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Phage Futures Congress 2019 | January 29-30 2019 | Washington D.C., USA

With antimicrobial resistance a rising international crisis, western medicine's interest is turning into phage therapy as an alternative to antibiotics.  Challenging past doubt in phage therapy's commercial viability, recent developments such as highly positive outcomes of compassionate use cases in the US has excited the area and the next step is successful phase II clinical trials. Phage Futures Congress is a translational phage treatment conference where Steffanie Strathdee, Tom Patterson, the FDA, and others are going to discuss how we proceed phage treatment forward in the usa.  Numerous A Smaller Flea writers will be speaking or in presence: Jessica Sacher of Phage Directory, Ben Chan of Yale Univeristy, Shawna McCallin of PhageForward.  I'm pleased to announce that I have also joined the Scientific Advisory Board for the congress The Phage Futures Congress will bring together peers from biotech companies and academia, together with experts from regulatory bodies, pharmaceutical companies and government institutions, to discuss how to actively advance clinical science and workable routes to advertise.  You will learn about: Regulatory advice to achieve clinical information from Cara Fiore, FDA Strategies to get the marketplace through the veterinary, personalized medicine and conventional pharmaceutical routes Insights into investment drivers from NIH and Boehringer Ingelheim The truth on how to manufacture GMP phage Approaches to conquer multi-drug immunity such as combining phage treatment and antibiotics Phage use in new indications like IBD

"The Phage Futures Congress has the capability to serve as a catalyst to further concerted and  collaborative efforts to develop alternative Phage based approaches to the antibiotic catastrophe.  Additionally, the location in the Washington DC area will facilitate an opportunity for Government Agencies, responsible for public health, like the NIH, FDA, USDA and DOD to participate and interact with educational study teams and biotechnology companies developing phage treatments and initiating clinical testing."  -- Carl Merril, Adaptive Phage Therapeutics

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Inside Earth, Microbes Approach Immortality

Last month, the Deep Carbon Observatory declared an astonishing fact: the bulk of the microbes living beneath the planet's surface amounts to 15 to 23 billion tons of carbon dioxide, a sum some 245 to 385 times greater than the carbon mass of all people.  That's remarkable.  It was not so long ago we weren't even certain life at depth was possible. But buried in the media release was a detail that I discovered a whole lot more surprising and intriguing than the bulk of underground life: its era. Back in the late 1920s, a scientist named Charles Lipman, a professor at the University of California, Berkeley, started to suspect there were bacteria in rocks.  Not fossil bacteria.  Alive bacteria. He was considering the fact that bacteria in his lab may be reanimated after 40 years in dry dirt in sealed bottles.  If they could endure four years, was there any limitation? Coal seemed like a rock ripe for testing, made as it is from swamp muck.  He started crushing lumps of coal to find out if he could get anything to grow from the dust.  He did. When placed in solutions of coal dust and sterile water, in two to three weeks he started to see what seemed like germs.  When put in solutions enriched with germs chow called peptone, it took as little as five hours. Intriguingly, he found a rehydration period of at least a couple of days in liquid was essential for revivification.  When the crushed coal was wetted but instantly placed on food-infused gelatin-like agar in a Petri dish, nothing grew. He had, of course, included controllers and taken precautions to ensure no contaminants led to the growth.  His draconian cleaning and sterilization process of the pre-crushed lumps involved scrubbing, soaking, baking, or pressurizing the lumps of coal for days or weeks before pulverization.  In actuality, he discovered that heating the sample for hours at 160°C never managed to kill the germs within the coal.  If anything, it only seemed to encourage them.  The longer they had been baked -- up to an unbelievable 50 hours the better they seemed to grow when the coal was then crushed (If his results were real, they might not be altogether surprising given both the states that produce coal as well as the effects of heat shock proteins). Lipman didn't feel that the germs that he coaxed from coal were residing in the sense that the bacteria in your gut are living.  Instead, he considered that during the process of forming coal, the germs had dried up and entered suspended animation. ". . [T]he microorganisms found in coal are now survivors, imprisoned at the coal at the time it was formed, from material that originally was probably very full of microorganisms because it was peat-like in nature," he wrote in the Journal of Bacteriology. "It's my opinion that here and there sprinkled through the masses of the coal measures an occasional spore or any similarly resistant resting period of a microorganism has survived the vicissitudes of time and circumstance and kept its own living character, its capability to become a vegetative form, and its capability to multiply when circumstances are left handed for it." This dessicated condition we now call anhydrobiosis, and it's in this state that organisms such as water bears can withstand the vacuum of space and bombardment with radiation. Lipman's coal came from Wales and Pennsylvania, where some was pulled from a depth of 1,800 feet.  Pennsylvania coal inspired the title of a whole geologic subperiod -- the Pennsylvanian. It's at least 300 million years old. The year was 1931.  His coworkers probably thought he was nuts.  But from where we sit in 2019, it is looking increasingly possible that Lipman wasn't nuts.  The world's oldest surviving people might not be gnarled bristlecone pines or shimmering aspen clones, but small microbes locked in stone miles under the surface whose purpose is to not to grow or replicate, but only to cheat death. An increasing number of newspapers published in the past decade indicate that bacteria living -- many of them in a hydrated, active state -- in sediments, in stones, and in pockets and fissures buried deep underground are old beyond belief. For example, in the early 2000s, scientists demonstrated that the rate at which microbes in aquifers and sediments were breathing was significantly slower than that of germs in the surface.  The biomass turnover rates -- the time in which is needed to replace the molecules in a cell -- were measured on the order of hundreds to thousands of years. "We don't know if the microbes of those subsurface environments replicate at such slow rates of biomass turnover," wrote Frederick Colwell and Steven D'Hondt in a review named Nature and Extent of the Deep Biosphere in 2013,"or reside without breaking for countless tens of centuries." A 2017 paper in the Proceedings of the National Academy of Science discovered low densities of bacteria (although"low" remains 50-2,000 cells per cubic centimeter) in 5 to 30 million-year-old coal and shale beds situated two km beneath the floor of the Pacific Ocean from the coast of Japan. They were actively, if exceptionally slowly, living.  Their creation times ranged from months to over 100 years.  However, this quote was probably low, the authors conceded.  The production time of E. coli from the laboratory: 15 to 20 minutes. A 2018 study published in Geobiology of microbes living in deep sea sediments from the South Pacific Gyre reasoned that the fitness in these sediments is about growing but only surviving.  Such microbes' only food source is whatever happened to be buried together, the authors concluded.  The quantity of carbon they have for upkeep and repair annually is only 2% of the cell's own carbon material.

