May 23, 2017

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Today’s microbiome is packed with thought-provoking insights from the status of Microbiology today and in-depth look at what is REALLY in our drinking water.

General Microbiome and Microbiology

Big Questions in Microbiology Mizrahi V. Cell

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Rath S. Microbiome

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.Hibberd MC. Science Translational Medicine

Human microbiome and immune system

Potential Impact of Nutrition on Immune System Recovery from Heavy Exertion: A Metabolomics Perspective.Nieman DC. Nutrients

Animal and insect microbiome

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. Gontang EA. Plus One

A metagenomic approach to discover a novel β-glucosidase from bovine rumens. Suwan E. Pure and Applied Chemistry, 2017

Plant, soil, and air microbiome

Tomato root microbiota and Phytophthora parasitica-associated disease. Larousse M. Microbiome

Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Oono R. Environmental Microbiology

Carbon‐driven enrichment of the crucial nitrate reducing bacteria in limed peat soil microcosms. Zhu Y. Letters in applied Microbiology

Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash. Cruz-Paredes C. Soil Biology and Biochemistry.

Inland waters and ocean microbiome

Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor.Gantt SE.FEMS Microbiology Letters.

Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pond. Lee ZMP.  Frontiers in Microbiology

Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance’s perspective. Zhang Y. Environmental Microbiology

Faecal microbiome 

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.Khanna S. Microbiome

Probiotics

Antioxidant Properties of Probiotic Bacteria. Wang Y. Nutrients

 STUDYING HOST-MICROBIOTA MUTUALISM USING GNOTOBIOTIC DROSOPHILA. Ma D.Old Herborn University Seminar Monograph 30

Virology

Pre-Symptomatic Diagnosis of Ebola Virus Infection. Navalkar K. Emerging disease and Virology   2017

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.Vigneron A. The ISME Journal

Preprint 

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. Laroche O. PeerJ

May 22, 2017

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Events and jobs
Microscopist Asbestos/Microbiology – EMSL Analytical, Seattle, WA

Technician (Microbiology Team) – AsureQuality (AQ), Christchurch, Canterbury, New Zealand

Laboratory Technician I (Microbiology & Genetics) – IDEXX, Columbia, MO, US

Associate Scientist Molecular Microbiology – CheckMark Labrecruitment, South Holland

Human respiratory microbiome
Review: Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides – Wilmore C. Webley – Respiratory Research

Human gut microbiome
Review: The bidirectional gut-brain-microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease – Mark Sundman – Brain, Behavior, and Immunity

Clinical Trial Watch: ‘Targeting the gut-liver axis in liver disease’ – Reiner Wiest – Journal of Hepatology

Gluten-degrading bacteria are present in the human small intestine of healthy volunteers and celiac patients – Alexandra R. Herran – Research in Microbiology

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans – Lloyd S. Robinson – Journal of Biological Chemistry

Plant, root, and soil microbiome
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation – José A. Siles A. Siles – Scientific Reports

Review: Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens – Ikkei Shikano – Journal of Chemical Ecology

Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots – Robert J. Dorosky – Applied and Environmental Microbiology

Water and extremophile microbiome
Review: A multiomics approach to study the microbiome response to phytoplankton blooms – Liyan Song – Applied Microbiology and Biotechnology

Antibiotics/probiotics/prebiotics
The Resistome Of Important Human Pathogens – Christian Munck – bioRxiv

Phages and viruses
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer – Marie Touchon – Current Opinion in Microbiology
Part of a themed issue on MGE-HGT in prokaryotes

Bioinformatics
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees – Märt Roosaare – PeerJ

Microbes in the news
Bacteria could lead to cleaner methane power – Jon Fingas – Engadget

Luminous bacteria will help to measure radioactivity – Siberian Federal University – EurekAlert!

