Posts Tagged ‘microbes’

Reporter and Curator: Dr. Sudipta Saha, Ph.D.


The trillions of microbes in the human gut are known to aid the body in synthesizing key vitamins and other nutrients. But this new study suggests that things can sometimes be more adversarial.


Choline is a key nutrient in a range of metabolic processes, as well as the production of cell membranes. Researchers identified a strain of choline-metabolizing E. coli that, when transplanted into the guts of germ-free mice, consumed enough of the nutrient to create a choline deficiency in them, even when the animals consumed a choline-rich diet.


This new study indicate that choline-utilizing bacteria compete with the host for this nutrient, significantly impacting plasma and hepatic levels of methyl-donor metabolites and recapitulating biochemical signatures of choline deficiency. Mice harboring high levels of choline-consuming bacteria showed increased susceptibility to metabolic disease in the context of a high-fat diet.


DNA methylation is essential for normal development and has been linked to everything from aging to carcinogenesis. This study showed changes in DNA methylation across multiple tissues, not just in adult mice with a choline-consuming gut microbiota, but also in the pups of those animals while they developed in utero.


Bacterially induced reduction of methyl-donor availability influenced global DNA methylation patterns in both adult mice and their offspring and engendered behavioral alterations. This study reveal an underappreciated effect of bacterial choline metabolism on host metabolism, epigenetics, and behavior.


The choline-deficient mice with choline-consuming gut microbes also showed much higher rates of infanticide, and exhibited signs of anxiety, with some mice over-grooming themselves and their cage-mates, sometimes to the point of baldness.


Tests have also shown as many as 65 percent of healthy individuals carry genes that encode for the enzyme that metabolizes choline in their gut microbiomes. This work suggests that interpersonal differences in microbial metabolism should be considered when determining optimal nutrient intake requirements.





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Molecular On/Off Switches in Bacterial Design

Larry H. Bernstein, MD, FCAP, Curator



Controlling Synthetic Bacteria

“Kill switches” ensure that genetically engineered bacteria survive only in certain environmental conditions.

By Kate Yandell | Dec 7, 2015


Two synthetic gene circuits allow researchers to keep genetically engineered (GE) microbes alive only under specific conditions, and to kill them when their services are no longer needed. The circuits, described today (December 7) in Nature Chemical Biology,could help pave the path to safe diagnostics, therapies, or environmental remediation strategies that rely on GE bacteria.

“This is yet another step forward towards better biosafety and biocontainment based on certain aspects of existing technology,” said Guy-Bart Stan, a synthetic biologist at Imperial College London who was not involved in the study.

Study coauthor James Collins, a synthetic biologist at MIT, began to design these gene circuits, or “kill switches,” after becoming interested in using GE microbes for diagnostic and therapeutic purposes. “We were motivated to begin working on the topic as synthetic biology has moved increasingly toward real-world applications,” Collins told The Scientist. Other groups are working to engineer microbes for bioremediation and industrial processes, among other things.

But with genetic modification comes the concern that scientists will create new and uncontrollable species that outcompete or share their genes with wild-type organisms, permanently altering the environment or endangering people’s health.

Earlier this year, two research teams led by Yale bioengineer Farren Isaacs and Harvard geneticist George Church showed that they could genetically modify Escherichia coli to incorporate synthetic amino acids into essential proteins. When the bacteria are not fed the amino acids, they cannot produce these essential proteins, and so they die. This strategy yields bacteria that are very unlikely to survive without support from scientists but requires intensive engineering of the bacterial genome. (See “GMO ‘Kill Switches,’” The Scientist, January 2015.)

In contrast, Collins and his colleagues set out to create kill switches that could work in a more diverse range of microbes. “Our circuit-based safeguards can be conveniently transferred to different bacterial strains without modifying the target cell’s genome,” he wrote in an email.

First, Collins and his colleagues generated a kill switch called “Deadman,” named for a locomotive braking system in which the train will only run if the engineer is affirmatively holding down a pedal. In the microbial version of Deadman, a researcher must feed bacteria a substance called anhydrotetracycline at all times, or else the microbes will express a toxin and self-destruct.

