Tag Archives: genes

Unique combination of intestinal bacteria in Japanese centenarians may be the key to long life

We are pursuing the dream of eternal life. We fast to stay healthy. And each year, we spend billions of kroner on treatment to make sure we stay alive. But some people turn 100 years old all by themselves. Why is that?

Researchers from the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen have set out to find the answer.

Studying 176 healthy Japanese centenarians, the researchers learned that the combination of intestinal bacteria and bacterial viruses of these people is quite unique.

We are always eager to find out why some people live extremely long lives. Previous research has shown that the intestinal bacteria of old Japanese citizens produce brand new molecules that make them resistant to pathogenic – that is, disease-promoting – microorganisms. And if their intestines are better protected against infection, well, then that is probably one of the things that cause them to live longer than others.”

Postdoc Joachim Johansen, first author of the new study

Among other things, the new study shows that specific viruses in the intestines can have a beneficial effect on the intestinal flora and thus on our health.

“Our intestines contain billions of viruses living of and inside bacteria, and they could not care less about human cells; instead, they infect the bacterial cells. And seeing as there are hundreds of different types of bacteria in our intestines, there are also lots of bacterial viruses,” says Associate Professor Simon Rasmussen, last author of the new study.

Joachim Johansen adds that aside from the important, new, protective bacterial viruses, the researchers also found that the intestinal flora of the Japanese centenarians is extremely interesting.

“We found great biological diversity in both bacteria and bacterial viruses in the centenarians. High microbial diversity is usually associated with a healthy gut microbiome. And we expect people with a healthy gut microbiome to be better protected against aging-related diseases,” says Joachim Johansen.

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Once we know what the intestinal flora of centenarians looks like, we can get closer to understanding how we can increase the life expectancy of other people. Using an algorithm designed by the researchers, they managed to map the intestinal bacteria and bacterial viruses of the centenarians.

“We want to understand the dynamics of the intestinal flora. How do the different kinds of bacteria and viruses interact? How can we engineer a microbiome that can help us live healthy, long lives? Are some bacteria better than others? Using the algorithm, we are able to describe the balance between viruses and bacteria,” says Simon Rasmussen.

And if the researchers are able to understand the connection between viruses and bacteria in the Japanese centenarians, they may be able to tell what the optimal balance of viruses and bacteria looks like.

Optimizing intestinal bacteria

More specifically, the new knowledge on intestinal bacteria may help us understand how we should optimize the bacteria found in the human body to protect it against disease.

“We have learned that if a virus pays a bacterium a visit, it may actually strengthen the bacterium. The viruses we found in the healthy Japanese centenarians contained extra genes that could boost the bacteria. We learned that they were able to boost the transformation of specific molecules in the intestines, which might serve to stabilize the intestinal flora and counteract inflammation,” says Joachim Johansen, and Simon Rasmussen adds:

“If you discover bacteria and viruses that have a positive effect on the human intestinal flora, the obvious next step is to find out whether only some or all of us have them. If we are able to get these bacteria and their viruses to move in with the people who do not have them, more people could benefit from them.”

Even though this requires more research, the new insight is significant, because we are able to modify the intestinal flora.

“Intestinal bacteria are a natural part of the human body and of our natural environment. And the crazy thing is that we can actually change the composition of intestinal bacteria. We cannot change the genes – at least not for a long time to come. If we know why viruses and intestinal bacteria are a good match, it will be a lot easier for us to change something that actually affects our health,” says Simon Rasmussen.

Source:
Journal reference:

Johansen, J., et al. (2023). Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan. Nature Microbiology. doi.org/10.1038/s41564-023-01370-6.

Identifying what makes some gut bacteria strains life-threatening in pre-term babies

Researchers from the Quadram Institute and University of East Anglia have identified what makes some strains of gut bacteria life-threatening in pre-term babies.

The findings will help identify and track dangerous strains and protect vulnerable neonatal babies.

A major threat to neonatal babies with extremely low birth weight is necrotizing enterocolitis (NEC).

Rare in full-term babies, this microbial infection exploits vulnerabilities destroying gut tissue leading to severe complications. Two out of five cases are fatal.

One bacterial species that causes especially sudden and severe disease is Clostridium perfringens. These are common in the environment and non-disease-causing strains live in healthy human guts.

So what makes certain strains so dangerous in preterm babies?

Prof Lindsay Hall and Dr Raymond Kiu from the Quadram Institute and UEA led the first major study on C. perfringens genomes from preterm babies, including some babies with necrotizing enterocolitis.

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The research team analyzed C. perfringens genomes from the faecal samples of 70 babies admitted to five UK Neonatal Intensive Care Units (NICUs).

Based on genomic similarities, they found one set had a lower capacity to cause disease. This allowed a comparison with the more virulent strains.

The less virulent group lacked genes responsible for production of a toxin called PFO and other factors needed for colonization and survival.

This study has begun to construct genomic signatures for C. perfringens associated with healthy preterm babies and those with necrotizing enterocolitis.

Exploring genomic signatures from hundreds of Clostridium perfringens genomes has allowed us potentially to discriminate between ‘good’ bacterial strains that live harmlessly in the preterm gut, and ‘bad’ ones associated with the devastating and deadly disease necrotizing enterocolitis.

We hope the findings will help with ‘tracking’ deadly C. perfringens strains in a very vulnerable group of patients – preterm babies.”

Prof Lindsay Hall, UEA’s Norwich Medical School and the Quadram Institute

Larger studies, across more sites and with more samples may be needed but this research could help identify better ways to control necrotizing enterocolitis.

The team previously worked alongside Prof Paul Clarke and clinical colleagues at the Norfolk and Norwich University Hospital NICU. And they demonstrated the benefits of providing neonatal babies with probiotic supplements.

The enterocolitis gut microbiome of neonatal infants is significantly disrupted, making it susceptible to C. perfringens overgrowth.

