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Researchers Reveal New Ways To Identify Bacteria More Easily

Antibiotics are used far too frequently all over the world. Bacteria are getting resistant as a result. Curing bacterial infections is becoming increasingly challenging because antibiotics are one of our most powerful tools in the fight against them. The good news is that finding better ways for identifying infections is a crucial step towards requiring fewer antibiotics.

"We have developed a simple tool that can identify all of the genetic material in bacteria. This allows us to find out more quickly what kind of bacteria a sick person or animal is affected by, or what kind of bacteria are found in food or the environment. We can then also decide whether it is necessary to use antibiotics against the bacterium, and if so what kind, so we don't have to use as much medication," says Professor Erika Eiser at Norwegian University of Science and Technology's (NTNU)Department of Physics. An international research group is behind the latest findings. The results have been presented in the prestigious Proceedings of the National Academy of Sciences (PNAS) journal. Playing a key role in the work was Dr Peicheng Xu from the Institute of Physics Chinese Academy of Sciences in Beijing, for whom Eiser was previously an academic supervisor.

One reason why the new method is faster is that users do not have to go through a step called 'gene amplification'. This involves making several copies of the genetic material so it is easier to analyse, but this step can now be skipped. "We can analyse all of the bacterium's DNA without gene amplification by using a method previously used in simulations," says Professor Eiser.

Eiser was part of a research group led by Tine Curk from Johns Hopkins University that developed the theory behind the method, which also works in reality. "We get excellent results when we apply the theoretical method to real samples," said Professor Eiser.

This paragraph might be a bit difficult to understand, but basically, DNA is made up of rows of so-called nucleotides. The new method enables researchers to find short sequences of the bacteria's DNA. They do this by seeing how these sequences bind to different variants of DNA that are grafted onto colloids, which are particles dissolved in a liquid. If you are interested in finding out more, you can read about the process in more detail here. What it means, however, is that researchers can quickly identify the bacteria, because they bind themselves to these colloids in various ways and cause them to clump together.

The bottom line is: you don't have to analyse so much material. You can skip the step of having to copy them, and this saves time and money. "Using this method, we saw how as few as five E. Coli bacteria caused the colloids to create clusters," said Professor Eiser.

All of this is currently in its early stages. Eiser has published a proof-of-principle experiment. This means that there is still a lot of work to be done before it becomes a widely used method. "The findings can provide us with a reliable method for identifying pathogens in disciplines such as food safety, disease control and environmental monitoring," said Professor Eiser. (ANI)

(This story has not been edited by Devdiscourse staff and is auto-generated from a syndicated feed.)

New Method For Identifying Bacteria More Easily

Far too many antibiotics are used around the world. As a result, bacteria are becoming resistant to these drugs. Curing bacterial diseases is becoming more difficult than before because antibiotics are perhaps our foremost weapons in the fight against them.

An important step towards using fewer antibiotics is to find better methods for identifying pathogens, and here is the good news.

"We have developed a simple tool that can identify all of the genetic material in bacteria. This allows us to find out more quickly what kind of bacteria a sick person or animal is affected by, or what kind of bacteria are found in food or the environment. We can then also decide whether it is necessary to use antibiotics against the bacterium, and if so what kind, so we don't have to use as much medication," says Professor Erika Eiser at NTNU's Department of Physics.

No need to copy genetic material

An international research group is behind the latest findings. The results have been published in the Proceedings of the National Academy of Sciences. Playing a key role in the work was Peicheng Xu from the Institute of Physics Chinese Academy of Sciences in Beijing, for whom Eiser was previously an academic supervisor.

One reason why the new method is faster is that users do not have to go through a step called "gene amplification." This involves making several copies of the genetic material so it is easier to analyze, but this step can now be skipped.

"We can analyze all of the bacterium's DNA without gene amplification by using a method previously used in simulations," says Professor Eiser.

Eiser was part of a research group led by Tine Curk from Johns Hopkins University that developed the theory behind the method, which also works in reality.

"We get excellent results when we apply the theoretical method to real samples," says Eiser.

The method creates clumps

This paragraph might be a bit difficult to understand, but basically, DNA is made up of rows of so-called nucleotides. The new method enables researchers to find short sequences of the bacteria's DNA. They do this by seeing how these sequences bind to different variants of DNA that are grafted onto colloids, which are particles dissolved in a liquid.

If you are interested in finding out more, you can read about the process in more detail here. What it means, however, is that researchers can quickly identify the bacteria, because they bind themselves to these colloids in various ways and cause them to clump together.

The bottom line is that you don't have to analyze so much material. You can skip the step of having to copy them, and this saves time and money.

"Using this method, we saw how as few as five E. Coli bacteria caused the colloids to create clusters," says Professor Eiser.

Still a way to go

All of this is currently in its early stages. Eiser has published a proof-of-principle experiment. This means that there is still a lot of work to be done before it becomes a widely used method.

"The findings can provide us with a reliable method for identifying pathogens in disciplines such as food safety, disease control and environmental monitoring," says Professor Eiser.

In a world where more and more bacteria are becoming resistant to antibiotics, this is particularly good news.

