August 6, 2018

In today’s digest, look for probiotic trials for renal insufficiency and metabolic syndrome, experimental dysbiosis in SIV-infected primates, bacterial and fungal network analyses in soils, and recombination in the human virome. Plus, bacteria in the popular press, hints for scientists using Twitter, the first stem cell therapies for Parkinson’s Disease, and more!

Human gut microbiome
Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease – Linda Stewart – Clinical and Experimental Immunology

Animal experiments
Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz – Nature Medicine

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs – Marion Lemaire – Scientific Reports

Animal microbiome
Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs – Sara C. Bell – Frontiers in Microbiology

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart – American Journal of Veterinary Research

Plant, root, and soil microbiome
Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes – Andrew T. Nottingham – Ecology

Soil bacterial networks are less stable under drought than fungal networks – Franciska T. de Vries – Nature Communications

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits – Miguel A. Redondo – The ISME Journal

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.) – Xue-Xue Chen – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Evaluation of performance and microbial community successional patterns in an integrated OCO reactor under ZnO nanoparticle stress – Zhenghui Liu – RSC Advances

Screening of quorum quenching activity of the bacteria isolated from dairy industry waste activated sludge – J. Kaur – International Journal of Environmental Science and Technology

Food Microbiology
Identification of Mesophilic Spore-formers in Whey Powder using Shotgun Metagenomic Sequencing – Aoife J. McHugh – Applied and Environmental Microbiology

An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD) – Mariadelina Simeoni – European Journal of Nutrition

Probiotic and synbiotic supplementation could improve metabolic syndrome in prediabetic adults: A randomized controlled trial – Nazila Kassaian – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Phages and viruses
Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff – Scientific Reports

Microbes in the news
Hong Kong Subway Study Shows How Quickly Bacteria Travel Across a City – Gizmodo

Bacteria hysteria
Please Don’t Give Up Your Pet Over The Fear Of Dog-Lick Bacteria – Huffington Post

Science, publishing, and career
Scientists on Twitter: Preaching to the choir or singing from the rooftops? – Isabelle Côté – Facets

Alyson’s non-microbiology picks
‘Reprogrammed’ stem cells to be tested in people with Parkinson’s

These tiny, stretchy speakers and microphones let your skin play music

April 5, 2017

Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology


Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins


SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ


Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

New book claiming cancer caused by pasteurized milk

One of my Google alerts pointed me towards the press release of a new book that claims to have found the cure to cancer: the lack of lactic acid bacteria in milk. The book is written by a Dutch writer called Don Elsman and is titled: “Cancer, Cause and Prevention”. Although the press release and book title were in English, the book is actually written in Dutch – which is my first language.

Here is the link to the book’s website.

Here is a short summary – If you are a true scientist it s hard to read this without your eyes starting to bleed.

Cancer is caused by an overgrowth of Candida in our bodies. Candida invasion is inhibited by lactic acid bacteria that make a layer of acid. This is true because Candida does not grow at pH 4. Since pasteurizing destroys the lactic acid bacteria in milk we are all going to die of cancer. 

The press release appears to be full of false statements, persons claiming to be doctors, non-existing universities and fake PhDs. I especially did not like the “I have discovered the cure for cancer – buy my book and I will tell you all about it” vibe. I lost my sister last year to cancer, and I am pretty sure that it was not caused by Candida overgrowth or milk.

Which led me to a Twitter rant that I tried to summarize in this Storify.

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Storify: My rant about new book claiming cancer caused by pasteurized milk



June 1, 2016

Cystic fibrosis, microbial detoxification in the Sage Grouse, salinity gradient in the Baltic Sea, and testing different 16S rRNA gene primer pairs.

Human respiratory microbiome

Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients – H. Al-momani – Scientific Reports

The Dynamics of Disease Progression in Cystic Fibrosis – Frederick R. Adler – PLOS ONE

Human gut microbiome

Alterations and correlations of the gut microbiome, metabolism, and immunity in patients with primary biliary cirrhosis – Long-Xian Lv – Environmental Microbiology

Review: Analysis and Interpretation of the Human Microbiome – Ashton, James J. – Inflammatory Bowel Diseases

Review: Gut microbiota and colorectal cancer – Mayuko Yamamoto – Genes and Environment

Animal experiments

The Impact of Lactobacillus casei on the Composition of the Cecal Microbiota and Innate Immune System Is Strain Specific – Busra Aktas – PLOS ONE

Metagenomic Analysis of the Rumen Microbiome of Steers with Wheat-Induced Frothy Bloat – D. W. Pitta – Frontiers in Microbiology

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens – Lingling Wang – Frontiers in Microbiology

Animal microbiome

Snapshot of a Bacterial Microbiome Shift during the Early Symptoms of a Massive Sponge Die-Off in the Western Mediterranean – Andrea Blanquer – Frontiers in Microbiology

Microbial detoxification in the gut of a specialist avian herbivore, the Greater Sage-Grouse – Kevin D. Kohl – FEMS Microbiology Letters

Plant, root, and soil microbiome

Understory herb layer exerts strong controls on soil microbial communities in subtropical plantations – Kai Yin – Scientific Reports

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Diversity Enhances NPP, N Retention, and Soil Microbial Diversity in Experimental Urban Grassland Assemblages – Grant L. Thompson – PLOS ONE

Water and extremophile microbiome

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea – Tue O. O. Hu – Frontiers in Microbiology

Superimposed Pristine Limestone Aquifers with Marked Hydrochemical Differences Exhibit Distinct Fungal Communities – Ali Nawaz – Frontiers in Microbiology

Culture-independent characterization of novel psychrophilic magnetotactic cocci from Antarctic marine sediments – Fernanda Abreu – Environmental Microbiology

Food microbiology

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine – Xutao Hong – Scientific Reports

Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar – Zong-Min Wang – Scientific Reports

Bioreactor microbiology

Mycoalgae biofilm: development of a novel platform technology using algae and fungal cultures – Aravindan Rajendran – Biotechnology for Biofuels


Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies – Bram Beckers – Frontiers in Microbiology

Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases – Victor Satler Pylro – Journal of Microbiological Methods

Microbes in the news

Unlocking the secrets of bacterial biofilms – to use against them – Karin Sauer – The Conversation

CDC to set up network of labs to fight tough bacteria – Dale Shoemaker – The Morning Call

Stick insects produce bacterial enzymes themselves. In the course of evolution, genes of gut microbes ‘jumped’ to their insect host – EurekAlert

Tobacco Smoke Makes Germs More Resilient – University of Louisville – NewsWise

Malaria, Zika and Dengue Could Meet Their Match in Mosquito-Borne Bacteria. A common bacteria that infects mosquitoes seems to prevent them from carrying more deadly diseases – Brian Handwerk – Smithsonian

Wild Culture: The Wild Side of Beer Brewing – Anna Brones – Paste Magazine

Unlocking the Mysteries of the Microbiome – J Craig Venter Institute

Science, publishing, and career

Nondisclosure of Financial Interest in Clinical Practice Guideline Development: An Intractable Problem? – Hilda Bastian – PLOS Medicine

Financial Relationships between Organizations That Produce Clinical Practice Guidelines and the Biomedical Industry: A Cross-Sectional Study – Paul Campsall – PLOS Medicine


Why Is Big Naturopathy Afraid Of This Lone Whistleblower? – Kavin Senapathy – Forbes

May 11, 2016

Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.


The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

April 19, 2016

A review about breastmilk with a great name, skin microbiome in different populations, a mouse model for Sjögren’s, the office microbiome, Guam reef sponges, the Alaska tundra ecosystem, and taxonomic classification. Note that I will be traveling internationally in the next couple of days due to (another) tragic family situation, so posting will be irregular. But I will try my best!

