Sometimes I come across a stock photo that is unintentionally funny. Here is another one.
An artist’s rendition of how microbes grow in the intestinal tract. Here you can see bacteria circling around microvilli. Or are they shiny pills in straight lines circling around sausages, or decaying fingers in plastic gloves?
Same villi but different bacteria. It’s a Fecal Microbiota Transplant!
And this one has no bacteria at all. I guess it represents the Germ Free Mouse.
There were almost no papers this weekend, so today’s digest is short.
Events and jobs
Assistant Professor of Horticulture – Plant Microbiome Research – University of Kentucky
Postdoctoral Scientist – Microbiome, Mycobiome, Mucosal Immunology – Weill Cornell Medicine, New York City
Water and extremophile microbiome
Whole community metagenomics in two different anammox configurations: process performance and community structure – Ananda S. Bhattacharjee – Environmental Science Technology
Phages and viruses
All of today’s posts are genome announcements:
Genomic Characterization of Three Melon Necrotic Spot Viruses Detected in Human Stool Specimens – Rachel Marine – Genome Announcements
Genome Sequence of Cauliflower Mosaic Virus Identified in Earwigs (Doru luteipes) through a Metagenomic Approach – Márcio Tadeu Godinho – Genome Announcements
Bioinformatics
metaSPAdes: a new versatile metagenomic assembler – Sergey Nurk – Genome Research
Science, publishing, and career
All biology is computational biology – Florian Markowetz – PLoS Biology
No – all biology is not computational biology – Jonathan Eisen – Tree of Life
A nice collection of articles this Sunday. We look at the potential benefits of Fecal Microbiota Transplantation, a number of probiotic articles, and microbiota manipulations in animals.
Events and jobs
Pharmaceutical Microbiology Laboratory Manager – Derbyshire / Edinburgh
General microbiome
Role of the small intestine, colon and microbiota in determining the metabolic fate of polyphenols – Gary Williamson – Biochemical Pharmacology
Free Radical Biology and Medicine
PREPRINT: Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics – Ashish A Malik – BioRxiv
Human respiratory microbiome
Review: Normal Oral Flora and the Oral Ecosystem – Lakshman Samaranayake – Dental Clinics of North America
Oral Bacterial Infections : Diagnosis and Management – Glendee Reynolds-Campbell – Dental Clinics of North America
Human gut microbiome
The gut microbiota metabolism of pomegranate or walnut ellagitannins yields two urolithin-metabotypes that correlate with cardiometabolic risk biomarkers: comparison between normoweight, overweight-obesity and metabolic syndrome – María V. Selma – Clinical Nutrition
Animal experiments
Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout – David Huyben –
Aquaculture
Host Intestinal Epithelium Derived Mirnas Shape The Microbiota And Its Implication In Cardiovascular Diseases – Lianbi Zhao – Journal of the American College of Cardiology
The effect of penicillin administration in early life on murine gut microbiota and blood lymphocyte subsets – Jaroslaw Daniluk – Anaerobe
Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw – E. Gozde Ozbayram – Anaerobe
Animal microbiomes
Hunting for healthy microbiomes: determining the core microbiomes of Ceratina, Megalopta, and Apis bees and how they associate with microbes in bee collected pollen – Peter Graystock – Conservation Genetics
Water and extremophile microbiome
Bacterial Microbiota Associated with the Glacier Ice Worm Is Dominated by Both Worm-Specific and Glacier-Derived Facultative Lineages – Takumi Murakami – Microbes and Environments
Food microbiology
Biopreservation potential of lactic acid bacteria from Andean fermented food of vegetal origin – Alba Yépez – Food Control
Metaproteomic analysis of microbiota in the fermented fish, Siniperca chuatsi – Chaofan Ji – LWT – Food Science and Technology
Probiotics / prebiotics
The use of potential probiotic Lactobacillus plantarum DW12 for producing a novel functional beverage from mature coconut water – Duangporn Kantachote – Journal of Functional Foods
Autochthonous lactic acid bacteria with probiotic aptitudes as starter cultures for fish-based products – Barbara Speranza – Food Microbiology
Functional probiotic products based on fermented buckwheat with Lactobacillus rhamnosus – Zuzana Matejčeková – LWT – Food Science and Technology
Techniques
