What do microbes do?

Inner Workings: Hunting for microbial life throughout the solar system

Of Mars and Microbes

Efforts to look for life on other worlds got off to a rocky start in the 1970s, when the Viking 1 and Viking 2 spacecraft descended to the Martian surface. They each carried three biological experiments. The most intriguing outcome came from the Labeled Release experiment, which added a drop of nutrient-rich water tagged with radioactive carbon-14 to soil samples and then detected the isotope in gases rising from the material, suggesting that microorganisms might have metabolized and excreted the carbon-14. But the other experiments found no evidence of organic compounds on Mars, leaving researchers with a mixed bag of findings. “You had an ambiguous result,” says geochemist Ariel Anbar of Arizona State University in Tempe, AZ. “And we ran away from the ambiguity.”

Because the experiments looked like a failure to much of the public, Anbar says for decades NASA balked at projects intent on finding microbial life. But the passage of time and new evidence, including the discoveries of hardy microbial organisms on Earth and the prevalence of water on other worlds in the solar system, are renewing interest in life detection, says Anbar.

Mars, in particular, is a favored destination. Because of periodic swings in the tilt of the planet’s axis, Mars’ northernmost region was much warmer and potentially habitable as recently as 5 million years ago, so there’s incentive to revisit the region. To avoid the uncertainty of Viking’s findings, astrobiologist Marc Neveu of NASA headquarters in Washington, DC, and his colleagues used findings from the past 20 years of astrobiology research to develop the “Ladder of Life Detection,” which they published in June. The ladder has 15 “rungs,” each a measurable criterion that gets increasingly suggestive of evidence of life elsewhere—ranging from identifying habitability to detecting biomolecules to spotting metabolizing, evolving organisms—for researchers to use in their investigations (7).

For instance, finding amino acids, the building blocks of proteins, might be an early indication that some particular rock is interesting, especially if the amino acids are in ratios typical of microorganisms on Earth. More complex organic molecules, which seem too intricate to have been generated by abiotic processes, might be the next hint. Evidence of metabolic processes, such as waste heat coming from the sample, would be more revealing. The most convincing would be to study the sample with a microscope and see tiny cells moving around.

Yet, life detection is tricky, and the document details how astrobiologists can be led astray. “It’s important to us to explain to the public why it’s not a slam dunk thing to do,” says Mary Voytek, director of NASA’s astrobiology program in Washington, DC. “If we found a planet with cows on it, it would be really easy. But we’re looking for microbial life.”

One mission that could assist in the search for such microbial life is the Mars 2020 rover, a follow-up to Curiosity (which found complex organic molecules on Mars in June). Although Mars 2020 won’t be detecting signs of life, it will cache 0.5 kilogram of biologically interesting material. In April, NASA and the European Space Agency agreed to work together to bring the samples back to Earth for rigorous analysis. They could launch Curiosity’s cache into Martian orbit and use a spacecraft to capture and return the material, possibly by the end of the next decade. “To do this seriously, you need to bring things to Earth,” says geochemist and Mars 2020 project scientist Ken Farley of the California Institute of Technology in Pasadena, CA.

Icebreaker could do lab work on Mars itself, using a suite of complementary instruments, including the Signs Of LIfe Detector (SOLID), a small chip containing hundreds of antibodies that recognize common organics such as amino acids (which make up proteins) and nucleic acids (which make up DNA and RNA), as well as proteins common to extremophile bacteria on Earth. Such molecules could survive for millions of years in ice even if Martian life went extinct long ago.

SOLID’s focus on proteins found in earthbound microorganisms has been criticized, says instrument designer Victor Parro of the Centro de Astrobiologia in Madrid, but his team thinks it makes sense to search for such compounds because life on Earth and Mars may have evolved similar mechanisms to deal with tough environmental conditions, such as extreme cold, salinity, or dryness. Chris McKay of NASA’s Ames Research Center in Mountain View, CA, is readying Icebreaker to compete in NASA’s next round of Discovery funding, and the mission could be selected in the next few years and be ready by 2026.

