Category Archives: Microbiology

Microbiology

This course teaches students how to connect with older adults to forge intergenerational bonds and help alleviate loneliness and isolation

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Uncommon Courses is an occasional series from The Conversation U.S. highlighting unconventional approaches to teaching.

“Legacy Building with Older Adults – Students Re-Humanizing Health Care”

In March 2020 – as the COVID-19 pandemic was causing widespread lockdowns across the U.S. – I heard from a chaplain friend about older adults who were dying in assisted living facilities and skilled nursing homes indirectly because of social isolation and loneliness.

I was finishing my dissertation, focused on developing a curriculum to assist underrepresented and underserved university students. But after hearing about the needs of older adults, I was moved to do something to help them.

So I shifted my focus and geared my curriculum toward bridging the needs of older adults, who are also often underserved, with young people who are learning the principles of health care.

I developed the concept and then piloted it at my alma mater, the University of Toledo, with counseling and pre-med students. I then further developed it to be suitable for a course aimed at connecting university students in health-care-related fields with older adults who may feel isolated and alone.

This course covers issues in social and cultural determinants of health. Social determinants of health are the conditions in the environments where people live, play, work, attend community events – and where they age. These environments can influence what decisions people make, and the decisions they make can affect a wide range of health and quality-of-life results.

Students in this course connect with older adults once a week, for one hour, in person, via phone or through virtual visits. Throughout the course, students receive training materials in growth mindset, resiliency, mindfulness and goal-setting both for themselves and for the older adults. Students are also trained in reminiscence therapy, which is an approach to help students guide or support the older adult, reaffirming the value of the adults’ stories as they reminisce.

The sessions that involve discussions between students and older adults focus on building rapport and connecting. They also allow for an older adult to impart wisdom and share stories of their past with the students. At the end of the sessions, the older adult participants receive a digital or physical book – which I call a legacy book – that summarizes the stories the older adult shared with the student, to help reinforce that their story matters.

One of the most profound lessons from the pandemic has been that staying connected is important for one’s health.

Emerging research shows how social isolation and loneliness before and during the COVID-19 pandemic are correlated with many physical and mental health problems, including heart disease, diabetes, high blood pressure, heart failure, stroke, dementia, anxiety, depression and suicide.

Researchers estimate that health issues caused by isolation and loneliness increase the risk of early death by 26% and have been equated to smoking 15 cigarettes a day. One of the major ways to build a foundation for addressing isolation and loneliness is building connection between generations.

Many older adults said the most valuable part of the program for them was the relationship and friendship they developed with their legacy builder. One older adult reported back that it was uplifting to know that she could communicate well with the younger generation, and that she is now more confident in talking with her young adult grandchildren.

Older adults can also learn new technology skills from their legacy builder. Many have started texting for the first time and learned how to send pictures via text. Another learned from her legacy builder to create a Facebook account for herself, and she now stays connected with the student through Facebook.

The critical lesson that I hope students take away from the course is that every person has value, and it is worthwhile to listen to the person’s stories to understand what they value and why it matters so much.

I want students to learn how they can reinforce the strengths and self-efficacy in another individual by valuing their stories and lived experiences. I also want health care students in particular to understand that those they serve are the experts of their own lived experiences and have a story worth listening to. On top of that, each person has something to be learned from the other. Ultimately, both leave the conversation feeling edified and uplifted.

The content mainly focuses on communication and listening skills, with mindfulness, growth mindset and goal-setting strategies. Emphasis is placed on gaining skills in interviewing, connection and building rapport.

The course will prepare students to treat the people they serve and care for as human beings, whether or not the student enters the health care field.

We all are children of someone. We all have birthdays. I believe we all deserve to live a life with a sense of dignity, respect and honor. We all need connection, and, whether it be in health care or everyday life, this is a skill that must not be left out of the curriculum.


Jeremy Holloway

The Conversation

Microbiology

Americans’ personal savings rate is near an all-time low – an economist explains what it means as a potential recession looms

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The rate at which Americans are saving money has dipped close to an all-time low, according to the Bureau of Economic Analysis. The personal savings rate was 2.3% as of October, down from 7.3% a year earlier. It’s the lowest since July 2005, when the rate hit a record low of 2.1%.

We asked Arabinda Basistha, an economist at West Virginia University, to explain the personal savings rate, what’s driving it so low and what it means as a potential recession looms in 2023.

The personal savings rate measures how much of Americans’ after-tax, or disposable, income is left over after spending on bills, food, debt and everything else. Calculated and reported by the U.S. Bureau of Economic Analysis, it is an important component of the financial security of American families.

The latest data shows Americans are saving just 2.3%, or US$2.30 of every $100 they earn after paying taxes, down from 7.5% as recently as December 2021. Historically, that’s very low.

