Bacterial cells transmit memories to offspring

Bacterial cells can 'remember' brief, temporary changes to their bodies and immediate surroundings, a new study has found. And, although these changes are not encoded in the cell's genetics, the cell still passes memories of them to its offspring -- for multiple generations.

 

Although these changes are not encoded in the cell's genetics, the cell still passes memories of them to its offspring -- for multiple generations.

 

Not only does this discovery challenge long-held assumptions of how the simplest organisms transmit and inherit physical traits, it also could be leveraged for new medical applications.

 

For example, researchers could circumvent antibiotic resistance by subtly tweaking a pathogenic bacterium to render its offspring more sensitive to treatment for generations.

 

A central assumption in bacterial biology is that heritable physical characteristics are determined primarily by DNA. But, from the perspective of complex systems, we know that information also can be stored at the level of the network of regulatory relationships among genes.

 

The researchers wanted to explore whether there are characteristics transmitted from parents to offspring that are not encoded in DNA, but rather in the regulatory network itself.

 

It was found that temporary changes to gene regulation imprint lasting changes within the network that are passed on to the offspring. In other words, the echoes of changes affecting their parents persist in the regulatory network while the DNA remains unchanged.

 

Since researchers first identified the molecular underpinnings of genetic code in the 1950s, they have assumed traits are primarily -- if not exclusively -- transmitted through DNA. However, after the completion of the Human Genome Project in 2001, researchers have revisited this assumption.

 

The objective of the study is to one day see if it is [possible to isolate the causes for the simplest single-cell organisms, since researchers can control their environment and interrogate their genetics. If they canwe observe something in this case, it shouldbe possible to attribute the origin of non-genetic inheritance to a limited number of possibilities -- in particular, changes in gene regulation.

 

The regulatory network is analogous to a communication network that genes use to influence each other. The research team hypothesized that this network alone could hold the key to transmitting traits to offspring.

 

The research team used a mathematical model of the regulatory network to simulate the temporary deactivation (and subsequent reactivation) of individual genes in Escherichia coli.

 

They discovered these transient perturbations can generate lasting changes, which are projected to be inherited for multiple generations. The team currently is working to validate their simulations in laboratory experiments using a variation of CRISPR that deactivates genes temporarily rather than permanently.

 

If the changes are encoded in the regulatory network rather than the DNA, the research team questioned how a cell can transmit them across generations. The researchers propose that the reversible perturbation sparks an irreversible chain reaction within the regulatory network.

 

As one gene deactivates, it affects the gene next to it in the network. By the time the first gene is reactivated, the cascade is already in full swing because the genes can form self-sustaining circuits that become impervious to outside influences once activated.

 

The study also suggests that other organisms have the necessary elements to exhibit non-genetic heritability. "In biology, it's dangerous to assume anything is universal.

 

See: Yi Zhao, Thomas P. Wytock, Kimberly A. Reynolds, Adilson E. Motter. Irreversibility in bacterial regulatory networks. Science Advances, 2024; 10 (35) DOI: 10.1126/sciadv.ado3232

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Safe and effective operation of wastewater plants (article)

Image by Tim Sandle

Key aspects of the wastewater treatment steps, together with some examples of operational problems, are discussed in this paper, together with some examples of what happens when things go wrong.

Read the full article here.

Reference:

Sandle,T. (2024)  Safe and effective operation of wastewater plants, EJPPS, 29 (2) DOI: https://www.ejpps.online/post/safe-and-effective-operation-of-wastewater-plants 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Ramble with Sandle: Fungi and cleanrooms

 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Industrial Pharmaceutical Microbiology: Standards and Controls

Reviewed by Melissa Patel, QA Compliance, Bio Products Laboratory

The modern microbiologist, be they based in healthcare, pharmaceuticals, or industry, should only spend part of their time at the laboratory bench. Modern industrial and pharmaceutical microbiology has moved beyond the quality control paradigm and requires the microbiologist to spend considerable time in the manufacturing environment.

This repositioning also requires the microbiologist to broaden their skill set and taken on aspects of validation, engineering, chemistry, experimental design, technology transfer and quality assurance.

Finding sources of advice to develop this skill set can be just as challenging as developing the skills. Fortunately, the latest edition of Industrial Pharmaceutical Microbiology: Standards and Controls (the 6th edition, published by Euromed and the PDA) offers an insight into the latest thinking.