Pregnancy and birth

Review: Breastfed at Tiffany’s – Thierry Hennet – Trends in Biochemical Sciences

Human skin microbiome

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome – Guillermo I. Perez Perez – PLOS ONE

Pathogenic bacteria profile and antimicrobial susceptibility patterns of ear infection at Bahir Dar Regional Health Research Laboratory Center, Ethiopia – Derese Hailu – SpringerPlus

Human oral microbiome (also see Animal models, below)

Comparison of the Oral Microbiome of Siblings Using Next-generation Sequencing: a Pilot Study – Hyo-Seol Lee – Oral Diseases

Human gastric microbiome

Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures – E. R. Shanahan – Alimentary Pharmacology & Therapeutics

Human gut microbiome

Conference Abstract: Walnut Consumption Influences the Human Gut Microbiome – Heather M Guetterman – The FASEB Journal

Conference Abstract: Anemia and Iron Status are Predictors of Gut Microbiome Composition and Metabolites in Infants and Children in Rural Kenya – Daniela Paganini – The FASEB Journal

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles – J. R. Allegretti – Alimentary Pharmacology & Therapeutics

Effects of sardine-enriched diet on metabolic control, inflammation and gut microbiota in drug-naïve patients with type 2 diabetes: a pilot randomized trial – Mariona Balfegó – Lipids in Health and Disease

Review: From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways – G B Rogers – Molecular Psychiatry

Review: Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? – Jodi E. Nettleton – Physiology & Behavior

Book chapter, some plagiarism: Impact of Probiotics and Gut Microbiota on Host Behavior – Sarabjit Singh Kanwar – Microbes in Food and Health

Animal models of microbiome research

Mouse model: Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome – Cintia S. de Paiva – Scientific Reports

Systemic Characterization of an Obese Phenotype in the Zucker Rat Model Defining Metabolic Axes of Energy Metabolism and Host-Microbial Interactions – Jutarop Phetcharaburanin – Journal of Proteome Research

Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model – Imran Khan – Frontiers in Pharmacology

Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition – M-L Wong – Molecular Psychiatry

Animal microbiome

The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers – Nicola Segata – Scientific Reports

In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity – Georg Steinert – PeerJ

Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali – Vincensius S.P. Oetama – Marine Pollution Bulletin

Diversity of endosymbiont bacteria associated with a non-filarial nematode group – Stela S. Lazarova – Nematology

Master thesis: Effects of Roundup (glyphosate) on gut microorganisms of farm animals – Charlotte Lynggaard Katholm – Aarhus University

Plant, root, and soil microbiome

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

Bacterial communities of the cotton aphid Aphis gossypii associated with Bt cotton in northern China – Yao Zhao – Scientific Reports

Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe – Cancan Zhao – Scientific Reports

Bioaerosol Deposition to Food Crops near Manure Application: Quantitative Microbial Risk Assessment – Michael A. Jahne – Journal of Environmental Quality

Effects of biofumigation using Brassica juncea and Raphanus sativus in comparison to disinfection using Basamid on apple plant growth and soil microbial communities at three field sites with replant disease – Bunlong Yim – Plant and Soil

Bacterial and eukaryal diversity in soils forming from acid mine drainage precipitates under reclaimed vegetation and biological crusts – Claudia Rojas – Applied Soil Ecology

Assessment of Bacterial Communities and Predictive Functional Profiling in Soils Subjected to Short-Term Fumigation-Incubation – Lin Chen – Microbial Ecology

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China – Wei Li – Journal of Soils and Sediments

Metagenomics reveals pervasive bacterial populations and reduced community diversity across the Alaska tundra ecosystem – Eric R. Johnston – Frontiers in Microbiology

Water microbiome

Bacterioplankton biogeography in the Atlantic Ocean: a case study of the distance-decay relationship – Mathias Milici – Frontiers in Microbiology

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities – Jeffrey Marlow – Frontiers in Microbiology

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean – Tallita Cruz Lopes Tavares – Science of The Total Environment

Dissolution Tests and Microbial Community Analysis Using the Bottom Sediment before and after a Heavy Storm – Ikuo Tsushima – Journal of Water and Environment Technology

Carbohydrate production by microbial mats communities in tidal flat from Bahía Blanca Estuary (Argentina) – E. M. Fernández – Environmental Earth Sciences

Built environment microbiome

Geography and Location Are the Primary Drivers of Office Microbiome Composition – John Chase – mSystems

Waste and pollution microbiology

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years – Xiao-Tao Jiang – Scientific Reports

Quantification of microbial load in diesel storage tanks using culture- and qPCR-based approaches – Pedro M. Martin-Sanchez – International Biodeterioration & Biodegradation

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns – Shuo Jiao – Soil Biology and Biochemistry

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates – Okoro Chuma Conlette – Microbial Ecology

Phages and viruses

Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system – Alex Betts – Evolution

Research highlight: More of the world’s a phage – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomics

Fast and sensitive taxonomic classification for metagenomics with Kaiju – Peter Menzel – Nature Communications

META-pipe – Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data – Espen Mikal Robertsen – ArXiv

Fast and sensitive mapping of nanopore sequencing reads with GraphMap – Ivan Sović – Nature Communications

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity – Beverly E. Flood – Frontiers in Microbiology

Editorial: A tale of two tardigrades – Thomas A. Richards – PNAS

Review: A guide through a family of phylogenetic dissimilarity measures among sites – Sandrine Pavoine – Oikos

Review: Compositional analysis: a valid approach to analyze microbiome high throughput sequencing data – Gregory B Gloor – Canadian Journal of Microbiology

More microbiology

Accessing Nature’s diversity through metabolic engineering and synthetic biology – Jason R. King – F1000 Research

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories – Vinoth Wigneswaran – F1000 Research

Microbes in the news

Your Invisible Neighbors: Each City Has Unique Microbes – Katherine Du – NPR

Can the bacteria on your skin reveal where you are from? Floors, walls and people in different cities have distinct microbial ‘signatures’ – Abigail Beall – Daily Mail

6 surprising facts about sugar-laden, virus-fighting breast milk – Megan Thielking – STAT News

Gut microbiota development driven by specific enzyme in breast milk – Yvette Brazier – Medical News Today

Mothers’ milk and the infant gut microbiota: An ancient symbiosis – Science Daily

Microbiome-Brain Research to Get $2.8M Boost from NIDA, NCCIH – Genome Web

Earth Day: New insights into coral health hidden in reefs’ microbiomes – National Science Foundation

Downwind safety on the farm. Manure application research aims to improve food safety – American Society of Agronomy

Heartburn Meds Alter the Gut. Acid blockers reduce the diversity of bacteria in the intestines—and that could lead to trouble – Melinda Wenner Moyer – Scientific American

Bacteria that ‘breathes’ iron: Microbes that might change our search for life in space – Dawn Papple – Inquisitr

Microbes and art
This artist uses bacteria as paint: Paint by Microbes – Steph Yin – PopSci

Science, publishing, and career

From #realtimechem to #whywedoresearch: Who are the Tweeting scientists? – Andrew Marsh – Piirus

Tips for Using Social Media to Promote Your Research – Emma Hedington – NPJ Biofilms and Microbiomes

About Joseph MercolaKnown Quack Forced to Refund Customers for Lying About Effects of Tanning Beds – Bryan Menegus – Gizmodo

Bik’s Picks

Meet the woman who makes fake fingers for Japan’s reformed gangsters – Justin McCurry – The Guardian

Microbiome Medicine Summit, part 5

Here is another transcript of the Microbiome Medicine Summit from last week. This transcript was made by the awesome Michelle Beaumont, Research Associate at King’s College London. Thank you, Michelle, for enduring this 45-min long talk and typing in all the text! That’s hours of work, so thank you very much.