"Only the fact that intact microbial cells are found in this ancient habitat has remarkable consequences regarding the durability of the organisms," the authors wrote. In their own computer versions running multi-million year simulations, after four thousand years, all cells had ceased growth.  They were only putting whatever tools they could scrounge into maintaining the old jalopy running, such as the desperate survivors in a Mad Max movie. How long does that zero-sum game go on?  Will they finally starve?  Will they metamorphose to the dessicated, suspended state that Charles Lipman promised to find in Pennsylvania coal?  Or does that need the particular conditions of coalification? Evidence is also accumulating that such nutrient-deprived, superannuated germs aren't"microbial zombies".  To the contrary, a lot of studies have found that if deep subsurface microbes are put in more moderate environments, they immediately animate. Taken together, these findings are not as absurd as they may appear when you consider that germs buried deep beneath the planet's surface are protected from cosmic radiation -- a frequent killer of the preternaturally obsolete -- by thick overburdens of sediment, water, or stone (Muons, the form in which cosmic radiation reaches Earth's surface, can only penetrate tens of meters into stone ).  Such radiation mutates the DNA of organisms living on Earth's surface. Panspermia hypotheses that life seeded the world by hitchhiking inside asteroids have always seemed very tin-foil hat for me.  But these findings, along with the recent understanding that life might have appeared on Earth almost as soon as it was possible, induce me to reconsider.  Although distance is immense, life is insistent. To sum up, Earth's crust seems to be just lousy with idling, historical bacteria parked in power-save manner, prepared at almost a minute's notice to throw the gearshift into drive.  But what a life!  Eons spent entombed in a dark, airless, quiet matrix, hardly eating, hardly breathing, hardly moving, hardly living.  But not dead.  Not dead.

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10 Predictions for the Future of Your (Microbial) Health

Every day it seems like some new discovery is shown ab0ut the microbial life on our own bodies, in our bodies, and around our homes.  The tendency in writing concerning this research is to make sweeping decisions about what is and isn't and, of course, how we should live and what we ought to do.  But the reality is these new studies are a part of a large lunge science is making into wonderful darkness.  The lights we're shining are showing discoveries and paintings, but nobody has a lens large enough to see the entire image, not yet anyway.  The temptation would be to stand at the website of every new discovery and attempt to make the prediction about what's next.  I am going to do something else here.  I'm going to attempt and predict not another discovery but rather in the next ten decades.  You may check back in ten years to tell me if I had been full of it.  I probably am, but what fun is a site if you can not speculate a little.  For what it's worth, these crazy ideas come mostly from extrapolating what we know about the ecology of non-human species generally and applying it to people and the microbes around us.  To put it differently, if humans comply with the environmental regularities the past fifty years of ecology have shown then it'll be discovered that...