A ‘Superbug’ Fungus Is Spreading Across The US – Kristen V. Brown – Gizmodo

Research shows that gut bacteria tells their hosts what to eat – Cordis News

Indian researchers use a novel route to kill TB bacteria – R. Prasad – The Hindu

Bacteria Hysteria
Cash is even grosser than you knew: Dangerous bacteria survive on paper money, study finds – James Dennin – AOL

May 21, 2017

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Events and jobs

FULLY FUNDED POSTDOCTORAL FELLOW POSITION TO STUDY MICROBIOME-BEHAVIOR INTERACTIONS: PORTUGAL

General microbiome

Bioinorganic antimicrobial strategies in the resistance era – Regiel-Futyra et al, Coordination Chemistry Reviews

Biofilm microenvironment induces a widespread adaptive amino-acid fermentation pathway conferring strong fitness advantage in Escherichia coli – Letoffe et al, PLoS Genetics

A bloodstream infection by Ruminococcus gnavus in a patient with a gall bladder perforation – Kim et al, Anerobe

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater – Zhu et al, Chemical Engineering Journal

Thermophilic Moorella thermoautotrophica-immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO2 – Yu et al, Bioelectrochemistry

Arumberiamorph structure in modern microbial mats: implications for Ediacaran palaeobiology – Kolesnikov et al, Bulletin de la Société Géologique de France

Succession in the petroleum reservoir microbiome through an oil field production lifecycle – Vigneron et al, ISME

Human respiratory microbiome

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307 – Long et al, Mbio

Human oral microbiome

Pro-resolving mediators in the regulation of periodontal disease – Van Dyke, Molecular Aspects of Medicine

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome – Goulas et al, Journal of Biological Chemistry

Human gut microbiome

Is frozen fecal microbiota transplantation as effective as fresh fecal microbiota transplantation in patients with recurrent or refractory clostridium difficile infection: a meta-analysis? – Tang et al, Diagnostic Microbiology and Infectious Disease

Weight-loss interventions and gut microbiota changes in overweight and obese patients: a systematic review – Seganfredo et al, Obesity Reviews

 

Dysbiosis of Gut Microbiome and Its Impact on Epigenetic Regulation – Lee et al, Journal of Clinical Epigenetics

Hypoxia and Inactivity Related Physiological Changes (Constipation, Inflammation) Are Not Reflected at the Level of Gut Metabolites and Butyrate Producing Microbial Community: The PlanHab Study – Sket et al, Frontiers in Physiology

Is there a potential role of fecal microbiota transplantation in the treatment of inflammatory bowel disease? – Eun, Intestinal Research

Diet and contaminants: driving the rise to obesity epidemics? – Di Ciaula and Portincasa, Current Medical Chemistry

How to: Establish and run a stool bank – Terveer et al, Clinical Microbiology and Infection

Animal experiments

Transforming growth factor β: a master regulator of the gut microbiota and immune cell interactions – Bauche and Marie, Clinical and Translational Immunology

Aloin, a Component of the Aloe Vera Plant Leaf, Induces Pathological Changes and Modulates the Composition of Microbiota in the Large Intestine of F344/N Male Rats – Boudraeu et al, Toxicology Science

Diabetes-associated microbiota in fa/fa rats is modified by Roux-en-Y gastric bypass – Arora et al, ISME

Absorption and degradation of sulfated polysaccharide from pacific abalone in in vitro and in vivo models – Ai et al, Journal of Functional Foods

Dietary ZnO nanoparticles alters intestinal microbiota and inflammation response in weaned piglets – Xia et al, Oncotarget

Dietary delta-tocotrienol favors abundance and diversity of beneficial microbiomes in obese male mice – Shen et al, FASEB

Bile acid binding resin prevents fat accumulation through intestinal microbiota in high-fat diet-induced obesity in mice – Kusumoto et al, Metabolism

In vitro ability of mastitis causing pathogens to form biofilms – Schonborn et al, Journal of Dairy Research

Dysbiosis of Intestinal Microbiota and Decreased Antimicrobial Peptide Level in Paneth Cells during Hypertriglyceridemia-Related Acute Necrotizing Pancreatitis in Rats – Huang et al, Frontiers in Microbiology

