Tag Archives: Microbiome

Microbiology

Urethra of Healthy Men Is Teeming With Microbial Life – Vaginal Sex Results in Distinct Microbiome

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Contrary to common beliefs, your urine is not germ-free. In fact, a new study shows that the urethra of healthy men is teeming with microbial life and that a specific activity—vaginal sex—can shape its composition. The research, published on March 24 in the journal Cell Reports Medicine, provides a healthy baseline for clinicians and scientists to contrast between healthy and diseased states of the urethra, an entrance to the urinary and reproductive systems.

“We know where bugs in the gut come from; they primarily come from our surroundings through fecal-oral transfer,” says co-senior author David Nelson, a microbiologist at Indiana University. “But where does genital microbiology come from?”

To flush out the answer, the team of microbiologists, statisticians, and physicians sequenced the penile urethra swabs of 110 healthy adult men. These participants had no urethral symptoms or sexually transmitted infections (STIs) and no inflammation of the urethra. DNA sequencing results revealed that two types of bacterial communities call the penile urethra home—one native to the organ, the other from a foreign source.

“It is important to set this baseline,” says co-senior author Qunfeng Dong, a bioinformatician at Loyola University Chicago. “Only by understanding what health is can we define what diseases are.”

The researchers found that most of the healthy men had a simple, sparse community of oxygen-loving bacteria in the urethra. In addition, these bacteria probably live close to the urethral opening at the tip of the penis, where there is ample oxygen. The consistent findings of these bacteria suggest that they are the core community that supports penile urethra health.

But some of the men also had a more complex secondary group of bacteria that are often found in the vagina and can disturb the healthy bacterial ecosystem of the vagina. The team speculates that these bacteria reside deeper in the penile urethra because they thrive in oxygen-scarce settings. Only men who reported having vaginal sex carry these bacteria, hinting at the microbes’ origins.

Delving into the participant’s sexual history, the team found a close link between this second bacterial community and vaginal sex but not other sexual behaviors, such as oral sex and anal sex. They also found evidence that vaginal sex has lasting effects. Vagina-associated bacteria remained detectable in the participants for at least two months after vaginal sex, indicating that sexual exposure to the vagina can reshape the male urinary-tract microbiome.

“In our study, one behavior explains 10% of the overall bacterial variation,” says Nelson, when discussing the influence of vaginal sex. “The fact that a specific behavior is such a strong determinant is just profound.”

Although current findings from the study show that vaginal bacteria can spread to the penile urethra, the team’s next plan is to test whether the reverse is true. Using the newly established baseline, the researchers also hope to offer new insights into bacteria’s role in urinary- and reproductive-tract diseases, including unexplained urethral inflammation and STIs.

“STIs really impact people who are socioeconomically disadvantaged; they disproportionately impact women and minorities,” says Nelson. “It’s a part of health care that’s overlooked because of stigma. I think our study has a potential to dramatically change how we handle STI diagnosis and management in a positive way.”

Reference: “Sexual behavior shapes male genitourinary microbiome composition” by Evelyn Toh, Yue Xing, Xiang Gao, Stephen J. Jordan, Teresa A. Batteiger, Byron E. Batteiger, Barbara Van Der Pol, Christina A. Muzny, Netsanet Gebregziabher, James A. Williams, Lora J. Fortenberry, J. Dennis Fortenberry, Qunfeng Dong and David E. Nelson, Cell Reports Medicine.
DOI: 10.1016/j.xcrm.2023.100981

This work was supported by the National Institute of Allergy and Infectious Diseases.

Cell Press

Microbiology

Vaginal sex can shape the composition of urethral microbiome in healthy men

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Reviewed by Emily Henderson, B.Sc.Mar 21 2023

Contrary to common beliefs, your urine is not germ free. In fact, a new study shows that the urethra of healthy men is teeming with microbial life and that a specific activity-;vaginal sex-;can shape its composition. The research, published March 24 in the journal Cell Reports Medicine, provides a healthy baseline for clinicians and scientists to contrast between healthy and diseased states of the urethra, an entrance to the urinary and reproductive systems.

We know where bugs in the gut come from; they primarily come from our surroundings through fecal-oral transfer. But where does genital microbiology come from?”

David Nelson, co-senior author, microbiologist at Indiana University

To flush out the answer, the team of microbiologists, statisticians, and physicians sequenced the penile urethra swabs of 110 healthy adult men. These participants had no urethral symptoms or sexually transmitted infections (STIs) and no inflammation of the urethra. DNA sequencing results revealed that two types of bacterial communities call the penile urethra home-;one native to the organ, the other from a foreign source.

“It is important to set this baseline,” says co-senior author Qunfeng Dong, a bioinformatician at Loyola University Chicago. “Only by understanding what health is can we define what diseases are.”