From 2015 to 2019, for example, this rate averaged around 7.6%. It rose dramatically during the COVID-19 shutdown in early 2020, to a record high of 33.8%. With restaurants, entertainment venues and almost everything else closed, Americans had fewer things to spend money on.

That’s changed as economies have opened up and people eager to travel and dine out have begun to spend the money they had saved.

American consumers usually do not change their consumption and saving behavior dramatically.

So to understand this decline, it’s important to add some historical context.

The last time the savings rate fell this low, in 2005, it was part of a trend that lasted several years. From 1998 to 2004, rates averaged about 5.4%, slipping to 3.3% from 2005 to 2007. Thus the 2.1% rate recorded in July 2005 should be seen as part of a low-savings rate phase.

In recent years, Americans have been saving more of their disposable income. The savings rate averaged nearly 9% in 2019 just before the pandemic stifled spending. This led to the massive swing upward in savings.

An October 2022 study by the Federal Reserve found that U.S. households accumulated $2.3 trillion during the pandemic, thanks in part to about $1.5 trillion in direct fiscal support.

Rates swung again in the other direction, as consumer spending has surged and people use up those excess savings. Against this backdrop, I believe it is quite unlikely that the current low rates will continue for long, as consumers adjust back to pre-2020 patterns.

While the savings rate is important, it doesn’t give us the full picture of Americans’ financial health. Moreover, one should not put too much importance on a single set of recent data, as future revisions can be large.

A few other measures are necessary to assess the state of household finances.

First, current delinquency rates – the share of all loans that are past due for at least 30 days – are at just 1.2%, the lowest since at least the 1980s. The rate is 1.9% for consumer loans and 2.1% for credit cards. Both rates have increased since 2021 but are still historically low.

The low rates are partly due to the pandemic forbearance programs and fiscal support, but still show Americans are in pretty good shape financially.

Another metric worth looking at is the household debt to gross domestic product ratio. This measures the debt burden of U.S. households relative to the size of the economy. The latest data from June 2022 shows the ratio at 76%, which is near the lowest in about two decades. Ahead of the 2007-2009 recession, the ratio was significantly higher, at about 100%.

A third measure of Americans’ financial health is the share of disposable income spent on payments for mortgages and other debts. U.S. households spent about 9.6% of their incomes servicing debts in the second quarter of 2022, well below the 12.8% average from 2005 to 2007.

Adding all this information together, household finances look quite stable and able to withstand moderate economic risks to the U.S. economy.

This is not to argue that a persistently low savings rate will not be an issue in the future. If the savings rate remains low for another year, it will weaken household financial positions.


Arabinda Basistha

The Conversation

Microbiology

Chickenpox and shingles virus lying dormant in your neurons can reactivate and increase your risk of stroke – new research identified a potential culprit

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Over 90% of the world population has the virus that causes chickenpox lying dormant in their nervous system. Most people contract the varicella zoster virus, or VZV, when they get chickenpox as children. For around a third of these people, this same virus will reactivate years later and cause shingles, also called herpes zoster.

While most people are familiar with the painful rash that VZV causes for shingles, a wide spectrum of other complications can also occur even without visible skin symptoms. Among the most severe is stroke, in particular ischemic stroke, which occurs when the blood supply to the brain is restricted by narrowing arteries or blocked by a clot.

People with shingles have an approximately 80% higher risk of stroke than those without the disease, and this risk stays elevated for up to a year after the rash has resolved. Stroke risk is nearly doubled for those with the rash on their face, and tripled for those under the age of 40.

The mechanism behind this long-term stroke risk is mostly unknown. Some researchers have proposed that direct infection of the arteries may be the cause. However, some features of VZV infections suggest that this is not the full picture. A common theme of VZV infections is chronic inflammation that spreads beyond the original infection site, which can persist for weeks to months after the virus is no longer detectable and presumably dormant again.

I am a neurovirologist, and my lab studies how VZV contributes to neurological disorders such as stroke and dementia. In our recently published research, we found that VZV reactivation triggers the formation of cellular sacs, or exosomes, carrying proteins that contribute to blood clotting and inflammation. An increase in these proteins may lead to an increased risk in stroke.

Exosomes are small vesicles, or fluid-filled sacs, made inside cells throughout the body. They’re like duffle bags that carry cargo, such as proteins and nucleic acids, from the cell to distant tissues. Although critical for essential biological functions like communication between cells, exosomes can also play a key role in disease progression and are drug targets for many diseases.

We wanted to see whether shingles patients develop exosomes that carry proteins involved in blood clotting, increasing their risk of stroke. So we isolated exosomes from the blood of 13 patients at time of shingles rash and compared them to exosomes isolated from healthy donors.

When we analyzed the contents of these exosomes, we found that shingles patients had nine times higher levels of clotting proteins than healthy patients. Moreover, we found the exosomes of shingles patients still had elevated levels of these proteins three months after their initial rash.