The researchers generated a genetic circuit containing genes for the proteins LacI and TetR, a toxin that is only expressed in the absence of LacI, and a protease that degrades LacI. Under normal circumstances, TetR is preferentially expressed over LacI. TetR expression also triggers expression of the protease, which degrades any LacI that has been expressed. Without LacI, cells express the toxin and die. But when the cells are fed anhydrotetracycline, TetR is inhibited and LacI is expressed. LacI represses the toxin and keeps the cells alive.

Other versions of the Deadman circuit can be designed to degrade essential proteins in the absence of anhydrotetracycline, said Collins.

A second kill switch, “Passcode,” similarly requires that researchers maintain a specific environment for cells lest they express a toxin. Passcode requires a combination of input molecules for cells to survive. The system relies on hybrid transcription factors, each with one component that recognizes a specific DNA sequence, and one component that is sensitive to specific small molecules, such as galactose or cellobiose. One hybrid transcription factor, factor C, turns off expression of a toxin. Two other hybrid transcription factors, factors A and B, suppress expression of factor C. But specific small molecules can keep them from interacting with C. Another small molecule could prevent C from repressing the toxin. Therefore, to keep the cells alive, researchers must provide them with two small molecules that keep factors A and B in check, and make sure not to give them a third small molecule that will interfere with C.

Scientists designing Passcode kill-switches could make hybrid transcription factors respond to whatever combination of small molecules they desired, said Collins. “The strength of our kill switches lies in their flexibility and their ability to detect complex environmental signals for biocontainment.” He noted that companies hoping to keep others from using their cells could keep the recipe for their feed a secret.

“The great advantage is that you can effectively scale this and create different combinations of environments that contain different cocktails of these small molecules, thereby allowing you to effectively create a suite of cells that are going to be viable in different environments,” said Isaacs.

But Church warned that Collins’s circuit-based approach might not as effectively contain bacteria as an amino acid-based method, like one his group developed, since the cells are not fundamentally dependent on foreign biology to survive.

“If you need to have the ability to really scale your containment across a number of different species, then I could see the Passcode kill switches would be incredibly valuable,” said Isaacs. “If you are very concerned about escape frequencies and your degree of biocontainment, maybe you’d opt for something where the organism has been recoded and it relies on a synthetic amino acid.”

Still, Stan said the new paper is a demonstration that creating easy-to-insert kill switches based on genetic circuits is feasible. “I think what they wanted to show in the paper is basically that using some existing genetic circuitry . . .  you can obtain biosafety for the here and now.”


C.T.Y. Chan et al., “‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment,” Nature Chemical Biology, doi:10.1038/nchembio.1979, 2015.  

Tags   synthetic biology, microbes, genetic engineering and biosafety


GMO “Kill Switches”

Scientists design bacteria reliant upon synthetic amino acids to contain genetically modified organisms.

By Kerry Grens | Jan 21, 2015–Kill-Switches-/

One of the biggest concerns about genetically modified organisms (GMOs) is that they can infiltrate wild populations and spread their altered genes among naturally occurring species. In Nature today (January 21), two groups present a new method of containing GMOs: by making some of their essential proteins reliant upon synthetic amino acids not found outside of the laboratory.

“What really makes this a valuable step change is that kill switches beforehand were very susceptible to mutation or other conditions, such as metabolic cross feeding, from basically inactivating them,” said Tom Ellis, a synthetic biologist at Imperial College London who was not involved in the studies. The new approach circumvents some of those problems by making it extremely unlikely for the genetically modified bacteria to be able to survive outside of the conditions dictated by their custom-designed genomes.

Both research teams—one led by George Church at Harvard Medical School and the other by Farren Isaacsat Yale University—based their work on so-called genetically recoded organisms (GROs), bacterial genomes that have had all instances of a particular codon replaced by another. Church and Isaacs, along with their colleagues, had previously developed this concept in collaboration. Since then, their respective groups designed the replacement codons to incorporate a synthetic amino acid, and engineered proteins essential to the organism to rely upon the artificial amino acid for proper function.