Screen Shot 2016-03-09 at 2.45.27 AM

Screen Shot 2016-03-09 at 1.25.03 AMToday’s transcript (shortened a bit by me) is from the podcast by Larry Dossey, MD. Read more about him on Wikipedia.

The host, as before, is Raphael Kellman, MD (shown here in Italics). Here is a link to the MP3 audio file (for as long as the Summit leaves it on). The title of the talk was: “How Consciousness and Mindset Affect the Microbiome and Overall Health.” Highlighted parts in red (by me) are good sentences to read if you are short on time.

Larry, tell us more about your background and your personal story that that segwayed into this incredible journey of consciousness and and the one mind and the role of spirituality and healing. Was there a particular event that triggered a change?

Well, there were several events. As you know as is often the case when physicians make these kinds of transitions in their lives, often it has to do with the physical illness, that was the case with me. I was afflicted beginning in the medical school (with) classical migraine headache, tipified not with just nausea, vomiting and headache but severe partial blindness and this got so bad during medical school that I actually tried to drop out. (…) Nothing worked. I tried everything and you may remember back in the late sixties and early seventies biofeedback popped up on the American scene and I was all over the country learning how to do this deep relaxation using these high-tech instruments that measure things you aren’t aware of usually and it was like a miracle. I had one of those overnight cures and there’s no going back after you discovered the power of consciousness in intention and in this sort of thing in your own personal life, so I was hooked Raphael, I mean I couldn’t deny the power of consciousness in my own medical problem area. 

But Larry, you took a big step forward from basically biofeedback to a much bigger picture to consciousness on a global, nonlocal level to the level of mind that then goes beyond energy, because you could certainly explain your experiences with biofeedback on a very energetic, even perhaps biochemical/mechanical perspective. You took many steps beyond that, so what catalyzed that further progression in your thinking?

It was a shock to my system. The first year in my medical practice as an intern in Dallas I had a series of what we call precognitive dreams. I dreamt of patients whom I would not see until the next day in complex detail, but the sort of experiences I had with these precognitive dreams just were not supposed to happen. (…) 

Screen Shot 2016-03-09 at 2.43.51 AMI came away thinking that there’s some well kept secrets here that we weren’t informed off, and so I developed a passionate interest in this business of non-local manifestations of consciousness whether you want to call it ESP, telepathy, clairvoyance, precognition, this whole area was something was entirely unknown to me. I came out of this search in this personal exploration thinking that all of this was one of the best kept secrets in medicine and people were just not willing to go there and I thought that was cowardly and I began to explore this in my own life and write about it. The thing is I couldn’t get any papers published in the traditional medical journals so I began to write books about this.

Wow, that was a big jump. Did it change your personal life as well, as you started exploring this new consciousness, this new domain, this new dimension?

Not only did change my personal life because my world view just really was transformed, my personal experiences and my delving into the literature. It also changed my professional life. After my first book came out in ’82, a book called “Space, Time and Medicine” I began to be invited around the country to talk to hospitals and hospital staffs and lay conferences, and I discovered that I was one of the few people who was willing, to you know open this can of worms and it made a lot of my colleagues, extremely uncomfortable. I was a member of a large internal medicine group in Dallas which I helped found and there were some real problems about my continuing to be integrated into the group with those kinds of interests. I was advised “Why don’t you just practice internal medicine?”. My feeling was that this was a decent, necessary part of internal medicine, so it was sort of a lonely journey early on, but it’s one that if I had to do it over again I wouldn’t change.

*** Deleted a part here where host Raphael Kellman expresses how Larry’s book help him a lot, and how he felt connected to Larry, followed by Larry saying how great he feels to be connected to him and many others. ***

Larry, you say that it was a well-kept secret (…) but I also believe that many people that are so deeply “entrenched in science” to say I think that science could be misinterpreted or taken in the wrong direction. They never knew this, they’re totally foreign to this knowledge that we all have in a point in our hearts or in our soul, but they never learn it, so it wasn’t a well-kept secret. (…) How does this way of thinking, that we are part of one consciousness, one mind, that there’s something deeper within us that will redefine how we understand the superficial perspective of who we are? How will that new way of thinking practically change the practice of medicine?

(…) I think this is one of the most exciting and fantastic moments to be a physician I’ve ever …I could concede. I think that the revolution is happening in terms of consciousness, spirituality, really because of two reasons. One is that doctors have their own internal experiences as well as experiences with patients which they cannot deny, although they may not choose to go public with him, but then in addition to doctors experiences we have to talk about experiments, we have to talk about that pesky little four letter word which is called data, and so I just must say that it is abundant. It is replicated around the world and the only way doctors are going to be able to hide from this is that they engaged in willful blindness. There is simply too much information out there to do this denial act which has appealed to a lot of doctors during a practice lifetime but it’s not going to work anymore. I think that you don’t get this picture if you listen to the diehard skeptics who basically will never change, but if you actually are willing to go to the literature and do some work, it becomes very clear that we are facing a complete revolution in what we mean by therapy doctor-patient relationships and the manifestations of consciousness.

(…) How do we get more people to, not just health professionals, doctors and scientists and the AMA etcetera, but the average person to be more in tune and more aware of a different reality, a different world that we live in? (…) Tell me what what do you suggest that we do, that people do, what would be a good idea, statement, some suggestion that may push humanity a bit forward?

(…) I’ve made every mistake in the business about how to do these things and how to bring people over to this new way of looking at things (…) I recall back in my practice days that I would get excited about a new study and I would make a copy for all of my colleagues and then on Monday morning I would have had this on their desk so they can share in my enthusiasm for the new study. That was a disaster! One of my colleagues came to me one day and he said “Larry, nobody reads this and you’re just running up the copy costs.” So I decided to just sort of give up, and when I sort of backed off that’s when my colleagues came forward and expressed an interest in some of this stuff. But even so we’re never going on the basis of data and experiments to bring skeptics along with us. Some of them will never come over in spite of the powerful data on their side. This is not a new problem. Max Planck, the physicist, ran into it the early part of the 19th centuries and he’s paraphrased as saying that “science changes funeral by funeral” so I sort of made peace with a lot of my colleagues but I have to tell you that in the past two years it has completely changed around. Just a couple years ago I gave a Harvard talk to a group of Harvard physicians who were gathered for a continuing medical education course and they wanted me to talk about what they call “that weird consciousness stuff”. So I did and I revealed to them some of my experiences which were you know, pretty amazing, precognitive dreams and so on. When the Q&A time came I thought you know, they’re not gonna buy this, I was ready for the tomatoes and that kinda thing, but I was really fooled because they began to share with me their experiences. One female intern stood up in the middle of this big group of doctors and she said “Well I get numbers in my dreams,” she said. “I dream specific lab values of my patients laboratory tests before I even ordered the tests!”. It was a really interesting to me because it revealed to me that in a safe environment a lot of doctors will come forward and reveal things which they have never shared with anybody else they will also usually begin the revelation of these experiences by saying something like “You know I’ve never told anybody this in my life, but…” then they would reveal this, so I’m much more sanguine and hopeful these days about the response of our colleagues than I used to be twenty years ago.

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Absolutely, I agree with you. Give me a good example of two health disorders, two diseases, two health challenges that this way of thinking, this one mind, the role of consciousness, the role of soul, whatever you want to call it, will influence and perhaps even change the the modalities of treatment, or how it could be an adjunctive component to the treatments that they’re receiving.

