Scientists Have Made a Human Microbiome From Scratch (2022)

Advertisement

Continue reading the main story

Supported by

Continue reading the main story

Matter

To better understand how microbes affect our health, researchers combined 119 species of bacteria naturally found in the human body.

  • Send any friend a story

    As a subscriber, you have 10 gift articles to give each month. Anyone can read what you share.

Scientists Have Made a Human Microbiome From Scratch (1)
(Video) Scientist have created human microbiome from scratch

By Carl Zimmer

Our bodies are home to hundreds or thousands of species of microbes — nobody is sure quite how many. That’s just one of many mysteries about the so-called human microbiome.

Our inner ecosystem fends off pathogens, helps digest food and may even influence behavior. But scientists have yet to figure out exactly which microbes do what or how. Many studies suggest that many species have to work together to do each of the microbiome’s jobs.

To better understand how microbes affect our health, scientists have for the first time created a synthetic human microbiome, combining 119 species of bacteria naturally found in the human body. When the researchers gave the concoction to mice that did not have a microbiome of their own, the bacterial strains established themselves and remained stable — even when the scientists introduced other microbes.

The new synthetic microbiome can even withstand aggressive pathogens and cause mice to develop a healthy immune system, as a full microbiome does. The findings were published on Tuesday in the journal Cell.

A better understanding of the microbiome could potentially lead to a powerful way to treat a host of diseases. Already, doctors can use the microbiome to treat life-threatening gut infections of the bacteria Clostridium difficile. They just have to transplant stool from a healthy donor, and the infection usually goes away.

“It works shockingly well,” said Dr. Alice Cheng, a gastroenterologist at Stanford University who led the new study.

Dr. Cheng and her colleagues can now use the new synthetic microbiome to learn about the role of each individual microbe, knowledge that could help doctors tackle other disorders. For example, the scientists could mix a cocktail of 118 of the 119 species in the lab and then see how the modified microbiome affects the health of mice.

(Video) scientists have created a human microbiome from scratch..

“It’s something that has been badly needed for some period of time,” said Dr. Gary Wu, a gastroenterologist at the University of Pennsylvania School of Medicine who was not involved in the research.

Each of us harbors about 30 trillion microbes, roughly the same number as our own cells. But since bacteria are much smaller, they make up only a few pounds of our weight.

Image

Before the 21st century, most of what was known about the human microbiome came from the few species that researchers managed to grow in a petri dish. In the early-2000s, scientists made a major advance by fishing DNA from samples of human spit, stool and skin. With those genetic sequences in hand, they created a catalog of species that live in our bodies.

The list was startlingly long, and many species were new to microbiologists. Making matters more confusing, most species live in some people but not others. There is no one human microbiome.

A number of researchers turned to mice to get better acquainted with some of these unfamiliar organisms. They reared germ-free animals in sterile cages and then put a broth made from human feces into the animals’ intestines. The microbes in that fecal transplant then started replicating in the animals.

These experiments have delivered some tantalizing results. For example, in some experiments, germ-free mice that received microbiomes from obese people put on more weight than did mice transplanted with microbiomes from people of average weight.

But pinpointing why these changes happen has proved harder. There’s no way to manipulate the microbiome in a stool sample, species by species. “It’s completely mixed up, and you can’t alter it,” Dr. Cheng said.

Some researchers have taken on this challenge by giving germ-free mice a single species of microbe and observing its effect. But those experiments have their own limits, since many microbes don’t work properly without ecological partners to help them.

Scientists have tried giving germ-free mice combinations of microbes. But so far, even the best efforts have left mice transplanted with fewer than 20 species — not the hundreds that live in humans. These miniature microbiomes leave the mice with poorly developed immune systems and metabolisms. “You get a mouse that doesn’t work,” said Lora Hooper, an immunologist at the University of Texas Southwestern Medical Center who was not involved in the new study.

In 2017, Dr. Cheng and her colleague at Stanford, Michael Fischbach, had long conversations about how to overcome the shortcomings of previous studies. “We needed to build an ecosystem from scratch,” Dr. Fischbach said.

