the best ways to convey science information to non-scientists? A number of avenues are open for outreach. For example, it may be possible to launch a campaign to present science information to the people who use public transportation: buses, trains, taxis, or in airports. The publication of popular books based on microbiological themes would also reach a significance audience. Science museums are a powerful outlet for educating young people, and interactive microbial exhibits could stimulate the minds of many future scientists in an engaging way. The mass media may also be employed. Some of these programs are already in place. For example, radio programs, like the American Society for Microbiology's “Microbe World” are well received and are proving to be highly effective.

It may be instructive to study in a systematic manner the quality of material related to microbiology that is currently being used for communication to the public. It is possible that the current lack of public savvy is due to the poor quality of information available, rather than to low availability.

Improving delivery of knowledge to the public requires engaging and informing communication professionals. Microbiological organizations should place a priority on reaching out to communication professionals and should aid in training of science writers.

Communicating with Decision-Makers

With respect to advancing the goals outlined in this report, the term “decision-makers” includes federal agencies, such as the National Science Foundation, National Institutes of Health, Environmental Protection Agency, Department of Energy, the Centers for Disease Control and Prevention, and the Department of Agriculture. Others include local and state boards of education, the Department of Homeland Security, the Food and Drug Administration, private foundations, and others.

Informed individuals who are affected by advancements in microbial science, but are not microbiologists themselves, may be among the best advocates for microbiology. Examples include representatives of biotechnology companies and their clients, business leaders who rely on the skills of highly-trained microbiologists, members of communities where property was remediated using microbes, and the beneficiaries of microbially-based therapies, including bacterially-derived antibiotics and other drugs.

The communications goals outlined in this report would be pursued most effectively by a consortium of professional societies, possibly including the American Society for Microbiology, the Society for Industrial Microbiology, the Infectious Diseases Society of America, and others.


Failure to acknowledge and weigh the pervasive effects of the microbial world deprives us of a powerful tool to assess the functioning of our planet and make decisions on its future as a live whole. In light of what is now known about the contributions of microorganisms to sustaining life and creating the physical and chemical properties of this planet, detailed studies in any branch of biology or geology must fully recognize the activities of microbes.

Since microbes are of fundamental importance to life and their activities must be taken into account in biology research, all biologists must have a firm background in microbial science. Coursework in micro-biology should be integrated into the core curriculum for all students in the life and earth sciences.

Building an understanding of microbes in young students will ultimately improve public awareness of the importance of microbes to the everyday health of the individual and of the planet. School science curricula in the elementary, middle, and high school levels must be amended to include lessons and lab exercises in microbiology.

The public is profoundly impacted by microbes and microbiology through disease-related matters, biotechnology, bioterrorism, and food safety. In order to improve the ability of individuals to manage their health and make informed judgments with respect to microbial science, microbiology-related professional societies should support programs that foster public microbial literacy.

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  • Cite this Page Microbiology in the 21st Century: Where Are We and Where Are We Going? This report is based on a colloquium sponsored by the American Academy of Microbiology held September 5–7, 2003, in Charleston, South Carolina. Washington (DC): American Society for Microbiology; 2004. doi: 10.1128/AAMCol.5Sept.2003
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Current Research in Microbiology

Aims and scope.

Current Research in Microbiology is a peer reviewed international journal aimed to publish current research and review articles on microorganisms, which are unicellular or cell-cluster microscopic organisms, includes eukaryotes such as fungi and protists, and prokaryotes, which are bacteria and archaea. CRM is a broad based journal which also includes articles on virology, mycology, parasitology, bacteriology and other branches. Current Research in Microbiology is a specialist journal in microbiology.

Science Publications is pleased to announce the launch of a new open access journal, Journal of Adaptive Structures. JAS brings together emerging technologies for adaptive smart structures, including advanced materials, smart actuation, sensing and control, to pursue the progressive adoption of the major scientific achievements in this multidisciplinary field on-board of commercial aircraft. 