I can give you some sensational examples. One was a woman who had retinitis pigmentosa and she was desperate. She was going to see an eye specialist for this problem. He sort of told her that he had done everything he could and there was nothing anybody else could do. She went to a Native American shaman – where I live, there’s a shaman behind every tree, it’s pretty easy to find one – and the shaman did whatever shamans do. He did a ritual healing for her and she went back to the eye specialist about six months later, and the problem had disappeared with no additional treatment of any kind. The ophthalmologist went into a rage. He said “This is an incurable situation,” he said “Never come back to my practice. This is impossible. I never want to see you again.”. So I went to see this woman and this is kind of a typical story you know, twenty years ago this would not be as likely to happen today I think, but at least that’s one way with intentionality, healing energy, or whatever you want to call it can be applied to the worst diseases for which medicine has not dealt very well with. You know, I have a file drawer full of these kinds of cases. The unfortunate thing is that we don’t know how to produce them on command and we can’t engineer these kinds of spontaneous remissions, but at least they are part of the medical lore and they they always have been.

Is there one thing that you would recommend as part of consciousness healing, mind healing, to a particular patient who has a specific disease? If there’s one thing that you could recommend that would be different than they would get if they just go to their physician?

I would advise in almost every disease entity I’m familiar with, that they need to make a place in there lives for some sort of contemplative practice whether they want to call that meditation, or contemplation or prayer or just timeout or sitting down for some a long time and so on. I think this is really crucial. It helps minimize stress responses of course. I mean we all know that now, but it also does a lot of other things. One I’m particularly interested in is it helps an individual get out of the sense of isolation and aloneness and feel some sort of connection with a larger entity that I call the One Mind, you know I wrote a major rant about this, my book “One Mind”, but I think that this is so easy to do that people underestimate the importance of this you know. Angie Ariand, the cultural anthropologist had four rules of life and she recommends them to everybody whether they’re sick or not. The first one was show up, the next one was tell the truth, the next one was be quiet, and the last one was probably the hardest thing, it was don’t be attached to the results, and I just think that says so much. This would be a generic approach I would recommend anybody, I don’t care what they’re dealing with.

That’s a nice way of helping people to kind of be catapulted to this One Mind, to collective energy, collected being. That’s beautiful. I think to be silent, to hear the the inner voice is wonderful as a vehicle to help people perhaps tap into that one mind that you speak about.

Well, I agree with you totally and I think that it’s getting even more difficult for people these days to follow these simple program and contemplation meditation. I’ve revised Angie’s rules to a less delicate form. The first one, for me is “Turn off your damn smartphone.”

I like that that’s real good practical advice. That’s gonna save lives, that little bit of advice but absolutely. (RK expresses again thanks to LD’s book that helped some many people in their loneliness. We’re 22 min in by now). 

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Talking about overcoming loneliness, I want to turn to the microbiome which is a very hot topic. I wrote a book on this, The Microbiome Diet. Actually, Larry, you know eight years ago, ten years ago I had a dream, I had a vision. I told it to my agent, to my wife and to my mother. I think everyone thought I was losing it. I said you know, the microbiome, I just felt intuitively that this is going to really help us transform medicine and we have to write about it. And my agent said he doesn’t know what I’m talking about and eight years later I wrote another proposal similar idea and she thought this was wonderful and this is this is going to be… I said “Janice is what I told you about eight years ago”, she said “Yes, yes you did but eight years ago no one was ready for it.” so there’s something that’s emerging today that we’re learning about. I think that the One Mind is teaching us new information about nature itself about the microbiome, the trillions of gut bacteria that play an incredible role in keeping us healthy, and my personal opinion is that the implications of the microbiome is going to really help us better understand what you’re writing about in the One Mind. Could you elaborate on that idea and would you agree with that idea and and if so why?

Absolutely, I agree with it, totally. I must say that you were ahead of your time when you sent that first book proposal and you know I must say that I remember seeing the microbiome on the horizon about twenty years ago. I don’t know if you remember Lynn Margulis, who is a biologist at Amherst, and she began to talk about you know, essentially the forerunner to this by microbial concept, how bacteria were included into the cell wall and they started invaded so that they became sort of tenants in our cellular makeup and that was sort of a state setting observation for the microbiome I think. Here’s what we know. I think that the microbiome is certainly factored into the One Mind idea. The reason I say that is because there are dozens of experiments, now I’m talking about hardcore controlled laboratory studies, which show that people, by using their intention, can interact with bacteria growing in test tubes, they can interact with fungi growing on Petri dishes, and they can use their intentions to increase the growth rate of bacteria or suppress it, and they can do this even though they’re not particularly skillful. We’re not talking about healers or shamans, we’re talking about skeptical college sophomores, who can do this. This is a widespread ability in the human race and it shows clearly that there is some nexus that in which is enveloped the consciousness of human beings in the behavior of microorganisms. I think we can predict with confidence that we’re going to see people intentionally learning how to regulate their microbiome through psychological techniques including intention, willing, wishing or praying, or whatever you want to call this stuff.

Do you have a particular idea or a type of thought or meditation or tapping into a particular type of idea that may particularly influence in a favorable way the microbiome?

I just incorporate into the energy and visualization that I use for practically any problem at all. Actually I’ve gotten so comfortable with bacteria, microbes in general that I don’t see them as a foreign substance anymore in my body. I played around with this idea so long that I see them as natural occupants and entities that are sharing what I call my corporeal body.

Larry, that’s what the science is showing, that this is the greatest turnaround in medicine in a hundred and fifty years, that bacteria are not the bad guy, there are no enemies out there, that in fact the bacteria are the good guys. That’s the greatest turnaround in a hundred and fifty years in medicine in my opinion.

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I really agree with you. I bump into people however and I bet you do too, who really don’t want much to do with this idea that they’re invaded by these microbes. I had one friend who just really got upset when I tried to tell him about how lucky he was to have these trillions of bacteria working in his behalf and he said “Don’t try to do that new age stuff for me, I don’t want anything to do with the bacteria my body.” Some people want to run in the other direction.

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You know what I tell my patients? I say you “You think you’re looking at me as a doctor person, as a person you know, but what you’re really looking at are trillions of bacteria dressed up in a suit, you know. We are mostly bacteria but you know to help people get comfortable with that idea, that the “me” that we think we are is really more like a beautiful “we”. We’re part of a bigger whole and by the way Larry, people love that idea. There’s a certain sense of comfort that people feel when they hear that.

Well I think this expanded concept that these are our friends and most of them really are there for a benefit, it really forces us to reinvestigate and rethink what we mean by antibiotics. I mean I know you deal with this all the time, most of the antibiotics we take are sort of like a nuclear bomb. It just destroys everything within its reach. And that’s crazy. If we hold on to the idea that these things are there to help us then you don’t want to destroy the good guys and so I know that people are working now on specific antibiotics that could be targeted to specific microorganisms, and that’s the smart way to go and I think that’s where we’re going to see antibiotic use headed in the future.

Just to close a little bit on the microbiome. I believe that the microbiome and its incredible interconnectedness to the outside bacteria and to every cell in every gene in our body, is a beautiful, physical example of that one-ness that you speak about. And that’s why you know, when I wanted to have people to talk about the microbiome I turned to you even though they say well “Larry Dossey talks about the One Mind.” but I said but no there’s a tremendous connection between the one mind and how it’s expressed here in the physical world.