The researchers found that most of the healthy men had a simple, sparse community of oxygen-loving bacteria in the urethra. In addition, these bacteria probably live close to the urethral opening at the tip of the penis, where there is ample oxygen. The consistent findings of these bacteria suggest that they are the core community that supports penile urethra health.

But some of the men also had a more complex secondary group of bacteria that are often found in the vagina and can disturb the healthy bacterial ecosystem of the vagina. The team speculates that these bacteria reside deeper in the penile urethra because they thrive in oxygen-scarce settings. Only men who reported having vaginal sex carry these bacteria, hinting at the microbes’ origins.

Delving into the participant’s sexual history, the team found a close link between this second bacterial community and vaginal sex but not other sexual behaviors, such as oral sex and anal sex. They also found evidence that vaginal sex has lasting effects. Vagina-associated bacteria remained detectable in the participants for at least two months after vaginal sex, indicating that sexual exposure to the vagina can reshape the male urinary-tract microbiome.

“In our study, one behavior explains 10% of the overall bacterial variation,” says Nelson, when discussing the influence of vaginal sex. “The fact that a specific behavior is such a strong determinant is just profound.”

Although current findings from the study show that vaginal bacteria can spread to the penile urethra, the team’s next plan is to test whether the reverse is true. Using the newly established baseline, the researchers also hope to offer new insights into bacteria’s role in urinary- and reproductive-tract diseases, including unexplained urethral inflammation and STIs.

“STIs really impact people who are socioeconomically disadvantaged; they disproportionately impact women and minorities,” says Nelson. “It’s a part of health care that’s overlooked because of stigma. I think our study has a potential to dramatically change how we handle STI diagnosis and management in a positive way.”

This work was supported by the National Institute of Allergy and Infectious Diseases.

Source:

Cell Press

Journal reference:

Toh, E., et al. (2023). Sexual behavior shapes male genitourinary microbiome composition. Cell Reports Medicine. doi.org/10.1016/j.xcrm.2023.100981

Microbiome

BioChek – A Hygiena® Company and Global Specialists in Animal Health

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BioChek’s innovative, user-friendly veterinary diagnostic tools and services consist of:

BioChek – more than experts in Veterinary Diagnostics
Infectious bronchitis, Newcastle disease, Gumboro, PCV2, PRRS… any Poultry and Swine farmer would rather do without these threats to the productivity of their animals and therefore, maximise business return. For every Poultry and Swine farmer, the health of the chicken flock or swine herd is the number one concern. This is something BioChek has supported since its formation in 1997. Our mission is to maximize Animal Health by partnering with Poultry and Swine vets and veterinary labs. BioChek utilises state-of-the art diagnostic products and systems to monitor and optimise the health of Poultry and Swine across the globe.

Smart Veterinary Diagnostics
In addition to service, innovation is key to BioChek’s success. We have a modern research and development department, which without doubt deserves the innovative label. A department staffed by an expert R&D team that guarantees the design and development of smart veterinary diagnostics. These diagnostic tools are developed in conjunction with the wishes and requirements of Poultry and Swine vets, which is of paramount importance to their chances of success.

Furthermore, BioChek invests intensively in collaboration with veterinary professionals and producers of vaccines. This collaboration results in a varied but focussed product portfolio which fully meets the requirements of the vets, laboratory technicians and professional livestock farmers. Our production facility is ISO 9001 certified and as such, our products are produced in accordance with the highest quality standards, which are often certified by, amongst others, the United States Department of Agriculture (USDA) and the World Organisation for Animal Health (OIE), among others.

2314_BioChek_RMB

For more information, please visit: www.biochek.com or use the Request Information button to contact the company directly.

RMB

Microbiology

Beware of the Microbial Mirage: Current Microbiome Analyses May Mislead Scientists With False Species Detection

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Research study of simulated microbial communities shows analyses are flawed by incomplete DNA databases.

Common approaches to analyzing DNA from a community of microbes, called a microbiome, can yield erroneous results, in large part due to the incomplete databases used to identify microbial DNA sequences. A team led by Aiese Cigliano of Sequentia Biotech SL, and Clemente Fernandez Arias and Federica Bertocchini of the Centro de Investigaciones Biologicas Margarita Salas, report these findings in a research paper published on February 8 in the open-access journal PLOS ONE.

Microbiomes have been the focus of intense research efforts in recent decades. These studies range from attempts to understand conditions such as obesity and autism by examining the human gut, to finding microbes that degrade toxic compounds or produce biofuels by studying environmental communities. The most commonly used methods for studying microbial communities rely on comparing the DNA obtained from a biological sample to sequences in genome databanks. Therefore, researchers can only identify DNA sequences that are already in the databases – a fact that may severely compromise the reliability of microbiome data in unexpected ways.

To test the consistency of current methods of microbiome analysis, researchers used computer simulations to create virtual microbiome communities that imitate real-world bacterial populations. They used standard techniques to analyze the virtual communities and compared the results with the original composition. The experiment showed that results from DNA analyses can bear little resemblance to the actual composition of the community, and that a large number of the species “detected” by the analysis are not actually present in the community.