To functionally confirm that the contents of these exosomes can induce clotting, we exposed platelets – cell fragments involved in blood clotting – of healthy people to exosomes from either shingles patients or healthy people. We found that exposing platelets to shingles exosomes triggered them to clump together and form aggregates with other types of blood cells, as they would in forming a blood clot.

These findings suggest that exosomes may be a potential mechanism for how the varicella zoster virus increases stroke risk for shingles patients.

A Food and Drug Administration-approved vaccine to prevent shingles, Shingrix, is available for adults age 50 and older and immunocompromised adults age 18 and older. However, those at highest risk of stroke are under the age of 40 and are ineligible for Shingrix. A large group of these individuals were likely not vaccinated for chickenpox as children, as the chickenpox vaccine was only approved in the U.S. in 1995 and uptake by adults was quite low at the time. While vaccination with the chickenpox vaccine significantly reduces the risk of shingles, it is still possible for a latent infection to reactivate and cause the disease.

While our study provides evidence for a potential way that shingles can cause an increased risk of stroke during and soon after infection, further research on how long this risk persists is needed. We are conducting follow-up studies to evaluate how long patients may have an increased tendency to form blood clots after their shingles infection has resolved. These longitudinal studies will also examine whether exosomes can be used as a biomarker to monitor stroke risk after shingles.

Meanwhile, we hope that our findings may provide a potential target for treatment development, and encourage people to get vaccinated for shingles.


Andrew Bubak

The Conversation

Microbiology

MGI’s DNBSEQ-T7* facilitates ultra-deep sequencing of high-complexity metagenomic samples

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From MGIDec 20 2022Reviewed by Emily Magee

Thanks to high-throughput sequencing technologies, shotgun metagenomic methods were made possible and had effectively transformed microbiology. Today, advances in both short- and long-read technologies are overcoming many of the previous challenges affecting metagenomic profiling, especially of highly complex samples and environment.

Researchers from France’s National Research Institute for Agriculture, Food, and Environment (INRAE) examined the performance of seven short- and long-read sequencing platforms in analyzing high-complexity metagenomic samples. The study, published in the Nature Portfolio journal Scientific Data, ran mock samples between 2018 and 2019 on various mainstream sequencers at the time, including MGI’s DNBSEQ-T7* and DNBSEQ-G400*.

Within this wide range of sequencing technologies tested, DNBSEQ-T7* was recognized for its ultra-high throughput and excellent accuracy. “We were surprised by the T7’s performance*,” said senior author Mathieu Almeida, a research fellow at INRAE.

It provides ultra-deep sequencing in a single run with similar low error rate compared to the other platforms, making it at the time of our study one of the most affordable technologies for metagenomic sequencing.”

Mathieu Almeida, Senior Author and Research Fellow, INRAE

In the study, three uneven synthetic microbial communities were constructed, consisting of up to 87 genomic microbial strains DNAs each and spanning 29 bacterial and archaeal phyla. They represented some of the most complex and diverse communities used for sequencing technology comparisons. The mock1 (71 strains) was sequenced using all platforms, mock2 (64 strains) was additionally sequenced to estimate the impact of various microbial richness, while MGI’s platforms were not performed on mock3.

To assess the impact of sequencing depth, the team ran a subsampling analysis and compared observed and theoretical genome abundances across samples at multiple depth from 10,000 to 1 million reads. Overall, Spearman rank correlations for all platforms were high at above 0.9 when mapping at least 100,000 reads. Among them, the correlations of T7* and G400* were the best in mock1 and remained excellent in mock2.

Overall comparison between observed and excepted mock compositions for each platform. Image Credit: MGI 

In addition, differential analysis between observed and excepted species abundances was performed in mock1. Results showed that over or under abundance estimation for most genomes had little to do with the sequencing platform, read length, taxonomy, GC-content, genome size and genome completeness, even at a low depth of 500,000 reads. In fact, most genomes were accurately estimated on all sequencers, with the observed normalized abundances generated by T7* charting very close to the excepted values.

 ​​​​​​​

Differential plot between observed and excepted species abundances in mock1. Image Credit: MGI ​​​​​​​

Based on performance analyses of the different sequencers, the study formed a microbial metagenomic sequencing benchmarking database, providing researchers and scientists a comprehensive and authentic reference for sequencing platform selection. In particular, the findings demonstrated the promising value of MGI’s DNBSEQ-T7* in metagenomic sequencing. 

Boasting high stability and accuracy as shown in the data, combined with outstanding throughput, T7* makes a strong platform for the identification of species and functional genes in highly complex microbial communities. Its upgraded biochemical, fluidics, and optical systems are not only making sequencing more efficient and productive, but also continuing to support research into the structure and diversity of microbial communities.​​​​​​​ 

*Unless otherwise informed, StandardMPS and CoolMPS sequencing reagents, and sequencers for use with such reagents are not available in Germany, Spain, UK, Sweden, Belgium, Italy, Finland, Czech Republic, Switzerland, Portugal, Austria, and Romania. Unless otherwise informed, StandardMPS sequencing reagents, and sequencers for use with such reagents are not available in Hong Kong. No purchase orders for StandardMPS products will be accepted in the USA until after January 1, 2023.