I happen to believe that the discovery of the microbiome is one of the most convincing pieces of evidence that we have uncovered so far pointing to the one-ness of ourselves in nature. If I had to pinpoint the most valuable lesson that may come out of the microbiome I think it’s the lesson that we cannot secede from nature. We’ve tried to do that and it has left us in a precarious position on this planet. The fact that we’re living with this incredible array of organisms in our own body says that we better get comfortable with nature and we are a part of the whole.

Right and a whole that’s not withholding, the whole that as a giving whole. Look what the microbiome is doing for us, sustaining us, keeping us alive. You know this is a little bit of theological medicine but you know that’s what the literature is pointing to, that we don’t live in a world that’s rooted in selfishness, you know I think that science is painting up a very very different picture. You know the one mind is teaching us, I believe, very important lessons and I really look forward to more of your work that will teach us more about this one mind. And to continue our dialogue. I want to go into prayer, Larry, because I know that’s a very important topic for you. Has your perspective changed over time, about the power and the value of prayer and the fact that it could be turned on at will and has your perspective changed on that?

Well my views have evolved, I’m happy to say but I have not lost my enthusiasm for prayer which I define basically so generically that you know, it disappoints a lot of people. I just think prayer is communication with something beyond the individual self, however that’s defined whether it’s god or goddess or all or universe or something else. The studies are very convincing that people who are willing to appeal to a greater power and follow a spiritual path through their years live longer on average and they have a lower incidence of all the major diseases you want to talk about. I mean this is big stuff you know, for years we just farmed out spirituality to rabbis and ministers and preachers and so on and we’re not going to be able to winnie out of the benefits of spiritual practice including prayer in my judgment. It’s time doctors took it on and we would go in that direction lot quicker. Doctors would develop the courage to actually look at the data, the prayer studies are very convincing in my judgment. If people don’t want to call it prayer that makes them sort of nervous and if they think that’s too squishy and they just would rather do intentionality… Who cares but the fact is that there’s something going on here that is highly relevant to health and longevity and we need to embrace it.

So basically your ideas have not really changed all that much and basically you’re saying that prayer, intentionality, focus and also letting go of a particular outcome, that state that a person taps into, can effect change in our world, in our lives?


Do you think that there is even something perhaps deeper that underlies the value of prayer? For example is it selflessness, just being in a certain inner state that also perhaps is even more important than the prayer or even the intentionality that you speak about?

Indeed I do. I think that there are some underlying commonalities that go beyond this word prayer. One I think is surrender. I think when Angie Arian lists her fourth rule of life which is “don’t be attached to results” I think there’s something really deeply important about that you know. We’ve been through all of this stuff in the past 20 years about the right mindset to adopt if you want to have one of these healings and so on and i think we went overboard with telling people to fight your illness, to be really aggressive in this sort of thing. I think for a lot of people it is just the opposite and I could quote you data to support that. An accepting abiding sense that no matter what happens it’s okay. Even if the wheels come off your illness and you die, my message is that you’re just gonna have to settle for immortality.

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And I used to counsel my patients with cancer, a patient who was approaching death and we would have what I used called The Conversation. The conversation was you know “Joe if things continue to go bad and you know, the wheels come off and you’re just gonna have to settle for immortality.” and he would laugh, you know, a nervous laugh, and then the next day would really get into things and if I may say so I think that this image that there’s some aspect of who we are, that’s non-local in time, which to say is infinite, is indirect evidence that some part of us couldn’t die if it tried, its not local with respect to time which means that it’s immortal and eternal. This is one of the major lessons that comes out of the consciousness and healing and prayer studies because it reveals a non-local aspect, a temporally non-local aspect of who we are. We might as well call it the soul but if that makes people nervous you know, we can end in other words to do the same thing.

We could call it the most inner point of who we are, our inner core, you know it doesn’t really matter what word we use. Let’s talk a little bit about spontaneous remission and that obviously is something that we can’t pursue.  We can’t force the experience of a spontaneous remission but you know there are some studies to point to the fact that spontaneous remissions exists. It’s something that actually happens in the physical world. What’s your take on it? What are the most convincing studies and how would that change the mindset of conventional doctors and conventional medicine and signs?

Well the first thing I want to say is the conventional notion of doctors really needs to be radically renovated on this subject. I bet you had the same experience, so I was in medical school, I was told by professors: “these things are rare, you’ll probably go through your life is an internist and never see one and this is just baloney.” Hirschberg and Reagan published a book in 1993 collecting thousands of these cases from all over the world is so we find these spontaneous remissions in practically any disease you want to look at. Acknowledging this would be a reason for hopefulness if nothing else in by just coming clean with the evidence, telling people you know, it may not be likely but there’s always the possibility that something nice would happen here. That would not be dishonest. There are several books. Andrew Weil has a book called “Spontaneous Healing”, Hirschberg and Barasch have a book called a “Remarkable Recovery” which I wrote the foreword to, so you know I recommend that book, so there’s a good literature out there about this. I want to say though that I take issue with some of the books that have been published in recent years that sort of give formulas about how to engineer these things. I mean I don’t think there is a formula. These things happen to religious people and atheists alike. If you ask people who had these spontaneous remissions what they did to have one, they are all over the ballpark. Some people talk about the virtues of exercise, music, dance, taking up a hobby, some people say they fought their disease, others say they accepted it. There’s no pattern that i’ve seen and really I think that one of the frustrating things that people encounter.

You know it’s definitely not about whether you’re an atheist or believer. (talks about God). It doesn’t matter whether you say you’re a believer or you’re not a believer, we’re all in the same space and language is meaningless to me at that point.

I could not agree more. Earlier this month my wife and I participated in a conference in Tucson called the Final Transition conference and there were people there who do work with the dying and this was one of the richest conferences I’ve ever been to because nobody held back, people were completely open in their presentations and what came out of this is that our fear of death and annihilation simply goes away and the journey through death can be an extremely fascinating and fearless experience for most people. And I think if we can really make this message real from the nonlocal consciousness perspective, that the most essential part of you couldn’t die if it tried.

(…) The future of medicine, how do you see it?

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(…) it’s going to get a lot more technical in terms of new medications, new surgical procedures, bionics is gonna be big, I mean things are going to be really high tech in ways that we can’t even imagine currently and I’m not particularly against that. What will be the big breakthrough in my judgment, will tend to be the insights into the nature of consciousness. I cannot imagine a more morbid approach to consciousness than has been engaged in by the medical profession for the past two hundred and fifty years which says that with death there is total annihilation of everything. I can’t think of worse things to tell a sick person. This is where the major humanitarian breakthroughs, the ethical and moral advances are going to come, from a reinvention of the nature of consciousness and a willingness to actually engage with the data that is already there. We’ve done a terrible job there and my prediction is in the future we’re going to turn that around.

And that’s why we need collaboration and we need to support each other. That’s a lot of people that are working in this direction. By the way, that’s why one of the reasons why I’m so interested in the microbiome because I’m interested in the implications of the microbiome and how that could be a vehicle and a medium to make the transformation go a little bit faster. By the way I think that what you said is so, so important and I’m going to remember some of these quotes to pass along to others, is that offering hope and offering a different worldview to patients and why that’s so important. If you believe that we live in a world of survival of the fittest, that we’re just a bunch of chemicals that just dissipate into nothingness when we die, how could you, and we live in a cold brute and hostile world, if that’s your inner feeling as a healer, as a doctor, as health professional, how can you really offer any hope and comfort to any patient you interact with. Deep down you can’t,  because they sense what you’re feeling.

If doctors really believe that in their heart they ought to go to choose another profession. I would suggest they go into computers or or sell real estate but they are not fit to prevail their skills on other human beings if that is their worldview they should never go into medicine in the first place.

