Densest Microbiome: the Human GI Tract

Dear Friends,

Over the last three weeks we have been begun our journey into the human microbiome using the roadmap set out for us by the HMP—the Human Microbiome Project. As we discussed last week, the first goal is the sequencing of 1000 organisms that will provide a benchmark against which further sequence data can be compared. The densest population of microbes in the human body lies in our gastrointestinal tract—the port of entry of our food and sustenance, but also the port of entry for toxins and pathogens.

We will focus initially on the GI tract microbiome looking at some of the organisms selected as part of the reference genome.

The Gastrointestinal Microbiome

Of the roughly 1000 microbes that represent the Reference Genome, approximately 307 different types of bacteria are from the GI tract—approximately. These numbers are constantly changing as newly discovered organisms are added and mischaracterized ones are deleted.

Of the 307 gut bacterial microbes there are 78 different Genus, with the rest representing different species and subspecies (strains). In other words, the 307 count contain 78 Genus and 129 species and sub species.

Notice the fact that many of the genus are unfamiliar to the commercial world: Alistipes, Bacillus, Bacteroides, Bdellovibrio, Bifidobacterium, Clostridium, Escherichia, Eubacterium, Fusobacterium, Kingella, Klebsiella, Lactobacillus, Malassezia, Methanobrewibacter, Mycoplasm, Neisseria, Oxalobacter, Pediococcus, Parvimones, Streptococcus, Veillonella and Yobenella.

In the Bacillus genus (a familiar genus but the following species of Bacillus are not) there are only 2 species now in the GI collection to be sequenced—alcalophilus and halodurans, whereas in the Bacteroides genus there are 32 different species and subspecies within the Reference Genome.

In the Bifidobacterium genus there are 12 species and subspecies (many familiar)—with species names such a B. adolescentis, B. angulatum, B. bifidum, B. breve, B. gallicum and B. longum, and subspecies (strains) like B. longum infantis CCUGS52386 and B. longum infantis ATCC 55813.

Other interesting numbers—the Bacteroides genus has 32 species and subspecies represented in the gut, Clostridium has 30, Escherichia has 4, Eubacterium has 12, Fusobacterium has 15, Klebsiella has 1 and Lactobacillus has 20.

Of the twenty Lactobacillus species, the following are some of the organisms (listed with their strain designations)—L. acidophilus ATCC 4796, L. brevis DSM 20054, L. hilgardii ATCC 8290, L. helveticus DSM 20075, L. plantarum ATCC 14917, L. paracasei ATCC 25302, L. reuteri CF48-3A and L. rhamnosis LMS 2-1.

The Lactobacillus genus has species in other sites—in fact, 39 other Lactobacillus species in the collection reside in other body microbiomes. Even though we are focusing on the gut in this email, I will list a few of them—L. casei (Airways), L. coleohominis DSM 14060 (Urogenital tract), L. crispatus CTV-05 (Urogenital tract), L. fermentum 28-3-CHN (Urogenital tract), L. jensenii 27-2-CHN (Urogenital tract), L. salivarius ATCC 11741 (Oral), L. johnsonii ATCC 33200 (Blood).

Each organism is listed in the HMP catalog under the following categories: Organism Name, Body Site, HMP Project Status, Finishing Goal, Gene Count, Sequence Center, Strain Repository. Here is a small sampling:

Bifidobacterium adolescentis L2-32—HMP Project Status-Complete; Genebank ID- AAYD000000000; Gene Count-2499; Body Site- GI Tract; Finishing Goal-High Quality Draft; Strain Repository-DSMZ; Sequencing Center- Washington University.

Bifidobacterium longum infantis CCUG52486— HMP Project Status-Complete; Genebank ID- ABOO000000000; Gene Count-2178; Body Site- GI Tract; Finishing Goal-High Quality Draft; Strain Repository-CCUG; Sequencing Center- Broad Institute.

Clostridium difficile NAP08— HMP Project Status-Draft; Gene Count-7349; Body Site- GI Tract Finishing Goal-High Quality Draft; Strain Repository-BEI HM-89; Sequencing Center-BCM-HGSC.

Lactobacillus hilgardii ATCC 8290— HMP Project Status-Complete; Genebank ID- ACGP000000000; Gene Count-2876; Body Site- GI Tract Finishing Goal-High Quality Draft; Strain Repository-ATCC 8290; Sequencing Center-BCM-HGSC.

Lactobacillus helveticus DSM 20075— HMP Project Status-Draft; Genebank ID- ACLM000000000; Gene Count-2154; Body Site- GI Tract Finishing Goal-High Quality Draft; Strain Repository-DSM 13335; Sequencing Center-BCM-HGSC.

Lactobacillus plantarum ATCC 14917— HMP Project Status-Complete; Genebank ID- ACGZ000000000; Gene Count-3314; Body Site- GI Tract Finishing Goal-High Quality Draft; Strain Repository-ATCC 14917; Sequencing Center-BCM-HGSC.

Lactobacillus reuteri CF48-3A—HMP Project Status-Complete; Genebank ID- ACHG000000000; Gene Count-2241; Body Site- GI Tract Finishing Goal-High Quality Draft; Strain Repository-BEI HM-102; Sequencing BCM-HGSC.

As you can see there are different strain repositories that the bacteria come from. There are a number of accredited microbial repositories in the world, all dedicated to the maintenance of accurate taxonomy and nomenclature, accurate sequencing and safe keeping of the microbial mother cultures in their care. The repository with the largest bacterial collection in the world is ATCC, located in Virginia. DSM -The German Collection of Microorganisms and Cell Cultures is locate in Braunschweig, Germany, and CCUG – Culture Collection University of Goteborg, in Sweden. Next to organism is the universal strain designation—the repository plus a number, representing their official scientific name down to the strain level. These repositories are the gold standard, accurately typing and properly naming each organism. That is why we can call them reference organisms. What must happen in the commercial probiotic world is to have organism typed by one of these repositories.

Notice the gene count of each of the above organisms. Most are around 2500 genes, but look at plantarum at 3300 and C. diff. at 7349. With bacteria each gene represents the ability to transcribe a one particular protein. This means that Clostridium difficile NAP08 can produce roughly three times more different kinds of proteins than the others listed here. Also realize that this isn’t even “a tip” from the tip of the iceberg of bugs in the gut. The HMP scientists are predicting that the collection of microbe in our human microbiome can produce 2 and ½ more proteins than our total human cells can. Isn’t it becoming clear how important this research is to our understandings of the workings of our human body in health and disease?

Next week we will go further into the current research regarding the sequencing of the different organisms, their protein producing abilities (their metabolic byproducts), and how these interact with our body’s pathways for good and for bad. I will be sharing with you my interviews with key researchers in the HMP.

Sincerely yours,

Seann Bardell

BioImmersion.com

Clinical Note:

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Here is an email from John Adams MD- Sedona, AZ.

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Of course, we would only make your thoughts public with your request.

The Last Quiz Answer: The Red Deer (Cervus elaphus) is one of the largest deer species. The Red Deer inhabits most of Europe, the Caucasus Mountains region, Asia Minor and parts of western and central Asia. It also inhabits the Atlas Mountains region between Morocco and Tunisia in northwestern Africa, being the only species of deer to inhabit Africa.

Normal healthy intestinal bacteria, like Bifidobacterium and Bacteroides, influence immune responses and protect against the development of inflammatory diseases. A Sydney-based research team describe in Nature 461, 1282-1286 (29 October 2009) how the combination of good bacteria in the gut and a whole food diet with lots of fiber enhance the production of SCFAs which join with certain immune system proteins to down regulate inflammation.