They knew it would be difficult to grow a wide variety of microbes in the lab. And it was entirely possible that once in a mouse, their ecosystem would crash. “At the time, we could not have expected this to work,” Dr. Fischbach said.

First, Dr. Cheng and her colleagues drew up a list of 166 species that have been found in a sizable fraction of people. When they reached out to labs and companies, they managed to get hold of 104 of them.

Each microbe came with its own instructions for staying alive. To Dr. Fischbach’s surprise, Dr. Cheng figured out how to satisfy each of their fussy requirements to produce colonies in the lab.

(Video) Hidden Secrets of the Human Microbiome

Image

Dr. Cheng mixed the 104 species together and put them into germ-free mice. Then she gave the microbes time to settle in — or die off. To see how her makeshift microbiome fared, she had to collect mouse droppings and work with colleagues to sequence all the DNA contained within.

Dr. Cheng found that the 104 species created a stable ecosystem inside the mice. Not only did the microbes endure in the animals, but the ecosystem’s structure didn’t change. Some microbes quickly became abundant and stayed that way. Others became rare but never disappeared. And the same ecosystem came into existence over and over again in different mice.

“It is remarkable how a hundred-plus human gut strains form a stable and resilient community,” said Kiran Patil, a University of Cambridge biologist who was not involved in the study. “It’s like a hundred-piece puzzle that looks daunting, but then you just mix and shake the pieces, and presto! The puzzle solves itself.”

(Video) scientists have created a human microbiome from scratch..

Next Dr. Cheng and her colleagues put their microbiome to a test: They gave the mice stool transplants from human volunteers. Would the animals’ synthetic microbiome be resilient enough to withstand the onslaught?

It was indeed. Only seven of the original species disappeared. Some of the new species found empty places in the ecosystem and became a stable part of the microbiome.

“I lay down on a couch and was looking at the skylight,” Dr. Cheng said. “I had that ‘I can’t believe that worked’ kind of feeling.”

From that second experiment, Dr. Cheng and her colleagues perfected their microbiome. They picked out the 22 most successful newcomer species and added them to their microbial zoo, for a total of 119 species.

This new microbiome, which they have dubbed hCom2, is even more resilient than the first version. When the scientists gave hCom2 mice a stool transplant, none of the newcomers could establish themselves in the animals.

The researchers also tested how well the mice could cope with a potentially lethal strain of E. coli. In previous experiments, scientists have found that this strain can explode in the intestines of mice that have a miniature microbiome of 12 species.

Dr. Cheng and her colleagues gave their hCom2 mice a dose of E. coli and found that they resisted the invaders just as well as did mice that received a full human stool sample.

The hCom2 microbiome also had the same kind of influence on its hosts as did a full microbiome. The mice produced healthy levels of digestive fluids in the gut and developed full-fledged immune systems not found in germ-free mice.

Dr. Cheng and her colleagues have already started running experiments in which they leave out certain microbes from the cocktail to better understand how their microbiome works. They are also providing their bank of microbes to other researchers who want to run experiments of their own.

When asked if she intended to use the synthetic microbiome for her own research, Dr. Hooper responded succinctly: “Heck yeah.”

She hopes to use hCom2 mice to understand how the microbiome influences obesity. Part of the answer clearly lies in how the microbes help our intestines absorb fatty lipids from our foods. But studies on mice have not shed much light on which microbes are helping and which are getting in the way.

“We’ve had a really hard time getting to the answer to this question,” she said. “So this type of experimental system will give us a path forward.”

Advertisement

(Video) The Invisible Universe Of The Human Microbiome

Continue reading the main story

FAQs

How is the human microbiome formed? ›

In humans, the composition of the gastrointestinal microbiome is established during birth. Birth by Cesarean section or vaginal delivery also influences the gut's microbial composition. Babies born through the vaginal canal have non-pathogenic, beneficial gut microbiota similar to those found in the mother.

How do scientists study the human microbiome? ›

Using markers, researchers can identify a microbe without having to sequence its entire genome. This shortcut allows them to identify all the species present in a huge number of samples very quickly. Even sequencing markers instead of entire genomes, researchers studying the microbiome generate massive amounts of data.

When did human microbiome research start? ›

The Human Microbiome Project was launched by the National Institutes of Health in 2007 with the mission to generate the resources and expertise needed to characterize the human microbiome and analyze its role in health and disease.