For the first time, the study demonstrates significant flaws in the techniques currently used to identify microbial communities. The researchers conclude that there is a need for increased efforts to collect genome information from microbes and to make that information available in public databases to improve the accuracy of microbiome analysis. In the meantime, the results of microbiome studies should be interpreted with caution, especially in cases where the available genomic information from those environments is still scarce.

The authors add: “This study reveals intrinsic constraints in metagenomic analysis stemming from current database limitations and how genomic information is used. To enhance the reliability of metagenomic data, a research effort is necessary to improve both database contents and analysis methods. Meanwhile, metagenomic data should be approached with great care.”

Reference: “The virtual microbiome: A computational framework to evaluate microbiome analyses” by Belén Serrano-Antón, Francisco Rodríguez-Ventura, Pere Colomer-Vidal, Riccardo Aiese Cigliano, Clemente F. Arias and Federica Bertocchini, 8 February 2023, PLOS ONE.
DOI: 10.1371/journal.pone.0280391

Funding: FB and CFA gratefully acknowledge support by the Roechling foundation. BS was partially supported by MINECO grant MTM2017-85020-P. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

PLOS

Microbiology

Host immune system forms small lesions in the intestines in response to bacterial infection

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Reviewed by Emily Henderson, B.Sc.Mar 14 2023

Yersinia bacteria cause a variety of human and animal diseases, the most notorious being the plague, caused by Yersinia pestis. A relative, Yersinia pseudotuberculosis, causes gastrointestinal illness and is less deadly but naturally infects both mice and humans, making it a useful model for studying its interactions with the immune system.

These two pathogens, as well as a third close cousin, Y. enterocolitica, which affects swine and can cause food-borne illness if people consume infected meat, have many traits in common, particularly their knack for interfering with the immune system’s ability to respond to infection.

The plague pathogen is blood-borne and transmitted by infected fleas. Infection with the other two depends on ingestion. Yet the focus of much of the work in the field had been on interactions of Yersinia with lymphoid tissues, rather than the intestine. A new study of Y. pseudotuberculosis led by a team from Penn’s School of Veterinary Medicine and published in Nature Microbiology demonstrates that, in response to infection, the host immune system forms small, walled-off lesions in the intestines called granulomas. It’s the first time these organized collections of immune cells have been found in the intestines in response to Yersinia infections.

The team went on to show that monocytes, a type of immune cell, sustain these granulomas. Without them, the granulomas deteriorated, allowing the mice to be overtaken by Yersinia.

“Our data reveal a previously unappreciated site where Yersinia can colonize and the immune system is engaged,” says Igor Brodsky, senior author on the work and a professor and chair of pathobiology at Penn Vet. “These granulomas form in order to control the bacterial infection in the intestines. And we show that if they don’t form or fail to be maintained, the bacteria are able to overcome the control of the immune system and cause greater systemic infection.”

The findings have implications for developing new therapies that leverage the host immune system, Brodsky says. A drug that harnessed the power of immune cells to not only keep Yersinia in check but to overcome its defenses, they say, could potentially eliminate the pathogen altogether.

A novel battlefield

Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica share a keen ability to evade immune detection.

“In all three Yersinia infections, a hallmark is that they colonize lymphoid tissues and are able to escape immune control and replicate, cause disease, and spread,” Brodsky says.

Earlier studies had shown that Yersinia prompted the formation of granulomas in the lymph nodes and spleen but had never observed them in the intestines until Daniel Sorobetea, a research fellow in Brodsky’s group, took a closer look at the intestines of mice infected with Y. pseudotuberculosis.

“Because it’s an orally acquired pathogen, we were interested in how the bacteria behaved in the intestines,” Brodsky says. “Daniel made this initial observation that, following Yersinia pseudotuberculosis infection, there were macroscopically visible lesions all along the length of the gut that had never been described before.”

The research team, including Sorobetea and later Rina Matsuda, a doctoral student in the lab, saw that these same lesions were present when mice were infected with Y. enterocolitica, forming within five days after an infection.

A biopsy of the intestinal tissues confirmed that the lesions were a type of granuloma, known as a pyogranuloma, composed of a variety of immune cells, including monocytes and neutrophils, another type of white blood cell that is part of the body’s front line in fighting bacteria and viruses.

Granulomas form in other diseases that involve chronic infection, including tuberculosis, for which Y. pseudotuberculosis is named. Somewhat paradoxically, these granulomas-;while key in controlling infection by walling off the infectious agent-;also sustain a population of the pathogen within those walls.

The team wanted to understand how these granulomas were both formed and maintained, working with mice lacking monocytes as well as animals treated with an antibody that depletes monocytes. In the animals lacking monocytes “these granulomas, with their distinct architecture, wouldn’t form,” Brodsky says.