Researchers suspect that the geysers of Saturn’s moon Enceladus, pictured here based on images from the 2010 Cassini-Huygens mission, could possibly contain microbial life. Image courtesy of NASA/JPL/Space Science Institute.

What Are Microbes: The Benefits Of Microbes In Soil

Farmers have known for years that microbes are critical for soil and plant health. Current research is revealing even more ways beneficial microbes help cultivated plants. Microbes in the soil and associated with plant roots provide a multitude of benefits, from improving the nutrient content of our crops to enhancing their resistance against diseases. Some soil microbes are even good for us too.

What are Microbes?

A microbe is usually defined as any living thing that is too small to be seen without a microscope. By this definition, “microbe” includes microscopic animals like nematodes along with single-celled organisms.

By an alternate definition, “microbe” means only single-celled living things; this includes microscopic members of all three domains of life: bacteria, archaea (also called “archaebacteria”), and eukaryotes (“protists”). Fungi are usually considered microbes, even though they can take single-celled or multicellular forms and produce both visible and microscopic parts above and below the ground.

Microbial life in soil includes living things in each of these groups. Huge numbers of bacterial

and fungal cells live in soil along with smaller numbers of algae, other protists, and archaea. These organisms play important roles in the food web and nutrient cycling within soil. Soil as we know it would not even exist without them.

What Do Microbes Do?

Microbes in soil are extremely important for plant growth and for the functioning of ecosystems. Mycorrhizae are symbiotic partnerships between plant roots and specific soil fungi. The fungi grow in close association with the plant roots, and in some cases, they even grow partially within the plant’s own cells. Most cultivated and wild plants rely on these mycorrhizal associations to obtain nutrients and to defend themselves against disease-causing microbes.

Legume plants like beans, peas, clover, and locust trees partner with soil bacteria called rhizobia to extract nitrogen from the atmosphere. This process makes the nitrogen available for plant use, and eventually for animal use. Similar nitrogen-fixing partnerships form between other groups of plants and soil bacteria. Nitrogen is an essential plant nutrient, and within plants it becomes part of amino acids and then proteins. Globally, this is a major source of the protein that humans and other animals eat.

Other soil microbes help break down organic matter from dead plants and animals and incorporate it into the soil, which increases the soil’s organic content, improves soil structure, and helps plants thrive. Fungi and actinobacteria (bacteria with fungal-like growth habits) begin this process by breaking down larger and tougher materials, then other bacteria consume and incorporate smaller pieces. If you have a compost pile, you’ve seen this process in action.

Of course, there are also disease-causing soil-borne microbes that affect garden plants. Crop rotation and practices that encourage the growth of beneficial microbes can help suppress the survival of harmful bacteria, fungi, and nematodes in the soil.

How does bacteria help plants thrive in salty conditions?

A plant needs salts, water, sunlight and different nitrogen-based compounds to grow. However, any of these in excess can adversely affect the plant and result in impaired growth or death. Salinity stress, caused by increased salt content in the soil, is a major issue faced by farmers as it affects the crop yield. In a recent study, researchers from the Birla Institute of Technology, Pilani, has uncovered the mechanism behind how some plants tolerate high levels of salinity in the soil. They see the helping hand of a soil bacterium called Enterobacter cloacae in keeping these plants alive in saline conditions.

But what makes it hard for the plants in saline conditions? Turns out, it is the difficulty in maintaining the structure of their cells. Due to high salt content, osmosis in the cells causes loss of water, leading to ultimately death of cells. To conserve water, stomata–small openings on the leaves that throw out excess water and take in carbon dioxide–remain closed. Hence, the availability of carbon dioxide, needed for photosynthesis, is adversely affected. However, some plants have developed their own strategies to adapt to salinity stress. They modulate the levels of proteins and in turn, the metabolic processes that ensure their survival.