What do scientists who study the human microbiome hope to achieve? ›

Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome profiling studies is to understand the role of microbes in health and disease.

Are babies born with sterile guts? ›

This study suggests that gut bacterial diversity is extremely limited at birth and supports the hypothesis that the neonatal gut is sterile and colonised rapidly thereafter.

Can you change your gut microbiome? ›

Probiotic foods contain beneficial live microbiota that may further alter one's microbiome. These include fermented foods like kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi, miso, and sauerkraut.

Who discovered the human microbiome? ›

Discovery. The diversity of the human microbiome was first observed by Antonie van Leewenhoek, a Dutch merchant. In the early 1680s he noted a striking difference between microbes found in samples taken from the mouth versus those in faecal stools.

What kind of scientist studies the microbiome? ›

Susan Lynch is a microbiologist who studies the human microbiome.

How long has the microbiome been studied? ›

2Study of the Human Microbiome. While study of what is now known as the human microbiome can be traced as far back as Antonie van Leeuwenhoek (1632–1723), advances in genomics and other areas of microbiology have spurred a resurgence of interest.

Are human microbes legit? ›

Yes!

The trillions of microbes that live in our guts impact & regulate every aspect of human health & development. This ecosystem of microbes -- comprising thousands of species of bacteria, viruses, archaea, and fungi -- makes up the gut microbiome.

Is the human microbiome project complete? ›

The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes.

How much of the human body is microbiome? ›

Because of their small size, however, microorganisms make up only about 1 to 3 percent of the body's mass (in a 200-pound adult, that's 2 to 6 pounds of bacteria), but play a vital role in human health.

What has the human microbiome project found? ›

In addition to establishing the human microbiome reference database, the HMP project also discovered several "surprises", which include: Microbes contribute more genes responsible for human survival than humans' own genes. It is estimated that bacterial protein-coding genes are 360 times more abundant than human genes.

Why is the human microbiome important? ›

The bacteria in the microbiome help digest our food, regulate our immune system, protect against other bacteria that cause disease, and produce vitamins including B vitamins B12, thiamine and riboflavin, and Vitamin K, which is needed for blood coagulation.

How do you measure your gut microbiome? ›

Microbiome tests — whether done in a doctor's office or at home — are conducted via a stool sample. Unlike other types of tests you may be able to do at home using blood or saliva samples, these are fecal tests that require fresh stool samples.

Are we born bacteria free? ›

Babies in the womb encounter no microbes until they are born. Most babies get their first big dose of microbes at birth, while traveling through the birth canal, then pick up more while breastfeeding. Early microbes helped shape your immune system, your digestive system, even your brain.

Are humans born with fungus? ›

Fungi are in the normal newborn gut at birth

Unlike the majority of the fungi we studied, which are naturally present in the gut, this made us wonder if having too much of this fungi too early in life might be one of the many causes of preterm birth.

Is milk good for gut bacteria? ›

Certain foods, such as natto, soy, pickles, sauerkraut, and milk and its derivatives contain good bacteria that help balance your gut flora. These microorganisms are known as probiotics and support overall health. Milk appears to be particularly beneficial.

What kills your gut flora? ›

A “western” diet that's high in fat and sugar and low in fiber can kill certain types of gut bacteria, making your microbiota less diverse. Limit use of antibiotics, which can wipe out healthy bacteria along with problematic bacteria, to only when necessary as determined by your doctor.

Is apple cider vinegar good for your gut? ›

Raw apple cider vinegar also contains: Natural probiotics (friendly bacteria), which may help with your immune system and gut health. Antioxidants, substances that can prevent damage to your body's cells.

What is the fastest way to heal gut microbiome? ›

In this article, we list 10 scientifically supported ways to improve the gut microbiome and enhance overall health.
  1. Take probiotics and eat fermented foods. ...
  2. Eat prebiotic fiber. ...
  3. Eat less sugar and sweeteners. ...
  4. Reduce stress. ...
  5. Avoid taking antibiotics unnecessarily. ...
  6. Exercise regularly. ...
  7. Get enough sleep.
28 May 2019

Can you live without your microbiome? ›

But as long as humans can't live without carbon, nitrogen, protection from disease and the ability to fully digest their food, they can't live without bacteria, said Anne Maczulak, a microbiologist and author of the book "Allies and Enemies: How the World Depends on Bacteria" (FT Press, 2010).