More information: Peicheng Xu et al, Whole-genome detection using multivalent DNA-coated colloids, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2305995120

Citation: New method for identifying bacteria more easily (2023, November 28) retrieved 29 November 2023 from https://phys.Org/news/2023-11-method-bacteria-easily.Html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

Examining What Smoking Does To Oral Bacteria

The father of Biotechnologist Giacomo Antonello, a dentist, sometimes amazed patients with his seemingly clairvoyant diagnostic abilities: one look in their mouth and he would advise them to see a specialist because, he explained, they might have a problem with their heart or diabetes. He often turned out to be correct.

While his patients were always very impressed, for experts, the dentist's diagnoses were justified: empirical studies show that there is often a connection between periodontitis and various cardiovascular diseases, even if the exact mechanisms are not fully understood.

Giacomo, who is currently conducting research for his Ph.D. At the Institute of Biomedicine, has now just completed a study with colleagues at the Eurac Research Institute for Biomedicine that points to one possible factor: in people who smoke, the alteration of the healthy community of oral bacteria could contribute to the increased risk of these diseases.

The study, which was conducted as part of the CHRIS study in Val Venosta, asks two central questions: What exactly happens to the bacterial community in the mouth, the so-called oral microbiome when we smoke? And what effect does quitting have on these same communities?

To find out, the research team in Bolzano, together with epidemiologist Betsy Foxman from the University of Michigan, analyzed saliva samples from more than 1600 people—a huge number of subjects for this research field, as bioinformatician Christian Fuchsberger, Giacomo's doctoral advisor, emphasizes, "There are hardly any large studies on the salivary microbiome."

"This is a young research field in which a lot is happening right now and one in which not everything is conducted so clearly. Many of the current studies are working with very small numbers of cases, for example, which means their results are not broadly applicable."

Microbiome research is a fairly young field: just a few decades ago, the communities of trillions of microorganisms that live on and in humans—mostly in the digestive tract—were considered of little significance by scientists. Now, the microbiome is taking center stage and is recognized to be important to our development and health. The intestinal microbiome is the subject of intensive research, with a major study currently underway at the Institute of Biomedicine.

Compared to the microbial density of the intestine, where thousands of strains of different bacteria live, our mouth is only sparsely populated. However, saliva has a particular advantage for studies: it is relatively easy to sample. Researchers can, therefore, acquire the data they need to investigate whether it is possible to identify changes in the oral flora (biomarkers) that indicate certain diseases, which, if found, could provide a valuable diagnostic tool that health care systems could easily employ.

In the CHRIS Study's examination, CHRIS participants were requested to spit 5 milliliters of saliva into a special collection tube. The participants were divided into groups according to whether they were current smokers, had stopped smoking, or had never started.

Those who had quit were asked exactly when they had quit, and those who still smoked were asked about the number of cigarettes they smoked per day. To get a picture of the microbial community in each mouth—which species were represented and at what frequency—the research team employed a universally used technology for identifying bacteria, namely sequence analysis of the 16S rRNA gene, a gene that represents something like an "identity card" for each different species.

Giacomo's research using the microbiome data collected in the CHRIS Study showed clear results. People who have never smoked carry a significantly different microbial community in their mouths than people who still smoke or have recently given up. Cigarette consumption primarily affects the bacteria that need oxygen: aerobic bacteria.

The number of these bacteria decreases continuously the more cigarettes one smokes; if one stops smoking, these aerobic bacteria gradually increase again. And the longer the smoke-free period, the more aerobic bacteria are found in the saliva. Only after five years of not smoking are former smokers indistinguishable, in terms of aerobic bacteria in their oral microbiome, from people who have never smoked.

"We have observed that the effects of smoking persist for years," Fuchsberger says. "So then, of course, it's interesting to ask whether these effects are related to certain diseases."

Smokers are known to have an increased risk of both periodontitis and cardiovascular disease. Could the changes in the oral microbiome caused by cigarette use play a role in this? This is where a function of the bacteria that live in the mouth comes into play, and like everything to do with our microbiome, it has been receiving increasing attention for some time—some of these bacteria, mainly aerobic ones, convert the nitrate we ingest with food into nitrite, which then becomes nitric oxide.

Nitric oxide is an important substance for regulating blood pressure, among other things. If too little nitric oxide is available, this could contribute to poorly perfused gums and cardiovascular disease. Now, the study in the Venosta valley did not measure nitric oxide in saliva, but it did examine the microbes in it; all the research team can say, therefore, is that the more the subjects smoked, the fewer nitrate-reducing bacteria lived in their mouths.

That this could be an additional explanation for why smokers have a higher risk of periodontal disease and cardiovascular disease is "a hypothesis that needs to be tested in further studies," Giacomo emphasizes.

He is already pursuing the next question based on the CHRIS samples. Namely, what are some of the other factors that influence our oral flora and to what extent? What role does genetics play, and what role do the people we share households with also play? He will only be able to answer this question in about a year's time, but one thing is already very clear: who we live with is very important.

The study is published in the journal Scientific Reports.

More information: Giacomo Antonello et al, Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population, Scientific Reports (2023). DOI: 10.1038/s41598-023-42474-7

Provided by Eurac Research

Citation: Examining what smoking does to oral bacteria (2023, November 29) retrieved 29 November 2023 from https://medicalxpress.Com/news/2023-11-oral-bacteria.Html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

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