Source:

MGI

Microbiology

Experiments Show Infection of Visceral Fat Cells May Contribute to Severe COVID-19

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Two types of adipocytes (fat cells) were infected in the laboratory: one obtained from human stem cells isolated from subcutaneous tissue and the other differentiated from stem cells taken from visceral fatty tissue.

Experiments show that visceral fat – fat around the liver, intestines, and other organs, considered a risk factor for cardiovascular disease, diabetes, and high blood pressure – contributes more to severe COVID-19 than subcutaneous fat (under the skin, as in “love handles”). The experiments were conducted in Brazil by researchers at the State University of Campinas (UNICAMP) and the University of São Paulo (USP).

In order to arrive at this conclusion, Marcelo Mori, a professor at the Institute of Biology at UNICAMP and one of the study’s leaders, infected in the lab two different types of fat cells: one obtained from human stem cells isolated from subcutaneous tissue and the other differentiated from stem cells taken from visceral fatty tissue.

“It was possible to observe that visceral adipocytes are more susceptible to infection by SARS-CoV-2. Viral load increased far more in this fat cell type than in subcutaneous adipocytes. We believe this was due mainly to higher levels of the protein ACE-2 [to which the virus binds to invade cells] on the cell surface,” Mori told Agência FAPESP.

Additionally, the researchers discovered that when visceral adipocytes were infected, they produced a larger amount of pro-inflammatory cytokines, which alert the immune system to the existence of a threat to be combated.

An article on the study was published recently in the scientific journal Nature Communications. Several research groups at UNICAMP collaborated with the group at USP, alongside colleagues at the Brazilian Bioscience National Laboratory (LNBio-CNPEM), National Cancer Institute (INCA) and D’Or Research and Education Institute (IDOR). The principal investigators were Luiz O. Leiria (USP), Mariana Osako (USP) and Daniel Martins-de-Souza (UNICAMP). The study was funded by FAPESP via 20 projects (17/08264-8, 20/05040-4, 20/04746-0, 19/00098-7, 19/05155-9, 20/04583-4, 20/15959-5, 19/26119-0, 16/00194-8, 20/04558-0, 20/04579-7, 21/10373-5, 20/08716-9, 13/07607-8, 20/04919-2, 17/01184-9, 17/23920-9, 16/24163-4, 19/04726-2 and 18/21635-8).

Mori’s team at UNICAMP was the first in the world to show – in July 2020 – that SARS-CoV-2 can infect human fat cells and to suggest that adipose tissue serves as a reservoir for the virus.

“After that, other studies confirmed that adipocytes can indeed be infected, and when we analyzed samples from patients who died of COVID-19, we found the presence of the virus in adipose tissue to be relatively frequent, corresponding to about 50% of cases,” Mori said.

The group then decided to investigate whether there were differences between the way visceral and subcutaneous adipose cells responded to infection. As far as metabolic diseases are concerned, the evidence in the scientific literature shows visceral fat to be the main villain, while subcutaneous fat tends to be neutral or even beneficial.

“We wanted to see if there was a similar association in the context of COVID-19,” Mori said. “And in fact, our model suggests that the more visceral adipose tissue there is in obese individuals, the more the virus can replicate, and this amplifies the inflammatory process.”

In subcutaneous adipocytes, on the other hand, the group observed a decrease in lipolysis, the breakdown of fats and other lipids by hydrolysis to release fatty acids, which can be used as a source of energy during physical activity or fasting periods.

“Our hypothesis is that this represents an antiviral cellular response,” Mori said. “There are studies showing that inhibition of lipolysis lowers the replicative capacity of SARS-CoV-2, which can be explained by the fact that the virus needs lipids to produce its envelope, as well as energy from cells to make copies of its genetic material.” Reduced lipolysis in subcutaneous adipose tissue, therefore, could be positive for the patient and bad news for the virus.

Visceral adipocytes were exposed to different strains of SARS-CoV-2: the ancestral lineage originally from Wuhan, China, and isolated from one of the first Brazilians diagnosed with COVID-19; and the gamma variant (P.1.), which emerged in late 2020 in Manaus, the capital of Amazonas state in Brazil. The difference in susceptibility compared to subcutaneous adipocytes was observed only in response to the ancestral virus.

“We concluded that the Manaus variant is less effective at infecting visceral fat cells than the ancestral strain,” Mori said. “A proteomic analysis [of all the proteins produced by the cells] showed that the Wuhan strain led to a reduction in several proteins associated with the cellular response to interferon [ an immune system mechanism to combat viruses], whereas the gamma variant led to an increase. In other words, the Manaus strain made adipocytes produce more proteins that promote an antiviral response.”