Why is the human microbiome losing diversity? ›

The Western diet also has a critical influence on the microbiota. Western diets high in saturated fats, refined carbohydrates and sugars, and low in fresh foods and fiber are associated with reduced microbial complexity, an imbalance of the gut ecosystem and disease.

When did the human microbiome project end? ›

The Human Microbiome Project (HMP) was supported by the National Institutes of Health (NIH) Common Fund from 2007 through 2016, with the mission of generating resources that would enable the comprehensive characterization of the human microbiome and analysis of its role in human health and disease.

How can I heal my gut health? ›

7 things you can do for your gut health
  1. Lower your stress levels. Chronic high levels of stress are hard on your whole body, including your gut. ...
  2. Get enough sleep. ...
  3. Eat slowly. ...
  4. Stay hydrated. ...
  5. Take a prebiotic or probiotic. ...
  6. Check for food intolerances. ...
  7. Change your diet.

What degree do you need to study the microbiome? ›

How do I get involved in microbiome research? An undergraduate degree in any life science subject (including physiology, biomedicine, medicine, sports science, neuroscience, genetics etc.) will open the door to a career in physiology research.

What is synthetic microbiome? ›

Altogether, synthetic microbiomes represent modular systems that allow various combinations of intestinal isolates based on their function to mimic physiological conditions of interest.

Did humans evolve from microbes? ›

It is likely that eukaryotic cells, of which humans are made, evolved from bacteria about two billion years ago. One theory is that eukaryotic cells evolved via a symbiotic relationship between two independent prokaryotic bacteria.

What's the difference between microbiome and microbiota? ›

The microbiome refers to the collection of genomes from all the microorganisms in the environment. Microbiota, on the other hand, usually refers to microorganisms that are found within a specific environment. Microbiota can refer to all the microorganisms found in an environment, including bacteria, viruses, and fungi.

How big is the microbiome? ›

The microbiome includes approximately 100 trillion bacterial cells. That's 100,000,000,000,000! You may have heard that there are 10 times more microbial cells than human cells in the human body, but that commonly-cited ratio was based on an estimate of 10 trillion cells in the human body.

Does human microbes actually pay? ›

Most donors, even reasonable healthy ones, only yield modest benefits. Human Microbes, an organization specialized in finding super-donors and connecting them with recipients, is paying super-donors $500 per stool. This adds up to $180,000/yr if donating a daily stool!

Where is the largest portion of a human's microbiome? ›

Stomach flora + Intestinal flora. The largest part of body microbiota.

Who is Michael Harrop? ›

I run Human Microbes, an organization finding super-donors for FMTs and connecting them with recipients. I am also the creator of HumanMicrobiome.info - the world's most comprehensive, up to date database on FMTs, gut health, and microbiome research, used by both professionals and laypeople.

How much did the human microbiome project cost? ›

This 10-year, $215-million initiative aimed to develop research resources for the emerging field of human microbiome research. The HMP was designed to increase our understanding of the complex and abundant microbial communities of the human body and their role in health and disease.

Can you test your microbiome? ›

Direct-to-consumer microbiome tests require little more than filling out a form online, paying a fee and sending in a stool sample. Two to three weeks later, you'll get a report that provides an overview of the microorganisms in your gut and whether they're associated with various diseases and disorders.

What is the human microbiome composed of? ›

The microbiome is defined as the collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa and viruses) that live inside and on the human body. We have about 10 times as many microbial cells as human cells.

What percentage of the human body is not human? ›

More than half of your body is not human, say scientists.

Human cells make up only 43% of the body's total cell count. The rest are microscopic colonists.

Where is the most bacteria found on the human body? ›

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 [1]. These microorganisms colonize the body, which means that they usually do not cause any harm.

What is your body basically made up of? ›

The four most abundant elements in the human body – hydrogen, oxygen, carbon and nitrogen – account for more than 99 per cent of the atoms inside you. They are found throughout your body, mostly as water but also as components of biomolecules such as proteins, fats, DNA and carbohydrates.