Effects of replacing Leymus chinensis with whole-crop wheat hay on Holstein bull apparent digestibility, plasma parameters, rumen fermentation, and microbiota – Niu et al, Scientific Reports

Physiological responses of insects to microbial fermentation products: insights from the interactions between Drosophila and acetic acid – Kim et al, Journal of Insect Physiology

Animal microbiome

Molecular detection by analysis of the 16S rRNA gene of fecal coliform bacteria from the two Korean Apodemus species (Apodemus agrarius and A. peninsulae) – Rahman et al, Genetics and Molecular Research

Detection and genetic characterization of Pasteurella multocida from alpaca (Vicugna pacos) pneumonia cases – Rimac et al, Tropical Animal Health and Production

Plant, root, and soil microbiome

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems – Zhang et al, Soil Biology and Biochemistry

Ground cover and slope exposure effects on micro- and mesobiota in forest soils – Gomez-Brandon et al, Ecological Indicators

Root chemical traits and their roles in belowground biotic interactions – Tsunoda and van Dam, Pedobiologia

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production – Li et al, Journal of Proteomics

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases – Valverde et al, AIMS Microbiology

Water and extremophile microbiome

The removal of nitrogen compounds from farming wastewater – The effect of different carbon substrates and different microbial activators – Mankiewicz-Boczek et al, Ecological Engineering

How do physicochemical properties influence the toxicity of silver nanoparticles on freshwater decomposers of plant litter in streams? – Batista et al, Ecotoxicology and Environmental Safety

The heterogeneity of composition and assembly processes of the microbial community between different nutrient loading lake zones in Taihu Lake – Zhao et al, Applied Microbiology and Biotechnology

Towards a sustainable biobased industry – Highlighting the impact of extremophiles – Kruger et al, New Biotechnology

Distribution and genetic diversity of microbial populations in the pilot-scale biofilter for simultaneous removal of ammonia, iron and manganese from real groundwater – Cheng et al, Chemosphere

Pilot plant demonstration of stable and efficient high rate biological nutrient removal with low dissolved oxygen conditions – Keene et al, Water Research

Study on The Removal of Hexavalent Chromium from Contaminated Groundwater using Emulsified Vegetable Oil – Wen et al, Process Safety and Environmental Protection

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea – Yang et al, Viruses

Oxidative Stickland reactions in an obligate aerobic organism — amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus – Stark et al, FEBS

Microbial Diversity in Extreme Marine Habitats and Their Biomolecules – Poli et al, Microorganisms

Methanogenic community was stable in two contrasting freshwater marshes exposed to elevated atmospheric CO2 – Lin et al, Frontiers in Microbiology

Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity – Ishaq, AIMS Microbiology

Effect of arbuscular mycorrhizal fungi on survival and growth of micropropagated Comanthera mucugensis spp. mucugensis (Eriocaulaceae) – Pereira et al, African Journal of Agricultural Research

Native communities of arbuscular mycorrhizal fungi associated with Capsicum annuum L. respond to soil properties and agronomic management under field conditions – Carballar-Hernandez et al, Agriculture, Ecosystems & Environment

Food microbiology

Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread – Cavallo et al, Food Chemistry

Analysis of the microbiota of refrigerated chopped parsley after treatments with a coating containing enterocin AS-48 or by high-hydrostatic pressure – Burgos et al, Food Research International

Microorganisms Found in MPR and Packaged Produce and Their Detection Methods – Acar and Soyer, Minimally Processed Refridgerated Fruits and Vegetables, Food Engineering Series

Applications of Kluyveromyces marxianus in Biotechnology – Varela et al, Yeast Diversity in Human Welfare

Mucin- and carbohydrate-stimulated adhesion and subproteome changes of the probiotic bacterium Lactobacillus acidophilus NCFM – Celebioglu et al, Journal of Proteomics

Techniques

Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities – Speda et al, Biotechnology Biofuels

Microbes in the news

Probiotics are popular, but some questions remain – Reading Eagle

Microbiome Medicine Summit 2017

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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.

