Revealing the mysteries within microbial genomes

 

Image designed by Tim Sandle

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

 

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

 

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

 

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

 

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

 

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

 

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

 

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

 

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

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

 

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

 

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

 

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

 

See:

 

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

 

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

Manipulation of gut microbiota with flaxseed could reduce breast cancer risk

 

A study demonstrates that the human gut microbiome may be a factor in breast health. In the study, flaxseed components called lignans were shown to influence the relationship between gut microorganisms and the expression of mammary gland microRNAs (miRNAs).

miRNAs are short, noncoding RNAs that regulate gene expression by targeting the 3' untranslated region of target mRNAs. A subset of these miRNAs regulates the genes involved in breast cancer, including genes that control cell proliferation and migration. 

Monitoring science

The gastrointestinal microbiota appears to play an important role in modifying many components of our diet to impact human health. The researchers studied the effects of flaxseed lignans on the microbiota of young female mice.

One flaxseed oil lignan requires microbial processing to release bioactive metabolites, small-molecule chemicals produced during metabolism that influence physiology and disease -- in this case, having antitumor effects.

Hence, the investigators found correlations between diets enriched in flaxseed, caecal microbiota composition, and miRNA profiles in the mammary gland that regulate many pathways, including those involved in cancer development.

Lignans, fibre-associated compounds found in many foods and particularly plentiful in flaxseed, are associated with reduced breast cancer mortality in postmenopausal women.

The researchers found that lignan components generate specific miRNA responses in the mammary gland.

The preliminary results support further research into the role that the microbiota plays in dietary approaches to reduce risk factors associated with disease.

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Reference:

Diana Wu, Lilian U. Thompson, Elena M. Comelli. Cecal microbiota and mammary gland microRNA signatures are related and modifiable by dietary flaxseed with implications for breast cancer risk. Microbiology Spectrum, 2023; DOI: 10.1128/spectrum.02290-23

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

How Your Microbes Adapt to New Environments

 

Traveling is a thrilling adventure that allows us to experience other surroundings, cultures, and temperatures. Whether you go on adventures in a tropical paradise, trek in the mountains, or live in the center of a busy city, your body adapts to the various conditions you put it through. The bacteria we gathered will offer information on how your microbiota adapts, how to stay healthy, how the vacations affect your well-being, and suggestions on maximizing your trip experiences. It is a fascinating part of our biology that is important to the process.

 

By Brittany Cotton

 

 

The Process By Which The Human Body Adapts to Novel Environments During Vacation Periods

 

 

When an individual commences a vacation, their physical being is exposed to many novel stimuli, encompassing diverse climatic conditions, culinary variations, disrupted sleep routines, and encounters with unfamiliar microorganisms. These alterations induce physiological adjustments in your body, including your microbiome, to promote health and wellness. The microbial organisms present in an individual's body play a significant role in facilitating these adaptations.

 

The Topic of Interest Pertains to Microbial Diversity and Composition

 

 

The microbiome is a highly intricate ecological system with many microorganisms, including bacteria, viruses, fungi, and other organisms. This ecosystem inhabits the gastrointestinal tract and is in the integumentary system and other anatomical regions. Every individual harbors a distinct microbiome shaped by many factors, including genetic predisposition, dietary choices, lifestyle practices, and exposure to the surrounding environment.

 

When individuals embark on a journey to an unexplored destination, they encounter various microorganisms distinct from those in their familiar domestic surroundings. This phenomenon could induce alterations in the composition and diversity of your microbiome. Research findings have indicated that travel has the potential to impact the quantity and variety of bacteria present in various bodily regions, such as the gut, skin, and other anatomical sites. These alterations in microbial composition are believed to result from microbial adaptations to novel environments encountered during travel.

 

The Modulation of The Immune System

 

 

The microbiome and the immune system have a close interaction, crucial for developing and regulating the immune system. Introducing individuals to novel environments elicits a response from the immune system, prompting it to adjust and adapt accordingly. The immune response can be influenced by the diverse microorganisms encountered during travel, which have the potential to enhance or regulate immune function.

 

While traveling, the immune system may encounter novel pathogens, thereby presenting new challenges to its functionality. Besides, meeting with a broader spectrum of microorganisms can enhance the immune system's functionality by expanding its antibody and resistant cell collection. This process enhances the body's ability to combat infections and strengthens the immune response.

 

The biochemical reactions inside an organism that change nutrients into forms the body can use are called "nutrient metabolism."