Are viruses part of a healthy human microbiome? ›

Archaea, viruses, fungi, and other eukaryotes

The study of the healthy microbiome has been greatly enriched for bacteria [7, 9], with less attention given to other microbial domains. The human microbiome, though, spans the tree of life and thus includes archaea, viruses, and eukaryotes.

How much bacteria is in your mouth? ›

There are about 6 billion bacteria in a human's mouth.

Yes, bacteria are lurking in your mouth, and it has almost the same number as the total human population on Earth. Aside from mouthparts, the oral microbiome contains good and bad bacteria too.

How many good bacteria do we have in our body? ›

In fact, our bodies are home to an estimated 100 trillion “good” bacteria, many of which reside in our gut. Not only do we live in harmony with these beneficial bacteria, but they are actually essential to our survival.

What is the best food for microbiome? ›

Another way to nourish your gut microbiota is by eating fermented foods like yogurt, kimchi, sauerkraut, kombucha and kefir. The microbes in fermented foods, known as probiotics, produce vitamins, hormones and other nutrients.

What would happen if microbes didn't exist? ›

Annihilation of most humans and nonmicroscopic life on the planet would follow a prolonged period of starvation, disease, unrest, civil war, anarchy, and global biogeochemical asphyxiation.

What do scientists who study the human microbiome hope to achieve? ›

Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome profiling studies is to understand the role of microbes in health and disease.

Are gut microbiome tests legit? ›

The FDA has not approved home microbiome tests, meaning that it has not tested them for accuracy or safety. Microbiome tests cannot diagnose health conditions. People should only purchase these products if they are interested in finding out which bacteria are in their stool.

How do you know if your gut bacteria is off? ›

Frequent discomfort, gas, bloating, constipation, diarrhea, and heartburn could be signs that your gut is having a hard time processing food and eliminating waste. You feel tired more often than not. People with chronic fatigue may have imbalances in the gut.

How do you know your gut is unhealthy? ›

Signs of poor gut health
  1. Autoimmune problems, such as thyroid issues, rheumatoid arthritis and type 1 diabetes.
  2. Digestive issues, such as irritable bowel syndrome, constipation, diarrhea, heartburn or bloating.
  3. Sleep issues.
  4. Skin rashes and allergies.
  5. Sugar cravings.
  6. Unexplained fatigue or sluggishness.

What makes up the microbiome? ›

The microbiome is defined as the collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa and viruses) that live inside and on the human body. We have about 10 times as many microbial cells as human cells.

Where do gut microbes come from? ›

In humans, a gut flora similar to an adult's is formed within one to two years of birth as microbiota are acquired through parent-to-child transmission and transfer from food, water, and other environmental sources.

What does the human gut microbiome consist of? ›

The human microbiome comprises of collective genomes of microbiota inhabiting us, namely protozoa, archaea, eukaryotes, viruses and predominantly bacteria that live symbiotically on and within various sites of the human body.

What is the human microbiome and why is it important? ›

The human microbiome comprises bacteria, archaea, viruses, and eukaryotes which reside within and outside our bodies. These organisms impact human physiology, both in health and in disease, contributing to the enhancement or impairment of metabolic and immune functions.

Can you live without your microbiome? ›

But as long as humans can't live without carbon, nitrogen, protection from disease and the ability to fully digest their food, they can't live without bacteria, said Anne Maczulak, a microbiologist and author of the book "Allies and Enemies: How the World Depends on Bacteria" (FT Press, 2010).

What kills your gut flora? ›

A “western” diet that's high in fat and sugar and low in fiber can kill certain types of gut bacteria, making your microbiota less diverse. Limit use of antibiotics, which can wipe out healthy bacteria along with problematic bacteria, to only when necessary as determined by your doctor.

How much of the human body is microbiome? ›

Because of their small size, however, microorganisms make up only about 1 to 3 percent of the body's mass (in a 200-pound adult, that's 2 to 6 pounds of bacteria), but play a vital role in human health.