Recent research points to a downtrend in the number of severe cases of COVID-19 due to novel variants among people with obesity. “But this could be influenced by other factors, such as vaccination or prior infection. Or these individuals may have been taking extra care because they knew they belonged to a high-risk group,” Mori explained.

To try to deepen their understanding of all these processes, the group plans further experiments involving adipocytes cultured with the delta and omicron variants.

Another plan for future research is to investigate possible medium- to long-term metabolic impacts of infection by SARS-CoV-2. “We want to find out whether infection changes the risk of developing diabetes or cardiovascular disease, for example,” Mori said. “One way of doing so could be to analyze samples from patients who had COVID-19 and were later submitted to bariatric surgery, in order to see if morphological and functional alterations occurred in visceral adipose tissue as a result of the infection.”

Reference: “SARS-CoV-2 infects adipose tissue in a fat depot- and viral lineage-dependent manner” by Tatiana Dandolini Saccon, Felippe Mousovich-Neto, Raissa Guimarães Ludwig, Victor Corasolla Carregari, Ana Beatriz dos Anjos Souza, Amanda Stephane Cruz dos Passos, Matheus Cavalheiro Martini, Priscilla Paschoal Barbosa, Gabriela Fabiano de Souza, Stéfanie Primon Muraro, Julia Forato, Mariene Ribeiro Amorim, Rafael Elias Marques, Flavio Protasio Veras, Ester Barreto, Tiago Tomazini Gonçalves, Isadora Marques Paiva, Narayana P. B. Fazolini, Carolina Mie Kawagosi Onodera, Ronaldo Bragança Martins Junior, Paulo Henrique Cavalcanti de Araújo, Sabrina Setembre Batah, Rosa Maria Mendes Viana, Danilo Machado de Melo, Alexandre Todorovic Fabro, Eurico Arruda, Fernando Queiroz Cunha, Thiago Mattar Cunha, Marco Antônio M. Pretti, Bradley Joseph Smith, Henrique Marques-Souza, Thiago L. Knittel, Gabriel Palermo Ruiz, Gerson S. Profeta, Tereza Cristina Minto Fontes-Cal, Mariana Boroni, Marco Aurélio Ramirez Vinolo, Alessandro S. Farias, Pedro Manoel M. Moraes-Vieira, Joyce Maria Annichino Bizzacchi, Tambet Teesalu, Felipe David Mendonça Chaim, Everton Cazzo, Elinton Adami Chaim, José Luiz Proença-Módena, Daniel Martins-de-Souza, Mariana Kiomy Osako, Luiz Osório Leiria and Marcelo A. Mori, 29 September 2022, Nature Communications.
DOI: 10.1038/s41467-022-33218-8

São Paulo Research Foundation (FAPESP)

Microbiology

Why Does Shingles Lead to Stroke? Scientists Might Have an Answer

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According to recent research from the University of Colorado Anschutz Medical Campus, scientists looking into why people who have had shingles are at a higher risk of stroke now believe the answer lies within lipid vesicles called exosomes that transport proteins and genetic information between cells.

The study explores the mechanisms behind the connection between shingles and strokes and was recently published in The Journal of Infectious Diseases.

“Most people know about the painful rash associated with shingles, but they may not know that the risk of stroke is elevated for a year after infection,” said the study’s lead author Andrew Bubak, Ph.D., assistant research professor in the Department of Neurology at the University of Colorado School of Medicine. “Importantly, the rash is often completely healed and individuals feel normal but nonetheless are walking around with this significant elevation in stroke risk.”

The varicella-zoster virus, which also causes chicken pox, is what causes herpes zoster (HZ), often known as shingles. The virus lingers in the ganglionic neurons and has the potential to reactivate and cause excruciating pain. However, researchers have discovered that shingles can also raise the risk of stroke, particularly in individuals under the age of 40, for whom the shingles vaccination is not normally recommended.

People who have rashes on their faces are more at risk, possibly because of how close the rash is to the brain.

Bubak and his colleagues began researching exosomes more closely to better understand how this works.

“Exosomes carry pathogenic cargo that can cause thrombosis and inflammation distant from the site of actual infection,” Bubak said. “That could ultimately lead to a stroke in patients.”

Researchers collected plasma samples from 13 patients with shingles and 10 without. The samples were taken at the time of infection and at 3-month follow-ups for a subset of patients and exosomes were extracted from the plasma.

The researchers found prothrombotic exosomes which could cause blood clots in those with the infection. They also discovered proinflammatory exosomes that also pose risks for stroke at the 3-month follow-up.

Bubak said the findings suggest that in a subset of people with shingles, the virus may not return to latency, or the circulating exosomes that induce a prolonged prothrombotic state may persist even after therapy is done and the rash is gone. He said using antiviral agents longer with the addition of antiplatelet and anti-inflammatory agents could help.