Instead, a more disorganized and necrotic abscess developed, neutrophils failed to be activated, and the mice were less able to control the invading bacteria. These animals experienced higher levels of bacteria in their intestines and succumbed to their infections.

Groundwork for the future

The researchers believe the monocytes are responsible for recruiting neutrophils to the site of infection and thus launching the formation of the granuloma, helping to control the bacteria. This leading role for monocytes may exist beyond the intestines, the researchers believe.

We hypothesize that it’s a general role for the monocytes in other tissues as well.”

Igor Brodsky, senior author

But the discoveries also point to the intestines as a key site of engagement between the immune system and Yersinia.

“Previous to this study we knew of Peyer’s patches to be the primary site where the body interacts with the outside environment through the mucosal tissue of the intestines,” says Brodsky. Peyer’s patches are small areas of lymphoid tissue present in the intestines that serve to regulate the microbiome and fend off infection.

In future work, Brodsky and colleagues hope to continue to piece together the mechanism by which monocytes and neutrophils contain the bacteria, an effort they’re pursing in collaboration with Sunny Shin’s lab in the Perelman School of Medicine’s microbiology department.

A deeper understanding of the molecular pathways that regulate this immune response could one day offer inroads into host-directed immune therapies, by which a drug could tip the scales in favor of the host immune system, unleashing its might to fully eradicate the bacteria rather than simply corralling them in granulomas.

“These therapies have caused an explosion of excitement in the cancer field,” Brodsky says, “the idea of reinvigorating the immune system. Conceptually we can also think about how to coax the immune system to be reinvigorated to attack pathogens in these settings of chronic infection as well.”

Source:

University of Pennsylvania

Journal reference:

Sorobetea, D., et al. (2023). Inflammatory monocytes promote granuloma control of Yersinia infection. Nature Microbiology. doi.org/10.1038/s41564-023-01338-6.

Microbiology

The right combination of bile salt hydrolases may offer a new approach to treat C. diff

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Reviewed by Emily Henderson, B.Sc.Mar 13 2023

Not all probiotics are created equal. In a new study, researchers found that certain enzymes within a class known as bile salt hydrolases (BSHs) can restrict Clostridioides difficile (C. diff.) colonization by both altering existing bile acids and by creating a new class of bile acids within the gut’s microbial environment. The work could lead to “designer” probiotics that protect against disease by introducing specific BSHs to the gut after antibiotic treatment.

Selecting the right suite of BSH-producing bacteria is critical, because the study found that interactions between BSHs and bile acids differ depending upon the type of bacteria the BSHs come from.

Certain bacteria within the gut microbiota contain BSH enzymes, which chemically modify bile acids. Bile acids are made in the liver and play an important role in modulating cholesterol levels, regulating fat absorption, shaping the immune system, and affecting which bacteria can colonize the gut.

Although researchers had long suspected a connection between BSHs from beneficial bacteria, the bile acid pool, gut microbial composition and host health, until now relatively little was known about how BSHs function and their potential impacts on host health.

The old dogma – that BSHs are needed for gut colonization because they render toxic bile acids non-toxic – oversimplified what’s actually happening.”

Casey Theriot, associate professor of infectious disease at North Carolina State University and co-corresponding author of the study

“The reality is that BSHs’ interactions are context-dependent, meaning they’re affected by the type of bacteria they come from,” Theriot says. “And they don’t just interact with bile acids produced by the host. BSHs in the microbiota can create and interact with a new class of bile acids called microbial conjugated bile acids (MCBAs) – bile acids that we didn’t even know existed until recently.”

In the new study, Theriot led a collaborative research team that included microbiologists, chemists, biochemists, and clinicians from NC State, the University of North Carolina at Chapel Hill, and the University of California, San Diego on a deep dive into BSHs.

Specifically, they looked at hundreds of BSHs from different Lactobacillaceae bacteria (which houses most probiotic strains) and then included BSHs from the gut microbiota (nearly 1,000 unique BSHs in total).

Matthew Redinbo, Kenan Distinguished Professor of Chemistry in UNC-Chapel Hill’s College of Arts and Sciences, and his departmental colleagues (led by then graduate student Morgan Walker) were instrumental in determining the structure of BSHs and how they “choose” to interact with bile acids, by either adding or taking away certain amino acids.

“We found the tiny molecular fingerprint that defined whether a BSH would ‘turn left’ or ‘turn right’ in terms of what they processed,” Redinbo says. “Knowing that allowed Casey’s team to steer the bile acid pool in whatever direction they wanted.”

The researchers used a cocktail of Lactobacillus BSHs to figure out if they could change the bile acid pool enough to alter C. diff colonization in both human stool samples collected from patients susceptible to C. diff infection (CDI) and in a mouse model of CDI. In both human stool samples and mice, the researchers saw that pre-treatment with BSH cocktails impacted C. diff colonization. Interestingly, the researchers noted elevated levels of MCBAs in the gut microbiota of the BSH-treated mice.