This present study, published in the journal PLOS One highlights one such survival mechanism assisted by the bacteria Enterobacter cloacae–a plant growth promoting rhizobacteria (PGPR). These bacteria grow in the soil or on the roots of plants. The study finds that they aid in growth of the plant by helping it acquire necessary nutrients, modulating plant hormone levels and protecting the plant from pathogens.

The researchers of the study traced the biological changes at a molecular level brought about by the presence of the bacteria in wheat plant. They found changes in the protein levels of the plant under salinity stress, before and after exposing the plant to the bacteria. This observation reveals that PGPR influences the production of proteins involved in stress response pathways.
The researchers compared protein profiles of the control group, the group without bacterial treatment, and two experimental groups–one with only bacteria, and the another with salinity stress and bacteria. They observed differential expression of proteins involved in protein synthesis, cell division regulation, lipid biosynthesis, photosynthesis and stress related metabolism. These events collectively alter the metabolic status and help the plant to maintain the cell integrity. The researchers identified the differentially expressed proteins in each of these groups to fish out those unique for the response observed. They then clustered related proteins based on their physiological functions such as cell cycle, ion transport, defence, etc.

The observations suggest that the plants produce more of certain cytoskeletal and cell cycle proteins to reinforce the cell structure and to ensure that cell division goes on. In addition, the functions of the cell membrane was assisted by the fastened lipid biosynthesis. Exposure to bacteria seemed to alter the expression pattern of RuBisCO–a key enzyme in carbon dioxide fixation, which makes carbon compounds more available for other reactions and energy synthesis. Various osmoprotectant proteins that help in the water-holding were also synthesized in higher amounts. The protein profile implied that bacteria incorporates double advantage by reducing the harsh environment and also by helping plants to tolerate the stress levels they are exposed to.

All these effects are the cascading events following the reduction in the levels of ethylene, the major stress hormone in plants, by the bacteria. “1-aminocyclopropane-1-carboxylate (ACC) deaminase catalase breakdown of ACC, which is an immediate precursor of ethylene. This reduces the level of ethylene in plant”, says Dr. Prabhat Nath Jha from BITS, who is also the lead author of the study.

The observations of the study has implications on agricultural crop yields in high salinity areas. However, the authors opine that further investigations are required for in-situ applications. “There are several other factors such as soil factors and competition with natural microbial inhabitants, which can be taken into consideration when applied in natural conditions. We have not tested it, but it needs to be done before it is used as biofertilizer under farming conditions”, signs off Dr. Jha.

Plant roots support an array of microorganisms that can have either a deleterious or beneficial impact on plant health and growth. The use of beneficial microorganisms, called plant growth-promoting rhizobacteria (PGPR), increases plant growth and crop yield. In the March 31 Proceedings of the National Academy of Science, Choong-Min Ryu and colleagues from Auburn University, Alabama, US, show that some PGPRs release a blend of airborne chemicals — volatile organic compounds (VOCs) — that promote the growth of Arabidopsis thaliana seedlings (PNAS, DOI:10.1073/pnas.0730845100, March 31, 2003).

Ryu et al. investigated the role of VOCs from seven strains of PGPRs on total leaf surface area. They showed that 2,3-butanediol and acetonin, released exclusively from two bacterial strains triggered the highest levels of plant growth. Insertional analysis of enzymes involved in the synthesis of these two VOCs resulted in a removal of the growth promotion effect. Further, exogenous application of 2,3-butanediol to seedlings resulted in dose-dependent growth promotion.

“PGPR strains release different volatile blends and that plant growth is stimulated by differences in these volatile blends. The mechanism by which volatile components from PGPR promote growth via cell expansion and/or cell division and the interaction of 2,3-butanediol with established plant growth hormones are areas that now can be examined,” conclude the authors.

Bacteria Encourage Plants Growth

For centuries farmers have taken advantage of the beneficial relationship between some bacteria and plants to boost yield, improve soil fertility, and inhibit crop infections.

Today spirited efforts are ongoing towards sustainable crop production and at its core is the application of biological approaches as part of an integrated crop nutrient management system. In fact, there is a piling body of knowledge on how significant and revolutionary harnessing the power of nitrogen-fixing bacteria would have on agriculture and crop production.