“As well as initiatives to increase HZ vaccine uptake to decrease stroke risk, particularly in individuals with known preexisting stroke risk factors,” said Bubak. “If these findings are confirmed with a larger longitudinal study, then this could change clinical practice.”

Most physicians are unaware of the connection between shingles – which has an effective vaccine – and stroke.

“But it’s really important and so easily mitigated,” Bubak said. “Send them home with antiplatelet agents.”

Reference: “Zoster-Associated Prothrombotic Plasma Exosomes and Increased Stroke Risk” by Andrew N. Bubak, Christina Coughlan, Janelle Posey, Anthony J. Saviola, Christy S. Niemeyer, Serena W. R. Lewis, Sara Bustos Lopez, Adriana Solano, Stephen K. Tyring, Cassidy Delaney, Keith B. Neeves, Ravi Mahalingam, Kirk C. Hansen and Maria A. Nagel, 6 October 2022, The Journal of Infectious Diseases.
DOI: 10.1093/infdis/jiac405

University of Colorado Anschutz Medical Campus

Microbiology

MGI’s DNBSEQ-T7* recognized for its ultra-high throughput and excellent accuracy

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Reviewed by Emily Henderson, B.Sc.Dec 19 2022

Thanks to high-throughput sequencing technologies, shotgun metagenomic methods were made possible and had effectively transformed microbiology. Today, advances in both short- and long-read technologies are overcoming many of the previous challenges affecting metagenomic profiling, especially of highly complex samples and environment.

Researchers from France’s National Research Institute for Agriculture, Food, and Environment (INRAE) examined the performance of seven short- and long-read sequencing platforms in analyzing high-complexity metagenomic samples. The study, published in the Nature Portfolio journal Scientific Data, ran mock samples between 2018 and 2019 on various mainstream sequencers at the time, including MGI’s DNBSEQ-T7* and DNBSEQ-G400*.

Within this wide range of sequencing technologies tested, DNBSEQ-T7* was recognized for its ultra-high throughput and excellent accuracy. “We were surprised by the T7’s performance,” said senior author Mathieu Almeida, a research fellow at INRAE. “It provides ultra-deep sequencing in a single run with similar low error rate compared to the other platforms, making it at the time of our study one of the most affordable technologies for metagenomic sequencing.”

In the study, three uneven synthetic microbial communities were constructed, consisting of up to 87 genomic microbial strains DNAs each and spanning 29 bacterial and archaeal phyla. They represented some of the most complex and diverse communities used for sequencing technology comparisons. The mock1 (71 strains) was sequenced using all platforms, mock2 (64 strains) was additionally sequenced to estimate the impact of various microbial richness, while MGI’s platforms were not performed on mock3.

To assess the impact of sequencing depth, the team ran a subsampling analysis and compared observed and theoretical genome abundances across samples at multiple depth from 10,000 to 1 million reads. Overall, Spearman rank correlations for all platforms were high at above 0.9 when mapping at least 100,000 reads. Among them, the correlations of T7* and G400* were the best in mock1 and remained excellent in mock2.

In addition, differential analysis between observed and excepted species abundances was performed in mock1. Results showed that over or under abundance estimation for most genomes had little to do with the sequencing platform, read length, taxonomy, GC-content, genome size and genome completeness, even at a low depth of 500,000 reads. In fact, most genomes were accurately estimated on all sequencers, with the observed normalized abundances generated by T7* charting very close to the excepted values.

Based on performance analyses of the different sequencers, the study formed a microbial metagenomic sequencing benchmarking database, providing researchers and scientists a comprehensive and authentic reference for sequencing platform selection. In particular, the findings demonstrated the promising value of MGI’s DNBSEQ-T7* in metagenomic sequencing.

Boasting high stability and accuracy as shown in the data, combined with outstanding throughput, T7* makes a strong platform for the identification of species and functional genes in highly complex microbial communities. Its upgraded biochemical, fluidics, and optical systems are not only making sequencing more efficient and productive, but also continuing to support research into the structure and diversity of microbial communities.

Source:

MGI Tech Co., Ltd.

Journal reference:

Meslier, V., et al. (2022) Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Scientific Data. doi.org/10.1038/s41597-022-01762-z.

Microbiology

Vaccine Confidence Declined Significantly During COVID-19 Pandemic

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Researchers comparing pre and post-pandemic surveys discovered that confidence in vaccinations is considerably lower post-pandemic among all demographic groups.

Despite the success of the COVID-19 vaccination campaigns, vaccine confidence has declined significantly since the start of the pandemic. This is according to a new study published in Vaccine.

Two anonymous surveys in the winters of 2019 and 2022 were carried out to investigate people’s attitudes towards vaccinations and the factors that might underpin hesitancy and refusal by researchers from the University of Portsmouth in England.

By comparing the responses of more than 1,000 adults overall, they discovered that the post-pandemic group was considerably less confident in vaccines than the pre-pandemic group.