But this is the point that I think we need to make so sharp, which you know i i assist you with, is that we have two choices you can either believe that we live in a dog eat dog world, survival of the fittest, or you could begin to see differently because the science is pointing in a different direction if you just open your eyes, that we don’t live in such a world, we live in a world of survival of the wholest, we live in a world, in my opinion and I don’t believe any scientist could refute this, that we live in a world that’s rooted in kindness and if you have that perspective that’s how you offer hope to a patient and I believe, and then tell me if I’m getting it, that that’s the message of the One Mind at the deepest level.

You got it

Ok, ok well what I want people to hear that because there’s two paths, we can choose: Either the old way where scientists are rooted in and culture is rooted in, our society is rooted in, which is one way. Or a very different way which are the fundamental implications of the books that you’re writing, that I’m speaking about and I’m writing about and many others, but let’s make it clear that that’s a different world view and that world view is that ultimately it’s one mind and that it’s not survival of the fittest and that something continues and goes on and that ultimately it’s all a world of of kindness and hope and possibility and growth and forever transformation.

I agree yeah.

Larry, that’s the other possibility.

You know if we were to really get what you just said, as physicians, if we were to get there in our heart we would really feel that their medicine could resume being a spiritual path as it used to be you know, now it’s the path of the technician and the mechanic but it used to be a spiritual path and we can reclaim that.

Beautiful. And we will, as much as the physical and the technological will advance, so will the spiritual component advance you know, I really thank you on behalf of all listings for the work that you’re doing and that we continue this dialogue and you continue to write these wonderful books. Is there a new one coming?

Yeah. It’ll be out in the spring of 2016 and is called “What is consciousness?”

Oh boy, I like that.

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I have a little poem before we go. This is a little poem from the 14th century from Hafiz the great Persian poet:

“Let’s go deeper, go deeper
For if we do, our spirits will embrace and interweave.
Our union will be so glorious
That even God will not be able to tell us apart.”

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A sad story showing how alternative medicine can cause harm

This morning, there were several Tweets about a very sad story. Here is the first one:

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But soon many others followed. It was a very tragic story.

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In short, a 19 month old Alberta boy died of meningitis. Read more articles here and here. According to the story, his parents were running an alternative medicine website called TrueHope Nutritional Support Inc., a Canadian online story selling vitamin and mineral supplements.  The couple tried to treat their son, who was getting sicker and sicker, with all kinds of supplements but he did not get better, and eventually passed away.

TrueHope, the company run by the parents of the boy (according to one of the news sites above) claims that their supplements will cure a wide variety of behavioral conditions such as autism, ADHD, bipolar disorder, and depression. Their main product is EMPowerplus, a multivitamin product. Here is one of their claims (highlighting mine):Screen Shot 2016-03-09 at 12.31.33 AM

In a related story, a British Columbia man with schizophrenia who had been taking EMPowerplus and had stopped taking his prescription drugs, killed his father.

Truehope lists a collection of “clinical studies” on their website, but most of these are by the same 2 authors, and unblinded, not-placebo controlled studies, where people with mental illness were given pills, and asked if they felt better after a while. Read a critical analysis about their research here.

Natasha Tracy, a mental health writer, wrote some critical blogs about EmPowerPlus. She actually bought the product, but received a lot of pushy telephone calls afterwards, asking her to do additional tests. Tracy wrote a post about her experience called What I Know about EMPowerplus by Truehope that You Don’t. TrueHope of course was not amused, and threatened her with a lawsuit. But she did not remove her posts – and has not been sued so far. More about the lawsuit and Tracy’s story here.

The question remains why such a product can be advertised to treat diseases, and sold in Canada without the need for a prescription. Today we learned how dangerous and tragic selling dietary supplements with vague health claims can be.


Microbiome Medicine Summit, part 4

The Microbiome Medicine Summit has ended today, but I have downloaded all the talks. Tonight, I listened to Joseph Mercola’s talk, called The Basic Ways to a Healthy Microbiome (this link will download MP3 file). Dr. Joseph Mercola is one of the most popular alternative medicine gurus in the US. His website receives as many visitors as the pages from the National Institute of Health, and his Twitter account has over 200 million followers. He is not an MD, but he is a graduate of the Chicago College of Osteopathic Medicine (Source: Wikipedia). From Wikipedia:

Mercola has been criticized by business, regulatory, medical, and scientific communities. A 2006 BusinessWeek editorial stated his marketing practices relied on “slick promotion, clever use of information, and scare tactics.” In 2005, 2006, and 2011, the U.S. Food and Drug Administration warned Mercola and his company to stop making illegal claims regarding his products’ ability to detect, prevent, and treat disease. The medical watchdog site Quackwatch has criticized Mercola for making “unsubstantiated claims [that] clash with those of leading medical and public health organizations and many unsubstantiated recommendations for dietary supplements.”

Here is my transcript of parts from Joseph Mercola (JM)’s talk. It was not until 18 minutes in that the microbiome was mentioned for the first time. Some remarkable statements are highlighted in red, and I have also tossed in some responses and comments from Twitter. Host: Raphael Kellman (RK).

RK. What are the main ways that people can take control of their health?
I’m passionate about health. I’ve summarized health into 5 simple basics.
And interestingly, they work for about every disease. I view these as the essential foundational elements. Whatever disease you have you really need to integrate this into the base program. What are those principles?
1. Access to sun as much as you can. It’s not dangerous like every dermatologist will tell you.
2. Drink clean water. Stop drinking sodas.
3. Eat real food (…) When you eat real food, you avoid a lot of other additives and derivatives that are put in food that can really damage your health. And the timing of your food is absolutely key.
4. Movement – you simply got to move your body on a regular basis.
5. You’re not special. I’m not special. We all need 8 hours of sleep a day. There’s a small subset of people, 1:10,000 people have a genetic problem, and they only need 4 hours a night. But I almost guarantee you: You’re not one of those people. You need 8 hours.

(note EB 3/8/16: these 5 steps are all reasonable – although I would not recommend sitting in the sun for hours every day. These steps all are important to help us stay healthy, but they are not a guaranty to a healthy life, nor will they provide a miracle “for every disease”). 

RK. Do these same principles apply to someone who already has a serious disease? Do they need to add something?
No, they all have the same basic principles. Eating real food. By that you’re avoiding sugars, processed foods. There is a loop-hole in the government regulations that allows the food industry to classify many food ingredients as GRAS, Generally Recognized As Safe. By making that classification, they can avoid having to do any human food safety testing, and also do not have to put that on the label. You can look all you want, it won’t be there. If you eat real food you avoid exposure to all those potential toxins.

RK. There are many people with insulin resistance who are eating a very healthy diet, and they’re not overweight, and their insulin resistance or their outright diabetes is due to endocrine disrupters, and the chemicals in the environments. Would you agree with that?
Absolutely. There is no question. What is the solution? If you eat clean food, that’s a big issue. But there all the toxic exposure, the BPA phthalates that are in food containers, or plastic curtains in your shower. You got to limit the exposure to plastics.
But it could be other things, like sun exposure. Vitamin D deficiency is pervasive. Yes, you can take oral vitamin D. But exposure to the sun is the ultimate and absolute best way to increase your vitamin D.

RK: I’ve been saying this for years! Listen, if the sun is an integral part of nature, and we are part of nature, you don’t have to be a medical doctor to figure out that the two of us need to get together. What happens, when you go to medical school, is that you lose your common sense.
Why is exposure to sun better than swallowing a capsule? There’s different reasons. One of them is there’s different wavelengths, 1500 wavelengths. One of those wavelengths is the infrared wavelength. And we know that infrared exposure actually helps structure water in your body. That’s why infrared sonars are so good for detoxing.