OK, now you know using bacteria in crop production could potentially usher in a second green revolution, but you’d be wondering how these bacteria do it. How do they help them grow?

If you have an indoor garden, then you should invest in full spectrum LED grow lights, but it’s not an easy task to choose what’s the best for you. It’s a good investment!

That’s the focus of this article to look at the various methods these microbes influence the plant.

There are several bacteria around the root which through their activities make available nutrients which are typically inaccessible to them. They do this either by breaking down insoluble nutrients or secreting acidic compounds which lower the pH level of the surrounding area.

  • Take for instance the role of these bacteria in the phosphorous uptake by plants. Due to its highly reactive nature with Iron, Calcium, and Aluminum, it precipitates and hence becomes inaccessible by the plants. Some of the growth-promoting microbes (PGPB) converts phosphorous into a form that is readily available for the plants.

Another scarce primary nutrient in soil is Iron; the bacteria secrete a compound siderophore which in turn acquires ferric iron which the plant roots readily absorb.

  • Manages the ethylene levels – Studies have shown that a reduced level of Ethylene promotes their growth. Some growth-promoting microbes are known to contain ACC deaminase an enzyme which cuts the concentration of ethylene in stressed or developing plant.
  • Nitrogen fixation – this is probably one of the well-known benefits of PGPB, and that’s for a good reason. Nitrogen is one nutrient that is hardly accessible to the plants. However, there is some plant growth promoting microbes that can fix atmospheric nitrogen in the soil; hence making the nutrients readily available.

PGPB can help in the Suppression of pathogenic attacks

PGPB(plant growth-promoting bacteria) can prevent the infection of pathogens through competing with them for nutrients, secreting anti-fungal compounds, and producing antibiotics to ward off these pathogens from invading the crops. In order to have the energy to ward off these pathogens, plants store their energy while they perform cellular respiration, it’s the chemical process used by cells to unlock energies stored in starch into usable forms. This helps the plant to defend from these pathogens.

Apart from populating and competing with this pathogens PGPB also triggers the plant to develop an induced system resistance which is its defense mechanism kicking in due to the interactions with the growth-promoting microbes.

They are used as Biofertilizer

This is not the same as organic fertilizer. In this case, the live beneficial bacteria are injected into the soil, applied to seeds or on plant surfaces this encourages high yield by increasing the supply of primary nutrients to the host plant. However, not all PGPB are considered a biofertilizer.

In summary, growth promoting microbes play a vital role in the eco-balance of the soil, through their activities farmers have been able to improve crop yield and ward off crop diseases.

And with the current push to adopt this PGPB for more crops, we are on the verge of another green revolution.

The use of PGPB as an integral component of agricultural practice is a technology whose time has come. These bacteria are already being used successfully in a number of countries in the developing world and this practice is expected to grow. In the more developed world, where agricultural chemicals remain relatively inexpensive, the use of PGPB occupies a small but growing niche in the development of organic agriculture. In addition, it is reasonable to expect the increased use of PGPB in various phytoremediation strategies.

What is microbiology?

Micro-organisms and their activities are vitally important to virtually all processes on Earth. Micro-organisms matter because they affect every aspect of our lives – they are in us, on us and around us.

Microbiology is the study of all living organisms that are too small to be visible with the naked eye. This includes bacteria, archaea, viruses, fungi, prions, protozoa and algae, collectively known as ‘microbes’. These microbes play key roles in nutrient cycling, biodegradation/biodeterioration, climate change, food spoilage, the cause and control of disease, and biotechnology. Thanks to their versatility, microbes can be put to work in many ways: making life-saving drugs, the manufacture of biofuels, cleaning up pollution, and producing/processing food and drink.

Microbiologists study microbes, and some of the most important discoveries that have underpinned modern society have resulted from the research of famous microbiologists, such as Jenner and his vaccine against smallpox, Fleming and the discovery of penicillin, Marshall and the identification of the link between Helicobacter pylori infection and stomach ulcers, and zur Hausen, who identified the link between papilloma virus and cervical cancer.