Prof Hall said: “Our genomic study gives us more data that we can use in the fight against bacteria that cause disease in babies – where we are harnessing the benefits of another microbial resident, Bifidobacterium, to provide at-risk babies with the best possible start in life.”

Dr Raymond Kiu, from the Quadram Institute, said: “Importantly, this study highlights Whole Genome Sequencing as a powerful tool for identifying new bacterial lineages and determining bacterial virulence factors at strain level which enables us to better understand disease.”

This research was supported by the Biotechnology and Biological Sciences Research Council, part of UKRI, and the Wellcome Trust.

The study was led by researchers at Quadram Institute and the University of East Anglia, in collaboration with colleagues at Imperial College, London, the University of Glasgow, the University of Cambridge, Newcastle University and Northumbria University.

‘Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains’ is published in Nature Microbiology.

Source:
Journal reference:

Kiu, R., et al. (2023). Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nature Microbiology. doi.org/10.1038/s41564-023-01385-z.

New tool shows early promise to help reduce the spread of antimicrobial resistance

A new tool which could help reduce the spread of antimicrobial resistance is showing early promise, through exploiting a bacterial immune system as a gene editing tool.

Antimicrobial resistance is a major global threat, with nearly five million deaths annually resulting from antibiotics failing to treat infection, according to the World Health Organisation.

Bacteria often develop resistance when resistant genes are transported between hosts. One way that this occurs is via plasmids – circular strands of DNA, which can spread easily between bacteria, and swiftly replicate. This can occur in our bodies, and in environmental settings, such as waterways.

The Exeter team harnessed the CRISPR-Cas gene editing system, which can target specific sequences of DNA, and cuts through them when they are encountered. The researchers engineered a plasmid which can specifically target the resistance gene for Gentamicin – a commonly used antibiotic.

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In laboratory experiments, the new research, published in Microbiology, found that the plasmid protected its host cell from developing resistance. Furthermore, researchers found that the plasmid effectively targeted antimicrobial-resistant genes in hosts to which it transferred, reversing their resistance.

Antimicrobial resistance threatens to outstrip covid in terms of the number of global deaths. We urgently need new ways to stop resistance spreading between hosts. Our technology is showing early promise to eliminate resistance in a wide range of different bacteria. Our next step is to conduct experiments in more complex microbial communities. We hope one day it could be a way to reduce the spread of antimicrobial resistance in environments such as sewage treatment plants, which we know are breeding grounds for resistance.”

David Walker-Sünderhauf, Lead Author, University of Exeter

The research is supported by GW4, the Medical Research Council, the Lister Institute, and JPI-AMR.

Source:
Journal reference:

Walker-Sünderhauf, D., et al. (2023) Removal of AMR plasmids using a mobile, broad host-range, CRISPR-Cas9 delivery tool. Microbiology. doi.org/10.1099/mic.0.001334.

Study identifies key genetic mechanism of drug resistance in the deadliest malaria parasites

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An important genetic mechanism of drug resistance in one of the deadliest human malaria parasites has been identified in a new study published in Nature Microbiology.

A second key gene, pfaat1, responsible for encoding a protein that transports amino acids in the membrane of Plasmodium falciparum, is involved in its resistance to the major anti-malaria drug, chloroquine.

The findings may have implications for the ongoing battle against malaria, which infects an estimated 247 million people worldwide and kills more than 619,000 each year, most of which are young children.

Chloroquine is a major antimalaria drug, however in recent years, resistance has emerged in malaria parasites, first spreading through Southeast Asia and then through Africa in the 1970s and 1980s. Although alternative antimalarial drugs have been developed, resistance to chloroquine remains a big challenge.

Since its discovery in 2000, only one gene has been believed to have been responsible for resistance to chloroquine – the resistance transporter pfcrt which helps the malaria parasite transport the drug out of a key region in their cells, subsequently rendering it ineffective.

In this study, researchers from the Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene & Tropical Medicine (LSHTM) analysed more than 600 genomes of P. falciparum that were collected in The Gambia over a period of 30 years. The team found that mutant variants of  a second gene, pfaat1, which encodes an amino acid transporter, increased in frequency from undetectable to very high levels between 1984 and 2014. Importantly, their genome-wide population analyses also indicated long term co-selection on this gene alongside the previously-known resistance gene pfcrt.

In the laboratory, a further team of researchers including from Texas Biomed, University of Notre Dame and Seattle Children’s Research Institute found that replacing these mutations in parasite genomes using CRISPR gene-editing technology impacted drug resistance. A team from Nottingham University also found that these mutations could impact the function of pfaat1 in yeast, resulting in drug resistance.

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Complementary analysis of malaria genome datasets additionally suggested that parasites from Africa and Asia may carry different mutations in pfaat1 which could help explain differences in the evolution of drug resistance across these continents.

Alfred Amambua-Ngwa, Professor of Genetic Epidemiology at MRC Unit The Gambia at LSHTM said: “This is a very clear example of natural selection in action – these mutations were preferred and passed on with extremely high frequency in a very short amount of time, suggesting they provide a significant survival advantage.

“The mutations in pfaat1 very closely mirror the increase of pfcrt mutations. This, and other genetic analyses in the paper demonstrate that the transporter AAT1 has a major role in chloroquine resistance.”

Grappling with drug resistance, for malaria and other pathogens, requires taking a holistic approach to both drug development and pathogen surveillance. We must be aware that different genes and molecules will be working together to survive treatments. That is why looking at whole genomes and whole populations is so critical.”

David Conway, Professor of Biology, LSHTM

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Source:
Journal reference:

Amambua-Ngwa, A., et al. (2023). Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nature Microbiology. doi.org/10.1038/s41564-023-01377-z.