To determine whether the MCBAs were also involved in inhibiting C. diff germination and growth, they tested the MCBAs against C. diff in vitro. In most cases, the presence of MCBAs inhibited multiple steps of the C. diff life cycle.

“This is more evidence that BSHs are driving changes in the bile acid pool – including making MCBAs – that could serve to inhibit C. diff,” Theriot says. “We’ve uncovered a new function for BSH enzymes.”

“This work highlights the importance of BSHs as key intestinal enzymes and promising new therapeutics,” says Matt Foley, research scholar at NC State and co-first author of the study. “Using BSHs in combination with other strategies may offer a new approach to treat C. diff.“

The researchers see the work as the first step toward potential probiotics that could be customized to protect against a variety of bacterial infections and intestinal diseases. But first, more work must be done to determine how and why the BSHs decide which MCBAs to produce and/or target.

“This is an important illustration of how deciphering the biochemical and genetic basis for probiotic functionality both leads to a better understanding of how we can combat gut disease with novel modalities, and also practically design and formulate next-generation commercial probiotics,” says Rodolphe Barrangou, the Todd R. Klaenhammer Distinguished Professor in Probiotics Research at NC State and co-corresponding author of the study.

The work appears in Nature Microbiology and was supported by the National Institutes of Health, the National Science Foundation, IFF Corporation and the U.S. Environmental Protection Agency. The MCBA detection work was done by Erin Baker, formerly of NC State and currently at UNC-Chapel Hill, Allison Stewart of NC State, and Emily Gentry and Pieter Dorrestein from UCSD.

Source:

North Carolina State University

Journal reference:

Foley, M. H., et al. (2023). Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. Nature Microbiology. doi.org/10.1038/s41564-023-01337-7.

Microbiology

New study focuses on genetic diversity of E. coli bacteria in hospitalized patients

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Reviewed by Emily Henderson, B.Sc.Mar 13 2023

The human intestine is an environment inhabited by many bacteria and other microorganisms collectively known as the gut microbiome, gut microbiota or intestinal flora. In most people, it contributes to wellness. A healthy gut indicates a stronger immune system, improved metabolism, and a healthy brain and heart, among other functions.

Escherichia coli is one of the bacteria found in practically everyone’s gut microbiota, where it performs important functions, such as producing certain vitamins.

But there’s a vast amount of genetic diversity in the species. Some of its members are pathogenic and can cause diseases such as urinary tract infections. E. coli is the main agent of this type of infection among both healthy people and hospitalized patients or users of healthcare services.”

Tânia Gomes do Amaral, Head of the Experimental Enterobacterial Pathogenicity Laboratory (LEPE), Federal University of São Paulo’s Medical School (EPM-UNIFESP), Brazil

Amaral is first author of an article published in the journal Pathogens on the virulence of these bacteria and their resistance to antibiotics in hospitalized patients.

“Our study focused on hospitalized patients because patients who stay in hospital for a long period are more likely to undergo various procedures, such as urine catheter insertion or venous access. Although these procedures are performed to assure life support, they may facilitate the entry of bacteria into the organism and cause an infection,” Amaral explained.

She earned a PhD in microbiology from EPM-UNIFESP in 1988, conducting part of her research at New York University Medical School and the Center for Vaccine Development at the University of Maryland, Baltimore (UMB) in the United States.

The article reports the findings of a broader study led by Amaral, with 12 co-authors who are researchers and graduate students, on the virulence and drug resistance of E. coli strains associated with urinary tract infections. The study was supported by FAPESP via three projects (18/17353-7, 19/21685-8 and 17/14821-7).

The main aim of this part of the study, described in the master’s dissertation of José Francisco Santos Neto, was to evaluate the diversity and drug resistance of pathogenic E. coli strains isolated from the gut microbiota of inpatients, and to analyze the frequency of endogenous infection (caused by bacteria from the patient’s own microbiota).

The UNIFESP group first investigated the genetic diversity and drug resistance of E. coli strains isolated from the gut microbiota of hospitalized patients, sequencing these strains as well as others isolated from their urine and comparing the results in order to evaluate dissemination of the bacteria in the hospital environment.

“We also compared the genomes of these strains with those of E. coli strains isolated in different parts of the world in order to see if any globally disseminated pathogenic bacteria were present in the study sample,” said Ana Carolina de Mello Santos, a postdoctoral researcher working on the LEPE team.

Urinary tract infections proved to be endogenous for the vast majority of the patients in the study (more than 70%). The results also showed that the patients’ gut microbiota contained at least two genetically different populations of E. coli and that about 30% were colonized by non-lactose-fermenting E. coli strains, which are less common, with some of the patients studied having only such strains in their gut microbiota.

“This finding is most interesting because previous research conducted in other countries to analyze the composition of human gut microbiota didn’t investigate non-lactose-fermenting E. coli,” Santos said.

