3 Types of Bacteria Environments in the Gut

[LNN]

Saw this NYT article and it reminded me of the recent discussions on how some probiotics that work wonders in people some cause problems for others.

http://www.nytimes.com/2011/04/21/science/21gut.html

 

April 20, 2011

Bacteria Divide People Into 3 Types, Scientists Say

By CARL ZIMMER

 

In the early 1900s, scientists discovered that each person belonged to one of four blood types. Now they have discovered a new way to classify humanity: by bacteria. Each human being is host to thousands of different species of microbes. Yet a group of scientists now report just three distinct ecosystems in the guts of people they have studied.

 

Blood type, meet bug type.

 

“It’s an important advance,” said Rob Knight, a biologist at the University of Colorado, who was not involved in the research. “It’s the first indication that human gut ecosystems may fall into distinct types.”

 

The research team, led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, found no link between what they call enterotypes and the ethnic background of the European, American and Japanese subjects they studied.

 

Nor could they find a connection to sex, weight, health or age. They are now exploring other explanations. One possibility is that infants are randomly colonized by different pioneering species of gut microbes. The microbes alter the gut so that only certain species can follow them.

 

Whatever the cause of the different enterotypes, they may end up having discrete effects on people’s health. Gut microbes aid in food digestion and synthesize vitamins, using enzymes our own cells cannot make.

 

Dr. Bork and his colleagues have found that each of the types makes a unique balance of these enzymes. Enterotype 1 produces more enzymes for making vitamin B7 (also known as biotin), for example, and Enterotype 2 more enzymes for vitamin B1 (thiamine).

 

The discovery of the blood types A, B, AB and O had a major effect on how doctors practice medicine. They could limit the chances that a patient’s body would reject a blood transfusion by making sure the donated blood was of a matching type. The discovery of enterotypes could someday lead to medical applications of its own, but they would be far down the road.

 

“Some things are pretty obvious already,” Dr. Bork said. Doctors might be able to tailor diets or drug prescriptions to suit people’s enterotypes, for example.

 

Or, he speculated, doctors might be able to use enterotypes to find alternatives to antibiotics, which are becoming increasingly ineffective. Instead of trying to wipe out disease-causing bacteria that have disrupted the ecological balance of the gut, they could try to provide reinforcements for the good bacteria. “You’d try to restore the type you had before,” he said. Dr. Bork notes that more testing is necessary. Researchers will need to search for enterotypes in people from African, Chinese and other ethnic origins. He also notes that so far, all the subjects come from industrial nations, and thus eat similar foods. “This is a shortcoming,” he said. “We don’t have remote villages.”

 

The discovery of enterotypes follows on years of work mapping the diversity of microbes in the human body— the human microbiome, as it is known. The difficulty of the task has been staggering. Each person shelters about 100 trillion microbes. (For comparison, the human body is made up of only around 10 trillion cells.) But scientists cannot rear a vast majority of these bacteria in their labs to identify them and learn their characteristics.

 

As genetics developed, scientists learned how to study the microbiome by analyzing its DNA. Scientists extracted DNA fragments from people’s skin, saliva and stool. They learned how to recognize and discard human DNA, so that they were left with genes from the microbiome. They searched through the remaining DNA for all the variants of a specific gene and compared them with known species. In some cases, the variants proved to be from familiar bacteria, like E. coli. In other cases, the gene belonged to a species new to science.

 

These studies offered glimpses of a diversity akin to a rain forest’s. Different regions of the body were home to different combinations of species. From one person to another, scientists found more tremendous variety. Many of the species that lived in one person’s mouth, for example, were missing from another’s.

 

Scientists wondered if deeper studies would reveal a unity to human microbiomes. Over the past few years, researchers have identified the genomes — the complete catalog of genes — of hundreds of microbe species that live in humans. Now they can compare any gene they find with these reference genomes. They can identify the gene’s function, and identify which genus of bacteria the microbe belongs to. And by tallying all the genes they find, the scientists can estimate how abundant each type of bacteria is.