MGI Empowers the Completion of Nearly 60,000 Samples for The Million Microbiome of Humans Project

SHENZHEN, China, 10 May 2023 – MGI Tech Co. Ltd. (MGI), a company committed to building core tools and technology to lead life science, today shared that a total of nearly 60,000 samples have been sequenced among 21 institutes and over 10 participating nations throughout Europe, as part of the Million Microbiome of Humans Project (MMHP) that was officially launched in 2019.

Image Credit: MGI

The project was launched as a joint effort by the Karolinska Institute of Sweden, Shanghai National Clinical Research Center for Metabolic Diseases in China, the University of Copenhagen in Denmark, Technical University of Denmark, MetaGenoPolis at the National Research Institute for Agriculture, Food and Environment (INRAE) in France, and the Latvian Biomedical Research and Study Center. Relying on MGI’s core DNBSEQ™ technology, MMHP aims to sequence and analyze microbial DNA from a million human samples to construct a microbiome map of the human body and build the world’s largest human microbiome database.

“Countless studies have highlighted the importance of the microbiome in human health and disease. Yet, our knowledge of the composition of the microbiome in different parts of the body across countries, ages, sexes, and in relation to human health and disease remains limited,” said Duncan Yu, President of MGI. “Through MMHP, we are pushing forward microbial metagenomic research while empowering researchers within the microbiology community with access to MGI’s innovative sequencing technology. Despite a brief interruption by the COVID-19 pandemic, we are delighted to see such a monumental milestone merely four years into the project.”

The rise of microbial metagenomic sequencing​​​​​​​

Since the first description of human microbiome was published in 2010, the field of human microbiome has moved fast from sampling hundreds of individuals to thousands. Advances in genome sequencing has enabled researchers to better characterize the composition of the microbiome through identification of unculturable microbes. It has also allowed them the opportunity to study how the microbiome influences the development of some cancers and drug responses.

Metagenomics, coupled with high-throughput sequencing technologies, have revolutionized microbial ecology. Today, metagenomic sequencing has become both a powerful and popular tool for identifying and classifying complex microbial communities. It facilitates accelerated discovery of new markers that translate to virulence or antibiotic resistance, as well as de novo discovery and characterization of novel species and assembly of new genomes. Besides human microbiome, it is highly applicable in agricultural microbiome studies, environmental microbiome studies, pathogen surveillance and identification, and monitoring of antimicrobial resistance genes.

Indeed, the global metagenomic sequencing market was estimated to be worth USD 1.86 billion in revenue in 2022 and is poised to reach USD 4.33 billion by 2027, growing at a CAGR of 18.4% during the forecast period. In particular, Europe and Africa account for approximately 29.7% market share from the globe, ranking second after North America at 45.6%. Thanks to continuous technological innovations in high-throughput sequencing platforms, the metagenomic sequencing market within Europe and Africa is projected to grow from USD 551.7 million in 2022 to 1.29 billion by 2027, presenting huge market opportunities and providing local institutions with the impetus to invest and get involved.

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Image Credit: MGI

An optimized workflow with MGI’s cutting-edge technology

Equipped with MGI’s innovative lab systems, the MMHP Consortium guarantees high-throughput processes, extreme precision, and high quality data output. The dedicated, one-stop workflow begins with sample transfer on MGISTP-7000* high-throughput automated sample transfer processing system. It then goes through nucleic acid extraction and library preparation on MGISP-960 high-throughput automated sample preparation system, a flexible and fully automated workstation capable of processing 96 samples per run. MGISP-960’s fully automatic operation design allows DNA extraction of 50,000 samples per year and library preparation of 25,000 samples per year. MGISP-Smart 8, the professional automated pipetting robot, equipped with an independent 8 pipetting channel can be used for the pooling, normalization and DNB making. Lastly, DNBSEQ-T7* ultra-high throughput sequencer and DNBSEQ-G400* versatile benchtop sequencer enables an efficient, productive, and streamlined sequencing experience.

“We are very focused on data quality, cost and time. After contrasting DNBSEQ™ technology by MGI with other sequencing technologies, we are convinced that MGI’s products have met high industry standards and provide a very good user experience,” commented Professor Lars Engstrand, Research Director of Center for Microbial Translational Research (CMTR) at Karolinska Institutet. “MGI’s platforms have enabled our team to upgrade our original microbiological research from 16SrRNA gene amplicon sequencing to shotgun metagenomic sequencing. I look forward to introducing more equipment and super-large projects as human microbiome emerges as a crucial diagnostic and treatment method in precision medicine.”

The next chapter in microbiomics

“Microbiomics will be part of precision medicine in the future, and data from the microbiome biobank that will result from MMHP will be leveraged for therapeutic R&D,” said Professor Stanislav Dusko Ehrlich of University College London, UK. “With 21 public and private institutions and 10+ countries currently involved in MMHP, we are actively looking for more research groups to take part in this landmark international microbiological research partnership and help generate the world’s biggest free-access human microbiome database.”

Since the inception of MMHP, MGI has played an important role in providing the program with state-of-the-art research platforms and technologies. Now entering its second phase towards sequencing and analyzing a final total of one million samples, the project welcomes further exchange and participation from relevant organizations to jointly promote research and applications of cutting-edge translational medicine in the field of microbiome. Those interested can fill the application form on www.mgi-tech.eu/mmhp.

About MGI

MGI Tech Co. Ltd. (MGI), headquartered in Shenzhen, is committed to building core tools and technology to lead life science through intelligent innovation. Based on its proprietary technology, MGI focuses on research & development, production and sales of sequencing instruments, reagents, and related products to support life science research, agriculture, precision medicine and healthcare. MGI is a leading producer of clinical high-throughput gene sequencers*, and its multi-omics platforms include genetic sequencing*, medical imaging, and laboratory automation. MGI’s mission is to develop and promote advanced life science tools for future healthcare. For more information, please visit the MGI website or connect with us on TwitterLinkedIn or YouTube.

