Category Archives: General Microbiome

March 18, 2017

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Events and jobs

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

General microbiome

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

Human respiratory microbiome

The relationship between nasopharyngeal CCL5 and microbiota on disease severity among infants with bronchiolitis – Kohei Hasegawa – Allergy

Human gut microbiome

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

Animal experiments

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

Animal microbiome

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

Built environment

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

Techniques

*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

Microbes in the news

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

Microbes on the market

Seres doubles down on a microbiome do-over as the FDA clears a make-or-break study – John Carroll – Endpoint News

Bacteria Hysteria

Revealed: Which supermarket’s chicken is most likely to contain food poisoning bacteria? – Tom Belger – Liverpool Echo

March 17, 2017

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Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day.In the first highlighted paper the authors present the structural basis of the day-night transition in a cyanobacterial circadian clock. The second highlighted paper evaluated the effects of antibiotic treatment on the honeybee gut microbiome. The authors found that exposure to antibiotics significantly alters the honeybee gut microbial community structure and leads to decreased survival.

General microbiome

Biohybrid Microtube Swimmers Driven by Single Captured Bacteria – Morgan M. Stanton – Small

Structural basis of the day-night transition in a bacterial circadian clock – Roger Tseng – Science

Pregnancy and early life

Breast Milk Polyamines and Microbiota Interactions: Impact of Mode of Delivery and Geographical Location – C Gómez-Gallego  – Annals of Nutrition and Metabolism

 
Human respiratory microbiome

Modulation of behaviour and virulence of a high alginate expressing Pseudomonas aeruginosa strain from cystic fibrosis by oral commensal bacterium Streptococcus anginosus – RD Waite  – PLOS One

Human gut microbiome

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism – Simon Nicolas – Molecular Systems Biology

Fecal microbiota transplantation induces hepatitis B virus e-antigen (HBeAg) clearance in patients with positive HBeAg after long-term antiviral therapy – Yan-Dan Ren – Hepatology

The Microbiome and Host Behavior – Vuong HE – Annual Review of Neuroscience

Nonalcoholic Fatty Liver Disease, the Gut Microbiome, and Diet – Zeinab Mokhtari – Advances in Nutrition

Animal experiments

Intestinal transcriptome modulation by functional diets in rainbow trout: A high-throughput sequencing appraisal to highlight GALT immunomodulation – Ana Teresa Gonçalves – Fish & Shellfish Immunology

Effects of Gliadin consumption on the Intestinal Microbiota and Metabolic Homeostasis in Mice Fed a High-fat Diet – Li Zhang – Scientific Reports

Oral administration of synthetic porcine beta-defensin-2 improves growth performance and cecal microbial flora and down-regulates the expression of intestinal toll-like receptor-4 and inflammatory cytokines in weaned piglets challenged with enterotoxigenic Escherichia coli – Zhiru Tang – Animal Science Journal

RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro – Elena Herrmann – BioMed Research International

Animal microbiome

Antibiotic exposure perturbs the gut microbiota and elevates mortality in honeybees – Kasie Raymann – PLOS Biology

Plant, root, and soil microbiome

Accessing the Carbofuran Degradation Ability of Cultures From Natural River Biofilms in Different Environments – Chien-Jung Tien – CLEAN – Soil, Air, Water

Impact of Agri-Usable Nanocompounds on Soil Microbial Activity: An Indicator of Soil Health – Priyanka Khati – CLEAN – Soil, Air, Water

Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites – Mitja N.P. Remus-Emsermann – SIGS Standards in Genomic Sciences

Is the methanogenic community reflecting the methane emissions of river sediments?—comparison of two study sites – Prem Prashant Chaudhary – Microbiology Open

Water and extremophile microbiome

Characterizing and predicting cyanobacterial blooms in an 8-year amplicon sequencing time-course – Nicolas Tromas – bioRxiv

Effect of pesticides on microbial communities in container aquatic habitats – Ephantus J. Muturi – Scientific Reports

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – KI Twing – Frontiers in Microbiology

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer – Ping Zhang – Environmental Science & Technology

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment – Pauliina Rajala – Frontiers in Microbiology