 

The dietary composition frequently undergoes modifications during periods of vacation or travel. The role of an individual's microbiota is of utmost importance in the processing and metabolizing of nutrients derived from various meals, whether exploring local culinary traditions or adjusting to diverse food options. The capacity of an individual's microbiome to degrade intricate carbohydrates, synthesize vital vitamins, and regulate the assimilation of nutrients contributes to the optimization of the body's metabolic processes.

 

When individuals are exposed to novel foods and dietary patterns while traveling, their microbiome undergoes adaptations by modulating the expression of genes associated with the metabolism of nutrients. The capacity for adaptability allows the human body to optimize the use of available food sources, guaranteeing enough nutritional intake throughout one's vacation.

Strategies for Maintaining Optimal Health During the period of leisure and relaxation known as vacation

 

The act of journeying to unfamiliar surroundings can elicit a sense of revitalization. Yet, it is imperative to adopt measures that safeguard one's physical and mental welfare during the entirety of the holiday. The following are several pragmatic suggestions to take into account:

 

One Should Engage in Proactive Planning and Remain Well-informed

 

 

Before beginning your journey, you should research the climate of your destination and the accessibility and caliber of the local healthcare facilities. You should also report any pertinent health recommendations that might be applicable. Individuals can enhance their preparedness and mitigate health-related uncertainties by comprehending potential hazards and implementing requisite measures, such as receiving vaccinations or ensuring the inclusion of suitable medications in their travel kit.

 

Stay Hydrated

 

 

Hydration is crucial for optimal microbial health. When traveling, particularly to warmer climates, the risk of dehydration increases. Ensure you drink adequate water throughout the day to stay hydrated. Carry a reusable water bottle and refill it regularly, especially when engaging in outdoor activities or the sun. Proper hydration supports the function of your digestive system and helps maintain the balance of your microbial communities. It also aids in regulating body temperature and promoting well-being.

 

Follow The Best Hygiene Guidelines

 

 

Proper hygiene practices are essential, especially when traveling to new places. Maintaining good hygiene habits recommended in routine hand hygiene practices, such as washing hands frequently with soap and water or using hand sanitizer when necessary to reduce the chances of harmful infection, plays a vital role in tissue and microbial balance in the skin.

 

Maintain a Balanced Diet

 

 

 

Sampling new and exciting cuisines is an integral part of traveling. But making mindful food choices to support your microbial health is essential. Here are a few tips:

 

Introduce new foods: Allow your microbiome time to adjust to unfamiliar ingredients and flavors by incorporating fresh foods into your diet.

 

Eat more excellent foods high in fiber

In the digestive tract, fiber serves as a meal for the most astounding bacteria. To get enough fiber in your diet, you must recognize that consuming clean produce, whole grains, and beans is necessary.

 

Eat Fermented Food Products

 

Yogurt, kimchi, sauerkraut, and kefir are some examples of fermented foods that incorporate live microorganisms beneficial to healthy gut microbiota. Please include them in your food plan while you can.

 

Exercise moderation

While enjoying the local cuisine is a part of traveling, be aware of portion sizes and avoid consuming too many processed or unhealthy meals.

 

Protect Yourself from Sun Exposure

 

 

Protecting your skin from harmful UV radiation is essential regardless of travel destination. Apply sunscreen with a high SPF regularly, wear a wide-brimmed hat and sunglasses, and seek shade during peak sun hours to minimize the risk of sunburn and long-term skin damage.

 

 

Ensure Enough Rest

 

 

Obtaining enough restorative sleep is paramount for one's holistic health, particularly when engaging in travel-related activities. Establishing a consistent sleep regimen that aligns with your travel itinerary is advisable. Additionally, it may be beneficial to bring along items such as earplugs or an eye mask to help you sleep in unfamiliar surroundings.

 

Participate in Physical Exercise

 

Integrating physical activities into your itinerary allows you to sustain a physically active lifestyle while on vacation. Engaging in activities such as hiking, swimming, or exploring the local surroundings on foot contributes to physical and mental well-being, thereby underscoring the significance of regular exercise.

 

Engage in Periodic Intervals of Relaxation

 

 

 

Although there may be a solid inclination to fill one's schedule with various activities and sightseeing ventures, it is crucial to consider the significance of incorporating regular relaxation intervals. Excessive physical or mental exertion can induce fatigue and elevate susceptibility to illness. Pay attention to your body's signals and prioritize maintaining your health and wellness.