Organism and Microbiome Analysis: Techniques and Implications for Chronic Rhinosinusitis – Ashleigh A. Halderman – Otolaryngologic Clinics of North America
Microbes in the news
Vitamin May be Key to Killing Cancer-Causing Bacteria Carole Ellis ContagionLive
Changes in gut microbiota after unhealthy diet may protect from metabolic disease – Medical Press
Porridge really is that good for you – The Independent
Antibiotics and the honeybee microbiome – Kerry Evans – Labroots
Research Fellow in Omics analysis – King’s College London – Apply by April 12, 2017
Postdoctoral Research Position in Marine Microbial Ecology – University of Southern Mississippi
Microbial Influences in Cardio–Metabolic Diseases – Rachel Petersen – New York Academy of Sciences
*Review: Microbiota: a key orchestrator of cancer therapy – Soumen Roy – Nature Reviews Cancer
*Review: Caenorhabditis elegans as a model for microbiome research – Fan Zhang – Frontiers in Microbiology
The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy
The Food Contaminant Deoxynivalenol Exacerbates the Genotoxicity of Gut Microbiota – Delphine Payros – mBio
Delayed utilization of some fast-fermenting soluble dietary fibers by human gut microbiota when presented in a mixture – Yunus E. Tuncil – Journal of Functional Foods
Deciphering the combinatorial influence of diet and the microbiota on experimental colitis – Sean R. Llewellyn – bioRxiv
The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish – Keaton Stagaman – ISME J
Comparison of bacterial populations in bedding material, on teat ends, and in milk of cows housed in compost bedded pack barns – R. L. Albino – Animal Production Science
Community analysis of microbial sharing and specialization in a Costa Rican ant–plant–hemipteran symbiosis – Elizabeth G. Pringle – Proceedings of the Royal Society Biological Sciences
Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment – Till Röthig – Scientific Reports
Root microbiota drive direct integration of phosphate stress and immunity – Gabriel Castrillo – Nature
Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment – G. Rodríguez-Caballero – Soil Biology and Biochemistry
Plant growth promoting rhizobacteria are more effective under drought: a meta-analysis – Rachel L. Rubin – Plant and Soil
Effect of biodynamic soil amendments on microbial communities in comparison with inorganic fertilization – Sibylle Faust – Applied Soil Ecology
Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico) – Miguel Medrano-Santillana – Extremophiles
Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica) – Rosabruna La Ferla – Microbial Ecology
Microbial communities of aquatic environments on Heard Island characterized by pyrotag sequencing and environmental data – Michelle A. Allen – Scientific Reports
A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater – Flavia Flaviani – Viruses
Microbial dynamics in anaerobic digestion reactors for treating organic urban residues during the start-up process – Rocio J. Alcántara-Hernández – Letters in Applied Microbiology
Variability of airborne bacteria in an urban Mediterranean area (Thessaloniki, Greece) – Savvas Genitsaris – Atmospheric Environment
*Review: A review of microscopy and comparative molecular-based methods to characterize “Plastisphere” communities – Caroline De Tender – Analytical Methods
*Review: Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data – Jian Xu – Engineering
*Review: Metaproteomic strategies and applications for gut microbial research – Mingming Xiao – Applied Microbiology and Biotechnology
Bacteria-Enriched Lotion Battles Skin Infections – Jenna Flannigan – Live Science
Frozen, Freeze-dried Products for Fecal Microbiota Transplantation as Effective as Fresh? – Pharmacy Times
Study by Irish scientists finds porridge to be good for the heart and gut – RTE
Certain Bacteria Within Gut Microbiome May Halt Inflammation Naturally, Study Says – Patricia Inacio – IBD News Today
Antibiotic overuse might be bad for bees – Mary Beth Griggs – Popular Science
Microbiome research Studies aim to help health, environment – David Wahlberg – The Times Record
My cats poop for science – Jonathan M. Giltin – ars Technica
Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News
Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo
A long review today, lots of environmental microbiome, a few papers on the methods, virus and microbial biotechnology sections and at the end a Nature announcement for transparency policy updates, aiming for better research reproducibility.