1-Many ailments result from using a very low diversity of good bacteria in your skin, on your nose or on your gut.  The advantages of having a high diversity of bacteria that are good are multiple.  They protect you by interacting with your immune system, but also by actively doing battle with newly arrived species. 2-Antibiotic wipes, soaps, toothpaste, underpants and other antimicrobial compounds, especially those with Triclosan, make you more likely to become sick rather than to get healthier.  In a decade, people will start to wonder how we maybe considered using them. 3-The advantage of hand washing is because of the capability of washing with water and soap to differentially kill the germs which have shown up instead of the good bacteria which are better established.  Since they wash their hands over most folks, the hands of physicians and nurses have fewer species on them, but are more prone to invasion by poor species if physicians or nurses ever stop washing their hands. 4-Being exposed to a diversity of bacteria is beneficial and reduces allergy and autoimmune disorders, but figuring out precisely which germs matter is difficult and depends on individual genotype .  This is true today, but will appear even truer in the future. 5-In the lack of a complete comprehension of which bacteria are essential, companies develop sprays with simple to grow germs which you can spray around your property.  A few of those sprays are beneficial.  Some aren't.  All of them cost more than they should and are poorly controlled.  Businesses will also create a device to assess the diversity of bacteria in your house and when your home (necessarily ) fails to be sufficiently varied, the exact companies will offer you the"diverse microbiota" spray. Picture 2.  Artist Kalliopi Monoyios wonders if one day we will discover Bacterial Wipes on the shelves of the supermarket cleaning products aisle. 6-The beneficial microbes in skin and in your gut prove to be composed mainly of a package of individual lineages with romantic and specific co-evolutionary relationships with individuals.  Different human populations have different lineages of those principal species, some of which are more valuable and some less.  The advantages of the others depend on the circumstance. 7-Human bodies possess many features that affect the particular lineages of microbes in various parts of our bodies.  The appendix functions as a reserve of valuable species.  The acidity of the stomach serves to filter out several pathogens.  The ears and nose both exert a strong effect on which species reside in them.  The armpits end up being an important organ connected with health and well-being in addition to signaling identity of people or quality of mates among individuals.  In the armpits many germs are fed in large densities by technical feeding glands. 8-At least three things about the relationship between bacteria and people which are entirely inconceivable now are discovered.  Once detected, they come to seem ordinary. 9-Several places in our houses that we envision to be completely lifeless prove to possess unique microbial species which evolved in those habitats because the building of homes. 10-Microscopic species are exerting more control over our behavior than we envisioned.  Some differences in behaviour among humans are accounted for by different exposures to microscopic organisms. And here are five additional as a bonus : 11-The common fungi in our lungs really prove to have some advantage and are engaged in complex connections with the bacteria in lungs.  The equilibrium between lung bacteria and parasites is tenuous and easily disrupted. 12-Bacteriophages end up being significantly more important in regulating the composition of germs on bodies than valued. 13-The surplus of perspiration on your feet evolved partly to nourish an excess of bacteria which help fight off fungi.  Individuals with stinking feet are less likely to become severe foot fungus infections. 14-Some of the very common species on human skin weren't common a couple of hundred years back.  A few of the species shared a couple of hundred years back, when washing was infrequent, are now completely absent from human skin except under unusual conditions like those in which body lice are now found for example in homeless shelters. 15-I'll leave this to your predictions about the bacteria, phages, viruses, fungi, and protists around us.  What do you predict we'll find on bodies or in homes about the trillions of microbial cells residing on and around us? Having found myself somewhat drunk by considering the future I also polled my microbially likely friends for their ideas on the future, which revealed that together my friends are much more wild-eyed  about the future than me.  

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NEW MICROBES DISCOVERED IN THE MARIANA TRENCH, NEW ZEALAND RIVERS AND HUMANS

Monthly, the Microbiology Society publishes the International Journal of Systematic and Evolutionary Microbiology (IJSEM), which details recently discovered species of bacteria, fungi, and protists.  Below are a few of the new species which were discovered and the places they have been found.

This month new microbes were reported at the deepest portion of the sea; the Mariana Trench.  Sphingomonas profundi was isolated from a marine sediment sample collected on the TS01 hadal trench cruise by the R/V Tan Suo Yi Hao.  The Mariana Trench is the deepest oceanic trench measuring about 2,550 km in length and 69 km in diameter, estimates of depth vary from between 10,984 km to 11,034 km.  This was not the only microbe found in the depths of the sea, researchers found Marinobacter salinexigens from the Mariana Trench.  Unlike the last discovery, this microbe was found in the water column, from a water sample collected at a depth of 9,600 m.

Along with deep sea trenches, a microbe was also found on a seamount this month.  Seamounts are big underwater mountains that rise from the sea floor but don’t reach to the water’s surface.  Seamounts are usually made from extinct volcanoes.  Researchers found Flavobacterium profundi on the surface of a marine sponge isolated by a seamount in the tropical western Pacific.  The marine sponge has been collected at a depth of 288 m.

Several microbes were discovered on creatures this month.  Researchers in New Zealand found Campylobacter novaezeelandiae on bird species and in rivers.  The birds were non-native mallards and starlings.  Campylobacter species are often related to the gastrointestinal tracts of birds, especially chickens, but also have been detected in wild birds which range from albatross into zebra finch.