 

In the recent work, Dr. Bork and his team carried out an analysis of the gut microbes in 22 people from Denmark, France, Italy and Spain. Some of their subjects were healthy, while others were obese or suffered from intestinal disorders like Crohn’s disease. Dr. Bork and his colleagues searched for fragments of DNA corresponding to the genomes of 1,511 different species of bacteria. The researchers combined their results with previous studies of 13 Japanese individuals and four Americans.

 

The scientists then searched for patterns. “We didn’t have any hypothesis,” Dr. Bork said. “Anything that came out would be new.”

 

Still, Dr. Bork was startled by the result of the study: all the microbiomes fell neatly into three distinct groups.

 

And, as Dr. Bork and his colleagues reported on Wednesday in the journal Nature, each of the three enterotypes was composed of a different balance of species. People with type 1, for example, had high levels of bacteria called Bacteroides. In type 2, on the other hand, Bacteroides were relatively rare, while the genus Prevotella was unusually common.

 

“You can cut the data in lots of different ways, and you still get these three clusters,” Dr. Bork said.

 

Dr. Bork and his colleagues found confirmation of the three enterotypes when they turned to other microbiome surveys, and the groups continue to hold up now that they have expanded their own study to 400 people.

 

This article has been revised to reflect the following correction:

 

Correction: April 20, 2011

 

An earlier version of this article misstated the number of microbes relative to the number of cells in the human body. Each person shelters about 100 trillion microbes, not 10 trillion, and is made up of about 10 trillion cells, not one million.

[peglem]

Wow, that is fascinating!

[trggirl]

Wow, that is fascinating!!

[Ozimum]

LLM - Thanks for posting this article! I can't help thinking it's a really important discovery.

 

Our Biomed/DAN! dr organised a stool screen for DS which gave us a profile of what was happening in his gut. He put him on two different probiotics, along with vit supps and we've been recolonising E.coli in his gut - he's doing really well. Improvements continue. He hasn't had antibiotics since August and he's cruised through a couple of colds and wisdom teeth extractions since... Something's working for him! Long may it last!

 

The following was sent to me today and thought I would pass it on FYI:

 

Antibiotics Disrupt Gut Ecology, MetabolismScienceDaily (Apr. 19, 2011) Humans carry several pounds of microbes in our gastro-intestinal tracts. Recent research suggests that this microbial ecosystem plays a variety of critical roles in our health. Now, working in a mouse model, researchers from Canada describe many of the interactions between the intestinal microbiota and host, and show that antibiotics profoundly disrupt intestinal homeostasis. The research is published in the April 2011 issue of the journal Antimicrobial Agents and Chemotherapy.

"Intestinal microbes help us digest our food, provide us with vitamins that we cannot make on our own, and protect us from microbes that make us sick, amongst other things," says L Caetano M. Antunes of the University of British Columbia, a researcher on the study. In this study, the investigators used powerful mass spectrometry techniques to detect, identify, and quantify more than two thousand molecules which they extracted from mouse feces. They then administered antibiotics to the mice, to kill off most of their gut microbiota, and analyzed the feces anew.

The second round of mass spectroscopy revealed a very different metabolic landscape. The levels of 87 percent of the molecules detected had been shifted up or down by factors ranging from 2-fold to 10,000-fold.

The most profoundly altered pathways involved steroid hormones, eicosanoid hormones, sugar, fatty acid, and bile acid. "These hormones have very important functions in our health," says Antunes. "They control our immune system, reproductive functions, mineral balance, sugar metabolism, and many other important aspects of human metabolism."

The findings have two important implications, says Antunes. "First, our work shows that the unnecessary use of antibiotics has deleterious effects on human health that were previously unappreciated. Also, the fact that our gut microbes control these important molecules raises the possibility that manipulating these microbes could be used to modulate diseases that have hormonal or metabolic origins (such as inmmunodeficiency, depression, diabetes and others). However, further studies will be required to understand exactly how our microbial partners function to modulate human physiology, and to devise ways of using this information to improve human health."

(L.C.M. Antunes, J. Han, R.B.R. Ferreira, P. Lolic, C.H. Borchers, and B.B. Finlay, 2011. Effect of antibiotic treatment on the intestinal metabolome. Antim. Agents Chemother. 55:1494-1503.)

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Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by American Society for Microbiology, via EurekAlert!, a service of AAAS.