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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

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Marco Ruggiero – The Study of Brain Microbiota and HealthScreen Shot 2017-05-20 at 4.34.09 PM.png

Donna Gates – Cleansing the Microbiome

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May 19, 2017

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Microbiome research

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs

Ursula M. McCormack et al., Applied and Environmental Microbiology

Modulation of the Gut Microbiota by Krill Oil in Mice Fed a High-Sugar High-Fat Diet

Chenyang Lu et al., Frontiers in Microbiology

Opinion: Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet?

Eamonn M. M. Quigley, Nature Reviews Gastroenterology & Hepatology (Online since March 30, 2017; however this has not been pointed out here before)

 

Pathogen microbiology

Mini review: The Role of Ribonucleases and sRNAs in the Virulence of Foodborne Pathogens

Rute G. Matos et al., Frontiers in Microbiology

Pathogenic Characteristics of Staphylococcus aureus Endovascular Infection Isolates from Different Clonal Complexes

Dafne Pérez-Montarelo et al., Frontiers in Microbiology

Pseudomonas aeruginosa Exolysin promotes bacterial growth in lungs, alveolar damage and bacterial dissemination

Stéphanie Bouillot et al., Scientific Reports (Nature)

Intrinsic Toxin-Derived Peptides Destabilize and Inactivate Clostridium difficile TcdB

Jason L. Larabee et al., mBio

 

Probiotics – Prebiotics

Vaginal Lactobacillus Inhibits HIV-1 Replication in Human Tissues Ex Vivo

Rogers A. Ñahui Palomino et al., Frontiers in Microbiology

Assessing the Risk of Probiotic Dietary Supplements in the Context of Antibiotic Resistance

Min Zheng et al., Frontiers in Microbiology

Review: Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

Daniel M. Linares et al., Frontiers in Microbiology

In silico Prediction, in vitro Antibacterial Spectrum, and Physicochemical Properties of a Putative Bacteriocin Produced by Lactobacillus rhamnosus Strain L156.4

Letícia de C. Oliveira et al., Frontiers in Microbiology

Health benefit of vegetable/fruit juice-based diet: Role of microbiome

Susanne M. Henning et al., Scientific Reports (Nature)

Characterization of bile salt hydrolase from Lactobacillus gasseri FR4 and demonstration of its substrate specificity and inhibitory mechanism using molecular docking analysis

Rizwana Parveen Rani et al., Frontiers in Microbiology

Lactobacillus johnsonii ameliorates intestinal, extra-intestinal and systemic pro-inflammatory immune responses following murine Campylobacter jejuni infection

Stefan Bereswill et al., Scientific Reports (Nature)

News and Views: Paediatrics: Are human milk oligosaccharides the magic bullet for necrotizing enterocolitis?

Michael S. Caplan, Nature Reviews Gastroenterology & Hepatology

Assessing the Challenges in the Application of Potential Probiotic Lactic Acid Bacteria in the Large-Scale Fermentation of Spanish-Style Table Olives

Francisco Rodríguez-Gómez et al., Frontiers in Microbiology

 

Antimicrobials

A broad-spectrum bactericidal lipopeptide with anti-biofilm properties

Ohad Meir et al., Scientific Reports (Nature)

The anticancer peptide TAT-RasGAP317-326 exerts broad antimicrobial activity

Mathieu Heulot et al., Frontiers in Microbiology

 

Genomics

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Sang Woo Seo et al., Scientific Reports (Nature)

High-Definition Electronic Genome Maps From Single Molecule Data

John S. Oliver et al., BioRxiv

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

Ben Pascoe et al., PeerJ (not peer reviewed)

Feature: Mining microbes: Creating genomic tools to fight disease

Amber Dance, Science

 

Microbiology – Other

Variation in soil microbial community structure associated with different legume species is greater than that associated with different grass species