Are humans born with bacteria in their guts? ›

This is a big day for baby and microbiome alike, because unlike the womb, the birth canal is chock full of bacteria. Newborn babies get their first microbiome from their mother during birth. During that journey, a newborn baby gets completely covered with bacteria, giving it a brand-new microbiome.

Did humans evolve from microbes? ›

It is likely that eukaryotic cells, of which humans are made, evolved from bacteria about two billion years ago. One theory is that eukaryotic cells evolved via a symbiotic relationship between two independent prokaryotic bacteria.

How do you regenerate gut flora? ›

Here are 9 science-based ways to improve your gut bacteria.
  1. Eat a diverse range of foods. ...
  2. Eat lots of vegetables, legumes, beans, and fruit. ...
  3. Eat fermented foods. ...
  4. Eat prebiotic foods. ...
  5. If you can, breastfeed for at least 6 months. ...
  6. Eat whole grains. ...
  7. Eat a plant-based diet. ...
  8. Eat foods rich in polyphenols.

How do I restore my gut microbiome? ›

In this article, we list 10 scientifically supported ways to improve the gut microbiome and enhance overall health.
  1. Take probiotics and eat fermented foods. ...
  2. Eat prebiotic fiber. ...
  3. Eat less sugar and sweeteners. ...
  4. Reduce stress. ...
  5. Avoid taking antibiotics unnecessarily. ...
  6. Exercise regularly. ...
  7. Get enough sleep.
28 May 2019

How can I heal my gut naturally? ›

7 things you can do for your gut health
  1. Lower your stress levels. Chronic high levels of stress are hard on your whole body, including your gut. ...
  2. Get enough sleep. ...
  3. Eat slowly. ...
  4. Stay hydrated. ...
  5. Take a prebiotic or probiotic. ...
  6. Check for food intolerances. ...
  7. Change your diet.

How can I improve my gut microbiome in a day? ›

Here are some tips to get your gut going:
  1. Increase your fibre intake. ...
  2. Eat as many types of fruit and veg as possible, and try to eat seasonally. ...
  3. Pick high-fibre vegetables. ...
  4. Choose food and drinks with high levels of polyphenols. ...
  5. Avoid snacking. ...
  6. Eat plenty of fermented foods containing live microbes. ...
  7. Drink a bit of alcohol.
10 Feb 2020

Are human microbes legit? ›

Yes!

The trillions of microbes that live in our guts impact & regulate every aspect of human health & development. This ecosystem of microbes -- comprising thousands of species of bacteria, viruses, archaea, and fungi -- makes up the gut microbiome.

Why is the human microbiome losing diversity? ›

The Western diet also has a critical influence on the microbiota. Western diets high in saturated fats, refined carbohydrates and sugars, and low in fresh foods and fiber are associated with reduced microbial complexity, an imbalance of the gut ecosystem and disease.

Where is the largest portion of a human microbiome? ›

Stomach flora + Intestinal flora. The largest part of body microbiota.

Videos

1. The Vital Cells of Existence: The Science of Your Microbiome
(World Science Festival)
2. The Human Microbiome: A New Frontier in Health
(University of California Television (UCTV))
3. Scientists re-define what's healthy in newest analysis for Human Microbiome Project
(Michigan Medicine)
4. Behind the Science - The Ancestral Human Microbiome
(Illumina)
5. Why is the Gut Microbiome Important? (Part #1) | Suzanne Devkota Ph.D
(Dr. Gabrielle Lyon)
6. Gut Microbiome Explained in Simple Words
(Science ABC)

Top Articles

You might also like

Latest Posts

Article information

Author: Rob Wisoky

Last Updated: 12/23/2022

Views: 6240

Rating: 4.8 / 5 (48 voted)

Reviews: 95% of readers found this page helpful

Author information

Name: Rob Wisoky

Birthday: 1994-09-30

Address: 5789 Michel Vista, West Domenic, OR 80464-9452

Phone: +97313824072371

Job: Education Orchestrator

Hobby: Lockpicking, Crocheting, Baton twirling, Video gaming, Jogging, Whittling, Model building

Introduction: My name is Rob Wisoky, I am a smiling, helpful, encouraging, zealous, energetic, faithful, fantastic person who loves writing and wants to share my knowledge and understanding with you.