Oral Microbiome
Targeting of Streptococcus mutans Biofilms by a Novel Small Molecule Prevents Dental Caries and Preserves the Oral Microbiome
S. S. Garcia – Journal of Dental Research
Human nearly-sterile sites
Review: Microbiome effects on immunity, health and disease in the lung
Shakti D. Shukla – Clinical & Translational Immunology
Animal Microbiome
The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle
Sigmund Jensen – Marine Ecology
Animal experiments
Influence of dairy by-product waste milk on the microbiomes of different gastrointestinal tract components in pre-weaned dairy calves
Y. F. Deng – Scientific Reports
Antiprotozoal Effect of Saponins in the Rumen Can Be Enhanced by Chemical Modifications in Their Structure
Eva Ramos-Morales – Frontiers in Microbiology
Plant, root, and soil microbiome
Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands
Xiao-Bo Wang – The ISME Journal
Phosphate solubilizing microbes: an effective and alternative approach as
biofertilizers
Kumar Anand – International Journal of Pharmacy and Pharmaceutical Sciences
Master’s thesis: An Investigation Of The Tri-Trophic Interactions In
The Rhizosphere Of Medicago Truncatula Using A
Functional Microbiome Approach
Amanda Anne Rosier – University of Delaware
Water and extremophile microbiome
Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal
Jing Wang – Frontiers in Microbiology
Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis
Niranjan Nitin Parulekar – PlOS One
Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment
Daniel F. R. Cleary – Marine Ecology
Built environment
Impact of water heater temperature setting and water use frequency on the building plumbing microbiome
Pan Ji – The ISME Journal
Food microbiology
Effects of cellulase-producing bacteria on bacterial community structure and diversity during fermentation of Chinese liquor grains
J. H. Guo – The Journal of The Institute of Brewing
Microbial Biotechnology
The role of inoculum and reactor configuration for microbial community composition and dynamics in mainstream partial nitritation anammox reactors
Shelesh Agrawal – Microbiology Open
Diversity of Cultivable Protease-Producing Bacteria in Laizhou Bay Sediments, Bohai Sea, China
Yan Li – Frontiers in Microbiology
General Microbiology
Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria
Masahiro Kanno – Nature Communications
Short communication: Membrane vesicle-mediated bacterial communication
Masanori Toyofuku – The ISME Journal
Brief Report: Influence of the alginate production on cell-to-cell communication in Pseudomonas aeruginosa PAO1
Jiayue Yang – Environmental Microbiology Reports
Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio
Anne-Catherine Ahn – PlOS One
Review article: The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics
Caroline S. Rempe – Frontiers in Microbiology
Phages and viruses
Mini-Review: Driving HIV-1 into a Vulnerable Corner by Taking Advantage of Viral Adaptation and Evolution
Shigeyoshi Harada – Frontiers in Microbiology
Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome
Daniel Aguirre de Cárcer – PlOS One
Review: The concept of commensal viruses almost 20 years later: redefining borders in clinical virology
Diem-Lan Vu & Laurent Kaiser – Clinical Microbiology and Infection
Statistics / Bioinformatics
A fast small-sample kernel independence test for microbiome community-level association analysis
Xiang Zhan – Biometrics
Revealing large metagenomic regions through long DNA fragment hybridization capture
Cyrielle Gasc & Pierre Peyret – Microbiome
Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies
Sara Ciucci – Scientific Reports
Microbes in the news
Snow Bacteria, A Pandora’s Box? – GlacierHub
Phage therapy shown to kill drug-resistant superbug (link to original paper included) – HealthCanal
A Microbe Hunter Plies Her Trade In Space – NPR
Science, publishing, and career
Announcement: Transparency upgrade for Nature journals – Nature
Today’s digest is full of environmental, soil/plant/root, and water related studies among a few gut microbiome studies and some opinion pieces.