*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents are not available in Germany, Spain, UK, Sweden, Italy, Czech Republic, Switzerland and Hong Kong (CoolMPS is available in Hong Kong).

*For Research Use Only. Not for use in diagnostic procedures (except as specifically noted).

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Study may provide new avenues for addressing somatosensory symptoms of long COVID

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COVID-19, the disease resulting from SARS-CoV-2 infection, is associated with highly variable clinical outcomes that range from asymptomatic disease to death. For those with milder infections, COVID-19 can produce respiratory infection symptoms (cough, congestion, fever) and sensory phenotypes such as headache and loss of sense of smell. In more severe cases, SARS-CoV-2 infection can affect nearly every organ and result in strokes from vascular occlusion, cardiovascular damage and acute renal failure. A substantial number of actively infected patients suffering from both mild and severe infections experience sensory-related symptoms, such as headache, visceral pain, Guillain-Barre syndrome, nerve pain and inflammation. In most patients these symptoms subside after the infection ends, but, for other patients, they can persist.

In a new study, researchers from Boston University Chobanian & Avedisian School of Medicine, Icahn School of Medicine at Mount Sinai (Icahn Mount Sinai) and New York University (NYU), have found that thousands of genes were affected by SARS-CoV-2-mediated disease even after the viral infection had been cleared. These genes were associated with neurodegeneration and pain-related pathways, suggesting lasting damage to dorsal root ganglia (spinal nerves that carry sensory messages from various receptors) that may underlie symptoms of Post-Covid Conditions also known as Long Covid.

Several studies have found that a high proportion of Long Covid patients suffer from abnormal perception of touch, pressure, temperature, pain or tingling throughout the body. Our work suggests that SARS-CoV-2 might induce lasting pain in a rather unique way, emphasizing the need for therapeutics that target molecular pathways specific to this virus.”

Venetia Zachariou, PhD, corresponding author, chair of pharmacology, physiology & biophysics at BU Chobanian & Avedisian School of Medicine

This work was performed in collaboration with Benjamin tenOever, PhD, professor of microbiology and medicine at NYU, formerly at Icahn Mount Sinai.

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Using an experimental model infected with SARS-CoV-2, the researchers studied the effects of infection on sensitivity to touch, both during active infection and well after the infection had cleared. They then compared the effects of SARS-CoV-2 to those triggered by influenza A virus infection. In the experimental model, they observed a slow but progressive increase in sensory sensitivity over time – one that differed substantially from viral control, influenza A virus, which caused quick hypersensitivity during active infection but returned to normal by the time infection was over.

According to the researchers, this model can be used to gain information on genes and pathways affected by SARS-CoV-2, providing novel information to the scientific community on gene expression changes in sensory ganglia several weeks after infection.

“We hope this study will provide new avenues for addressing somatosensory symptoms of long COVID and ME/CFS (myalgic encephalomyelitis/chronic fatigue syndrome), which are only just now beginning to be addressed by mainstream medicine. While we have begun using this information by validating one promising target in this study, we believe our now publicly available data can yield insights into many new therapeutic strategies,” adds Zachariou.

These findings appear online in the journal Science Signaling.

This study was supported by National Institute of Neurological Disorders and Stroke NS086444S1 (R.A.S), the Zegar Family Foundation (B.T.) and the Friedman Brain Institute Research Scholars Program (V.Z., B.T., R.A.S., J.J.F.).

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Source:
Journal reference:

Serafini, R. A., et al. (2023) SARS-CoV-2 airway infection results in the development of somatosensory abnormalities in a hamster model. Science Signaling. doi.org/10.1126/scisignal.ade4984.

How the COVID pandemic has improved genomics

insights from industryDavide CacciharelliMolecular Biology and Genomics ProfessorUniversity of Naples

In this interview, Davide Cacchiarelli, Molecular Biology and Genomics Professor at the University of Naples talks to NewsMed about how the COVID pandemic has highlighted the vital role of genomic surveillance and improved genomics.

Please introduce yourself and what inspired your career in molecular biology and genomics?

My name is Davide Cacchiarelli, and I am a molecular biology and genomics professor at the University of Naples. I was inspired by the fact that genomics is classed as an effective tool to improve human health, dissect the molecular events happening in the cell and nucleus, and better understand how cells and organisms work.

Image Credit: ShutterStock/pinkeyes

In The Telethon Institute of Genetics and Medicine, you combine various disciplines with cell biology, molecular biology, and genomics. Why is having a multidisciplinary approach useful when making discoveries, particularly surrounding infectious diseases such as COVID?

The majority of the time, a single omic, measuring only gene expression by RNA sequencing, measuring only epigenetics, or measuring only phenotype, is insufficient to understand how a cell works.

The best solution is to combine all efforts to understand how these events happen, from the nucleus to the cell’s exterior. COVID, in particular, has been a case where acquiring one single omic or a single view of how the system works is ineffective in understanding how COVID behaviors occur in the population or clinically hospitalized patients.

We, therefore, try to combine the general information and patient outcome to get the best result regarding COVID infection.

Davide Cacciarelli at ICG17 – How the COVID pandemic has improved genomics

On what research areas are you and your team at TIGEM currently focusing?

Our group aims to answer various questions, from basic microbiology to developmental biology. Then we can re-engineer it for real regenerative medicine purposes. We also look at how we can effectively use genomics as a medical instrument that can be used to impact the healthcare of patients in our healthcare system.

You have recently co-authored a paper, “Improved SARS-CoV-2 sequencing surveillance allows the identification of new variants and signatures in infected patients.” Can you expand on that?

One of the significant issues in Italy regarding SARS-CoV-2 genome sequencing was the cost. Sequencing the COVID genome was also a tedious and elaborate procedure.

Image Credit: ShutterStock/Kateryna Kon

The main objective was first to make this approach economically affordable and create a proof of printing pulled by which this approach could become a cost-effective method for anyone and any country.