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I have structured my life so that I don’t need vitamin D. I have not swallowed a vitamin D pill in over 5 or 6 years.  (Note EB: He lives in Florida. You know, where it’s sunny).

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But if you’re not able to do that, then you have to swallow and then you have to do a blood test.
RK: Get out in the sun! If you have 15-20 min, roll up your sleeves and sit out in the sun!
Take your shirt off! Don’t be embarrassed. If you’re a woman, of course you have a sports bra on, you know, we don’t wanna get indecent public exposure.

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RK: Your passion is to change the Paradigm of Medicine. What do you think is wrong with the current paradigm, and what is the new paradigm that you like to replace it with?
Everything that I mention reflects back to the simple principles of “RAP”, Replicate Ancestral Practice, so ancestral food, ancestral movements. What did our ancestors do hundreds of thousands of generations ago?

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Our genes and our metabolism (EB: mumbled here) were not optimized for what happened in the last hundred years. So when you remove yourself from that exposure you’re not going to achieve optimal health.

RK: My niece just got into medical school. So I asked her: Do they teach you in biochemistry or in cell biology that all these compounds like CoQ10 and PQQ and niacinamide, that you could actually use those compounds and improve cellular function, and there is research to support that? None of that is being taught. It’s just to know about these compounds in the cell, and then they get onto Pharmacology, what drugs to use.

Yeah, that’s just dead reality. I’m a big believer in CoQ10 or the reduced version which I think is higher quality becase that’s the actual portion that works, it’s biquinol.
Why? Because it supports mitochondria health. Why are mitochondria important? Mitochondria are derivatives of bacteria, they’re ancient bacteria, and each one of your cells has between a 100 and a 100,000 of these organelles (Note: Wikipedia lists an upper limit of 2000 per cell), and what do they do? They produce you energies. When you eat food, your body metabolically and enzymatically breaks that down to the food’s fuels, like fat and sugar, that eventually find their way to these the mitochondria. The mitochondria take that, combine it with oxygen, along the electron transport chain and create energy, distributed through ATP.
Why is this important? The timing of your food. When you eat fuel, one of the artifacts, the byproducts of this fuel generation is not terribly efficient, because it makes free radicals. It produces excessive electrons, and those few radials, you need some, but in excess they can cause cellular damage, can break up your cell membrane, destroy your DNA, kill your mitochondria prematurely. So what? Here is the key. (mentions a book)
Don’t eat food at least 3 hours before you go to bed. Personally I don’t eat food for 5 to 6 hours. Restricting your calories to about a 6h window is a powerful way to address that insulin resistance that I talked about earlier.

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But when you eat before you go to bed you’ve got fuel your body isn’t using. And it backs up, and creates all these excessive electrons and free radicals and damages your health. There is no way that you need fuel when you’re sleeping like that. That’s one of the worst things you can do, is to eat before you go to sleep.
Most of us do not need three meals a day. If you have insulin resistance, restricting your calories to a 6 to 8h window, and especially not eating loooong before you go to sleep, is one of the most powerful interventions, that will actually help eradicate, make almost magically disappear your food (inaudible).

18 min in. The host is gently steering the conversation to the topic of the microbiome.
RK: We’re talking about how the mitochondria actually come from ancient bacteria. We and bacteria have a special relationship that goes back for millions or billions of years, that has been totally overlooked. In fact we have always thought that bacteria are the bad guys, but in the last 10 years there’s been one of the greatest scientific turnarounds in the last 100-150 years, from thinking about bacteria as the bad guy to now changing that conception 180 degrees that bacteria is the ultimate good guy.

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Your gut is your second brain. When you eat bad food, the processed foods, the sugars, it goes in there. There’s only so much space in your gut. You can only hold so many bacteria back there. So when you fertilize it with bad material, you get the pathogenic yeast, bacteria, fungi, viruses, bacteriophages, that should not be there. There are pathogenic disease-causing microbes which will negatively influence your health. We’ve known about this for…, I forget the name… there was this Russian researcher about a century ago…
RK: Metchnikoff?

Talk about that bacteria are outnumbering us. And bacteriophages outnumber them. And the amount of genetics.
JM: At least we’re waking up. We’re starting to understand it. The more you know, the more you realize you don’t know.
RK: Ah! I love it.
(some talk about wise men and the bible).

RK: What is the main health issue where microbiome medicine can really make a difference?
JM: I really believe it has an impact on virtually every single health issue. There is just no question about in my mind. But if you have to target it to a specific group, the answer would be the gut diseases, like colon cancer and irritable bowel syndrome and inflammatory bowel disease and peptic ulcer. But it has an influence on almost every disease. There is no question in my mind.

RK: What would be the first step you would tell people to do to improve the microbiome and to improve their gut?
JM: Easy answer to that. You’ve got to take your foot off the gas pedal.
What does that mean? It means, you cannot feed the pathogenic yeast, bacteria, and fungi, You’ve got to stop eating sugar. You can take hundreds of trillions of beneficial microbes, but if you’re eating sugar, it’s like trying to stop your car with your foot on the gas pedal.

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Screen Shot 2016-03-08 at 1.31.42 AMOats is particularly high in phyatic (?) acids which can bind minerals. I liked oatmeal. When I was growing up that was one of my biggest – life cereals – when I didn’t know any better. Cause I did not come from a healthy family. I mean, I love them, but they were just clueless about nutrition.

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Orange juice is OK if freshly squeezed. I literally have 5 or 6 dozen fruit trees and about 3 dozen citrus, mostly tangerine, on my property that I consume regularly. I live in Florida so I can grow citrus.

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RK: What would you say is the second most important step to improve the microbiome?
JM Probably to eat real food. As as a subset to that, it’s really important to eat fermented food. If you are going swallow oral vitamin D (…) you have to take vitamin K2. Not K1, but K2. What does K2 do? It actually sucks the calcium out of the lining of the bloodvessels so that you prevent and actually reverse atherosclerosis, and it plugs it back into your bones, where it’s supposed to be. So you get stronger denser bones, so you don’t get osteoporosis, break your hip and die a few months later when you get older. 

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If you find fermented food and fermented vegetables specifically, you can get clinically significant amounts of vitamin K2 for free. I personally think that fermenting your own vegetables is a wise strategy. It’s not that hard to do. It’s not like you are creating a science experiment, gonna kill yourself and your family.

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(Around 30 min in, talking about prebiotics and butyrate enemas).
RK: Let’s talk about the targeted use of probiotics to improve various health conditions. More and more research is focussing on certain probiotics, certain types of bacteria that seem to be helpful with specific diseases. I feel there is a certain role for targeted probiotics.

JM: Most people can just benefit from a shotgut broad approach, to not only improve their gut flora, but improve all their health and decrease these chronic degenerative diseases that we are all exposing and they don’t have to die prematurely from Alzheimers, 50% of the people, have diabetes, 50% it’s so terrible. And they’re related. When you are looking at Alzheimers, it’s Type 3 diabetes.

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RK: Explain the connection between the gut and the microbiome and neurological health and how improving the gut and improving the microbiome can – to a great degree – prevent Alzheimers.
JM: Well, there are more connections from your gut to your brain than the other way around. It has enormous amounts of serotonin and other neurotransmitters that are actually produced by your gut.

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RK (shouting enthusiastically): By bacterial cells! They’re producing these neurotransmitters!
JM (shouting): That’s where it is! It’s in your gut! Not in your brain! In your gut!
RK (shouting): Gut feelings are real! It’s not poetry!
JM: You just follow Ancestral Practices. Do it right. Don’t follow what your friends and neighbors and relatives are doing, follow what your ancient relatives were doing. Follow their sleep patterns, bacteria, food, clean water, stay away from toxins. And when you do that your health will just improve automatically. There is no science involved. It’s just an automatic reflex.