Events and jobs
Event: Gut Feeling – How bacteria influence our wellbeing – EMBL-EBI – 21-May-2017
Event: Meeting of the Microbiome Minds – Colorado State University
General microbiome
Opinion: The study of microbiota needs both microbiologists and medical doctors – Didier Raoult – CMI
Pregnancy and early life
Review: Distinct Roles of Cervical Epithelia and Stroma in Pregnancy and Parturition – Shanmugasundaram Nallasamy – Seminars in Reproductive Medicine (Thieme)
The shape of the microbiome in early life – Erika von Mutius – Nature Medicine
Multi-site human microbiome
Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment – Jeanette M. Carlson – J. Vis. Exp.
Human respiratory microbiome
Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa – Laurence Pages-Monteiro – PLOS One
Human skin microbiome
Review: Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome – Mohammed Ashrafi – Future Microbiology
Human vaginal microbiome
Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, an Sexually Transmitted Diseases – Felicia M. Lewis – Obstetrics & Gynecology
Women view key sexual behaviours as the trigger for the onset and recurrence of bacterial vaginosis – Jade E. Bilardi – PLOS One
Human oral microbiome
Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study – Sebastien Boutin – Frontiers in Microbiology
Human gut microbiome
*The altered gut microbiota in adults with cystic fibrosis – D.G. Burke – BMC Microbiology
Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: a randomised crossover study – Lee Kellingray – Molecular Nutrition & Food Research
Gastric Acid Suppression Is Associated with an Increased Risk of Adverse Outcomes in Inflammatory Bowel Disease – Shah R – Digestion
NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology
Gut microbiome diversity and high fibre intake are related to lower long term weight gain – Menni C – International Journal of Obesity
We are not alone: a case for the human microbiome in extra intestinal diseases – S. Shivaji – Gut Pathogens
The intestinal microenvironment in sepsis – Katherine T Fay – BBA – Molecular Basis of Disease
The Gut Microbiome and Its Role in Cardiovascular Diseases – W. H. Wilson Tang – Circulation
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion – Wei Sun – Bioresource Technology
Dietary Broccoli Alters Rat Cecal Microbiota to Improve Glucoraphanin Hydrolysis to Bioactive Isothiocyanates – Xiaoji Liu – Nutrients
Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens – Eduardo Crisol-Martinez – PeerJ
Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice – Paul M. Ryan – Microbiome
Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome – Daniel Aguirre de Cárcer – PLOS One
Animal microbiome (for animals in the wild)
Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time – Sheila Torres – PeerJ
Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens – Carolina Ramirez – Frontiers in Microbiology
Use of signature-tagged mutagenesis to identify genes associated with colonization of sheep by E. coli O157:H7 – Nancy A. Cornick – Veterinary Microbiology
The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology
The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens – Gerard M. Murray – PLOS One
Plant, root, and soil microbiome
Analysis of microbiota involved in the aged natural fermentation of indigo – Takahiro Okamoto – World Journal of Microbiology and Biotechnology
Microbial solvent formation revisited by comparative genome analysis – Anja Poehlein – Biotechnology for Biofuels
Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities – Wepking, C – Proceedings of the Royal Society B-Biological Science
Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms – Tobias Weil – Microbiome
Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW) – Chunkai Huang – Biochemical Engineering Journal
Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog – Tomasz Mieczan – European Journal of Protistology