Our second approach, therefore, included integrating the genome information and the transcriptomic profiling of the patient airway epithelia. This helps us to understand how the genome evolves and allows us to track its evolution, in addition to seeing the response of the host respiratory epithelium. Finally, we implemented new ways to classify viral variants based on different characteristics using this approach.

What are the advantages of better identifying new cells, or two variants, for healthcare centers and patients?

The European Center for Disease Control has issued several requirements for next year focused on tracking respiratory viruses. One of these is tracking emerging variants as soon as possible, which we have done with COVID-19. We now know that new, specific variants can emerge in a short timeframe, so immediate tracking is crucial to help contain or at least delay the spreading of possible pathogenic variants.

MGI offers a variety of tools and technology surrounding genomics. Can you tell us more about some of the products used during your research and your experience with them?

At MGI, we have typically applied the COVID and whole genome solutions. We also have the freedom to test the stereo-seq they have in production this month. MGI can offer alternative solutions for various genome sequencing needs.

Image Credit: ShutterStock/peterschreiber.media

At present many sequencing genomic companies are coming up with different solutions. At MGI, we understand that the best genomic solution is the one that better fits your needs. With our experience, for example, with COVID, MGI had the right solution at the right moment.

How important is selecting the right sequencing technology for your research? When undertaking new research, what do you look for in a product/sequencer?

When the primary focus is not on identifying genes or mapping gene expression but on identifying or qualifying gene variants, there must be no issues in the sequencing, as the sequencing issue might be an error in the sequencing and misinterpreted data.

The error rate of MGI technology on DNB sequencing is extremely low, which offers significant benefits. Users can confidently rely on the data at the level of leaders in the field, which is what we look for when we start COVID genome sequencing.

You have often collaborated with other researchers throughout your research projects, especially concerning COVID. How vital have these collaborations been in accelerating your research?

Like many scientists who faced the COVID pandemic, I had much to learn. We used our knowledge in medical genetics and variant interpretation, and the crosstalk we had with virologists, MGI scientists, and genomic specialists was a step towards acquiring the best solution and the best effort to try to get those results as soon as possible, which is crucial for COVID sequencing.

Surprisingly, some scientists who had no interest in healthcare possessed knowledge valuable in tackling COVID issues. The circumstances and contingencies around the event forced them to think outside the box.

Do you believe that if we can understand SARS-CoV-2 better, we could better use this knowledge to prepare ourselves for future pandemics better? What advantages would this have for global health?

COVID did not give us any significant advantages for healthcare, but it may have for science. It highlighted how vital advanced genomics is to track diseases which influenced decisions at the governmental level.

Image Credit: ShutterStock/CKA

Today, several diseases require advanced genome sequencing, such as cancer diagnostics and medical genetics. Given that the issues with this problem affect a small population, you do not feel the urgency to improve specific knowledge or tests.

Therefore, the COVID pandemic has highlighted the vital role of genomic surveillance and improved genomics. Today, we have laboratories that, until two years ago, thought they could never afford to set up a genomic workflow; the pandemic forced them to enter the genomics field. Our mission as genomic scientists is to help them implement this solution in their lab because improving genomics in any lab is the best for healthcare in the future.

There is a saying, “omics for all.” As a scientist, what does that mean to you?

‘Omics for all’ has to be understood in two ways. It is critical to give everybody the chance to have access to omics. However, we need to remember that it is still a medical procedure. Thus, the omics flow offers everybody access to high-quality omics profiling of their genome, but under medical supervision.

Finally, what is the future for you in your research?

I will continue my basic research in my lab: studying how pluripotent cells and stem cells can be manipulated and organized for medical purposes. We also want to use the knowledge accumulated in the COVID pandemic to apply fast, cost-effective, and reliable genome sequencing to other types of screening.

Image Credit: ShutterStock/Anusorn Nakdee

With this in mind, we hope to screen for several hereditary cancers, for example, breast cancer inheritance. Therefore, we can effectively use the COVID strategies we set up for COVID sequencing as proof of principle to apply the sequencing to human and human disease-driving genes.

About MGI

MGI Tech Co., Ltd. (referred to as MGI) is committed to building core tools and technology to lead life science through intelligent innovation. MGI focuses on R&D, production, and sales of DNA sequencing instruments, reagents, and related products to support life science research, agriculture, precision medicine, and healthcare. MGI is a leading producer of clinical high-throughput gene sequencers, and its multi-omics platforms include genetic sequencing, mass spectrometry, medical imaging, and laboratory automation.

Founded in 2016, MGI has more than 1000 employees, nearly half of whom are R&D personnel. MGI operates in 39 countries and regions and has established multiple research and production bases around the world. Providing real-time, comprehensive, life-long solutions, its vision is to enable effective and affordable healthcare solutions for all.


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Fighting tuberculosis with the new MTB Strip Test Kit

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Lecturers of the Faculty of Allied Health Sciences, Chulalongkorn University have developed MTB Strip Test Kit for Tuberculosis (TB) diagnosis that’s accurate and easy to use, guaranteed by the 2023 Invention Award from the National Research Council of Thailand (NRCT) -; Another hope to reduce the spread of tuberculosis in Thailand.

Tuberculosis is one of the most contagious diseases that continues to challenge the public health system today. Although the World Health Organization (WHO) aims for 2035 (the next 12 years) to be the year to end the global tuberculosis crisis, the disease trend is still worrisome.

Thailand is one of the 14 countries with the most severe TB incidence. Fortunately, drug-resistant tuberculosis in Thailand has been removed from the WHO’s list of highest-incidence countries. Only ordinary tuberculosis cases remain.”

Dr. Panan Ratthawongjirakul, Associate Professor, Department of Transfusion Medicine, Faculty of Allied Health Sciences, Chulalongkorn University

Tuberculosis is an airborne disease caused by a bacterium called “Mycobacterium tuberculosis“. It is spread from TB patients to others through small respiratory secretions (AKA droplets) that come from coughing, sneezing, or talking. It is easy to contract and it spreads quickly.