RK: Will this change the way that doctors understand health and healing?
JM: I hope it will, especially with all the DNA sequencing going on. Science changes relatively slowly. It might take a while, may take another generation. Because there’s these vested interests that are highly conflicted and have enormous influence over powerful federal regulatory agencies that dictate policies, and the media of course. There’s a lot of – huh – negative impacts we have to overcome.

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Something even as simple as stopping sugar is still challenged and not widely adopted or accepted by traditional medicine because of these conflicted interests that I referenced earlier. It’s obvious, if you are rational, if you are not biased, and you are non-conflicted, and you’re sincerely seeking the truth, there is no other rational conclusion that you could reach. But unfortunately we have to battle these forces that are pushing us the other way, not of different beliefs, but because it is affecting their pocketbook.

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JM: I’ve been doing my website for almost 20 years. I’ve been educating people. We have literally 10 million unique visitors every month. But it’s not just about teaching. We have to play an activist role, to be a leader to erase some of these challenges. And the most classic one is these GMO foods, which we know have contained Roundup, which is actually more pronicious that its main ingredient glyphosate. Glyphosate has been shown to decimate your gut microbes. That’s one of the ways it works, it destroys your gut microbes!
We brought it to the public 4 years ago with the direct ballot initiative in California, which failed, but we increased consciousness about this. Right now, people have no clue that the food they’re buying contains GMOs which is gonna their gut health.
We are also working on getting mercury out of dentistry, fluoride out of the water, educating people about the importance of vaccine safety. And about biosolids, where cities are combining human waste with industrial waste, and sell it as organic fertilizer that you buy at Home Depot or Lowes. (rant continues)

RK: How do you see the future of microbiome research?
A: I’m not sure. It’s not an area that I study real carefully. So I’m sure there will be some improvements. (Quickly moves on into his other passion, i.e., extending life beyond 120 years.)

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JM: I’m delighted that you really went above your classmates and your local medical community and outcast probably, for recognizing the truth and applying that and being honest and taking a rational approach. Because it works.

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An example of how pseudoscientists and quacks are contorting science

This weekend I have been tweeting and posting about the Microbiome Medicine Summit, an online collection of talks by self-proclaimed “microbiome experts”. Some of these were MDs, some were PhD’s, and many others had titles I had never heard of before, but there was not a lot of science or medicine that was discussed here. In fact, a lot of the talks I listened to tried to first scare people about ingredients in their food or bad bugs in their guts, immediately followed by a mention of the speaker’s book or online cleansing products that the audience should buy.

Screen Shot 2016-03-07 at 12.36.08 AMAs an example of this scare tactic, I found a disturbing “factoid” on the website of Ann Louise Gittleman, who calls herself the First Lady of Nutrition (although I think that Michelle Obama is way ahead of her!). ALG held one of today’s Microbiome Summit talks called “Parasites May be the Hidden Cause of Your Health Issues”. You can find my transcript of parts of her talk here.

In her talk, ALG mentioned that a large part of the US population are infected by parasites. She mentioned that her mentor parasitologist estimated that 1970’s this number was 8 out of 10 Americans. She also claimed that most stool tests won’t detect these parasites. They are so hidden inside our guts, she said, that a regular stool test will easily miss them. But they are there! Anyone with GI problems, diarrhea, constipation, gas, GERD, or even sleep problems, Crohn’s Disease, asthma, arthritis and pretty much anything else you can think off, all these symptoms, she says, are an indication that you are infected with parasites. She even went on to say that these parasites are easier to detect “4 days before and after a full moon.”

So this is the point where she lost all my sympathy. She is really trying to scare the audience by telling them that pretty anyone is infested with invisible and undetectable parasites. But low and behold, she offers a solution (I am sarcastic here). You can go to her website where she sells a product called “My Colon Cleansing Kit“. And it’s even for sale! For $96 you will get 3 jars of herbs and probiotics.

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But here is what caught my eye. On the Details tab, she writes the following:

A study in The American Journal of Tropical Medicine and Hygiene found that 32% of a nationally representative sample of the US population tested positive for parasites. From microscopic organisms to 15-foot tapeworms, intestinal parasites can cause weight gain, damage organs, create toxicity, and infiltrate the bloodstream and brain. Parasites are often overlooked, however, because their symptoms can mirror other illnesses.

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Oh, that is scary. It sounds like she is writing that one third of the US populations is infected with parasites, right? Don’t you already feel a bit itchy down under? Could these invisible parasites you never realized you had be the cause that you don’t feel so well lately?

But is it really true? I guess I am a skeptical scientist, so I did not immediately believed this. So I dived into the American Journal of Tropical Medicine archives to dig up the study that she forgot to properly cite. It took me some ninja Google skills, but I found the study. And here it is, the real science behind ALG’s statement:

Seasonal prevalence of intestinal parasites in the United States during 2000 – Omar M Amin – Am J Trop Med Hyg June 2002 vol. 66 no. 6 799-803

Abstract: One-third of 5,792 fecal specimens from 2,896 patients in 48 states and the District of Columbia tested positive for intestinal parasites during the year 2000. Multiple infections with 2-4 parasitic species constituted 10% of 916 infected cases. Blastocystis hominis infected 662 patients (23% or 72% of the 916 cases). Its prevalence appears to be increasing in recent years. Eighteen other species of intestinal parasites were identified. Cryptosporidium parvum and Entamoeba histolytica/E. dispar ranked second and third in prevalence, respectively. Prevalence of infection was lowest (22-27%) in winter, gradually increased during the spring, reached peaks of 36-43% between July and October, and gradually decreased to 32% in December. A new superior method of parasite detection using the Proto-fix-CONSED system for fixing, transport, and processing of fecal specimens is described. In single infections, pathogenic protozoa caused asymptomatic subclinical infections in 0-31 % of the cases and non-pathogenic protozoa unexpectedly caused symptoms in 73-100% of the cases. The relationship between Charcot-Leyden crystals and infection with four species of intestinal parasites is examined and the list of provoking parasitic causes is expanded.

After reading the whole paper here’s my scientific interpretation: Yes, it is true that one third of the tested patients (916 of 2896) tested positive for at least one parasite. But here is the catch: it says *patients*. Every word in a scientific paper should be read carefully and is probably important. These were patients. These were not healthy people. All these samples were sent in by a physician to a specialized parasitic center for parasitic evaluation. In other words, their doctor suspected that their patients might have a parasite, based on e.g. a combination of GI complaints and recent travel to a foreign country, which about half of them had done.

So instead of writing that one third of the US population tested positive for parasites, it should read “One third of US patients suspected to be infected with a parasite indeed were found to be infected with a parasite. ” That is very different than the general population, where the real percentage is probably orders of a magnitude lower.

It’s just sad that people who are not trained to carefully interpret science are tweaking research findings to fit their own plan – and to fill their own pockets. It is even more sad if these persons are trying to attract people with chronic disorders such as arthritis, Crohn’s disease, and autism. That is just flat-out misleading and quackery. Please don’t fall for this.

Fun fact: Quackery means “the promotion of fraudulent or ignorant medical practices” (source: Wikipedia). It is derived from the Dutch word “kwakzalver”  meaning something like “a person who tries to sell ointments (“zalven”) that probably won’t work”. The Medieval word quack referred to the sound a duck or frog makes, but was also used to refer to exaggeration or overstatements (source: EtymologieBank).