The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands – Dominquez MT – Sci Total Environment
Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar – Jaiswal AK – Scientific Reports
Growth and 137Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain – Salem Djedidi – Journal of Environmental Radioactivity
Antibiotic mixture effects on growth of the leaf-shredding stream detritivore Gammarus fossarum – Mirco Bundschuh – Ecotoxicology
Microbial community changes during different empty bed residence times and operational fluctuations in an air diffusion reactor for odor abatement – Elisa Rodriguez – Science of the Total Environment
Response of indigenously developed bacterial consortia in progressive degradation of polyvinyl chloride – Mohammad S Anwar – Protoplasma
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Conference: Effects of simulated deep-sea mining impacts on microbial communities and functions in the DISCOL experimental area – Vonnahme, T – EU FP7 MIDAS final meeting,
Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities – Wei Xing – Journal of Environmental Sciences
PrePrint: Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive2 presence of metal resistance genes – Ankita Kothari – bioRxiv
Climate, soil and plant functional types as drivers of global fine-root trait variation – Gregoire T. Freschet – Journal of Ecology
Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function – Konstantin Gavazov – Science of the Total Environment
Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes – Emily B. Graham – Environmental Microbiology
Review: Microbiome involved in microbial electrochemical systems (MESs): A review – Saratale RG – Chemosphere
Chapter Four – Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology
The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings – Xinli An – Environmental Science and Pollution Research
Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis – Niranjan Nitin Parulekar – PLOS One
Food microbiology
Editorial: Inner Workings: Fermented foods offer up a versatile microbial model system – Alla Katsnelson – PNAS
Probiotics / prebiotics
News article: IBS cure? Probiotics could REDUCE irritable bowel syndrome symptoms AND stress – Olivia Lerche – express.co.uk
Bioinformatics
Applied Metagenomics for Biofuel Development and Environmental Sustainability – Antonio Djalma Nunes Ferraz Junior – Advances of Basic Science for Second Generation Bioethanol from Sugarcane
DEMOGRAPHICS INDUCE EXTINCTION OF DISEASE IN AN SIS MODEL BASED ON CONDITIONAL MARKOV CHAIN – XIAOFENG LUO – Journal of Biological Systems
Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters – Yu Shang – PLOS One
Techniques
Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods – Beibei Wang – Science of The Total Environment
*How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity – Camille Truong – New Phytologist
Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research – Shaocun Zhang – Frontiers in Cellular and Infection Microbiology
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods
Ed’s non-microbiology picks (news articles)
First Time Ever: Gene Therapy Reverses Sickle Cell Disease
Earth’s oceans are warming 13% faster than thought, and accelerating
MIT researchers create new form of matter
Gene therapy treats muscle-wasting disease in dogs
Quite a few picks from Nature Reviews Microbiology as a fresh issue was released today. We also see some nice papers on microbial diseases. The post author’s highlight today goes to the interesting review from Thurber et al. on the virus section: Virus–host interactions and their roles in coral reef health and disease. Have a great week!
General microbiome
Review: Timing the day: what makes bacterial clocks tick?
Carl Hirschie Johnson – Nature Reviews Microbiology
Microbial diseases
Evolutionary Constraints on the Norovirus Pandemic Variant GII.4_2006b over the Five-Year Persistence in Japan.