The authors also note the presence of bacteria with all the genetic markers required for classification as pathogenic and the detection of pathogenic bacteria in the gut microbiota of all patients that had not yet developed an infection. “Hospitalized patients are more susceptible to infection because by definition they are already unwell. Colonization by pathogens is the first step in the spread of hospital-acquired infections now so frequent worldwide,” Santos said.

With regard to antibiotics and other antimicrobials, the authors stress that drug resistance is also a growing global problem, and enterobacterial resistance to third-generation cephalosporins as well as colistin is critical. In all patients whose gut microbiota was colonized by drug-resistant bacteria, the same bacteria also caused endogenous urinary tract infections. In other words, the multidrug-resistant bacteria colonized the gut and traveled to the urinary tract, where they caused an infection.

“In light of these findings, early assessment of gut microbiota in hospitalized patients, at least in cases of E. coli infection, can facilitate and guide their treatment, while also identifying patients who risk progressing to extra-intestinal diseases such as urinary tract infections, which were part of the focus for our study,” Amaral said. “We don’t yet know whether the findings also apply to other bacteria found in gut microbiota, such as the genera Klebsiella, Enterobacter, Pseudomonas and others that can cause infections when they travel to extra-intestinal sites.”

These bacterial genera tend to be even more drug-resistant than E. coli, representing a major public health problem in the hospital environment. As the researchers noted, the World Health Organization (WHO) considers E. coli strains resistant to cephalosporin and colistin to be a critical global health threat. “The presence in human gut microbiota of drug-resistant bacteria associated with severe infectious disease is a matter of great concern, not least because they could spread to people outside the hospital environment,” Amaral said.

Another point raised by the study is the importance of finding out when colonization of the patient’s gut by drug-resistant virulent bacteria occurred. The authors of the article were unable to determine whether the bacteria resistant to cephalosporins and colistin colonized the patients before or after they were hospitalized.

By analyzing the genomes of the strains, however, the researchers were able to identify global risk clones that can cause severe disease and are associated with antimicrobial resistance. “One such clone found in the gut microbiota of two patients was identical to others isolated from urinary tract infections in Londrina, Paraná [a state in South Brazil], and in the United States, as well as European and Asian countries. This shows that some strains found in the study are clones generally associated with infections in all regions of the world,” Amaral said.

This type of information is important when patients are hospitalized. Knowledge of bacterial virulence and drug resistance can be used to prevent infection in parts of the organism outside the intestine and stop the bacteria from spreading to other patients in the same hospital.

Source:

São Paulo Research Foundation (FAPESP)

Journal reference:

Santos-Neto, J.F., et al. (2023) Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens. doi.org/10.3390/pathogens11121528.

Microbiology

Review on factors related to variations in human microbiota

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Pooja Toshniwal PahariaBy Pooja Toshniwal PahariaMar 8 2023Reviewed by Aimee Molineux

In a recent review published in Current Opinion in Microbiology, researchers reviewed existing data on variations in human microbiota, emphasizing on ageing- and ethnicity-associated changes in the microbiota.

Study: Human microbiome variance is underestimated. Image Credit: Troyan/Shutterstock
Study: Human microbiome variance is underestimated. Image Credit: Troyan/Shutterstock

Background

Human microbial heterogeneity lays the foundation for precision therapeutics, and thus, the potential of personalized microbiota-based diagnostic and therapeutic strategies can be tapped fully by understanding human microbial variations. However, the factors associated with alterations in the human microbiome have yet to be well-characterized.

Further, most of the human microbiota data has been obtained from residents of westernized and socioeconomically developed nations, with the probable skewing of microbiota variations and their associations with health. Moreover, the under-sampling of ethnic minorities in microbiota analyses must be addressed for assessing the history, context, and evolving dynamics of the human microbiota in the context of disease risks.

About the review

In the present review, researchers highlighted recent advances in characterizing human microbiota variations associated with ageing and various ethnicities globally.

Age-related changes in the microbiota of humans

Factors that shape the human microbiota include birth type, family sizes, cohabitation, housing, domestic animals, age, sex, physical fitness, diet, antibiotics, non-antibiotic drugs, and alcohol intake. At the societal level, complex associations of health inequalities, socioeconomic status, and social networks with the human microbiome balance have been reported.

Studies have demonstrated an inverse association between the microbiota and an individual’s age, and conversely, microbial compositional variations contribute to the process of ageing and age-associated diseases. All individuals do not age uniformly, and the differential ageing rates reflect in the human microbiota. Therefore, the human microbiota abundance is evolving as a biomarker to evaluate differences in the biological age and chronological age and between health and disease. Human microbiomes lacking Bacteroides species have been strongly associated with a healthy type of ageing.

Other factors related to variations in the human microbiota composition

Mediterranean diets, involving reduced intake of saturated-type fats, red meat, and milk products, with high consumption of fruits, vegetables, fish, legumes, nuts, and olive oil, have been reported to reverse age-associated microbiota alterations and delay cognitive decline. Studies have reported the co-evolution of human beings and intestinal microbes, with notable variations in Helicobacter pylori diversity associated with human migration.