Microbiology research has been, and continues to be, central to meeting many of the current global aspirations and challenges, such as maintaining food, water and energy security for a healthy population on a habitable earth. Microbiology research will also help to answer big questions such as ‘how diverse is life on Earth?’, and ‘does life exist elsewhere in the Universe’?

Introducing microbes


  • Bacteria

    More than just pathogens – can be friend or foe.


  • Viruses

    Smallest of all the microbes, but are they alive?


  • Fungi

    More than just mushrooms.


  • Protozoa

    Microbes with a taste for poo and so much more.


  • Algae

    Microbial powerhouses essential for life.


  • Archaea

    First found existing on the edge of life.


  • Prions

    Mysterious misfolding proteins.

Microbes in the world


  • Microbes and the human body

    Ever wondered why when we are surrounded by microbes we are not ill all the time?

  • Microbes and food

    Food for thought – bread, chocolate, yoghurt, blue cheese and tofu are all made using microbes.

  • Microbes and the outdoors

    The function of microbes as tiny chemical processors is to keep the life cycles of the planet turning.

  • Microbes and climate change

    How are microbes contributing to climate change?

We Are Never Alone: Living with the Human Microbiota

Abstract

The human body is inhabited by millions of tiny living organisms, which, all together, are called the human microbiota. Bacteria are microbes found on the skin, in the nose, mouth, and especially in the gut. We acquire these bacteria during birth and the first years of life, and they live with us throughout our lives. The human microbiota is involved in healthy growth, in protecting the body from invaders, in helping digestion, and in regulating moods. Some changes in the microbiota may occur during our growth, depending on the foods we eat, the environment in which we live, the people and animals that interact with us, or medicines that we take, such as antibiotics. The human microbiota helps us to keep us healthy, but sometimes these bacteria can also be harmful. We need to take good care of our microbiota to avoid the development of some diseases, such as obesity and asthma. We should eat healthy foods that contribute to the development of a healthy microbiota.

We live with and surrounded by microbes (also called microorganisms), even though we cannot see them with our eyes. Microbes are the smallest living organisms known. They are everywhere: in soil, rivers, plants, animals, tap water, on your keyboard, on your pillow and in your body. Some microorganisms live with us and inside our bodies. Bacteria represent the majority of the microorganisms living in the body. Did you know that you have more bacteria in your body than you have human cells? Do you have any idea why these bacteria live in your body? We carry these neighbors with us every day and usually they do not make us sick. Are they friendly? Or can they make us ill? How do they get in? What is their role in the body?

What are Bacteria?

Bacteria are tiny living microorganisms that are too small to be seen by the naked eye. They are a 1,000 times smaller than a pencil tip. We have to use an instrument called a microscope, which makes the image of the bacteria big enough to be seen. There are many different kinds of bacteria with diverse shapes and sizes. Some look like a baseball bat, others are round like a basketball (but millions of times smaller) (Figure 1).

  • Figure 1 – Shapes of bacteria.
  • A. Bacteria can be round like a basketball, long like a baseball bat, or can look like beans or waves. Sometimes bacteria can group together and look like a bunch of grapes or like a train. B. Bacteria can be seen using a microscope with 1,000× magnification. Staining is often used to help see the bacteria, which are actually transparent. Bacteria colored in pink are called bacilli and those in purple are called cocci.

Where are Bacteria in the Human Body?

Bacteria live on the skin, inside the nose, in the throat, in the mouth, in the vagina, and in the gut. The majority of the bacteria found in the body live in the human gut. There are billions of bacteria living there (Figure 2). We call the group of all the microbes found in the body the human microbiota . These microorganisms colonize the body, which means that they usually do not cause any harm. When a microorganism causes sickness, that is called an infection.

  • Figure 2 – The human body is the home of millions of bacteria.
  • Several body sites are full of bacteria and they are especially concentrated in the gut, in the throat and mouth, and on the skin.

Where Do the Bacteria That Live in the Human Body Come from?