Edited by the internationally famous microbiologist Tim Sandle, this book offers cutting edge insights beyond the QC microbiology space.

The book assembles a group of globally recognised experts and covers a range of essential topics.

These topics are presented as groups in a logical order. The book opens with areas around qualification and validation. This includes two cutting edge chapters relating to validation and the application of rapid microbiological methods. As Jeanne Moldenhauer expertly explains, alternative methods in particular are useful for taking into the industrial environment, enabling real-time assessments to be made. Such assessments are in tune with the notion of the contamination control strategy.

The contamination control strategy requires an appreciation and understanding of risk management and risk assessment processes. The next area of the book includes practical chapters by two leading industry gurus –Tim Eaton –and Tim Sandle both of which expertly apply risk based methodologies.

Risk assessment also requires control and detection. The book moves on to look at environmental monitoring strategies (by academic Rosalind Bird) and disinfection best practices (from Sandle, who is a specialist in this field). The text moves on to consider pharmaceutical water systems and takes a deep dive into biofilm control.

After Sandle’s review of microbial identification approaches, a review of cleanrooms and barrier technology is presented by John Neiger, the editor of Clea Air and Containment Review. There are few, if any, people who know more about airflow protection than Neiger.

Important industrial applications follow: media fills, sterile filtration, biological indicators and endotoxin. The latter is particularly detailed, in a chapter full of rich detail from Karen Zink McCullough. Again, Sandle has assembled a leading global subject matter expert.

The section ends with an overview of container-closure integrity technologies and cutting-edge pharmaceutical development in the form of advanced therapy medicinal products (ATMPs). Both of these chapters come from Sandle.

The next section assesses the regulatory space, considering biotherapeutics, non-sterile pharmaceuticals, pharmacopeial requirements and another cutting edge application in the form of bacteriophages. The non-sterile chapter is crafted by Edel Fitzmaurice, who is Ireland’s most in-demand microbiology consultant.

In all, the book is comprised of 25 chapters. The fact that it has reached a sixth edition and that the content is regularly reviewed and updated, with redundant chapters removed and new ones added, is testament to Sandle’s and the publisher’s commitment to being non-topic and current.

To be an advanced microbiologist in the modern age requires you to have this text on your bookshelf.

To order a copy, see PDA Bookstore 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

New dual therapeutic strategy shows promise against multidrug-resistant Salmonella

Antibiotic-resistant bacterial infections stand as one of the critical biological threats to human health on a global scale. One example is with multidrug-resistant (MDR) Salmonella enterica. The rise of MDR strains, coupled with the constrained array of treatment options, requires continuous innovation of therapeutic approaches.

 

According to Pharmaceutical Microbiology Resources: “Salmonella enterica serovar Typhimurium bacteria (S. Typhimurium) commonly cause human gastroenteritis, inflammation of the lining of the intestines. The bacteria live inside the gut and can infect the epithelial cells that line its surface.”

 

Image: NIAID, Public Domain, https://commons.wikimedia.org/w/index.php?curid=450281
 

A new study charts the discovery and application of a new therapeutic strategy to target the multidrug-resistant bacterium Salmonella enterica, with promising results.

 

The research was carried out at the University of Eastern Finland, as well as from the Rosario National University, Argentina, and the University of the Republic, Uruguay. The research introduces a strategy to enhance the efficacy of colistin, a last-resort antibiotic.

 

Commenting on this, Senior Researcher Christopher Asquith states: “Through the utilisation of a non-antibiotic anti-virulence quinazoline compound, we investigated a dual-pronged therapeutic methodology.”

 

The combined treatment with the quinazoline and colistin targets Salmonella by simultaneously inhibiting its resistance mechanisms against colistin and disrupting the bacterium’s envelope electrochemical equilibrium.

 

This synergistic interplay not only introduces a new route to counter MDR bacteria but also lays the groundwork for potentially addressing resistance challenges associated with other antibiotics.

 

The quinazoline compound specifically affects the key regulatory pathway used by the bacterium for both the advancement of infection and the development of resistance. The outcomes presented within this study underscore the potential of leveraging this pathway to target bacterial disease.

 

This should also provide a blueprint for tailored interventions beyond Salmonella to a spectrum of bacterial infections.