It is with great pleasure that we announce the SGAMR Annual Awards 2020. This award is given annually to Researchers and Reviewers of International Journal of Structural Glass and Advanced Materials Research (SGAMR) who have shown innovative contributions and promising research as well as others who have excelled in their Editorial duties.

This special issue "Neuroinflammation and COVID-19" aims to provide a space for debate in the face of the growing evidence on the affectation of the nervous system by COVID-19, supported by original studies and case series.

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Study Provides Clues to Developing Better Treatments for Lung Damage

graphic of lungs in the chest cavity with glowing bronchi and alveoli

Scientists and clinicians at the Duke University School of Medicine have discovered new details about how lung tissue heals after injury caused by toxins such as air pollution or cigarette smoke.  

The researchers found that a cascade of interacting steps involving two different cell types is crucial for healing. An imbalance in these steps can lead to damage that resembles emphysema or lung fibrosis, the study found.  

The study , published November 2, 2023, in the journal Cell Stem Cell, paves the way for future investigations to identify possible new treatments to prevent or reverse these diseases.  

Purushothama Rao Tata, PhD

"A long-standing question in the field of wound healing is how our body organs know to regrow and build the same structure after a wound," said co-senior author Purushothama Rao Tata, PhD, assistant professor of cell biology and medicine , and co-director of the Duke Regeneration Center . The study's other senior author was Aleksandra Tata, PhD, assistant research professor of cell biology. 

Tata explained that lung tissue is like a big balloon draped by a structure akin to a fishnet:  the extracellular matrix scaffold, which creates multiple compartments with strong, flexible walls that expand and contract as we breathe. This study focused on how the lungs rebuild this scaffold after injury. 

To study this question, the scientists used a variety of methods, including single cell transcriptome analysis and other computational tools, to build "time-lapse molecular circuits" to reconstruct wound repair in mouse lungs. 

"We refer to it as molecular circuits because we are not looking at one or two genes, but a collection of genes associated with a particular cell state or phenotype," Tata said. "These are like electrical circuits that all come together to switch on a light, for example. All of these genes together exert a collective function." 

Aleksandra Tata, PhD

"Disruption of these circuits revealed key druggable molecules to target two currently incurable lung diseases — emphysema and fibrosis," he said. "These diseases are like two sides of the same coin. In a lung with emphysema, we lose the walls of the scaffold. In the case of fibrosis, the wall thickness increases so they are no longer flexible." 

The study revealed that after a healing "program" is activated, a cascade of events ensues, involving both epithelial cells (cells that line the lungs) and mesenchymal cells (support cells). 

The researchers outlined three crucial steps or "transitional states" that happen during this process. If certain transitional states involving epithelial cells persist too long, the result is fibrosis (buildup of scar tissue). "If there is a blockade in the transition of these cell states, the result is loss of tissue that resembles emphysema," Tata said. 

In a preview article highlighting the work, scientists not affiliated with the Duke study pointed out that one of the intermediate cell states identified as crucial in the healing process has previously been termed a "bad actor" in lung fibrosis research. Two drugs currently approved for fibrosis (nintedanib and pirfenodone) actually kill this cell state, Tata said. "Our study shows that treating with these drugs may actually be a bad thing," he said. 

Other authors of the study are:  Arvind Konkimalla, MD, PhD, currently a resident at Duke University Hospital; postdoctoral associate Satoshi Konishi, MD, PhD; laboratory research analyst Lauren Macadlo; PhD candidates Jeremy Morowitz and Zachary Farino; postdoctoral fellow Naoya Miyashita, PhD; and bioinformatician Pankaj Agarwal, all in the Duke Department of Cell Biology; Department of Pediatrics postdoctoral research associate Lea El Haddad, MD, PhD; Mai K. ElMallah, MD, associate professor of pediatrics; Christina E. Barkauskas, MD, associate professor of medicine ; and Tomokazu Souma, MD, PhD, assistant professor in medicine; and Yoshihiko Kobayashi, PhD, now an assistant professor at Kyoto University in Japan. 

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