We begin to be colonized by bacteria during birth. During the birth process and immediately after birth, we get our first microorganisms. Babies get microorganisms from their moms during delivery, when they pass through the vagina, or from contact with the mom’s skin, if the delivery is by cesarean section. Lactobacilli, a type of bacteria considered to be one of the “good guys,” live in the mother’s vagina and they colonize the baby’s intestines to help in the digestion of milk, which contains a sugar called lactose. If the baby is delivered by cesarean section, Lactobacilli will not immediately become part of the baby’s microbiota, which will be made up mostly by bacteria from the mom’s skin and the baby’s environment. These differences in a baby’s microbiota, resulting from the type of birth that baby experienced, will remain until the baby is 12–24 months of age. All babies also acquire bacteria from the skin of the nurses and medical doctors and the environment they live in. After babies begin to eat, they get microbes from their diet. In the first days of life, the type of the microorganisms that colonize their intestines will be different, depending whether the baby is breast feeding or drinking formula. Breast feeding is healthy for the baby, because it helps the baby to acquire bacteria from the mother’s skin that will then colonize the baby’s intestines, and there are also other components of the mother’s milk that protect the baby from disease. As babies grow, they get microorganisms from the solid food they eat, from crawling on the floor, from putting their hands in their mouths, from licking toys, and from many other sources!

The microbes that live in the human body change during our growth, until we are 3 years old. At that point, the microbiota becomes more or less stable until adult life. Each individual has his or her own microbiota, which depends in part, but not only, on the types of food eaten, the environment where the person lives, and the other people and animals that the person interacts with (Figure 3) .

  • Figure 3 – Factors that influence our microbiota are showed in the small circles around the middle circle.
  • During birth, the first microorganisms that we get depend on the birth delivery process (natural or c-section). The baby feeding method (mom’s milk or drinking formula) will influence the microbiota in our first years of life. Diet will influence the composition of microbiota in all stages of our life. As we get older (age), microbiota alterations depend on our diet, environment where we live, and life style. Antibiotics will also alter the composition of our gut microbiota (see text for detailed explanation).

What is the Role of the Human Microbiota?

When we mention bacteria in the human body, you might immediately think of a disease, called a bacterial infection. At some point in your life, you have probably had an infection that was treated by antibiotics prescribed by your doctor. Antibiotics are medicines that kill or prevent the growth of bacteria.

However, the majority of the microbes are harmless and actually help to maintain our health. The microbes of the skin, mouth, and nose fight against bad bacteria that want to enter the body to cause disease. These good bacteria act like guards that keep away the harmful bacteria that make us sick. The bacteria that colonize the vagina are another example of good bacteria. They maintain an acidic environment in the vagina that prevents the growth of other microorganisms that might cause disease. Disease-causing microorganisms are called pathogens.

Even though most of the time they are harmless or even helpful, in certain conditions some of the bacteria that are part of the human microbiota can harm us. For example, bacteria that live on the skin can become a problem. If you cut yourself, the bacteria that live on the surface of your skin may be able to enter into your body through the cut, getting in where they do not belong. In this instance, these bacteria sometimes might be harmful to the body and trigger an infection. Symptoms of an infection include pain, swelling, redness, and fever.

Another example of how the microbiota can harm us is when you let too many bacteria accumulate in your mouth. These bacteria can stick to the surface of your teeth. Some types of bacteria will produce acidic products from the food you eat (especially sugars) that can destroy your teeth and gums. That is why we need to brush our teeth at least two times a day for 3 min to avoid the multiplication of bacteria that can cause painful disease and, in severe cases, loss of teeth.

As we mentioned earlier, the intestines contain the largest portion of the human microbiota. The intestinal microbiota produces some vitamins that are good for us, such as vitamins B12 and K. These vitamins are not produced by human cells. The intestinal microbiota also helps in the digestion of food and protects the intestinal walls from invasion by pathogens.

