Last year I wrote about the Microbiome Medicine Summit, which was not really a summit/conference but rather a collection of interviews with “nutrition specialists” and “microbiome experts” – some real, others not so much – conducted by Raphael Kellman, who has been trained as an MD but is very eager to believe and report on non-scientific statements involving the human microbiome. RK has been award the “Overselling the Microbiome” Award by Jonathan Eisen.

Most of the talks at last year’s Microbiome Medicine Summit provided very little science, a lot about “nurturing your microbes” , some crazy stuff, and lots of promotions to buy overpriced probiotic drinks, minerals, and self-help books. Even more telling, there were very few interviews with real microbiome experts or scientists.

I wrote about some of these talks in my blog posts from last year: Microbiome Medicine Summit with Deepak Chopra et al, part 2 with Donna Gates, part 3 with Ann Louise Gittleman, part 4 with Joseph Mercola, and part 5 with Larry Dossey.

This year, the Microbiome Medicine Summit returned in its second edition, with lots of new interviews, but basically the same strange mix of a tiny bit of science and lots of quackery, snake oil, alternative facts, and of course links to dubious websites selling products claiming to cure diseases. As in last year’s collection, most of these interviews were with nutritionists and holistic doctors. And again, most interviews were conducted by Raphael Kellman, who sometimes talks more than the person he is interviewing, and never, ever, seems to ask a critical question.  The schedule can be found here.

I took on the (at times painful) task of sitting through several of these talks so that I could share with you what they were about. Some of these talks were not too bad, with lots of “feed your microbes by eating healthy” types of messages, but some were outright weird or even dangerous. I reported about these talks on Twitter and compiled the tweets and some responses on Storify.

Here are my reports on Storify.

John Gray – Healthy Microbiome and Personal Relationships

Marco Ruggiero – The Study of Brain Microbiota and Health

Donna Gates – Cleansing the Microbiome

Today’s Microbiome Digest brings quite a few jobs and a lot of news about bacteria. Other then that there is an interesting review about human gut microbiome from E. Thursby and a study from M.J. MacAnulty  about the  conversion of methane directly into electricity.

Jobs

Research Specialist – Department of Microbiology, Champaign, IL

Research Technician – School of Medicine, Microbiology, Boston, MA

Microbiology Technologist Position at Top Hosptial, Raleigh, NC

Postdoctoral Research Associate – Microbiology, Lake Forest Park, WA

Microbiology Team Leader-Reference Laboratory, Kansas City Missouri

Summer job in RNA sequencing of cyanobacteria, KTH Royal Institute of Technology, Stockholm, Sweden

General microbiome

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations – Richard E Lensk – The ISME Journal

Pregnancy and early life

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life – Linda Wampach – Frontiers in Microbiology

Human oral microbiome

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Theodoros Goulas – Journal of Biological Chemistry
Human gut microbiome

A gut microbiome signature for advanced fibrosis diagnosis in NAFLD – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha – James M. Davison – Genome Research

Review: Introduction to the human gut microbiota – Elizabeth Thursby- Biochemical journal

Edible Plants and Their Influence on the Gut Microbiome and Acne – Ashley K. Clark – International Journal of Molecular Sciences

In vivo fermentation of a Pleurotus eryngii polysaccharide and its effects on fecal microbiota composition and immune response – Gaoxing Ma – Food & Function

Fecal microbiota transplantation outcomes in immunocompetent and immunocompromised patients: A single-center experience – Sally Alrabaa – Transpant Infectious Disease

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolis – Milan J. A. van Hoek – BMC Systems Biology
Animal microbiome

Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens – Shaun Nielsen – PeerJ

Plant, root, and soil microbiome

Host Plant Compatibility Shapes the Proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Tomato root microbiota and Phytophthora parasitica-associated disease – Marie Larousse – Microbiome

Insights into the Mechanism of Proliferation on the Special Microbes Mediated by Phenolic Acids in the Radix pseudostellariae Rhizosphere under Continuous Monoculture Regimes – Hongmiao Wu – Frontiers in Plant Science

Water and extremophile microbiome

Microbial contributions to the persistence of coral reefs – Nicole S Webster – The ISME Journal

Environmental pollution

Niche Partitioning In Sympatric Populations Of Aquatic Stenotrophomonas Uncovered By Evolutionary Species Delimitation – Luz Edith Ochoa-Sanchez – bioRxiv

Efficient degradation of chlorimuron-ethyl by a bacterial consortium and shifts in the aboriginal microorganism community during the bioremediation of contaminated-soil – Chunyan Li – Ecotoxicology and Environmental Safety
Food microbiology

Applications of cold plasma technology for microbiological safety in meat industry – N.N. Misra – Trends in Food Science & Technology
Probiotics / prebiotics

