Finding Bifido

Bioinformatics; noun plural but singular in construction bio·in·for·mat·ics \ˌbī-ō-in-fər-ˈma-tiks\

...the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied to molecular genetics and genomics (Merriam Webster).

Apologies to Disney and MicrobeWiki

American Gut Project Data Mining Tutorial

Sorry, non-geeky types...most boring blog post ever!  I'm putting this up as a resource for anyone who wants to try it out.  If you do, and have any short-cuts, please post in the comments and I'll amend later.

First Semester Finished!

Woo-hoo! Party time at the Farthest North Frat House! "I Tappa Kegga" rulez! All finished with my first semester of grad school. 6 credits earned, 30 more to go. 4.0 average so far! I am seriously considering changing my specialty from Biotech Regulations to Bioinformatics as I really enjoyed learning about bioinformatics and all of the tools used in biotechnology. I hear that next semester will include more on-line panty raids and even an e-goat in the dean's office. Can't wait!

The Future of Antibiotics

This is the last in my weekly antibiotics updates.  I hope you enjoyed them.

The enormity of our love affair with antibiotics is staggering...we currently use over 7 million pounds per year of antibiotics for humans and over 26 million pounds per year for animals destined for the food chain, and this, nearly 60 years after Alexander Fleming issued numerous warnings that we should be diligent in unleashing antibiotics into the environment to prevent resistance from spreading.

In its recent annual report on global risks published in the New England Journal of Medicine in 2013, the World Economic Forum concluded that:

“Arguably the greatest risk … to human health comes in the form of antibiotic-resistant bacteria. We live in a bacterial world where we will never be able to stay ahead of the mutation curve. A test of our resilience is how far behind the curve we allow ourselves to fall.”

Resilience to antibiotic administration

If I’ve painted a bleak picture these last few weeks, don’t despair.  As I’ve said, antibiotics save lives—it’s the overuse of antibiotics that cause problems.  While I hope you never get into the situation where round after round of antibiotics is prescribed, if it does happen, there is still hope.

Gut bugs are extremely adaptable.^[43] Even after many rounds of harsh antibiotics, it’s possible to regain the vigor of a healthy microbiome. In long-term studies, gut bacteria has been irrevocably mucked up for up to four years following a single antibiotic administration, although, of course, it may be different for each individual person.  During and after a prescribed antibiotic course is provided, there are immediate steps that should be taken to ensure your gut bugs are treated right and the stage is set for the beneficial microbes to out-pace the bad in the race that is soon to follow.

Effects of antibiotic use

While antibiotics have saved countless lives that would have been lost due to infection, they are a double-edged sword.  Antibiotics are prescribed to kill a particular pathogen, for instance, one causing strep throat.  Sometimes, these antibiotics are targeted to a particular pathogen, often called Gram negative or Gram positive, but more often broad-spectrum antibiotics are prescribed to hasten the healing process.

  

Antibiotic-associated diarrhea^[41] is often the result of antibiotic use and directly caused by altering the gut flora.  When the gut flora is altered, as it is with a round of antibiotics, pathogens are allowed to grow out of control and biofilms develop that protect these pathogens.

Antibiotic Proliferation

There is a staggering array of antibiotics available to the modern clinician, from the old standby, penicillin, to the newest antibiotic available. “Old” antibiotics, penicillin and the sulfonamides, are effective most of the time in treating routine outpatient infections.^[38] When enough infections that don’t respond to the ‘old standbys’ arise, new antibiotics soon follow.

Between 1945 and 1968, drug companies invented 13 new categories of antibiotics, but between 1968 and today, just two new categories of antibiotics have been added. According to the National Institutes of Health the lack of new antibiotics is threefold:^[39]

• There is not much money in it;
• Inventing new antibiotics is technically challenging;
• In light of drug safety concerns, the FDA has made it difficult for companies to get new antibiotics approved.

Mass Production of Antibiotics

Since the discovery of antibiotics, natural products have been used as killers of disease causing bacteria.  This has prevented untold pain, suffering, and created a revolution in healthcare, however, it is now outdated and these early antibiotics are now largely ineffective. As new pathogens emerge, scientists struggle to keep up with ways to kill them. The “new” pathogens in this scenario being pathogens that have evolved resistance genes from unfettered use of antibiotics.  Antibiotics are now manufactured in three ways^[35]:

• Collected from live microorganisms
• Semi-synthetically produced from natural products
• Chemically synthesized based on the structure of natural products

Evolution in Action—Right Before your Very Eyes!