Yang Zhou et al.,  Frontiers in Microbiology

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Stephanie Turner et al., Frontiers in Microbiology

Autotrophic and heterotrophic acquisition of carbon and nitrogen by a mixotrophic chrysophyte established through stable isotope analysis

Ramon Terrado et al., The ISME Journal

Hypothesis & Theory: The hyperarid core of the Atacama Desert, an extremely dry and carbon deprived habitat of potential interest for the field of carbon science

Armando Azua-Bustos et al., Frontiers in Microbiology

 

non-Microbiology picks

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides

Shaun Stairs et al., Nature Communications

Virus origin could relate to the act of prey among primitive life forms

Eslam Abbas, PeerJ (not peer reviewed)

Beyond the protein-only hypothesis: A novel mineral-lipid hypothesis in prion and protein-misfolding disease

Kavitha Reddy, PeerJ (not peer reviewed)

Feature: Introducing ORCID

John Bohannon and Kirk Doran, Science

 

May 18, 2017

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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

 

Microbiome at BioData World West 2017

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Last month, from April 26th to April 27th, I attended the BioData World West conference representing GENEWIZ, where I am a Bioinformatics Analyst (developer) working primarily on metagenomics.  The focus of the conference were three major areas: Genomics & Health, Precision Medicine, and Artificial Intelligence.  The conference, in San Francisco, hosted a variety of forward thinking and interdisciplinary organizations ranging from the top academic institutions to big industry players from abroad (Google, Merck, Illumina, etc.) to start ups in AI/tech/biotech/pharma.  The talks and conversations I had there were exciting and educational and the networking opportunities were amazing – I believe a number of collaborations were born there.   You can see details about the conference through this link: BioData World West 2017

My highlighted talks were by Atul Butte (UCSF), Jeff Dean (Google), Ronald Pryzgodski (MVP), Steve Miller (USCF, developed SURPI), Ali Torkamani (Scripps), and Sylvain Costes (NASA).  However, every talk was fascinating in its own way and I’d highly recommend this conference to anyone in this space – I could write 10 posts about what I learned but I’ll focus on the microbiome below.  It seemed everyone loved to talk and learn from each other about microbiome-related science, even the people focused mainly on AI.

In regard to the microbiome, many if not most talks incorporated, mentioned, or focused on the importance of this area of research.  Here are some of my high level notes related to the microbiome:

  • Phenotyping is a big area that we need to develop and are establishing right now.  The microbiome is an aspect of our phenotype and should be considered a distinct biomarker.
  • Mobile / site of study lab and metagenomic techniques are important to develop
  • We need to work together to share our genomic data, including metagenomic data
  • AI can be used to find new information where we never thought to look – this, in my opinion, will have implications in studying the massive network of interactions between microbes but also in discovery of new microbes among other things
  • Steve Miller’s (SURPI) talk was fascinating.  Without going into too many details he is moving forward clinically with using metagenomics for pathogen detection and diagnoses – something I believe will be the future of infectious disease diagnostics (or at least could be used to establish accurate SNP-based panels).  I’d highly recommend following his publications and well as Dr. Chiu.  I believe exciting things are coming from his lab in the next year or so http://profiles.ucsf.edu/steve.miller
  • Cannabis microbiome studies are paramount because microbes are the only risk for cannabis – and pesticides typically cannot be used in production

I hope this post was interesting – the conference surely was – I can’t wait to see the advances we’ve made presented there next year!

Edward Messick

May 17, 2017

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Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans.  Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)

Events and jobs

* Scientist – Microbiomics – ZymoResearch

PhD in microbiology – Université Catholique de Louvain (UCL)

Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT

General microbiome

* Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal

* Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE

Pregnancy and early life

PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes

The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.

 

Human oral microbiome

The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity

Human gut microbiome

Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN

The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience

The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress

* Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection

Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig

Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery

* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America

Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology

Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.