Deleterious Metabolic Effects of High Fructose Intake: The Preventive Effect of Lactobacillus kefiri Administration – María Guillermina Zubiría – Nutrients

Biotechnology

Electricity from methane by reversing methanogenesis – Michael J. McAnulty – Nature Communications

Hydrogen Isotope Composition Of Thermoanaerobacterium saccharolyticum Lipids: Comparing Wild Type To A nfn- Transhydrogenase Mutant – bioRxiv

Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms – Francesca Mapelli – Trends in Biotechnology

Techniques
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys – William Walters – mSystems
Microbes in the news 

Super-sensitive nanofiber can hear individual cells and detect swimming bacteria

Gym Equipment May Contain More Bacteria Than You Thought

Are Vitamin Supplements Killing Our Gut Bacteria?

Ignore your gut reaction: scientists say microbes can help conquer fear

NASA Names Microbe Found In Space After APJ Abdul Kalam

Growing antimicrobial resistance a major health issue for NZ
Bacteria Hysteria 

TB bacteria evolve at alarming rate

Science, publishing, and career 

Modeling Science Trustworthiness Under Publish Or Perish Pressure – David Robert Grimes – bioRxiv

Our Tuesday Digest came a bit late but still it is packed with content! Lots going on, specially in the Plant & Soil Microbiome section. Good reading!

Events and jobs

Scientist for Food Microbiology and Modelling – nationale vacaturebank (Link in Dutch)

General human microbiome

The Threat of Antimicrobial Resistance on the Human Microbiome
Lauren Brinkac et al – Microbial Ecology

Human epitelial microbiome

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences
Emily K. Cope et al – Microbiome

Review: Is the role of human female reproductive tract microbiota underestimated?
D. Kaminska & M. Gajecka – Beneficial Microbes

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota
Silke Rath et al – Microbiome

Pre-print: The effect of treatment on the microbiota of patients diagnosed with colonic lesions
Marc A Sze et al – bioRxiv

Microbial diseases

Targeted Metagenome Based Analyses Show Gut Microbial Diversity of Inflammatory Bowel Disease patients
Zhibing Qiu et al – Indian Journal of Microbiology

Report: Zinc metalloproteinase ZmpC suppresses experimental pneumococcal meningitis by inhibiting bacterial invasion of central nervous systems
Masaya Yamaguchi et al – Virulence

Review: Fungal Biofilms and Polymicrobial Diseases
Caroline B. Costa-Orlandi et al – Journal of Fungi

Inflammatory bacteriome featuring Fusobacterium nucleatum and Pseudomonas aeruginosa identified in association with oral squamous cell carcinoma
Nezar Noor Al-hebshi et al – Scientific Reports

Identification of Atypical El Tor V. cholerae O1 Ogawa Hosting SXT Element in Senegal, Africa
Bissoume Sambe-Ba et al – Frontiers in Microbiology

General environmental microbiome

Following Rapoport’s Rule: The geographic range and genome size of bacterial taxa decline at warmer latitudes
Gavin Lear et al – Environmental Microbiology

Animal experiments

Examining the efficacy of intravenous administration of predatory bacteria in rats
Kenneth Shatzkes et al – Scientific Reports

Animal microbiome

Characterization of the juvenile green turtle (Chelonia mydas) microbiome throughout an ontogenetic shift from pelagic to neritic habitats
James T. Price et al – PLoS One

Temporal Variations of Microbiota Associated with the Immature Stages of Two Florida Culex Mosquito Vectors
Dagne Duguma et al – Microbial Ecology

Understanding the gut microbiome of dairy calves: Opportunities to improve early-life gut health
Nilusha Malmuthuge & Le Luo Guan – Journal of Dairy Science

Pre-print: Uncovering the drivers of animal-host microbiotas with joint distribution modeling
Johannes R. Björk – bioRxiv

Plant, root, and soil microbiome

Ecology and Genomic Insights on Plant-Pathogenic and -Nonpathogenic Endophytes
Günter Brader et al – Annual Review of Phytopathology

High-throughput sequencing reveals bacterial community composition in the rhizosphere of the invasive plant Flaveria bidentis
Z Song et al – Weed Research

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region
Dominika Chmolowska et al – Science of the Total Environment

Microbial Community Dynamics in Soil Depth Profiles over 120,000 Years of Ecosystem Development
Stephanie Turner et al – Frontiers in Microbiology

Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions
Stilianos Louca et al – Environmental Microbiology

Thesis: Culture-Independent Analysis of Microbial Communities Associated with Hydroponically Grown “Living Lettuce”
Abby Matthews – The University of Mississippi

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling
Jun Li et al – Environmental Pollution

Review: The influence of bacteria on multi-trophic interactions among plants, psyllids, and pathogen
Cecilia Tamborindeguy et al – Insect Science