There is a lot of research going on about the role of the intestinal microbiota. We are still trying to understand how the human microbiota contributes to health and disease. In general, healthy humans have a balanced microbiota, with a high diversity of bacteria in their guts. This means that they have a mix of different types of bacteria with different shapes, sizes, function, and names. More than 1,000 different types of bacteria exist in the human gut! By contrast, when only a small diversity of bacteria is present, meaning that only a few types of bacteria exist in the gut, in higher numbers than normal, disease may occur. Different levels of diversity in the gut bacteria may be related to obesity (the state of being extremely overweight), which can begin in childhood. Abnormal diversity in the intestinal microbiota may also play a role in the development of diabetes (increased sugar in the blood), asthma (long-lasting difficulty with breathing), and painful diseases in the intestine (chronic gut inflammation), among others . As an example, a healthy gut microbiota includes two main groups of bacteria called Firmicutes and Bacteroidetes, but it has been shown that, in the guts of obese people, Bacteroidetes are almost absent.

It is known that a healthy microbiota (which means a microbiota with a huge bacterial diversity, including plenty of good microbes) contributes to our health (Figure 3). Do you want to be healthy? Then you need to take care of your friendly intestinal bacteria. How can you do that?

Taking Care of the Gut Microbiota

Over the last few decades, many of the diseases mentioned above have been increasing. Many of these problems are related to changes in the types of food we eat . We eat a lot of sugar in things like cakes, biscuits, brownies, sweet jellies, and white bread, and we also eat a lot of burgers, meat with fat, and sauces, which, in excess, are not good for our health. These foods are also not good for some of our intestinal microbiota. Some of our microbes need veggies, fibers from beans, chickpeas, cereals, dark bread, seeds, and roots. These types of foods are called prebiotics and they help the growth of the microbiota, feeding bacteria that are able to break down this type of food into the nutrients that can be used by the human body to improve our health. We cannot digest some types of food properly if we do not have our tiny friends in our guts. Therefore, we do not want these good bacteria to die, because they are important to our health balance. The reduction of these good bacteria will allow the growth of the not-so-good bacteria that can eventually cause health problems.

Probiotics can help you replace the lost good microbiota. Probiotics are live bacteria that are good for us, that balance our good and bad intestinal bacteria, and that aid in digestion of food and help with digestive problems, such as diarrhea and bellyache. Bacteria that are examples of probiotics are Lactobacilli and Bifidobacterium. You can find probiotics in some foods, such as yogurts, sourdough bread, buttermilk, and sour pickles. Some infant formulas are also supplemented with probiotics, despite the fact that we do not really know yet how helpful they are in diseases of babies.

Antibiotics are medicines we take to treat infections caused by bacteria. Antibiotics are not active against infections by fungi or viruses. So, do antibiotics kill our good bacteria friends too? Yes, they do . However, if we have a bacterial infection, we have to treat it, so in many cases we must take antibiotics. Be sure to only take antibiotics when your doctor says you really need to, and take them during the time he advises. You do not need an antibiotic to treat a cold or the flu, because these diseases are caused by viruses. People who take a lot of antibiotics may get sick because the antibiotics destroy lots of the bacteria in their bodies, including the good ones. When lots of the bacteria in the gut are killed, the gut then has more free space and available food for the bad bacteria, which can then multiply. When these bad bacteria reach higher numbers, they can sometimes cause disease. As a consequence, individuals taking antibiotics frequently get diarrhea or more complicated intestinal diseases. When you take antibiotics without needing to do so, you might contribute to the emergence of “superbugs,” which are bacteria that are not killed by the majority of the antibiotics available today. These superbugs can survive in the presence of the antibiotic (which is called resistance to the antibiotic), so the infection continues even when the antibiotics are being used.

Conclusion

Humans need a diverse and balanced microbiota in their intestines to keep them healthy. Kids or adults who eat a lot of sugar and fats, but not veggies, and who do not have balanced nutrition, tend to become obese or to develop some diseases, even later in life. Do not take antibiotics without a prescription from your doctor. Always eat a healthy, balanced diet and never forget to include some green, orange, and red on your plate: make your plate colorful. With these tips, you will be taking the best care of your microbiota!

Glossary

Microbes/Microorganisms: Mostly one-celled organisms that include bacteria, some fungi (such as yeast), and microalgae.

Bacteria: Tiny living microorganisms that can be beneficial or dangerous for people.

Human Microbiota: The group of microbes that live in the human body and do not cause disease.

Colonization: Living in the body without causing any harm.

Digestion: To break down food into small pieces to be used by the human body.

Bacterial Infection: A disease caused by pathogenic bacteria.

Antibiotics: Special medicines used to fight against bacteria.

Pathogen: Microorganism that causes disease (sometimes also called a germ).

Prebiotics: Compounds that help the growth of the good microbes in the gut.

Probiotics: Live microorganisms are good for our health, especially the digestive system.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Blaser, M. J. 2014. Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues. Toronto, Ontario: HarperCollins Publishers, 273.

How and why do microbes rely on each other?

In the natural world, microbes live in communities where individuals rely on one another. The vast majority of microbes cannot produce all of the nutrients they require, and instead depend on other microbes to produce nutrients such as amino acids and vitamins. This type of microbial interaction, nutrient sharing, is a major driver of microbial community assembly and function.

To study how nutrient sharing occurs in microbial communities, we specifically focus on vitamin B12 and B12 analogs, collectively termed corrinoids. Corrinoids are cofactors involved in the biosynthesis of amino acids and DNA, carbon metabolism, and many specialized metabolic processes. With a focus on corrinoids, the Taga Lab dissects molecular interactions and interdependencies critical to communities. Interestingly, while the majority of microorganisms use corrinoids, only a subset of microbes can produce them. We study the biosynthesis of corrinoids, how bacteria obtain corrinoids from their environment, and the role of corrinoid sharing in microbial community dynamics. We take interdisciplinary approaches combining biochemistry, molecular biology, microbiology, computational modeling, and bioinformatics in innovative ways to investigate three main areas of cofactor sharing:

What factors determine an organism’s cofactor preference?

Organisms require corrinoids with particular structures for growth. However, the molecular basis of preference (selectivity) between corrinoids is poorly understood and cannot yet be predicted. Using biochemistry and molecular biology, we characterize corrinoid-dependent enzymes to identify protein residues responsible for discriminating between different corrinoids. We also investigate the regulatory responses of organisms to the presence of different corrinoids.

One of the main goals of our work is to bridge sequence and function: to predict from an organism’s genome how different corrinoids will interact with corrinoid-binding proteins. We aim to uncover determinants of corrinoid selectivity in DNA sequences and predict which corrinoids microbes require for growth and survival. Ultimately, we hope to use these predictions to develop new ways to manipulate microbial communities, and help scientists to culture a wider range of microbes.

How do microbes “share” nutrients?

The majority of organisms cannot produce corrinoids and instead must obtain corrinoids from their environment. Curiously, in contrast to other nutrients, scientists have not discovered a cellular system for exporting corrinoids. The question thus remains: how do corrinoids, produced by a small subset of bacteria, exit cells and become a resource in the environment for consumption by other microbes? Using synthetic co-cultures of cross-feeding bacterial strains, we investigate the role of cell death in nutrient release into the environment.

Furthermore, in addition to scavenging complete corrinoids, microbes can scavenge precursors to corrinoids. We work to characterize the variety of corrinoid precursors that may be shared by microbes in microbial communities by predicting possible shared precursors with bioinformatics, and testing predictions in culture.

How do microorganisms that share nutrients coexist and coevolve?

The details of how microbes depend on one another nutritionally remains enigmatic. What is the metabolic cost of producing a shared metabolite? How does nutritional interdependence shape the evolutionary trajectory of microbes? To address these questions, we developed synthetic co-cultures of metabolically interdependent bacterial strains. To test hypotheses about vitamin B12 interdependence in microbial communities we experimentally manipulate these co-cultures, carry out laboratory evolution experiments, and use computational approaches to model co-culture dynamics.

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