Built environment

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community – Fei Pan – Scientific reports

Probiotics / prebiotics

Achieving High Yield of Lactic Acid for Antimicrobial Characterization in Cephalosporin-Resistant Lactobacillus by the Co-Expression of the Phosphofructokinase and Glucokinase – Gong Y – Journal of Microbiology and Biotechnology

Phages and viruses

Inflammation boosts bacteriophage transfer between Salmonella spp.– Médéric Diard – Science

Bioinformatics

microclass: an R-package for 16S taxonomy classification – Kristian Hovde Liland – BMC Bioinformatics

Microbes in the news

Team finds new way that bacteria lay siege to neighboring cells by hijacking two factors involved in protein synthesis – Phys.Org

 

March 15, 2017

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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

World’s oldest plant fossil discovered by student pushes evolution of complex life back 400 million years

 

March 14, 2017

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A short Digest today, many news pieces, a new bioinformatics tool from the Rob Knight lab, and papers on genome-scale metabolic models.

General microbiology

Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance – Jonathan M. Stokes – Nature Microbiology

Press: Antiprotozoal drug, Pentamidine, used with antibiotics effective against ‘superbugs’: McMaster research – Outbreak News Today

Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis – Gang Luo – Environmental Science & Technology

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families – Ana Popovic – Scientific Reports

Animal experiments

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis – Huijuan Jia – Scientific Reports

Animal microbiome

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants – Jon G. Sanders – bioRxiv

Plant, root, and soil microbiome

Book chapter – Chapter 16: Growth Promotion Features of the Maize Microbiome: From an Agriculture Perspective – Ubiana de Cássia Silva – Plant-Microbe Interaction: An Approach to Sustainable Agriculture

Metabolomics

Evaluating the Capabilities of Microbial Chemical Production Using Genome-Scale Metabolic Models – Hugh M. Purdy and Jennifer L. Reed – Current Opinion in Systems Biology

Model-based quantification of metabolic interactions from dynamic microbial-community data – Mark Hanemaaijer – PLoS One

Review: Current state and applications of microbial genome-scale metabolic models – Won Jun Kim – Current Opinion in Systems Biology

Bioinformatics

Deblur: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping – Amnon Amir – mSystems

Deblur: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns – Amnon Amir – mSystems

Microbes in the news

Common Bacteria May Control Disease-Carrying Insects – Jessica Berman – VOA

Study finds new evidence that viruses and bacteria may be found in some public water supply wells – Home Town Source

Your mobile phone has more germs than a toilet seat, but should you worry? – The News Minute

Mining nature for the next groundbreaking antibiotic – Julia Franz – PRI

March 12, 2017

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The first day of daylight saving time in the USA and if your Sunday morning started in a (relative) darkness just read about the viruses in the oceanic basement.  Then find out why yogurt can help your mood.  More interesting papers about the gut-brain connection, a microbiota-centric view of diseases of the upper gastrointestinal tract, microbiome and Type 1 & 2 diabetes, and a new method of detecting bacteria during root canal treatments.

General microbiome

Review: Calling All Hosts: Bacterial Communication In Situ – Jessica L. Cleary – Chem

Gut-Brain connection

The Association Between Temperament and Microbiota in Healthy Individuals: A Pilot Study  – Kim H – Psychosomatic medicine

Gut-brain actions underlying comorbid anxiety and depression associated with inflammatory bowel disease –  Aine Abautret-Daly -Acta Neuropsychiatrica

Human gut microbiome

A microbiota-centric view of diseases of the upper gastrointestinal tract – Gerardo Nardone- Gastroenterology & Hepatology

Review: Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine – Jens Nielsen – Cell Metabolism

Intestinal Microbiota in Type 2 Diabetes and Chronic Kidney Disease – A. Sabatino – Current Diabetes Reports

The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins  – Elsa Pinto – Microbiology

Therapeutic efficacy of oral immunization with a non-genetically modified Lactococcus lactis-based vaccine CUE-GEM induces local immunity against Helicobacter pylori infection – Wei Liu – Applied Microbiology & Biotech