Pre-print: Yeasts dominate soil fungal communities in three lowland Neotropical rainforests
Micah Dunthorn et al – bioRxiv

Bacterial inoculants for enhanced seed germination of Spartina densiflora: Implications for restoration of metal polluted areas
Paredes-Páliz K et al – Marine Pollution Bulletin

A Phloem-Feeding Insect Transfers Bacterial Endophytic Communities between Grapevine Plants
Sebastiàn Lòpez-Fernàndez et al – Frontiers in Microbiology

Water, estuarine and sediment microbiome

Spatiotemporal analysis of microbial community dynamics during seasonal stratification events in a freshwater lake (Grand Lake, OK, USA)
Jessica M. Morrison et al – PLoS One

Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting
Megan J. Huggett et al – FEMS Microbiology Ecology

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond
Aurélien Saghaï et al – Environmental Microbiology

Extremophile and space microbiome

Thesis: Microbial Biogeography of the Arctic Cryosphere
Aviaja Zenia Edna Lyberth Hauptmann & Thomas Sicheritz-Pontén – Technical University of Denmark

Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis
F. Mandelli et al – Extremophiles

Aspergillus atacamensis and A. salisburgensis: two new halophilic species from hypersaline/arid habitats with a phialosimplex-like morphology
Livia Martinelli et al – Extremophiles

Built environment

Variation of microbial communities and functional genes during the biofilm formation in raw water distribution systems and associated effects on the transformation of nitrogen pollutants
Wei Chen et al – Environmental Science and Pollution Research

Microbiota and Particulate Matter Assessment in Portuguese Optical Shops Providing Contact Lens Services
Carla Viegas et al – Healthcare

QAC modified PVDF membranes: Antibiofouling performance, mechanisms, and effects on microbial communities in an MBR treating municipal wastewater
Mei Chen et al – Water Research

Microbial biotechnology

Green energy generation from plant microbial fuel cells (PMFC) using compost and a novel clay separator
A. Carmalin Sophia & S. Sreeja – Sustainable Energy Technologies and Assessments

Dynamics of two methanogenic microbiomes incubated in polycyclic aromatic hydrocarbons, naphthenic acids, and oil field produced water
Bohanis J. Oko et al – Biotechnology for Biofuels

Optimization of the extraction and purification of the compatible solute ectoine from Halomonas elongate in the laboratory experiment of a commercial production project
Ruifeng Chen et al – World Journal of Microbiology and Biotechnology

Review: Large scale cultivation of genetically modified microalgae: A new era for environmental risk assessment
Tracey A. Beacham et al – Algal Research

Subcellular localization based comparative study on radioresistant bacteria: A novel approach to mine proteins involve in radioresistance
Divya Vishambra et al – Computational Biology and Chemistry

Food microbiology

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology

Sulfites and the Wine Metabolome
Chloé Roullier-Gall et al – Food Chemistry

Meta-omics insights in the microbial community profiling and functional characterization of fermented foods
Gu Chen et al – Trends in Food Science & Technology

Biofilms

Pre-print: Bifunctionality of a biofilm matrix protein controlled by redox state
Sofia Arnaouteli et al – bioRxiv

General microbiology and evolution

The biology and the importance of Photobacterium species
Ibrahim Musa Moi et al – Applied Microbiology and Biotechnology

Review: A Metagenomic Approach to Cyanobacterial Genomics
Danillo O. Alvarenga et al – Frontiers in Microbiology

In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus
Michael Banasik et al – Journal of Biotechnology

Report: Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1
Yue Guan et al – Environmental Microbiology Reports

Phages and viruses

Characterization of prophages of Lactococcus garvieae
Giovanni Eraclio et al – Scientific Reports

Review: Viruses and miRNAs: More Friends than Foes
Patrice Bruscella et al – Frontiers in Microbiology

Bioinformatics and statistics

SteadyCom: Predicting microbial abundances while ensuring community stability
Siu Hung Joshua Chan et al – PLoS Computational Biology

Techniques and methods

Preview: An Elegan(t) Screen for Drug-Microbe Interactions
Alison Vrbanac et al – Cell Host & Microbe

Microbes in the news

Gut microbiome may predict response to biologic therapy for inflammatory bowel disease
ScienceDaily – Original Paper

Diseased Microbiome Varies From Condition to Condition
Ciara Curtin – GenomeWeb

Vini’s non-microbiology picks

Sociomics: Using Omic Approaches to Understand Social Evolution
Melanie Ghoul et al – Trends in Genetics

A short digest this Sunday with most studies focusing on associations with microbiota and host health, plus a look at a novel sampling method for assessing human-pathogen interactions.