Microbiome compositions vary among individuals residing in industrialized or non-industrialized regions. Non-industrialized region-associated microbiomes or ancestral microbes have adapted to metabolizing complex-type carbohydrates from diets with high fibre content. The microbial compositions vary by season, climatic fluctuations, and accessibility to unprocessed-type foods. The microbiome of individuals living in non-industrialized regions reportedly has lower Bacteroides/Prevotella spp. ratio, elevated counts of Treponema species, and varying abundance of parasites that affect the immunity of the host.

Naturally maintained palaeofaeces microbiome genomes resemble the genomes of non-industrialized human intestinal microbiota. Socioeconomic developments and industrialization have been associated with microbiome diversity losses, lowered parasitism, reduced counts of ancestral microbes like Helicobacter pylori species and elevated counts of microbes associated with non-communicable and chronic metabolic and inflammatory diseases.

Immigration has been related to an increased abundance of microbes associated with obesity. A study on Irish travellers reported three key factors influencing the human microbiota composition, i.e., living conditions, closeness to domestic pets during childhood and family sizes, with the average number of siblings among traveller families and other families being 10, and one, respectively).

Conclusions

Based on the review findings, the human microbiome is influenced by age, diet, ethnicity and immigration. Further research is required to improve understanding of age-related microbiome changes to identify targets and develop tailored microbiota-based therapeutic interventions. The increase or decrease in microbial abundance associated with changes in dietary patterns and modernization needs to be assessed further to develop highly specific precision medicine catered to the residential locations and food consumed.

The co-diversification of microbes with humans globally warrants in-depth analysis of microbial compositions by ethnicity, region, diet, and industrialization status to maximize the benefit of microbiota-based interventions to one and all. Microbial analyses were performed to evaluate the risk of disease in relation to microbiome dysbiosis and abrupt changes following immigration could inform policy-makers and decision-making and aid in developing personalized therapeutics to improve the standard of care for all individuals across the globe.

Journal reference:
Microbiology

Do seasonal changes in food types lead to changes in the composition and structure of gut microbiota?

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Bhavana KunkalikarBy Bhavana KunkalikarMar 6 2023Reviewed by Danielle Ellis, B.Sc.

In a recent study published in the Frontiers in Microbiology, researchers assessed the impact of diet or macronutrient consumption on the function and structure of gut microbiota.

Study: Does diet or macronutrients intake drive the structure and function of gut microbiota? Image Credit: Alpha Tauri 3D Graphics/Shutterstock
Study: Does diet or macronutrients intake drive the structure and function of gut microbiota? Image Credit: Alpha Tauri 3D Graphics/Shutterstock

Background

Shifting ingestive behavior is crucial for animals to adjust to environmental change. Studies have recognized that changes in animal feeding habits lead to gut microbiota structure alterations. However, further research is required to understand the alterations incident in the structure as well as the function of the gut microbiota that occur in response to alterations in nutrient consumption or food types.

About the study

In the present study, researchers explored how animal feeding techniques influence nutrient consumption and further affect the content and digestive function of the gut microbiota.

The study observation site was in the Guanyin Mountain National Natural Reserve in the Qinling Mountains, northwest of Fuping County, Shaanxi Province, China. During a year, this area experiences conventional and four different seasons. According to climate, the seasons are as follows: Spring between March and May, Summer between June and August, Autumn between September and November, and Winter between December and February.

The team compiled feeding information for the four seasonal groupings. For data collection, a month with typical phenological characteristics for each season: March for Spring, June for Summer, October for Autumn, and December for Winter.

All of the 78 golden snub-nosed monkeys in the study group were accustomed to the presence of researchers. The team identified both adult and young individuals in the study cohort. Due to the necessity for quantitative observational data, the natural feeding area of the study animals was restricted. The team provided five kilograms of maize twice daily at 10 am and 3 pm as supplemental nourishment for the group. The feed grounds were evenly strewn with corn kernels.

The team randomly selected one individual per day and observed the subject animal continuously from sunrise to dusk to record data related to its feeding pattern. Furthermore, the type of food, quantity, preset units, and feeding duration were recorded. After the subject had finished eating, food samples were gathered from the leftovers.

Food samples were collected using conventional procedures, their nutritional content was assessed, and their energy content was computed. The lipid, starch, water-soluble carbohydrate (WSC), acid detergent fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), ash content of each food, and available protein (AP) were evaluated.

Results

Data related to 96 days of feeding across four months were obtained from the target population. It was discovered that the normal diet of golden snub-nosed monkeys in the wild comprised 24 plant species from 16 families. A total of six plant parts, including branches, buds, seeds, barks, leaves, and stems, were consumed by the subjects.