“Here, for the first time, we’re showing that we’re able to engineer a dependency on synthetic biochemical building blocks for these proteins,” Isaacs told reporters during a conference call.

Both teams found that the cells perished in environments lacking the synthetic amino acid. Although the technology is not ready for industrial-scale deployment, the scientists suggested that such an approach could be applied as a safeguard against the escape of GMOs.



‘Deadman’ and ‘Passcode’ microbial kill switches for bacterial containment

Clement T Y ChanJeong Wook LeeD Ewen CameronCaleb J Bashor & James J Collins

Nature Chemical Biology(2015)  

Figure 2: The fail-safe mechanism for Deadman circuit activation.

The fail-safe mechanism for Deadman circuit activation.

To demonstrate active control over host cell viability, cells grown under survival conditions (with ATc) were exposed to 1 mM IPTG to directly induce EcoRI and mf-Lon expression. Cell viability was measured by CFU count and is displayed…


Biocontainment systems that couple environmental sensing with circuit-based control of cell viability could be used to prevent escape of genetically modified microbes into the environment. Here we present two engineered safeguard systems known as the ‘Deadman’ and ‘Passcode’ kill switches. The Deadman kill switch uses unbalanced reciprocal transcriptional repression to couple a specific input signal with cell survival. The Passcode kill switch uses a similar two-layered transcription design and incorporates hybrid LacI-GalR family transcription factors to provide diverse and complex environmental inputs to control circuit function. These synthetic gene circuits efficiently killEscherichia coli and can be readily reprogrammed to change their environmental inputs, regulatory architecture and killing mechanism.


Nontoxic antimicrobials that evade drug resistance

Stephen A DavisBenjamin M VincentMatthew M EndoLuke WhitesellKaren MarchilloDavid R AndesSusan Lindquist & Martin D Burke

Nature Chemical Biology 2015;11:481–487

Drugs that act more promiscuously provide fewer routes for the emergence of resistant mutants. This benefit, however, often comes at the cost of serious off-target and dose-limiting toxicities. The classic example is the antifungal amphotericin B (AmB), which has evaded resistance for more than half a century. We report markedly less toxic amphotericins that nevertheless evade resistance. They are scalably accessed in just three steps from the natural product, and they bind their target (the fungal sterol ergosterol) with far greater selectivity than AmB. Hence, they are less toxic and far more effective in a mouse model of systemic candidiasis. To our surprise, exhaustive efforts to select for mutants resistant to these more selective compounds revealed that they are just as impervious to resistance as AmB. Thus, highly selective cytocidal action and the evasion of resistance are not mutually exclusive, suggesting practical routes to the discovery of less toxic, resistance-evasive therapies.



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Gut microbiome and anti-tumor response

Larry H. Bernstein, MD, FCAP, Curator

Pharmaceutical Intelligence


Microbes Play Role in Anti-Tumor Response

Gut microbiome composition can influence the effectiveness of cancer immunotherapy in mice.

By Anna Azvolinsky | November 5, 2015


The presence of certain types of gut microbes in mice can boost the anti-tumor effects of cancer immunotherapy, according to two studies from independent research teams published today (November 5) in Science Express.

Cancer immunotherapies that block immune inhibitory pathways are now available as treatments for several tumor types, yet patients’ responses to these therapies vary. Aside from the presence of T cells within the tumor before the start of treatment, it has not been clear what other factors are linked to a response to these antibodies. The two studies published today, while not the first to suggest thatgut microbes can influence the efficacy of cancer therapy, provide a definitive link between gut microbiome composition and cancer immunotherapy response and implicate the positive role of specific bacterial species.

“These interesting papers combine two of the hottest areas in science—the microbiome and immunology—showing that gut bacteria can activate [host] anti-tumor responses,” said Timothy Hand of the department of immunology at the University of Pittsburgh who was not involved in either study.