 General microbiome

Review: Using systems biology approaches to elucidate cause and effect in host-microbiome interactions – Elizabeth A. Witherden – Current Opinion in Systems Biology

Human gut microbiome

Dynamic gastrointestinal digestion of grape pomace extracts: bioaccessible phenolic metabolites and impact on human gut microbiota – Irene Gil-Sánchez – Journal of Food Composition and Analysis

Gut Microbiota in Parkinson Disease in a northern German cohort – Franziska Hopfner – Brain Research

Outlier based literature exploration for cross-domain linking of Alzheimer’s disease and gut microbiota – Donatella Gubiani – Expert Systems with Applications

Animal experiments

Review: This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth–Microbiota Interactions in Veterinary Species – Laura E. Peachey – Trends in Parasitology

Lactobacillus johnsonii CJLJ103 attenuates colitis and memory impairment in mice by inhibiting gut microbiota lipopolysaccharide production and NF-κB activation – Su-Min Lim – Journal of Functional Foods

Effects of potato dextrin on the composition and metabolism of the gut microbiota in rats fed standard and high-fat diets – Renata Barczynska – Journal of Functional Foods

Antibiotics-induced gut microbiota dysbiosis promotes tumor initiation via affecting APC-Th1 development in mice – Chengming Xu – Biochemical and Biophysical Research Communications

Plant, root, and soil microbiome

Effectiveness of a full-scale horizontal slow sand filter for controlling phytopathogens in recirculating hydroponics: From microbial isolation to full microbiome assessment – Francesc X. Prenafeta-Boldú – Science of The Total Environment

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region – Dominika Chmolowska – Science of The Total Environment

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling – Jun Li – Environmental Pollution

Techniques

A novel sampling method for assessing human-pathogen interactions in the natural environment using boot socks and citizen scientists, with an application to the seasonality of Campylobacter – Natalia R Jones – Applied and Environmental Microbiology

Microbes in the news

The Coral Microbiome May Offer Protection in Warming Seas – Jeffrey Marlow – Discover

Grotty socks reveal surprising spread of gut-churning bacteria – Ben Guarino – Stuff

UK researchers develop low tech method for environmental sampling of campylobacter – ASM Press release

First, a job opportunity in my PI’s lab: please forward or apply! Papers today are spread over multiple topics, with more in soil and water, and an emphasis on ecological ideas for the general microbiome.

Events and jobs
Bioinformatics Research Associate – Harvard T.H. Chan School of Public Health

General microbiome
Perspective: Multi-stability and the origin of microbial community types – Didier Gonze – ISME

Microbial consortia at steady supply – Thibaud Taillefumier – eLife

Human oral microbiome
Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome – Steven Knapp – Frontiers in Cellular and Infection Microbiology

Human gut microbiome
Opinion: What happened to Koch’s Postulates in Diarrhea? – Shamima Sultana – Environmental Microbiology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics – Sonny T.M. Lee – Microbiome

Animal experiments
TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome – Robert D. Stedtfeld – FEMS Microbiology Ecology

A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep – Saad Al-Masaudi – Frontiers in Microbiology

Plant, root, and soil microbiome
Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances – Bingxin Li – Science of the Total Environment

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations – Yunfu Gu – PLoS One

Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence – Nicholas A. Barber – Environmental Microbiology

Arbuscular and Ectomycorrhizal Fungi Associated with the Invasive Brazilian Pepper Tree (Schinus terebinthifolius) and Two Native Plants in South Florida – Karim Dawkins – Frontiers in Microbiology

Water and extremophile microbiome
Differential responses of marine, mesohaline, and oligohaline bacterial communities to the addition of terrigenous carbon – DPR Herlemann – Environmental Microbiology

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia – Hauke F. Kegler – Frontiers in Microbiology

Built environment
Long-term successional dynamics of microbial association networks in anaerobic digestion processes – Linwei Wu – Water Research

Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition – A. Anisa Cokro – Water Research

Probiotics / prebiotics
Review: Effectiveness of Probiotic, Prebiotic, and Synbiotic Therapies in Reducing Postoperative Complications: A Systematic Review and Network Meta-analysis – Nongyao Kasatpibal – Clinical Infectious Diseases

Review: Effect of Probiotics on Metabolic Outcomes in Pregnant Women with Gestational Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials – Bonnie L. Taylor – Nutrients

Techniques
Rapid Pathogen Identification in Bacterial Pneumonia Using Real-time Metagenomics – Kathryn M Pendleton – American Journal of Respiratory and Critical Care Medicine

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics – Andrea C. Duarte – Frontiers in Microbiology

Microbes in the news
Gold processing bacteria help to recycle electronics – Tim Sandle – Digital Journal

Continued exposure to bacteria from decomposing bodies took its toll on workers – Mahesh Avadhuta – Deccan Chronicle

Bacteria Hysteria
Rob Mancini: Why do folks insist on providing bad food safety advice? – Ben Chapman – BarfBlog