Hironori Sato – Frontiers in Microbiology
Review: Anti-trypanosomatid drug discovery: an ongoing challenge and a continuing need Mark C. Field – Nature Reviews Microbiology
Commentary: The chicken or the egg? Changes in oral microbiota as cause or consequence of mucositis during radiation therapy
Stephen T. Sonis – EBioMedicine
Commentary: From bugs to brains: The microbiome in neurological health
Kyla A. McKay – Multiple Sclerosis and Related Disorders
Commentary: A Microbiome Foundation for the Study of Crohn’s Disease
Dirk Gevers – Cell Host & Microbe
Human gut microbiome
European consensus conference on faecal microbiota transplantation in clinical practice
Giovanni Cammarota – Gut
Commentary: Microbe Hunting Hits Home
Ivaylo I. Ivanov – Cell Host & Microbe
Commentary: Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control
Peter J. Turnbaugh – Cell Host & Microbe
Review: The gut microbiome and microbial translocation in multiple sclerosis
Ali Mirza – Clinical Immunology
Plant, root, and soil microbiome
COREXIT 9500 enhances oil biodegradation and changes microbial community structure of oil-enriched microcosms
Techtmann SM – Applied Environmental Microbiology
Soil formation and initial microbiological activity on a foreland of an Arctic glacier (SW Svalbard)
Dorota Górniak – Applied Soil Ecology
The response of soil microbial diversity and abundance to long-term application of biosolids
Abdul-Wahab Mossa – Environmental Pollution
Comparative analysis of metagenomes of Italian top soil improvers
Federica Gigliucci – Environmental Research
Water and extremophile microbiome
Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms
Weil T. – Microbiome
Built environment
Bacterial diversity on rock surface of the ruined part of a French historic monument: The Chaalis abbey
Agnes Mihajlovski – International Biodeterioration & Biodegradation
Food microbiology
Diversity of the dominant bacterial species on sliced cooked pork products at expiration date in the Belgian retail
Wim Geeraerts – Food Microbiology
Biotechnology
Agar-degrading bacteria isolated from Antarctic macroalgae – Folia Microbiologica
Roxana Alvarado & Sergio Leiva
Exploring the Antimicrobial and Antitumor Potentials of Streptomyces sp. AGM12-1 Isolated from Egyptian Soil
Maged S. Ahmad – Frontiers in Microbiology
Phages and viruses
Review: Virus–host interactions and their roles in coral reef health and disease
Rebecca Vega Thurber – Nature Reviews Microbiology
Review: Mimivirus: leading the way in the discovery of giant viruses of amoebae
Phillippe Colson – Nature Reviews Microbiology
Change in Emiliania huxleyi Virus Assemblage Diversity but Not in Host Genetic Composition during an Ocean Acidification Mesocosm Experiment
Highfield A. – Viruses
Techniques and methods
Review: Current state and applications of microbial genome‐scale metabolic models
Won Jun Kim – Current Opinion in Systems Biology
A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Lee S. Katz – Frontiers in Microbiology
FurIOS: A Web-Based Tool for Identification of Vibrionaceae Species Using the fur Gene
Henrique Machado – Frontiers in Microbiology
Research Highlights (a few from today’s issue of Nature Reviews Microbiology):
Bacterial Physiology: Treadmilling runs bacterial division – Ashley York
Symbiosis: Wolbachia’s matchmaking secret revealed – Ursula Hofer
Bacterial Physiology: Persisters running out of energy – Andrea Du Toit
Bacterial pathogenesis: Hitching a ride with DCs – Yvonne Bordon
Microbes in the news
Light rain can spread soil bacteria far and wide, study finds
Science Daily – Paper by Young Soo Joung available here.
Novel antibiotic combination therapy overcomes deadly drug-resistant bacteria
Case Western Reserve University – EurekAlert!
Researchers track spread of multidrug-resistant bacteria in hospital sinks
University of Virginia – Paper by Kotay S. available here.