 

The efficacy of the dual treatment in mitigating mortality was demonstrated using an in vivo insect infection model, presenting promise in terms of future therapeutic applications.

 

The research has been published in the journal Scientific Reports, titled “Enhancing colistin efficacy against Salmonella infections with a quinazoline-based dual therapeutic strategy”.

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Revealing the mysteries within microbial genomes

 

Image designed by Tim Sandle

A new technique developed at Lawrence Berkeley National Laboratory (Berkeley Lab) will make it much easier for researchers to discover the traits or activities encoded by genes of unknown function in microbes, a key step toward understanding the roles and impact of individual species.

 

The approach is called barcoded overexpression bacterial shotgun library sequencing, or Boba-seq. This involves taking random fragments of DNA from bacteria of interest and expressing them in host bacterial cells.

 

The term "barcode" in the name refers to a small sequence of DNA that the scientists use as an identifying tag for a much larger fragment of DNA, much like how a barcode at a grocery store identifies a specific item with a small code. The entire genome of the organism being studied is randomly separated into fragments containing single genes or clusters of several genes, then inserted into plasmids -- circular packages of DNA -- that have been tagged with unique barcodes.

 

The Boba-seq "library" refers to all the barcoded plasmids containing fragments from an organism. This library can be introduced into different bacterial hosts to generate a huge number of genetic variants, which are then screened for new behaviors or properties.

 

With Boba-seq, hundreds of thousands of barcoded fragments can be put into host cells and cultured under varying conditions to determine function in a single experiment. For example, if cells with a certain barcode grow happily when the whole culture is exposed to an antibiotic, but the others perish, you know that the gene or genes in that fragment encoded antibiotic resistance traits. And identifying the fragment responsible for this new ability is cheap and fast, thanks to the barcode.

 

The other significant breakthrough is that Boba-seq fragments can be tested in the same organism that they were pulled from (or a close relative), which is essential for getting an accurate picture of what a gene does. Previous techniques are limited because they only test genes inside model organisms like E. coli and yeast. Genes from organisms very different from E. coli are often not functional in E. coli, making it difficult or impossible to get a clear picture of what the genes do.

 

The computational tool used to process results from the laboratory work involved in Boba-seq is available to other researchers on an open-source platform.

 

The technique connects with the ENIGMA project, short for Ecosystems and Networks Integrated with Genes and Molecular Assemblies. This is a U.S. Department of Energy (DOE) Scientific Focus Area co-led by Arkin that is aimed at understanding how microbial communities cycle nutrients through ecosystems and detoxify toxic heavy metal contaminants.

 

After building and refining Boba-seq, the researchers tested the new technique by studying the genes in Bacteroidales, a taxonomic order of microbes that are abundant in the human gut and known to play many roles in our internal microbiome.

Bacteroidales are also major players in terrestrial soil processes, where they degrade organic matter and return the nutrients to plants. The team generated 305,000 barcoded fragments from libraries of six Bacteroidales species and evaluated more than 21,000 protein-coding genes in parallel.

 

Results from these proof-of-principle experiments revealed that genes encoding enzymes that build certain lipid molecules endow resistance to ceftriaxone, an antibiotic in the cephalosporin class. These genes have not been previously linked to antibiotic resistance, and warrant further investigation.

 

The researchers also discovered several new functions in carbohydrate metabolism, including an enzyme needed to metabolize glucosamine, a modified sugar molecule found in bones, connective tissue, and the exoskeletons of insects and crustaceans. In the gut, microbes use glucosamine as an energy molecule and to construct their cell walls, whereas human cells that form the lining of the intestine use it to produce the mucus membrane that helps maintain healthy nutrient uptake and prevent invasion of pathogens.

 

These insights into Bacteroidales will help health researchers better understand gut function, as this order acts as commensals most of the time and really maintain gut health. But in certain states, the nutrient released by Bacteroidales can be used by pathogens to support their own growth.

 

See:

 

Yolanda Y. Huang, Morgan N. Price, Allison Hung, Omree Gal-Oz, Surya Tripathi, Christopher W. Smith, Davian Ho, Héloïse Carion, Adam M. Deutschbauer, Adam P. Arkin. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nature Communications, 2024; 15 (1) DOI: 10.1038/s41467-024-50124-3 

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)