Throughout the year, wild snub-nosed monkeys eat 33.43% of bark, 3.09% of seed, 1.33% of bud, 3.25% of brunch, 0.17% of the stem, and 58.72% of the leaf. Nonetheless, there were significant variations in the number of plant materials consumed over the four seasons. Herbaceous stems were harvested only in tiny quantities in the Spring. Mostly, seeds were harvested in the Spring and fall. The harvesting of leaves occurred throughout the year. Throughout fall and Winter, when leaves become sparse, especially in Winter, barks, buds, and brunches were the principal sources of nutrition.

The species composition was evaluated to explore seasonal changes in gut microbiota in greater depth. Species annotation revealed that most OTUs could be assigned taxonomically at the phylum and order levels, but assignments reduced dramatically at the genus level.

The top 10 phyla out of 38 phyla recognized dominant phyla, including Bacteroidetes, Firmicutes, Spirochaetes, Proteobacteria, Tenericutes, Planctomycetes, Verrucomicrobia, Epsilonbacteriaeota, Euryarchaeota, and Fibrobacteres comprised 99% of the total abundance ratio. They comprised the majority of the golden snub-nosed monkeys’ gut microbiome.

Three hundred ninety-five metabolic pathways were found based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database’s function prediction. Gut microbes were primarily engaged in the metabolism of nucleotides, carbohydrates, glycans and their production, amino acids, terpenoids, lipids, cofactors, polyketides, and vitamins.

Moreover, some annotated functions pertaining to macronutrients exhibited relatively high abundance, including glycolysis/gluconeogenesis, pyruvate metabolism, sucrose and starch metabolism, glycerolipid metabolism, fatty acid synthesis in lipid metabolism, and pentose phosphate pathway in glycerophospholipid metabolism and carbohydrate metabolism.

Conclusion

The study findings showed a considerable seasonal change in the food consumption and nutritional intake of golden snub-nosed monkeys, with three macronutrients being higher in Autumn and Summer and lower in Winter and Spring. Seasonal dietary changes are the primary source of seasonal shifts in gut microbiota. The results indicated that bacteria in the gut compensate for inadequate macronutrient intake through microbial metabolic functions.

Journal reference:
Microbiology

In recent years, we have learned a lot about the crucial role gut microbes play in our health …

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In recent years, we have learned a lot about the crucial role gut microbes play in our health and well being. The extent of their influence can be surprising at times. Research has shown that gut microbes can impact the repair of tissue damage by fueling the production of a type of immune cell called Tregs, or regulatory T cells. These cells reside in various tissues and help regulate inflammation and immunity in different organs. But new work has shown that Tregs can also move around the body and respond when they are called to help fix injuries and tissue damage, such as in the muscles and liver. The findings, which used a mouse model and still have to be confirmed in humans, have been reported in the journal Immunity.

Image credit: Pixabay

There are Tregs that reside in the colon, and these cells are known to play an important role in the maintenance of gut health. The immune system in the gut has to protect us from infection while also ignoring the harmless or beneficial microbes in the gut microbiome. Gut microbes have also been known to affect Treg production. But colonic Tregs were thought to stay in the gut. In this study, the investigators found colonic Tregs among muscle cells.

First study author Bola Hanna, a research fellow in immunology at Harvard Medical School (HMS) noticed cells that looked like gut-derived Tregs among muscle tissue. The researchers wanted to known more about these mysterious cells. First, they confirmed the identity of the Tregs by analyzing gene expression and molecular characteristics. This indicated that these cells were just like colonic Tregs. Next, the investigators tagged those cells and watched as they moved around the bodies of a mouse model. The researchers assessed the antigens on these cells as well, confirming that they were equivalent to Tregs from the gut.

When a mouse model was created to lack these Tregs, and was then subjected to muscle injury, the mice had high levels of inflammation and difficulty healing. When healing did happen, it was accompanied by scarring.

In another experiment, mice were given antibiotics to reduce the levels of gut microbes. Once again, when muscle injury occurred, it took longer to heal. But if the gut microbiome was restored, normal healing commenced.

The colonic Tregs are promoting healing in muscles by reducing the levels of an inflammatory molecule called IL-17.

The investigators also found evidence of gut Tregs in different organs including the kidneys, liver, and spleen. In a mouse model of fatty liver disease, there were unusually high levels of colonic Tregs compared to healthy mice, suggesting that Tregs are influencing inflammation in a variety of tissues.

In the mouse model of fatty liver disease, symptoms got worse when the mice lacked Tregs, which also seems to confirm that colonic Tregs are playing an important role in countering the effects of inflammation due to fatty liver disease.

“Our observations indicate that gut microbes drive the production of a class of regulatory T cells that are constantly exiting the gut and act as sentries that sense damage at distant sites in the body and then act as emissaries to repair that damage,” explained senior study author Diane Mathis, a professor of immunology in the Blavatnik Institute at HMS. This work may also help scientists create therapies for fatty liver disease.

Sources: Harvard Medical School, Immunity


Carmen Leitch