 

Adhering to these recommendations can optimize their satisfaction during the vacation period while prioritizing their well-being. Besides, despite implementing preventive measures, unforeseen health complications may still occur. It is at this point that travel insurance shines. It is advisable to look into the travel health resources offered by Generali Travel Insurance to understand the significance of travel health insurance and its function in protecting people during their travels.

 

The Benefits of Vacations on Health and Well-being

 

 

While understanding how our microbes adapt to new environments during vacations is crucial, it is equally important to recognize the broader impact of leaves on our health and well-being. Holidays provide many benefits beyond microbial adaptation and are vital in promoting overall wellness.

The Reduction of Stress

 

 

Vacations afford individuals respite from the monotonous routine of daily life and present a valuable occasion to disengage from stressors associated with professional obligations. Engaging in pleasurable activities and disengaging from regular responsibilities can reduce stress levels, fostering relaxation and revitalization.

 

Enhancing Mental Well-being

 

 

The act of traveling provides individuals with the opportunity to encounter unfamiliar environments, cultures, and experiences, thereby stimulating cognitive processes and expanding one's worldview. Exposure to new and unfamiliar stimuli can augment creative thinking, enhance mental adaptability, and contribute to individual development. In addition, vacations allow individuals to engage in meaningful interactions with their close companions, cultivating social bonds and enhancing interpersonal connections, which are crucial in promoting psychological wellness.

 

Improved Physical Fitness

 

 

Vacations often encompass various physical activities, including walking tours, hiking expeditions, participating in swimming activities, or indulging in water sports. These activities present a valuable opportunity for individuals to experience consistent physical exercise and enhance their physical fitness. Physical activity plays a significant role in managing weight, strengthening cardiovascular health, fortifying the musculature and skeletal structure, and augmenting energy levels.

 

Enhancement of Sleep Quality

 

 

The act of seeking respite from the demands of daily life and adapting to a novel setting can yield beneficial effects on one's sleep behaviors. Many studies have demonstrated that vacations have the potential to enhance the quality of sleep, thereby facilitating a more profound and revitalizing state of rest. The alteration in environmental surroundings, diminished levels of stress, and heightened engagement in physical activity during vacation periods can contribute to regulating one's sleep-wake cycle and cultivating improved sleep patterns.

 

The augmentation of happiness and well-being

 

 

The pre-vacation anticipation, excitement, pleasurable experiences, and lasting memories formed throughout the journey contribute to an augmented state of happiness and well-being. Vacations allow individuals to deviate from repetitive patterns and engage in pursuits that elicit happiness, tranquility, and exploration.

 

Increasing Stress Resilience and Reducing Burnout: A Systematic Approach

 

 

It has been found that taking vacations helps people manage stress and reduces their risk of becoming burnt out. A person's physical and mental health may worsen due to ongoing stress. By integrating vacations into one's lifestyle, individuals can establish a genuine relaxation, revitalization, and self-preservation period. This practice enables them to replenish their energy levels and enhance their concentration upon re-engaging with their routine activities.

The Enhancement of Productivity and Creativity

 

 

Vacations serve the dual purpose of offering respite from work-related obligations and fostering heightened productivity and creativity upon reintegration into professional endeavors. Temporarily removing oneself from a familiar environment and established routine can stimulate novel ideas, enhance one's capacity for resolving problems, and offer a renewed outlook on challenges encountered in the professional sphere. Engaging in periods of relaxation can result in heightened productivity and efficacy upon resumption of one's everyday tasks.

 

 

Conclusion

 

 

People's physiological systems, including the microbiome, adapt when they go on vacation or travel to new settings in response to changes in climate, dietary habits, and exposure to microbes. The maintenance of one's general health and well-being depends on the adoption of these modifications. People can make the most of their travel experiences by following sensible guidelines for maintaining health when traveling, such as proactive preparation, strict adherence to hygiene precautions, and prioritizing personal well-being.

 

 

Furthermore, vacations provide many advantages for physical and mental well-being, encompassing stress alleviation, enhanced sleep patterns, improved physical fitness, and heightened happiness and wellness. Engaging in periodic rest intervals and actively seeking novel encounters can significantly improve one's overall capacity for resilience, productivity, and creativity.

 

When embarking on a new journey, it is crucial to recognize the significance of travel health insurance in safeguarding oneself against unforeseen health complications. It is advisable to look into the travel health resources offered by Generali Travel Insurance for a thorough understanding of travel health insurance and its benefits. One should embrace the various opportunities that travel presents, as it allows for exploring novel environments and facilitates the adaptation and flourishing of both the body and mind within the dynamic realm of travel.

 

Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)