 

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Journal Reference:

1. L. C. M. Antunes, J. Han, R. B. R. Ferreira, P. Lolic, C. H. Borchers, B. B. Finlay. Effect of Antibiotic Treatment on the Intestinal Metabolome. Antimicrobial Agents and Chemotherapy, 2011; 55 (4): 1494 DOI: 10.1128/AAC.01664-10

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Antimicrobial Agents and Chemotherapy, April 2011, p. 1494-1503, Vol. 55, No. 4

0066-4804/11/$12.00+0 doi:10.1128/AAC.01664-10

Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Effect of Antibiotic Treatment on the Intestinal MetabolomeL. Caetano M. Antunes,1 Jun Han,2 Rosana B. R. Ferreira,1 Petra Loli,1,3 Christoph H. Borchers,2, and B. Brett Finlay1,3*

Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada,1 University of Victoria Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada,2 Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada3

Received 1 December 2010/ Returned for modification 8 January 2011/ Accepted 21 January 2011

 

http://www.sciencedaily.com/releases/2011/04/110419214734.htm

 

 

The importance of the mammalian intestinal microbiota to human health has been intensely studied over the past few years. It is now clear that the interactions between human hosts and their associated microbial communities need to be characterized in molecular detail if we are to truly understand human physiology. Additionally, the study of such host-microbe interactions is likely to provide us with new strategies to manipulate these complex systems to maintain or restore homeostasis in order to prevent or cure pathological states. Here, we describe the use of high-throughput metabolomics to shed light on the interactions between the intestinal microbiota and the host. We show that antibiotic treatment disrupts intestinal homeostasis and has a profound impact on the intestinal metabolome, affecting the levels of over 87% of all metabolites detected. Many metabolic pathways that are critical for host physiology were affected, including bile acid, eicosanoid, and steroid hormone synthesis. Dissecting the molecular mechanisms involved in the impact of beneficial microbes on some of these pathways will be instrumental in understanding the interplay between the host and its complex resident microbiota and may aid in the design of new therapeutic strategies that target these interactions.

 

http://aac.asm.org/cgi/content/abstract/55/4/1494

Edited April 27, 2011 by Ozimum

[LNN]

Ozimum - thanks for this! I was just thinking how much I miss seeing links to new research. I was particularly intrigued by the comments on hormones. My DS is on multiple abx and while his gut seems fine - based on what he does/doesn't crave and on the "output", I was just thinking the other day how his body seems "younger" than his peers. He's 8.5 and has only lost 4 teeth, and only two adult teeth have grown in. His lost his last two in the fall and the adult teeth are only now cutting through the gum. Is this normal? He suffers from enuresis but he's been sick for 3 yrs - is it some delay that wouldn't be there if he were healthy or is he just one of those 10% of boys that take a long time to mature in that area? Or is it the massacre we're waging on his gut flora?

 

So often, I feel like our kids are perfect guinea pigs for so many lines of research, if only we could hook up with the right science geeks and the right financiers...

 

Thanks for sharing!

[MomWithOCDSon]

Thanks, LLM and Ozmium! I, too, find myself "hungry" for fresh research!

 

LLM, as for hormonal components to our kids' overall conditions, I've had similar thoughts/concerns, though I'm as yet unconvinced which came first, the chicken or the egg. My DS has seemed to be "behind the curve" in terms of maturation almost all his life. The dentist and orthodontist have both described his mouth as "immature," and he too took a long time to lose baby teeth, get his adult ones in, etc. His height and weight are appropriate for a 14yo, and he's developed hair "in all the right places," but many of his friends have had their voices drop within the last year or so, and he still has his high-pitched kiddie voice.

 

While we suspect our DS had PANDAS well before he was diagnosed as such (likely as early as 3), and he was on and off 10-day courses of antibiotics frequently between the ages of 18 months and 3 years due to recurring otitis medea, he didn't start any "chronic" abx use until nearly 13. And yet his maturation delays go much further back than that.

 

So, once again, are these conditions related? Or are they unrelated but corrolaries . . . "phenotypes" of some sort? Does one cause the other or just tend to co-exist?

 

Where's Buster when you need him?