With every dose of antibiotics a person receives, the microbes that survive the medicine will be “antibiotic resistant.”  These antibiotic resistant microbes can then be passed to other people and even a fetus.  A person may have never had a course of antibiotics in their entire life, yet harbor many antibiotic resistant pathogens.  These resistant bacteria are transmitted in three ways:^[28]

• Consumption of animal products (such as meat, eggs, and milk)
• Close contact with animals or humans who harbor antibiotic resistant microbes
• Through the environment, as in water contaminated with animal or human waste

The Evolution of Antibiotic Resistance

Microbes developed interactive signalling systems over billions of years.  Scientists do not have a complete grasp on how antibiotics are produced or what they do in the natural world. There are several theories that involve gene transfer, evolutionary selection, and competition. At first it was believed that microbes produced antibiotics when competing microbes encroached on their territory, but this explanation was proved wrong when microbes began producing antibiotics in a laboratory setting with no other microbes present.

The Winds of War

Though the discovery of antibiotics went largely unnoticed, World War II changed everything. By 1945 Fleming’s penicillin was in full production as were many of the antibiotics pioneered by Waksman.  In fact, a large supply of penicillin was a prerequisite for the D-Day invasions of Normandy. At a time of great national pride the production of antibiotics was delegated to the War Department. A memo was sent to the manufacturers of antibiotics in 1943^[16]:

"You are urged to impress upon every worker in your plant that penicillin produced today will be saving the life of someone in a few days or curing the disease of someone now incapacitated. Put up slogans in your plant! Place notices in pay envelopes! Create an enthusiasm for the job down to the lowest worker in your plant."

Antibiotic Pioneers

In 1928, Scottish scientist Alexander Fleming was fiddling around with a strange mold he found growing on a Petri dish. This mold was known as Penicillium notatum and after an accidental exposure of the Penicillium to a Petri dish containing Staphylococcus (an infectious microbe), Fleming discovered that the exposure resulted in destruction of the Staphylococcus. This was an amazing discovery and he soon learned he now had the power of life and death over a wide range of Gram-positive bacteria that had been stymieing doctors for centuries!  Fleming toyed with the moldy medicine for well over a decade with little success in making a commercially viable, purified form of his invention: penicillin.

Antibiotics and Antibiotic Resistance

The antibiotic era is not confined to modern day. Tetracycline, an antibiotic first isolated from Actinobacteria in the dirt, is a cheap antibiotic that has been used to treat pneumonia, acne, and other infections.  It was first discovered in the 1940’s and by the 1950’s, tetracycline-resistant bacteria had quickly emerged.^[7] Ironically, tetracycline has been isolated from the bones of ancient skeletons from Sudan dating back to the year 350 AD and late Roman period skeletons from ancient Egypt. The tetracycline in these instances is presumed to have been introduced by the diet or through the use of botanical herbs or healing soils used as medicine, but no trace of tetracycline resistance has been found in these areas after thousands of years of consumption^[8].

RS2 vs RS3 Put to the (Gut) Test! Part 2

I love all of the gut tests available to us now!  The two that have gotten the most attention are American Gut and uBiome.  Neither require a doctor's orders and are relatively cheap ($99 and $89 respectively).  uBiome gets you a report in about 6 weeks, while AmGut takes 6 months.

I think both tests are far from perfect, as Mr. Heisenbug recently discussed:

Later,
Tim
 
Edit to add my full AmGut Taxa Report from 2013:

Kingdom	Phylum	Class	Order	Family	Genus	Relative Abundance (%)
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides	46.52
Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	---	13.06
Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium	11.32
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	---	5.27
Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Faecalibacterium	4.81
Bacteria	Firmicutes	Clostridia	Clostridiales	---	---	2.21
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	---	2.10
Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	---	1.69
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Paraprevotellaceae]	Paraprevotella	1.25
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Sutterella	0.96
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides	0.91
Bacteria	Tenericutes	Mollicutes	RF39	---	---	0.90
Bacteria	Firmicutes	Clostridia	Clostridiales	Veillonellaceae	Phascolarctobacterium	0.79
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnobacterium	0.78
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus	0.76
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia	0.76
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Barnesiellaceae]	---	0.64
Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillospira	0.53
Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus	0.50
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnospira	0.48
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia	0.41
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Paraprevotellaceae]	---	0.38
Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio	0.37
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	[Ruminococcus]	0.27
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Odoribacteraceae]	Butyricimonas	0.24
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Dorea	0.23
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella	0.21
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	---	---	0.13
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Odoribacteraceae]	Odoribacter	0.12
Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus	0.12
Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	[Eubacterium]	0.10
Bacteria	Firmicutes	Clostridia	Clostridiales	Christensenellaceae	---	0.10
Bacteria	Actinobacteria	Coriobacteriia	Coriobacteriales	Coriobacteriaceae	Collinsella	0.09
Bacteria	Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobiaceae	Akkermansia	0.07
Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	---	0.07
Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Anaerostipes	0.07
Bacteria	Lentisphaerae	[Lentisphaeria]	Victivallales	Victivallaceae	---	0.06
Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus	0.05
Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium	0.05
Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter	0.05
Bacteria	Firmicutes	Clostridia	Clostridiales	[Mogibacteriaceae]	---	0.04
Bacteria	Firmicutes	Clostridia	Clostridiales	Veillonellaceae	Dialister	0.04
Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Peptococcus	0.03
Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Bilophila	0.03
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	---	0.02
Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	SMB53	0.02
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Oxalobacter	0.02
Bacteria	Firmicutes	Clostridia	Clostridiales	[Tissierellaceae]	Finegoldia	0.02
Bacteria	Actinobacteria	Coriobacteriia	Coriobacteriales	Coriobacteriaceae	---	0.02
Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria	0.02
Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium	0.02
Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	---	0.02
Bacteria	Cyanobacteria	Chloroplast	Streptophyta	---	---	0.02
Bacteria	Firmicutes	Clostridia	Clostridiales	Dehalobacteriaceae	Dehalobacterium	0.01
Bacteria	Actinobacteria	Coriobacteriia	Coriobacteriales	Coriobacteriaceae	Slackia	0.01
Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia	0.01
Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	---	0.01
Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Holdemania	0.01
Bacteria	Firmicutes	Bacilli	Turicibacterales	Turicibacteraceae	Turicibacter	0.01
Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc	0.01
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	---	0.01
Bacteria	Firmicutes	Clostridia	SHA-98	---	---	0.01
Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella	0.01
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas	0.01
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Limnobacter	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Anaerotruncus	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	---	0.00
Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Lactococcus	0.00
Bacteria	Firmicutes	Bacilli	Lactobacillales	---	---	0.00
Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	[Weeksellaceae]	Chryseobacterium	0.00
Bacteria	Actinobacteria	Coriobacteriia	Coriobacteriales	Coriobacteriaceae	Adlercreutzia	0.00
Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium	0.00
Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas	0.00
Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus	0.00
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Morganella	0.00
Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter	0.00
Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	---	0.00
Bacteria	Proteobacteria	Betaproteobacteria	Rhodocyclales	Rhodocyclaceae	Thauera	0.00
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Janthinobacterium	0.00
Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	---	---	0.00
Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingobium	0.00
Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	Ochrobactrum	0.00
Bacteria	Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas	0.00
Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	cc_115	0.00
Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Coprobacillus	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	[Tissierellaceae]	Peptoniphilus	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	[Tissierellaceae]	Parvimonas	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	[Tissierellaceae]	Anaerococcus	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	Veillonellaceae	Veillonella	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Caloramator	0.00
Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	02d06	0.00
Bacteria	Firmicutes	Clostridia	---	---	---	0.00
Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus	0.00
Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	---	0.00
Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Aerococcus	0.00
Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus	0.00
Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	[Paraprevotellaceae]	[Prevotella]	0.00
Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	---	0.00
Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces	0.00

Beet Kvass

Summertime at my house means beet kvass.

Got probiotics?

Kvass is the forerunner to a host of water fermented probiotic drinks such as water kefir and kombucha.  Kvass was traditionally made with rye bread (sometimes flavored with berries, raisins, or birch sap) in Russia and is still popular in places with a Russian influence.  Somewhere along the line, some poor sucker who couldn't afford bread made kvass with a beet.

Vinegar Magic

Yesterday I got an out-of-the-blue email from one of my old lurker buddies asking about 'wild fruit vinegars.' Christine, aka, WildCucumber, told me she's been making vinegar in her kitchen from fruit she gets around her home in Quebec.  This made me remember a paper I had recently bookmarked about the health properties of vinegar, but hadn't gotten around to reading. 

I clicked on the vinegar paper and scrolled down, wow.  Vinegar is amazing stuff! 

My New 'Schtick'...Ancestral Biotechnology

Here's me swimming in our muddy farm pond circa 1975.  Before drying off, we had to pick off the leaches between our toes.  I can't count the times I stepped on a bee running to be the first one in.

Ancestral Biotechnology...hmmmmmm

Chaga

                                                              
A couple months ago I found out that I'm eligible for the "Post 9-11 GI Bill."  This is the Veteran's Administration's program for veterans who served during the current rounds of 'war' going on in Iraq and Afghanistan since 2001.

I retired from the Air Force, where I was a combat engineer, in 2004 and have been working in the Process Controls and Electronics industries since that time.  My first job as a civilian was in a local water plant, then I moved to a coal-burning power plant.  After a few years, I tired of coming home blowing black snot out of my nose and after narrowly missing being caught in a devastating explosion, I took a new job as the Electrical Systems Supervisor at a local hospital.  I've been crawling around the underbelly of the medical establishment since 2007, and absolutely love my job.