“One of the mechanisms to help end tuberculosis is identifying TB patients as early as possible to control and limit its transmission” said Assoc. Prof. Dr. Panan about the inception of the research project to develop MTB Strip (Mycobacterium tuberculosis Strip) that is easy to use, convenient to read by the naked eye, and with fast and accurate results. More importantly, the cost should not be high to make it accessible to local public health service systems.

“If we can distribute this test to small hospitals everywhere, we will be able to identify TB patients within two hours and screen positive patients quickly into the treatment system. We believe this will help reduce the number of TB cases in our country” said Assoc. Prof. Dr. Panan about the objective of MTB Strip innovation.

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Pros and Cons of the current methods of TB Testing

Assoc. Prof. Dr. Panan mentioned the various advantages and disadvantages of current testing methods for tuberculosis as follows:

  1. Microscopic examination using acid-fast staining is a simple method. It can be done in a small hospital, but the disadvantage is low sensitivity (the minimum bacterial concentration required for a positive signal when examining with a microscopic examination is 5000–10000 cells in 1 ml of sputum.
  2. Sputum culture is the standard method of diagnosing tuberculosis, but it can only be done in well-equipped large hospitals. This method must be done in a room with a high-safety system to prevent it from spreading outside. It takes more than a month to know the results which will result in delayed treatment.
  3. TB Genotyping involves taking the patient’s sputum to extract and amplify the genetic materials which are then tested by a Real-time PCR machine. The disadvantage of this method is that it is costly and requires a lab with specialized personnel, so it can be done only in some hospitals.

Based on the advantages and limitations of various methods used to detect tuberculosis, the research team developed the MTB Strip Test Kit.

Faster and easier TB Screening with MTB Strip

MTB Strip TB Test Kit consists of 2 main parts: 1. Genetic amplification using isothermal amplification with specifically modified and designed primers. 2. Genetic materials detection using developed test strips, which are manufactured from ISO13485-certified industrial plants for medical device manufacturing.

Assoc. Prof. Dr. Panan explained the process of using this test kit “after receiving sputum from the patient, the DNA will be extracted and used as a template. We will put a primer specially designed to amplify the amount of genetic material in the DNA of the pathogen in the patient’s sputum before entering the isothermal amplification process by using a recombinase polymerase amplification technique. It takes only 20 – 40 minutes at 37 degrees Celsius. Then, the developed test strip is dipped into the amplified genetic material. The results will appear on the test strip as positive and negative results like the ATK test that we are familiar with.”

The key feature of the MTB Strip is its sensitivity to tuberculosis. With a small amount of tuberculosis in the sputum, the test can detect it and display the result. In addition, the test process takes less than an hour and does not require any special tools.

“The results are up to 96 percent accurate compared to Realtime PCR and other commonly used acid-resistant dye methods. Importantly, this kit is cheaper than molecular biology tests because it does not require any special tools such as thermocycler” Assoc. Prof. Dr. Panan emphasized.

The MTB Strip kit uses the principle of amplifying genetic material under a single constant temperature in conjunction with a heat box. In a typical laboratory, this type of box is already available. Small hospitals can also use this technique.

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“The MTB Strip TB test kit we have developed will enable many existing small and medium-sized hospitals in Thailand to screen for TB cases so that patients can receive appropriate treatment quickly, thereby reducing the number of TB cases and the spread of TB.”

Fighting tuberculosis with the Distribution of MTB strips to the provinces

The MTB Strip Test prototypes have already been administered at Umphang Hospital, Tak Province in 2019-2020 and the results are good to a certain extent. However, Assoc. Prof. Dr. Panan has not stopped developing methods and innovations to reduce the number of cases of tuberculosis in Thailand.

“Although the MTB Strip kit works satisfactorily, we would still like to develop more sensitivity by making the DNA extraction easier to be used as the kit primer.”

In addition, Assoc. Prof. Dr. Panan also has plans to expand the testing of TB and related diseases by developing an easier-to-use DNA extraction kit and TB test kit that can identify drug-resistant variants of TB right from the outset, so that more specific treatment guidelines can be set.

“We are currently conducting in-depth research on the genetic modification of tuberculosis using a novel technique of genetic modification for a living organism called CRISPR Cas-9 Interference to modify certain TB genes, making the infection less aggressive and more responsive to antituberculosis drugs. CRISPR Cas-9 Interference can be used in conjunction with current antituberculosis drugs.”

If the study is successful, it will be a new TB treatment of the future, which Assoc. Prof. Dr. Panan is sure will help reduce the number of TB cases to reach WHO’s target. Small hospitals interested in the MTB Strip Test kits can contact Assoc. Prof. Dr. Panan Rathwongjirakul, the Research Unit of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University.

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How inert, sleeping bacteria spring back to life

Solving a riddle that has confounded biologists since bacterial spores -; inert, sleeping bacteria -; were first described more than 150 years ago, researchers at Harvard Medical School have discovered a new kind of cellular sensor that allows spores to detect the presence of nutrients in their environment and quickly spring back to life.

It turns out that these sensors double as channels through the membrane and remain closed during dormancy but rapidly open when they detect nutrients. Once open, the channels allow electrically charged ions to flow out through the cell membrane, setting in motion the shedding of protective spore layers and the switching on of metabolic processes after years -; or even centuries -; of dormancy.

The team’s findings, published April 28 in Science, could help inform the design of ways to prevent dangerous bacterial spores from lying dormant for months, even years, before waking up again and causing outbreaks.

This discovery solves a puzzle that’s more than a century old. How do bacteria sense changes in their environment and take action to break out of dormancy when their systems are almost completely shut down inside a protective casing?”