Animal experiments 

* Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology

Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science

The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research

Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology

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

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME

Plant, root, and soil microbiome

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal

A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data

Built environment (subways, indoor surfaces)

Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen

 

Probiotics / prebiotics

Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms

Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors

Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology

Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition

Bioinformatics

PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv

Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE

Techniques

Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews

Microbes in the news 

Cork scientists link gut bacteria to anxiety disorders

New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness

Optical nanofiber ‘hears’ bacteria swim, cancer cells move

Microbes on the market 

* BiomX raises $24 million to boost bacteria based drugs

 

Ed’s non-microbiology picks

Breakthrough in delirium research ‘solves 2,500-year-old mystery’

Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine

High levels of exercise linked to nine years of less aging (at the cellular level)

Migratory birds bumped off schedule as climate change shifts spring

PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members –  Megan S. Patterson – Human Kinetics

Edible insects could play key role in cutting harmful emissions – EurkAlert!

May 16, 2017

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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

May 15, 2017

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General microbiome

Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders – D Didier – Science of the Total Environment

Biodegradation and metabolic fate of levofloxacin via a freshwater green alga, Scenedesmus obliquus in synthetic saline wastewater – JQ Xiong – Algal Research

Ionic liquid-based reagents improve the stability of midterm fecal sample storage – L Hao – Journal of Microbiological Methods

Aerobic vaginitis: no longer a stranger – GGG Donders – Research in Microbiology –

The antibiotic resistome: gene flow in environments, animals and human beings – Y Hu – Frontiers of Medicine

 

Human respiratory microbiome

Neutrophil Extracellular Traps are associated with disease severity and microbiota diversity in Chronic Obstructive Pulmonary Disease – AJ Dicker – Journal of Allergy and Clinical Immunology

Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood – CY Chiu – Scientific Reports

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study – findings from Pretest 1 of the German National Cohort – MK Akmatov – Scientific Reports

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences – EK Cope – Microbiome

 

Animal microbiome

Response of turkeys fed wheat-barley-rye based diets to xylanase supplementation – G González Ortis – Animal Feed Science and Technology

Bifidobacterium CECT 7765 modulates early stress-induced immune, neuroendocrine and behavioral alterations in mice – A Moya Pérez – Brain, Behavior, and Immunity

 

Water and extremophile

UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities – MC Rasuk – Photochemistry and Photobiology

 

Techniques

A Tunable Protein Oscillator Controls Directional Movements In Myxococcus xanthus – M Guzzo – bioRxiv

Uncovering The Drivers Of Animal-Host Microbiotas With Joint Distribution Modeling – JR Bjork – bioRxiv

 

Microbes in news

Hospital superbugs – The Hans India

Market pressures and inadequate production are hampering access to essential antibiotics – EurekAlert

Learning the rules of antibiotics to make old drugs work on new bugs –  D Gitig – ARS Technica

Does Cooking Kill Probiotics? – KDA Traegner – Care2

Research team hopes to reduce size of tsunami using bacteria – The Mainichi

Antibiotic-resistant bacteria predate dinosaurs study reports – J Scalise – Science Recorder

Vexed childhood likely to cause irritable bowel syndrome (IBS) – NewsGram

Study suggests link between imbalanced gut microbiome and systemic sclerosis – UCLA Health

Microbiome leader Professor Borody joins researchers at the China Microbiota Transplantation Conference – MENAFN

How doctors could use viruses to kill drug-resistant bacteria – CTV News

Microbiologists find bugs, bacteria – and poo – lurking inside the UK’s cars – J Watkiss – Cambridge News

#Flint: As Mich. Gov. Snyder Signs $100,000,000 in Aid Into Law, Residents Warned Water Filters Harbor Bacteria – M Judge – The Root

Rutgers Researchers See Paper as a Defense Against Bacteria – J Murtha – Tap Into

Bacteria find clarified – S Silaitoga – The Fiji Times Online

The Filthiest, Most Bacteria Infested Places In Your Kitchen – Sky Valley Chronicle