Recently published in the medical journal Vaccine, the paper revealed nearly one in four participants reported a fall in confidence since 2020, and this was observed regardless of participants’ age, ethnicity, gender, religious belief, and education.

Dr. Alessandro Siani, Associate Head (Students) of the School of Biological Sciences at the University of Portsmouth, said: “While vaccine hesitancy is not a new phenomenon, COVID-19 vaccines have been met with particular hostility despite the overwhelming scientific evidence of their safety and effectiveness.

“This isn’t just among conspiracy theorists though, but also those who don’t consider themselves ‘anti-vaxxers’ and had supported other vaccination campaigns in the past.”

Participants were asked how much they agreed with statements including:

In both surveys, participants who held religious beliefs were significantly more vaccine-hesitant than atheist and agnostic ones, and individuals from Black and Asian backgrounds were more hesitant than those belonging to White ethnicities. However, gender showed no association with vaccine confidence.

While these overall trends remained largely similar between the two surveys, some noteworthy changes were observed in the post-pandemic survey. For example, the analysis revealed that while in 2019 middle-aged participants were considerably more apprehensive about getting vaccinated than younger groups, this was not the case in the 2022 survey.

“This could be because COVID-19 infections notoriously lead to more severe outcomes in older patients,” added Dr. Siani.

“Young people who are infected rarely experience severe symptoms that lead to hospitalization and death, so it’s possible that many have become complacent and don’t feel the need to get vaccinated. On the other hand, older people may have been more wary of the consequences of the infection, and more appreciative of the protection offered by the vaccine.”

While providing precious insight into how the pandemic affected the public perspectives on vaccinations, the study is not without limitations. The original survey was designed as a standalone piece of research, so a different group of people had to be sampled in 2022. This resulted in a cross-sectional study as opposed to a longitudinal one.

Dr. Siani explained: “We didn’t expect a worldwide pandemic to break out only a few months after carrying out the 2019 survey. Because our findings don’t reflect the changing opinions of the same group of people over time, but rather a comparison of responses provided by two different cohorts, they should be interpreted with a grain of salt.

“However, the study is consistent with other observations suggesting that vaccine confidence may be yet another victim of the COVID-19 pandemic.”

Reference: “Is vaccine confidence an unexpected victim of the COVID-19 pandemic?” by Alessandro Siani and Amy Tranter, 31 October 2022, Vaccine.
DOI: 10.1016/j.vaccine.2022.10.061

University of Portsmouth

Microbiology

Daylong wastewater samples yield surprises

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Testing the contents of a simple sample of wastewater can reveal a lot about what it carries, but fails to tell the whole story, according to Rice University engineers.

Their new study shows that composite samples taken over 24 hours at an urban wastewater plant give a much more accurate representation of the level of antibiotic-resistant genes (ARGs) in the water. According to the Centers for Disease Control and Prevention (CDC), antibiotic resistance is a global health threat responsible for millions of deaths worldwide.

In the process, the researchers discovered that while secondary wastewater treatment significantly reduces the amount of target ARG, chlorine disinfectants often used in later stages of treatment can, in some situations, have a negative impact on water released back into the environment.

The lab of Lauren Stadler at Rice’s George R. Brown School of Engineering reported seeing levels of antibiotic-resistant RNA concentrations 10 times higher in composite samples than what they see in “grabs,” snapshots collected when flow through a wastewater plant is at a minimum.

Stadler and lead authors Esther Lou and Priyanka Ali, both graduate students in her lab, reported their results in the American Chemical Society journal Environmental Science & Technology: Water.

The results could lead to better protocols for treating wastewater to lower the prevalence of antibiotic-resistant genes in bacteria that propagate at plants and can transfer those genes to other organisms in the environment.

The issue is critical because antibiotic resistance is a killer, causing an estimated 2.8 million infections in the U.S. every year, leading to more than 35,000 deaths, said Stadler, an assistant professor of civil and environmental engineering and a pioneer in the ongoing analysis of wastewater for signs of the SARS-CoV-2 virus responsible for COVID-19.

Those statistics have made it a long-standing focus of efforts at Rice that led to the foundation of a new center, Houston Wastewater Epidemiology, a partnership with the Houston Health Department and Houston Public Works. The center is one of two designated by the CDC announced this year to develop tools and train other state and local health departments in the sciences of monitoring wastewater-borne diseases.

The takeaway for testers is that snapshots can lead to unintended biases in their results, Stadler said.

“I think it’s intuitive that grabbing a single sample of wastewater is not representative of what flows across the entire day,” said Stadler, who is also a faculty member of the Rice-based, National Science Foundation-supported Nanotechnology Enabled Water Treatment (NEWT) Center. “Wastewater flows and loads vary across the day, due to patterns of water use. While we know this to be true, no one had shown the degree to which antibiotic-resistant genes vary throughout the day.”