David Rudner, study senior author, professor of microbiology, Blavatnik Institute at HMS

How sleeping bacteria come back to life

To survive adverse environmental conditions, some bacteria go into dormancy and become spores, with biological processes put on hold and layers of protective armor around the cell.

These biologically inert mini fortresses allow bacteria to wait out periods of famine and shield themselves from the ravages of extreme heat, dry spells, UV radiation, harsh chemicals, and antibiotics.

For more than a century, scientists have known that when the spores detect nutrients in their environment, they rapidly shed their protective layers and reignite their metabolic engines. Although the sensor that enables them to detect nutrients was discovered almost 50 years ago, the means of delivering the wake-up signal, and how that signal triggers bacterial revival remained a mystery.

In most cases, signaling relies on metabolic activity and often involves genes encoding proteins to make specific signaling molecules. However, these processes are all shut off inside a dormant bacterium, raising the question of how the signal induces the sleeping bacteria to wake up.

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In this study, Rudner and team discovered that the nutrient sensor itself assembles into a conduit that opens the cell back up for business. In response to nutrients, the conduit, a membrane channel, opens, allowing ions to escape from the spore interior. This initiates a cascade of reactions that allow the dormant cell to shed its protective armor and resume growth.

The scientists used multiple avenues to follow the twists and turns of the mystery. They deployed artificial intelligence tools to predict the structure of the intricately folded sensor complex, a structure made of five copies of the same sensor protein. They applied machine learning to identify interactions between subunits that make up the channel. They also used gene-editing techniques to induce bacteria to produce mutant sensors as a way to test how the computer-based predictions played out in living cells.

“The thing that I love about science is when you make a discovery and suddenly all these disparate observations that don’t make sense suddenly fall into place,” Rudner said. “It’s like you’re working on a puzzle, and you find where one piece goes and suddenly you can fit six more pieces very quickly.”

Rudner described the process of discovery in this case as a series of confounding observations that slowly took shape, thanks to a team of researchers with diverse perspectives working together synergistically.

Along the way, they kept making surprising observations that confused them, hints that suggested answers that didn’t seem like they could possibly be true.

Stitching the clues together

One early clue emerged when Yongqiang Gao, an HMS research fellow in the Rudner lab, was conducting a series of experiments with the microbe Bacillus subtilis, commonly found in soil and a cousin to the bacterium that causes anthrax. Gao introduced genes from other bacteria that form spores into B. subtilis to explore the idea that the mismatched proteins produced would interfere with germination. Much to his surprise, Gao found that in some cases the bacterial spores reawakened flawlessly with a set of proteins from a distantly related bacterium.

Lior Artzi, a postdoctoral fellow in the lab at the time of this research, came up with an explanation for Gao’s finding. What if the sensor was a kind of receptor that acts like a closed gate until it detects a signal, in this case a nutrient like a sugar or an amino acid? Once the sensor binds to the nutrient, the gate pops open, allowing ions to flow out of the spore.

In other words, the proteins from distantly related bacteria would not need to interact with mismatched B. subtilis spore proteins, but instead simply respond to changes in the electric state of the spore as ions begin to flow.

Rudner was initially skeptical of this hypothesis because the receptor didn’t fit the profile. It had almost none of the characteristics of an ion channel. But Artzi argued the sensor might be made up of multiple copies of the subunit working together in a more complex structure.

AI has entered the chat

Another postdoc, Jeremy Amon, an early adopter of AlphaFold, an AI tool that can predict the structure of proteins and protein complexes, was also studying spore germination and was primed to investigate the nutrient sensor.

The tool predicted that a particular receptor subunit assembles into a five-unit ring known as a pentamer. The predicted structure included a channel down the middle that could allow ions to pass through the spore’s membrane. The AI tool’s prediction was just what Artzi had suspected.

Gao, Artzi, and Amon then teamed up to test the AI-generated model. They worked closely with a third postdoc, Fernando Ramírez-Guadiana and the groups of Andrew Kruse, HMS professor of biological chemistry and molecular pharmacology, and computational biologist Deborah Marks, HMS associate professor of systems biology.

They engineered spores with altered receptor subunits predicted to widen the membrane channel and found the spores awoke in the absence of nutrient signals. On the flip side, they generated mutant subunits that they predicted would narrow the channel aperture. These spores failed to open the gate to release ions and awake from stasis in the presence of ample nutrients to coax them out of dormancy.

In other words, a slight deviation from the predicted configuration of the folded complex could leave the gate stuck open or shut, rendering it useless as a tool for waking up the dormant bacteria.

Implications for human health and food safety

Understanding how dormant bacteria spring back into life is not just an intellectually tantalizing puzzle, Rudner said, but one with important implications for human health. A number of bacteria that are capable of going into deep dormancy for stretches of time are dangerous, even deadly pathogens: The powdery white form of weaponized anthrax is a made up of bacterial spores.

Another dangerous spore-forming pathogen is Clostridioides difficile, which causes life-threatening diarrhea and colitis. Illness from C. difficile typically occurs after use of antibiotics that kill many intestinal bacteria but are useless against dormant spores. After treatment, C. difficile awakens from dormancy and can bloom, often with catastrophic consequences.

Eradicating spores is also a central challenge in food-processing plants because the dormant bacteria can resist sterilization due to their protective armor and dehydrated state. If sterilization is unsuccessful, germination and growth can cause serious foodborne illness and massive financial losses.

Understanding how spores sense nutrients and rapidly exit dormancy can enable researchers to develop ways to trigger germination early, making it possible to sterilize the bacteria, or block germination, keeping the bacteria trapped inside their protective shells, unable to grow, reproduce, and spoil food or cause disease.

Source:
Journal reference:

Gao, Y., et al. (2023) Bacterial spore germination receptors are nutrient-gated ion channels. Science. doi.org/10.1126/science.adg9829.