Microbes on the market
CRISPR patent results
Shimona Starling – Nature Reviews Microbiology
Global Microbiology Testing Market Present Scenario and Growth Prospects 2016-2021
medGadget
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis – M Pammi – Microbiome
Is the 25 year hepatitis C marathon coming to an end to declare victory? – Khulood T Ahmed – bioRxiv
Natural antimicrobial peptide complexes in the fighting of antibiotic resistant biofilms: Calliphora vicina medicinal maggots – N Gordya – PLoS One
Complement inhibition by Sarcoptes scabiei protects Streptococcus pyogenes – An in vitro study to unravel the molecular mechanisms behind the poorly understood predilection of S. pyogenes to infect mite-induced skin lesions – PM Swe – PLoS Neglected Tropical Disease
CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis – C Barthels – Nature Communications
Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal – I Khan – Medical Principles and Practice
Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy
*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology
*Review: Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy – UC Ghoshal – Gut and Liver
Beyond Digestion: The Pancreas Shapes Intestinal Microbiota and Immunity – H Tilg – Cell Metabolism
Melatonin prevents obesity through modulation of gut microbiota in mice – P Xu – Journal of Pineal Research
Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats – Vientós-Plotts AI – PLoS One
A gut reaction: The combined influence of exercise and diet on gastrointestinal microbiota in rats – R Batacan – Journal of Applied Microbiology
Parasitism perturbs the mucosal microbiome of Atlantic Salmon – MS Llewellyn – Scientific Reports
Probiotic efficiency of Bacillus sp. in Labeo rohita challenged by Aeromonas hydrophila: assessment of stress profile, haemato-biochemical parameters and immune responses – A Nandi – Aquaculture Research
Simplified and representative bacterial community of maize roots – B Niu – PNAS
Impact of three different fungicides on fungal epi- and endophytic communities of common bean (Phaseolus vulgaris) and broad bean (Vicia faba) – R Prior – Journal of Environmental Science and Health, Part B
Thermophilic microorganisms in arable land around medieval archaeological sites in Northern Caucasus, Russia: Novel evidence of past manuring practices – E Chernysheva – Geoarchaeology
In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – AR Rowe – Environmental Microbiology
Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – M Kwon – Environmental Microbiology
A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv
Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis – L D’Amico – Lab on a Chip
A fast small-sample kernel independence test for microbiome community-level association analysis – X Zhan – Biometrics
Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health – Leulier F – Cell Metabolism
Phage therapy is highly effective against chronic lung infections with Pseudomonas aeruginosa – EM Waters – Thorax
*Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology
Meibomian gland disease and the microbiotome: is it time for ocular probiotics? – S Watson – Clinical & Experimental Ophthalmology
*Review: Infection in Organ Transplantation – JA Fishman – American Journal of Transplantation
Azole resistance in Candida albicans from animals: Highlights on efflux pump activity and gene overexpression – MFG Rocha – Mycoses
The Synonymy of the Toxic Dinoflagellates Prorocentrum mexicanum and P. rhathymum and the Description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae) – F Gomez – Journal of Eukaryotic Microbiology
Gut microbiota analysis in rats with methamphetamine-induced conditioned place preference – T Ning – bioRxiv
What is Metagenomics? – Y Smith – News Medical
UCC researchers discover weapon to fight antibiotic resistance – D Ahlstrom – The Irish Times
Community gets an eye-opening lesson in human microbiome and our western lifestyle – C MacDonald – UToday
Microbiome Research Symposia Review: Microbiome and Diseases – J Phelan – Taconic Biosciences
Q&A with Zeus Capital’s Dr Gary Waanders: Live Biotherapeutics & 4D Pharma PLC (LON:DDDD) – A Stone – Directors Talk Interviews
Do You Have the Guts to Perform? Microbial Balance, the Brain and Athletic Performance – SJ Hewlings – Natural Products Insider
New probiotics meant to balance microbial, fungal communities in gut – H Schultz – NUTRAingredients
Google Leads $51M Investment in Startup Tackling Drug-Resistant Bacteria – R Bushey – R & D
Your bacteria-ridden makeup could be the reason you keep getting sick – A Mulvaney – Independent
Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.
General microbiome
The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology
The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology
Oral and nasal microbiome
Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Marino PJ. Journal of Critical Care
Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders
Gut microbiome
The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology
Water and extremophile microbiome
Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin
Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology
Probiotics
Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology
Techniques
Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology
Plant, root, and soil microbiome
How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research
Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology
Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA. DeCrappeo NM. Plant and Soil
Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils
Head, Microbiome Discovery Research – Johnson & Johnson
Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine
Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome
Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology
Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology
Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog
Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology
Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems
The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere
*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology
Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology
Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology
Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology
Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology
Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety
Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology
Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology
Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research
Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE
Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere
REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv
Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome
How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ
Gut bacteria affect intestines and brain in IBS patients – Medical News Today
Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News
Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine
Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist
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