For the study, the Rice team took both grab and composite samples in two 24-hour campaigns, one during the summer and another during winter, at a Houston-area plant that routinely disinfects wastewater.

They took samples every two hours from various stages of the wastewater treatment process and ran PCR tests in the lab to quantify several clinically relevant genes that confer resistance to fluoroquinolone, carbapenem, ESBL and colistin, as well as a class 1 integron-integrase gene known as a mobile genetic element (MGE) for its ability to move within a genome or transfer from one species to another.

The samples they collected allowed them to determine the concentration of ARGs and loads across a typical weekday, the variability in removal rates at plants based on the grab samples and the impact of secondary treatment and chlorine disinfection on the removal of ARGs, as well as the ability to compare grabs and composites.

The team found that the vast majority of ARG removal occurred due to biological processes as opposed to chemical disinfection. In fact, they observed that chlorination, used as the final disinfectant before the treated wastewater is discharged into the environment, may have selected for antibiotic-resistant organisms.

Because the results from snapshots can vary significantly during any given day, they had to be collected at a steady pace over 24 hours. That required Lou and Ali to spend several long shifts at the City of West University Place wastewater treatment plant. “They camped out,” Stadler said. “They set up their cots and ordered takeout.”

Such commitment will not be necessary if real-time wastewater monitoring becomes a reality. Stadler is part of a Rice collaboration developing living bacterial sensors that would detect the presence of ARGs and pathogens, including SARS-CoV-2, without pause at different locations within a wastewater system. The project underway at Rice to build bacterial sensors that emit an immediate electrical signal upon sensing a target was the subject of a study in Nature in November.

“Living sensors can enable continuous monitoring as opposed to relying on expensive equipment to collect composite samples that need to be brought back to the lab to analyze,” she said. “I think the future is these living sensors that can be placed anywhere in the wastewater system and report on what they see in real time. We’re working towards that.”

Rice undergraduate Karen Lu and Prashant Kalvapalle, a graduate student in the Systems, Synthetic and Physical Biology Ph. D. program, are co-authors of the study.

The National Science Foundation (2029025, 1805901, 1932000) and a Johnson & Johnson WiSTEM2D award supported the research.

Story Source:

Materials provided by Rice University. Original written by Mike Williams. Note: Content may be edited for style and length.

Journal Reference:

  • Esther G. Lou, Priyanka Ali, Karen Lu, Prashant Kalvapalle, Lauren B. Stadler. Snapshot ARG Removal Rates across Wastewater Treatment Plants Are Not Representative Due to Diurnal Variations. ACS ES&T Water, 2022; DOI: 10.1021/acsestwater.2c00467

    • Rice University
    Microbiology

    The microbes in the gut can metabolize some of the foods we eat to produce new molecules, some …

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    The microbes in the gut can metabolize some of the foods we eat to produce new molecules, some of which can affect our health. Researchers have previously shown that gut microbes can metabolize proteins in the diet to generate phenylacetylglutamine (PAG), a chemical that increases the risk of heart disease. New research has confirmed that link using human data, and expanded on what we know with an analysis of heart cells. The findings have been reported in Circulation: Heart Failure. This research may help scientists develop strategies to mitigate PAG-associated risks.

    Image credit: Pixabay

    This study assessed data from over 3,000 Americans and over 800 Europeans. It showed that increased PAG levels are linked to heart failure. Individuals with heart failure with preserved ejection fraction, in which there is a lack of heart muscle relaxation between beats, have elevated blood PAG levels, for example.

    Blood PAG levels may serve to predict who is at risk for heart failure, suggested corresponding study author Stanley Hazen, M.D., Ph.D., department chair of Cardiovascular & Metabolic Sciences at the Lerner Research Institute. “The data build a strong case that making this test available for clinicians would add to their arsenal of diagnostic tests for heart failure.”

    Hazen and colleagues reported that PAG can influence adrenergic receptors on platelets, which can affect things like blood clotting risks, in a study reported in Cell in 2020. That study is outlined in the video below.

    This latest rsearch also showed that PAG and the parallel molecule found in mice, phenylacetylglycine, promote changes in gene expression and conditions that are related to heart failure, such as a reduction in contractility in certain heart cells.

    Heart failure and cardiac disease is still a major cause of death around the world. Changes in diet that affect PAG levels may be one way to reduce the risk of heart disease.

    “This study substantially expands the breadth of possible links between our diet and how our gut microbiome serves as a filter of our diet, impacting our susceptibility to develop different diseases,” said Hazen. “In this case, gut microbes form a metabolite from the amino acid phenylalanine in dietary protein, adversely impacting the function of a beating cardiac muscle cell.”

    Hazen’s team is searching for the bacterium or bacteria and the enzymes they make that are involved in PAG production, and how to reduce PAG levels. Diet modifications might be a way to reduce risk too, added Hazen.

    Sources: Cleveland Clinic, Circulation: Heart Failure


    Carmen Leitch