Can a disrupted gut microbiota contribute to anorexia nervosa pathogenesis?

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In a recent study published in the journal Nature Microbiology, researchers investigated whether intestinal microbial alterations contribute to anorexia nervosa (AN) pathogenesis.

AN, a disorder associated with altered eating, has caused considerable mortality, especially among women. However, therapies based on scientific evidence are scarce. AN pathogenesis likely involves several environmental and genetic factors. Studies have reported intestinal microbial dysbiosis among AN-affected individuals. However, data were obtained from small sample sizes, and genus-level microbial alterations were analyzed by amplicon sequencing.

Study: The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Image Credit: Tatiana Shepeleva / ShutterstockStudy: The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Image Credit: Tatiana Shepeleva / Shutterstock

About the study

In the present study, researchers assessed the association between the intestinal microbiome and AN.

The team performed metabolomics and shotgun metagenomic analyses on serum and fecal samples, respectively, that were obtained from women with AN (n=77) and age- and sex-matched healthy controls (n=70). Further, the fecal microbiome was transplanted from anorexia nervosa cases to murine animals fed calories-limited diets over three weeks to simulate AN eating behavior for in vivo analysis. In addition, the team explored causal associations in silico by bidirectional mediation analysis. The intestinal microbiome was analyzed at functional, taxonomic, and genetic levels.

The team used the eating disorder inventory-3 (EDI-3) questionnaire to assess eating behaviors and insulin resistance was assessed using the homoeostatic model assessment for insulin resistance (HOMA-IR) tool. The team examined covariations between bacterial abundance at species and genus levels and clinical variables for AN cases and controls. Linear regression modeling was performed, adjusting for confounders such as age, smoking status, medications, and body mass index (BMI).

Further, the team evaluated the growth dynamics of gut bacteria by calculating peak-to-trough ratios (PTR) using the metagenomic dataset. The functional modules of gut bacteria were identified using gut-brain modules (GBMs) and gut metabolic modules (GMMs). Differences in bacterial genomics were explored based on the Canberra distance of bacterial structural variant profiles.

​​​​​​​Graphical abstract of the study workflow and findings.

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Results

Several bacterial organisms (including Clostridium) were altered among individuals with anorexia nervosa and were associated with mental well-being and eating behavior estimates. Bacterial functional-type modules related to neurotransmitter degradation were enriched among those with anorexia nervosa. Further, several structural variants (SVs) in bacterial organisms were associated with the metabolic characteristics of anorexia nervosa.

The findings indicated a probable role of the intestinal microbiome in AN-associated changes concerning satiety and the metabolism of secondary bile acids. The metabolomic analysis indicated an elevation in metabolites linked to lowered food consumption (including taurine-hyodeoxycholic acid, taurine-α-muricholic acid, and indole-3-propionic acid molecules). Causal inference analysis indicated that serological bacterial metabolites probably mediate the effect of gut microbial alterations on anorexia nervosa. At the phylum level, AN microbiome samples showed lowered Actinobacteriota and Bacteroidota counts. Among families of bacteria, Christensenellaceae species, particularly CAG-138, showed the most significant enrichment in AN.

At the genus level, elevated Lactobacillus counts were observed in the AN microbiota. The Ruminococcacea-enterotype was more prevalent in cases of AN. Species-level analysis indicated greater β-diversity among AN-affected women. In AN, Roseburia inulinivorans and Roseburia intestinalis were depleted, whereas those of Erysipelatoclostridium ramosum, Blautia species CAG, and Enterocloster bolteae innocuum (Clostridium) were increased. Clostridium counts correlated positively with eating disorder scores. The abundance of Bifidobacterium and Parasutterella, in absolute terms, showed positive correlations with perfectionism and body dissatisfaction, respectively.

Absolute Brachyspira count showed a positive association with ‘drive for thinness’ markers in anorexia nervosa. Median values for PTR markedly differed between individuals with AN and controls. Women with AN were leaner, had lower fasting serological insulin, glucose, and C-reactive protein (CRP) levels, and were more sensitive to insulin than controls. Bacterial organisms with significant growth retardation, among AN case individuals included Alistipes finegoldii, Akkermansia muciniphila, Eubacterium siraeum, Coprococcus catus, SS3/4, and Odoribacter splanchnicus.

In addition, the intestinal virome was altered among AN-affected individuals, including lowered bacterial-viral interactions, due to attenuated interactions of viruses with short-chain fatty acid (SCFA)-producing bacteria, including Roseburia inulinivorans, Roseburia hominis, and Faecalibacterium prausnitzii. The team observed greater viral richness and Shannon diversity in the fecal samples of AN cases compared to controls. Notably, 25/30 viruses increased in AN were Lactococcus bacteriophages. The abundance of GBMs for serotonin synthesis and degradation of tryptophan, glutamate, and dopamine, were enriched in AN.

The team detected 2,423 and 5,056 variable SVs and deletion SVs, respectively, across 56 species of bacteria, including Bacteroides uniformis, Faecalibacterium prausnitzii, Parabacteroides distasonis, Methanobrevibacter smithii. Individuals with AN lacking the genomic region of B. uniformis had greater scores for self-denial and bulimia. The genetic deletion in B. uniformis could result in the deficiency of thiamine, a vitamin associated with intestinal and mental health. The serotonin synthesis module causally affected BMI through glycoursodeoxycholic acid, which is upregulated by serotonin.

Serum leucine mediated the influence of B. vulgatus counts on glucose homeostasis. Mice receiving AN individuals’ fecal transplants initially lost more weight with a slower gain of weight with time than those receiving fecal transplants of control individuals. The finding was related to greater levels of hypothalamic appetite-suppressing genes and thermogenesis-associated genes in the adipose tissues of mice receiving fecal transplants from individuals with AN.

Based on the study findings, gut microbial disruptions may contribute to the pathogenesis of AN.

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Journal reference: