Stomach Virus : How does it affect the bacteria of the intestines?

Stomach Virus : How does it affect the bacteria of the intestines?

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When you have a stomach virus and it causes extreme bowel movements to the point of almost pure stomach acid, does this kill off the bacteria in our intestinal tracks?

No, since the pH and the conditions are different in the different compartments (stomach, small intestine, colon) of the bowel. See this figure (taken from this website) for the differences:

There are not that much bacteria in the stomach, so even even nothing else than acidic stuff comes out, the bacteria are not affected. And even when you have a severe diarrhea, there are still enough bacteria left to keep it colonized.

  • Close contact with an infected person or animal
  • Food poisoning, such as from eggs, raw vegetables, shellfish, or meat that is not fully cooked
  • Drinking water that is not clean, such as when you camp or travel
  • Diarrhea or gas
  • Nausea, vomiting, or poor appetite
  • Abdominal cramps, pain, or gurgling
  • Fever
  • Tiredness or weakness
  • Headaches or muscle aches with any of the above symptoms

SIBO (Small Intestinal Bacterial Overgrowth) Causes, Symptoms, Treatments, and Diet

The small intestine is a relatively clean place. The stomach receives food, mixes it with acid and digestive juices and turns it into a clean slurry that is pushed through the three parts of small intestine (duodenum, jejunum, ileum) where the nutrients are absorbed into the body. The refuse is dumped into the large intestine, or colon, where water is absorbed and the feces become more solid and are eliminated from the body.

The normal bacteria (flora) of the gut, perform important functions, helping to digest certain vitamins like folic acid and vitamin K, and they protect the intestine from being invaded by disease causing bacteria. However, if the normal function of the intestine is compromised, bacterial overgrowth may occur. This may be the result of a lack of adequate stomach acid, damage to the intestine by toxins like alcohol, or a decrease in the speed at which the small intestine transfers material to the colon.

The colon is not as clean as the small intestine and reflux, or backflow, of stool into the small intestine can colonize it with colonic bacteria.

This article will discuss only the type of SIBO associated with intestinal diseases and conditions.

Associated SIBO: Types of other diseases or conditions associated with it

Small intestine bowel overgrowth is often associated with another illness that affects the function of the small intestine. The body has many protective mechanisms to keep bacteria under control, including stomach acidity and intestinal motility, the ability for the intestine to move its contents downstream at an appropriate speed. Bacterial growth is hindered by the presence of bile and immunoglobulins. Finally, the ileocecal valve prevents stool from refluxing from the colon (large intestine) into the ileum or the last part of the small intestine.

Any illness or disease that affects the body's defense mechanism puts a person at risk for SIBO, but the majority of people develop SIBO because of an intestinal motility problem. These may include

  • complications from gastric bypass surgery,
  • bowel strictures and adhesions that can lead to intermittent bowel obstructions,
  • diverticuli or outpouchings of the small intestine, and
  • tumors.

Bowel motility may be affected by neurologic diseases including

People with diabetes with autonomic dysfunction (nerve damage) may also develop dysmotility.

Other intestinal diseases that may be associated with SIBO include:

  • Crohn's disease
  • Achlorhydria (chronic inflammation causes the stomach to become unable to produce acid) of the liver
  • Non-alcoholic steatohepatitis (NASH) , leukemia and lymphoma may also increase the risk of developing small intestine bacterial overgrowth.

SIBO and IBS: FODMAP Foods to Eat and Foods to Avoid

FODMAP is an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. High FODMAP foods have a lot of simple carbohydrates and sugar alcohols that aren't absorbed by the gut very well, and can pose a problem particularly if you have IBS or another bowel condition that puts you at risk for the condition. Examples of foods high in FODMAPs (foods that sit and ferment in the gut) include:

SIBO symptoms and signs

There are no specific complaints or physical findings that can make the diagnosis of SIBO. Instead, small intestine bacterial overgrowth should be considered in the presence of a compilation of many non-specific symptoms each by themselves would not be worrisome but together can point to the potential diagnosis.

Initial symptoms are specific to the gastrointestinal tract and abdomen and include:

A person with SIBO does not need to have all of these symptoms.

As the disease progresses, the bacterial overgrowth inhibits the body's ability to properly absorb nutrients from the diet. This can lead to vitamin and electrolyte abnormalities, protein deficiencies, and difficulties with fat absorption.

Inability to absorb vitamin B12 can lead to symptoms of pernicious anemia, including a low red blood cell count and peripheral neuropathy. Anemia also may be due to iron deficiency. Decreased Vitamin A may lead to night blindness. Metabolic bone disease may be due to Vitamin D deficiency and decreased calcium. This may also lead to muscle twitching and spasms.

Malnutrition may result in weight loss, and progress to excessive muscle wasting (cachexia). Inability to absorb fats in the diet may lead to steatorrhea (excess fat in the feces) that results in foul smelling oily stool, and may cause some anal leakage or fecal incontinence.

Is there a test to diagnose the condition?

The initial symptoms of small intestine bacterial overgrowth are non-specific and it may take time for the person and health care professional to consider SIBO as a potential cause. The clues may come from illnesses associated with malabsorption of proteins, fats and vitamins. When there is malabsorption it is important to look for SIBO.

Blood tests may be ordered looking for different causes of anemia, electrolyte imbalance, and vitamin deficiencies.

Breath tests may be considered to diagnose SIBO by looking for the byproducts of digestion , especially those produced by bacteria. Upper GI endoscopy allows a gastroenterologist to look at the inside of the upper part of the small intestine and take biopsies or small bits of tissue that can be examined under the microscope. Biopsies can determine if there is damage to the lining of the intestine that may be giving rise to the symptoms either through the mechanism of bacterial overgrowth or via another mechanism.

While these diagnostics tests are being performed, it is appropriate for the health care professional to look for conditions that are associated with SIBO. If such a condition is already known, then maximizing treatment of the associated condition may be undertaken at the same time the diagnosis of which SIBO is being considered and tested.


Antibiotic and probiotic treatment for SIBO

The treatment for SIBO includes controlling and treating any underlying associated illness. The goal is to control the symptoms of small intestine bacterial overgrowth since it may not be possible to "cure" the disease.

Antibiotics are one of the treatments that are helpful in controlling the excess bacteria. It is important that not all the bacteria in the intestine are eradicated, since some are required to help with normal digestion.

Amoxillin-clavulanate (Augmentin) and rifaxamin (Xifaxan) are the two common first line antibiotics that may be prescribed. Depending upon the situation, other antibiotics may also be considered, including:

While a single course of antibiotics for 1-2 weeks may be sufficient, SIBO has a tendency to relapse, and sometimes repeated courses of antibiotics may be required. In some people, the antibiotics will be routinely cycled, meaning that they will alternate a 1-2 weeks on the antibiotic with 1-2 weeks off.

In addition, underlying vitamin and nutrient deficiencies due to malabsorption should be treated.

How can the condition be prevented?

Since SIBO usually is a secondary illness that occurs because the intestine has in some way been affected by another disease, it is important to keep chronic diseases properly treated and under control as best as possible.

Does SIBO relapse? What's the prognosis?

Small intestine bacterial overgrowth is usually associated with another underlying illness. Even with appropriate treatment, the relapse rate is high and often depends upon how well the underlying illness is managed and controlled.

How Covid-19 affects the gut: Scientists uncover a rare side effect

Media reports earlier this week described a Queensland nurse with stomach pains who went on to test positive for Covid-19.

Could stomach pains be another symptom of Covid-19? And if you have stomach pains, should you get tested?

Although we might think of Covid-19 as a respiratory disease, we know it involves the gut. In fact, SARS-CoV-2, the virus that causes Covid-19, enters our cells by latching onto protein receptors called ACE2. And the greatest numbers of ACE2 receptors are in the cells that line the gut.

Covid-19 patients with gut symptoms are also more likely to develop severe disease. That’s partly because even after the virus has been cleared from the respiratory system, it can persist in the gut of some patients for several days. That leads to a high level of virus and longer-lasting disease.

We also suspect the virus can be transmitted via the fecal-oral route. In other words, the virus can be shed in someone’s poo, and then transmitted to someone else if they handle it and touch their mouth.

What type of gut symptoms are we talking about?

A review of more than 25,000 Covid-19 patients found about 18% had gastrointestinal symptoms. The most common was diarrhea followed by nausea and vomiting. Abdominal pain was considered rare. In another study only about 2% of Covid-19 patients had abdominal pain.

Some people believe Covid-19 causes abdominal pain through inflammation of the nerves of the gut. This is a similar way to how gastroenteritis (gastro) causes abdominal pain.

Another explanation for the pain is that Covid-19 can lead to a sudden loss of blood supply to abdominal organs, such as the kidneys, resulting in tissue death (infarction).

Are gut symptoms recognized?

The US Centers for Disease Control has added diarrhea, nausea, and vomiting to its list of recognized Covid-19 symptoms.

However, the World Health Organization still only lists diarrhea as a gastrointestinal Covid-19 symptom.

In Australia, nausea, diarrhea, and vomiting are listed as other Covid-19 symptoms, alongside the classic ones (which include fever, cough, sore throat and shortness of breath). But abdominal pain is not listed.

Advice of symptoms that warrant testing may vary across different states and territories.

How likely is it?

Doctors often use the concept of pre-test probability when working out if someone has a particular disease. This is the chance a person has the disease before we know the test result.

What makes it difficult to determine the pre-test probability for Covid-19 is we don’t know how many people in the community truly have the disease.

We do know, however, Covid-19 in Australia is much less common than in many other countries. This affects the way we view symptoms that aren’t typically associated with Covid-19.

It’s far more common for people’s abdominal pain to be caused by something other than Covid-19. For example, about a quarter of people at some point in their lives are known to suffer from dyspepsia (discomfort or pain in the upper abdomen). But the vast majority of people with dyspepsia do not have Covid-19.

Similarly, irritable bowel syndrome affects about 9% of Australians, and causes diarrhea. Again, the vast majority of people with irritable bowel syndrome do not have Covid-19.

So how about this latest case?

In the Queensland case, we know the nurse was worried he could have had Covid-19 because he was in close contact with Covid-19 patients.

As he seemed otherwise healthy before developing new abdominal symptoms, and considering he worked on a Covid ward, his pre-test probability was high. Doctors call this a “high index of suspicion” when there is a strong possibility someone may have symptoms due to a disease such as Covid-19.

What does this mean for me?

If you have new gastrointestinal symptoms and you’ve potentially been in contact with someone with COVID-19 or if you also have other classic Covid-19 symptoms (fever, cough, shortness of breath and sore throat) you should definitely get tested.

If you have just gastrointestinal symptoms, you may need to get tested if you’re in a “hotspot” area, or work in a high-risk occupation or industry.

If you have gastrointestinal symptoms alone, without any of these additional risk factors, there is no strong evidence to support testing.

However, if Covid-19 becomes even more common in the community, these symptoms now regarded as uncommon for Covid-19 will become more common.

If you have concerns about any gastrointestinal symptoms, seeing your GP would be sensible. Your GP will provide a balanced assessment based on your medical history and risk profile.

This article was originally published on The Conversation byVincent Ho at Western Sydney University. Read the original article here.


If you don’t have SIBO because of an anatomical problem, a simple step is to cut out sugary foods and drinks. This may be all it takes to feel better.

Other diet changes for SIBO include:

  • Quitting foods that seem to make your symptoms worse and waiting 3 days before putting them back on your menu. This way, you’ll know whether a certain food triggers your symptoms.
  • Avoiding fiber supplements as well as any liquid medications (such as cough syrup) that use sugar alcohols for flavor.
  • Avoiding lactose. If your small intestine is damaged, you might lose the ability to digest lactose, the sugar in milk products.
  • A low-FODMAP diet. FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. FODMAPs are a type of carbohydrate. But not every carb is a FODMAP. A nutritionist or a doctor experienced in nutrition can help you come up with the right plan.
  • The elemental diet. This is an eating plan that involves special nutritional formulas instead of typical foods. They’re designed to meet your body’s nutritional needs.
  • Prebiotics and probiotics. You can get probiotics in fermented foods like yogurt (look for “live, active cultures” on the label), kefir (a yogurt-based drink), and kimchi (a traditional Korean relish). To get more prebiotics from foods, include lots of fruits, veggies, and whole grains.

If you’re thinking about taking prebiotics or probiotics in supplements, talk with your doctor first to make sure they’re a good choice for you. Foods are always a good first step, since you’ll get lots of other nutrients that are good for you.

Do I have a stomach virus or food poisoning?

Sickness and pain in the abdomen is often passed off as either stomach flu or food poisoning. However, since the symptoms are similar, people often confuse the two conditions.

Knowing the difference between the two can support an accurate diagnosis.

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A viral infection that attacks the digestive system is commonly called a stomach virus.

People sometimes call the illness a ‘stomach flu‘, although this name is misleading, as influenza attacks the respiratory system. A stomach virus can also be known as viral gastroenteritis.

Different strains of the virus exist. According to the Centers for Disease Control and Prevention (CDC), the most common cause in the United States is norovirus.

Food poisoning, on the other hand, describes the ingestion of contaminated food. Bacteria, viruses or less commonly parasites can enter the body and cause symptoms of gastroenteritis through food that has spoiled, been unhygienically prepared or contaminated in any other way.

Stomach viruses

Stomach viruses are highly contagious and can spread quickly. People infected with a stomach virus are contagious from the moment they begin feeling ill and also for the first few days after they recover.

A stomach virus can spread in several different ways:

  • eating food or drinking liquids that have been contaminated with the virus
  • having direct or indirect mouth contact with an infected person or surface with the virus on it

The virus also inhabits the vomit and stools of people who have the infection.

Food poisoning

Cross-contamination is often the cause of food poisoning, during which harmful organisms transfer from one surface to another. Uncooked and ready-to-eat foods, such as salads, are particularly at risk of contamination.

Each year, approximately 48 million people in the United States experience a bout of food poisoning.

Bacteria can grow rapidly when a range of foods, including meats, dairy products, and sauces, are not kept at the right temperature. Bacteria and other harmful organisms produce poisonous substances that can cause inflammation of the intestines when eaten.

Contamination can also occur at home if raw meat is not handled or cooked properly.

Salmonella and E. coli are two common types of bacteria linked to food poisoning.

The symptoms of stomach viruses and food poisoning are very similar but there can be some differences.

Stomach viruses

The symptoms of a stomach virus include:

    that may be watery or bloody
  • a loss of appetite
  • nausea or vomiting
  • stomach cramps, muscle aches, or weakness
  • low-grade fever
  • light-headedness or dizziness

A stomach virus does not usually cause bloody stools. Stools that contain blood could signal a more serious infection.

These symptoms often last 3-4 days but can last for up to 14 days.

Food poisoning

Symptoms of food poisoning can occur within hours of eating. People may experience:

  • watery or bloody diarrhea
  • nausea
  • vomiting
  • stomach pain and cramping
  • a fever, chills, and body aches
  • dizziness and lightheadedness from dehydration

Sickness from food poisoning can last from a few hours to several days.

People can usually suspect food poisoning if they ate unrefrigerated food or other individuals who consumed the same food are experiencing similar symptoms.

Salads, raw or undercooked poultry, eggs, seafood, and other dairy-based products are high-risk foods for food poisoning.

There is no single method for diagnosing a stomach virus. A doctor will likely base a diagnosis on the presenting symptoms alone.

A rapid stool test can be used to detect the rotavirus or norovirus but it is not readily available at most clinics. There are no quick tests for other viruses. A stool sample can also be used to rule out bacterial or parasitic infection.

Diagnosing food poisoning can be difficult, especially if you cannot identify the particular cause. Stool tests may be able to identify the disease-causing pathogen.MEDICAL NEWS TODAY NEWSLETTERStay in the know. Get our free daily newsletter

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Treatment depends on the organism causing the infection.

Supportive therapy that includes increased hydration, rest, electrolyte replenishment, and medication for fever, are usually all that’s needed for viral illnesses. This is because viruses do not respond to antibiotics and simply need to run their course.

If it is determined that a bacteria, like Salmonella, is causing the symptoms, an antibiotic may be prescribed. For parasites, anti-parasitic medications may be available.

There are a few steps people can take at home to aid recovery from a stomach virus or food poisoning.

  • Let the stomach settle. Try not to eat any solid foods until you feel better.
  • Suck on ice chips or take small sips of water. People should drink plenty of liquids to prevent dehydration. Avoid juices or other beverages with a lot of sugar or sweeteners that can make diarrhea worse.
  • Ease yourself back into eating. Start with bland, easy-to-digest foods, such as soda crackers, toast, and rice. Stop eating if a feeling of nausea returns.
  • Avoid certain substances until feeling better, or for a few days to a week after symptoms have resolved cleared if your case was severe. These include dairy, caffeine, alcohol, sugar, and fatty or highly seasoned foods.

People should be cautious of taking over-the-counter (OTC) medications, unless advised by a healthcare provider, as some can worsen the infection. Even anti-diarrhea medications can make the situation worse in some cases.

Gastroenteritis will typically resolve within a few days or less without medication. However, hydration is vital to a speedy recovery and prevention of complications.

People should seek medical attention if they have have any of the following symptoms:

  • bloody stool or vomit
  • unable to keep liquid down for 12-24 hours
  • dizziness or lightheadedness
  • fever above 104 °Fahrenheit (°F)
  • severe, unrelenting abdominal pain

Stomach virus

The CDC estimate that norovirus causes 19 to 21 million illnesses each year. The following preventive measures can help reduce the risk of catching a stomach virus.

  • Practicing proper hand hygiene: People should always wash their hands with soap and water, especially after using the toilet, changing diapers, or before eating or preparing food.
  • Taking precautions when in the kitchen: It is important to rinse fruits and vegetables and cook all food thoroughly.
  • Cleaning and disinfecting potentially contaminated surfaces: People should immediately clean and disinfect contaminated surfaces after vomiting or diarrhea.
  • Washing laundry thoroughly: The stomach virus can easily be carried from person to person so any clothing contaminated with vomit or stool should be removed and washed in hot water.
  • Keeping a distance from anyone who is infected with the virus: If someone in a household is infected, they should use separate personal items such as plates and glasses, and use a separate bathroom if possible.

There is a vaccination available in some countries that counters certain stomach viruses. The vaccine can be effective in helping to prevent severe symptoms of the virus when given to children in the first year of their life.

Food poisoning

People can help prevent food poisoning by ensuring that meats, salads, dressings, and other foods are stored at the right temperature. Do not eat food that has been left out of storage for more than 2 hours.

It is important that people wash their hands when handling any raw meat. They should also make sure to cook it thoroughly, and to avoid eating raw meat, raw eggs, or sauces made with raw eggs. During picnics or parties, food that should be refrigerated should be kept on ice.

People should also be careful when eating in restaurants or other unfamiliar environments.

Clostridium Difficile (C. Diff) Prevention

If you're in a hospital or long-term health care facility, you can do several things to protect yourself from C. diff. For example:

  • Ask your health care professionals to wash their hands thoroughly before and after caring for you.
  • Request that all medical equipment be sanitized before being brought into your room. with soap and water after using the bathroom and before eating.


Another way to help prevent C. diff is to not take unnecessary antibiotics. Talk this over with your doctor and see if there are other treatment options. And don't take antibiotics without a doctor's OK.

Many C. diff infections are mild and short-lived, but others can be quite serious. Take precautions, and don't hesitate to seek medical help if you have symptoms.


Mayo Clinic: "C. Difficile Infection," "C. Difficile Infection: Symptoms and Causes," "C. Difficile Infection: Treatment."

CDC: "Clostridium Difficile Infection Information for Patients," "Clostridium Difficile (C. diff.)," "Prevent the Spread of C. diff."

Wisconsin Department of Health Services: "Clostridium difficile: Disease Fact Sheet."

California Department of Public Health: "Clostridium difficile infection (CDI)."

American Academy of Family Physicians: "Clostridium difficile (C. diff) infection."

You will most likely recover from the most common types of bacterial gastroenteritis in a couple of days. The goal is to make you feel better and avoid dehydration.

Drinking enough fluids and learning what to eat will help ease symptoms. You may need to:

If you have diarrhea and are unable to drink or keep down fluids because of nausea or vomiting, you may need fluids through a vein (IV). Young children may be at extra risk of getting dehydrated.

If you take diuretics ("water pills"), or ACE inhibitors for high blood pressure, talk to your provider. You may need to stop taking these medicines while you have diarrhea. Never stop or change your medicines without first talking to your provider.

Antibiotics are not given very often for most common types of bacterial gastroenteritis. If diarrhea is very severe or you have a weak immune system, antibiotics may be needed.

You can buy medicines at the drugstore that can help stop or slow diarrhea. Do not use these medicines without talking to your provider if you have:


The substances secreted through the process of digestion have an effect as to where gut bacteria proliferate. Stomach acid, bile acid, and pancreatic enzymes typically prevent the colonization of bacteria in the stomach or the beginning section of the small intestine. (Small intestinal bacterial overgrowth is a health problem in which excess bacteria are found in the small intestine.)

Therefore, gut bacteria are found to some extent in the last part of your small intestine, but overwhelmingly so in your large intestine. It is estimated that there are more than a thousand types of microbes in your body.   (A 2015 study reported that these microbes make up anywhere from 25% to 54% of your stool.) This world of microorganisms is separated internally from your body through a single layer of cells on your large intestine—cells known as epithelial cells.  

These resources provide more information about this condition or associated symptoms. The in-depth resources contain medical and scientific language that may be hard to understand. You may want to review these resources with a medical professional.

Where to Start

  • You can obtain information on this topic from the Centers for Disease Control and Prevention (CDC). The CDC is recognized as the lead federal agency for developing and applying disease prevention and control, environmental health, and health promotion and education activities designed to improve the health of the people of the United States.

In-Depth Information

  • Medscape Reference provides information on this topic. You may need to register to view the medical textbook, but registration is free.
  • The Merck Manual for health care professionals provides information on Klebsiella infection.
  • The Monarch Initiative brings together data about this condition from humans and other species to help physicians and biomedical researchers. Monarch’s tools are designed to make it easier to compare the signs and symptoms (phenotypes) of different diseases and discover common features. This initiative is a collaboration between several academic institutions across the world and is funded by the National Institutes of Health. Visit the website to explore the biology of this condition.