“These are beautiful studies that give mechanistic views of how the gut microbiota is critical for regulating the immune system in the context of an immune checkpoint blockade to encourage the immune system in fighting cancer,” agreed Justin Sonnenburg, a microbiome researcher at the Stanford School of Medicine who was also not involved in the research. “The microbiota is connected to our biology in both direct and

indirect ways, and these works are adding to the list of how the microbiota is incredibly important for our health.”

Thomas F. Gajewski, a cancer clinician and researcher at the University of Chicago, and his colleagues were interested to understand what leads some cancer patients to have a strong immune response against a tumor—in the form of T cells that infiltrate the tumor. “Differences in immune responses to cancer may be due to genetic variants, differences in the tumor mutations, environmental differences, or a combination of these factors,” explained Gajewski.

To explore the role of the gut microbiome, the researchers studied two groups of the same strain of laboratory mice that had been bred at two different mouse facilities and were known to harbor different commensal bacteria in their GI tracts. When both sets of mice were implanted with melanoma tumors, tumors grew less aggressively in the mice sourced from the Jackson Laboratory (JAX) and these mice had more robust T-cells responses against the tumors. When both mouse groups were housed together, the differences in tumor responses disappeared, leading the researchers to hypothesize that commensal microbes from the JAX mice had colonized the other mouse population, sourced from Taconic Biosciences. Sure enough, a fecal transplant from the JAX mice to the other group resulted in better anti-tumor T-cell responses and slower tumor growth in the Taconic Biosciences group, even when housed separately.

Next, the researchers decided to test the effects of an anti-PD-L1 immunotherapy antibody. The therapy slowed tumor growth to a greater extent in the JAX compared to the Taconic Biosciences mice. Taconic Biosciences mice treated with the antibody had similar tumor control and immune responses to mice who’d received a fecal transplant from the JAX animals, but combining the immunotherapy and the fecal transplant led to greater tumor control.

Sequencing the gut microbiome of the mice, the researchers found that Bifidobacterium species were linked to the anti-tumor immune response and that adding a cocktail of these microbes to the Taconic Biosciences mice with melanoma resulted in the same benefit as the fecal transplant. The team also found that the dendritic cells isolated from either the JAX mice or Bifidobacterium-treated Taconic Biosciences mice are able to better stimulate tumor-specific T cells in vitro.

“These effects of the gut microbiome on the anti-tumor immune response were stronger than we had anticipated,” said Gajewski.

In the second study, led by immunologist Laurence Zitvogel of INSERM in France, researchers found that the effect of treating mice harboring sarcomas, melanoma, or colorectal tumors with another immunotherapy antibody, against CTLA-4, depended on the presence of Bacteroides species; germ-free or antibiotics-treated mice did not enjoy tumor control as a result of the therapy. Adding Bacteroides species to the germ-free and antibiotics treated mice restored the immunotherapy’s anti-tumor benefit. Interestingly, adding murine memory T cells targeting the gut microbes to the mice had the same effect, suggesting that it is the immune system’s response to commensal microbes that readies it to fight tumors.

Analyzing gut microbiome of 25 metastatic melanoma patients, the INSERM researchers also found that some patients had Bacterioides as part of their gut microbiomes and that a fecal transplant from these patients into germ free mice also restored the anti-CTLA-4 therapy’s anti-tumor effects.

“What was quite exciting for us is that using microbes may be a way to improve the efficacy of immunotherapies without increasing their toxic side effects,” said study author Mathias Chamaillard, an immunologist at the Center of Infection and Immunity at the University of Lille in France. Both groups of researchers are now sorting out the details of how the gut microbes stimulate the immune system to act against tumors.

Of course, whether the gut microbial species identified in these mouse studies will have the same effect in people is not clear. “The impact of the gut microbiota is probably different depending on the context,” said Gajewski. “We’re starting to understand that that one type of bacteria is not going to cure everything.”

M. Vétizou et al., “Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota,” Science Express, doi:10.1126/aad1329, 2015. 

A. Sivan et al., “Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy,” Science Express, doi:0.1126/science.aac4255, 2015.  

Correction (November 6): This story has been updated from its original version to correctly name the origin of some of the study animals as Taconic Biosciences, not Taconic Farms. The Scientist regrets the error.



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