Water and extremophile microbiome

Viruses in the Oceanic Basement – OD Nigro -MBio

Models

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium -Yuli Wang – Biomaterials

Built environment

Review: Microbiome involved in microbial electrochemical systems (MESs): Rijuta G Saratale- Chemosphere

Microbes in the news

Probiotic found in yogurt can reverse depression symptoms, Researchers at the University of Virginia School of Medicine finds

New method of detecting bacteria during root canal treatments 

March 11, 2017

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General microbiome

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

 

Human skin microbiome

Prenatal antibiotics and atopic dermatitis among 18-month old children in the Danish National Birth Cohort – S Timm – Clinical and Experimental Allergy

 

Human vaginal microbiome

*Review: Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, and Sexually Transmitted Diseases – FM Lewis – Obstetrics and Gynecology

 

Human gut microbiome

*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

 

Animal microbiome

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

 

Plant, root and soil microbiome

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

 

Water and Extremophiles

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

 

Transcriptomics and Proteomics

A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide – Sardar Karash – bioRxiv

 

Techniques

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

 

More microbes

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

 

Microbes in news

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

March 9, 2017

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A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian

March 8th, 2017

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Today is the International Women’s Day! This is a day for awareness about the importance of support equality in rights and opportunities for women.

About International Women’s Day

Gender at Nature Ecology & Evolution

Helping women progress in traditionally male dominated fields

Rosalind Franklin: Navigating workplace politics to gain recognition in science

International Women’s Day 2017: pursuing a career in science

BMC Series Blog: International Women’s Day

Events and Webinars

3rd Annual Translational Microbiome Conference, April 12-13, 2017 in Boston, MA

Webinar: Nomadic nanopore sequencing of metagenomes with the MinION

Microbiome research

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island – Jiro Nakayama – Frontiers in Microbiology

Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora – Shirali Pandya – Journal of Medical Microbiology

Effect of predatory bacteria on the gut bacterial microbiota in rats – Kenneth Shatzkes – Scientific Reports

Methods article: Critical Issues in Mycobiota Analysis – Bettina Halwachs – Frontiers in Microbiology

Microbiota alteration is associated with the development of stress-induced despair behavior – Ioana A. Marin – Scientific Reports

Review: Beyond Hygiene: Commensal Microbiota and Allergic Diseases – Sung-Wook Hong – Immune Network

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens – Sandra Pinto-Cardoso – Scientific Reports

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Probiotics

Lactobacillus rhamnosus GG supernatant enhance neonatal resistance to systemic Escherichia coli K1 infection by accelerating development of intestinal defense – Xiaolong He – Scientific Reports

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat  – Elaine Patterson – Scientific Reports

Timely use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: a Systematic Review with Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Metagenomics

Review: Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Yu – bioRxiv

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Pathogens

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus – Ilse Vandecandelaere – PLoS ONE

Review: Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium – David Taylor-Robinson – Research in Microbiology

Case report: Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus – Emilie Sitterlé – Frontiers in Microbiology

The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes – Helena M.B. Seth-Smith – Genome Biology and Evolution

Extremophiles

Reducing salinity by flooding an extremely alkaline and saline soil changes the bacterial community but its effect on the archaeal community is limited – Arit S de León-Lorenzana – Frontiers in Microbiology

Early life

Paleoproterozoic sterol biosynthesis and the rise of oxygen – David A. Gold – Nature

March 7, 2017

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Events and jobs

Professor Of Microbiology – University of Western Australia – Last date: Friday, May 12, 2017

 

General microbiome

Biofilms: Microbial Cities Wherein Flow Shapes Competition – Su Chuen Chew – Trends in Microbiology

*Review: Critical Streptococcus suis Virulence Factors: Are They All Really Critical? – Mariela Segura – Trends in Microbiology

*Review: Collective Infectious Units in Viruses – Rafael Sanjuán – Trends in Microbiology

*Review: KSHV microRNAs: Tricks of the Devil – Jie Qin – Trends in Microbiology

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

 

Human oral microbiome

Chemotherapeutic decontamination of dental implants colonized by mature multispecies oral biofilm – Sebastien Dostie – Journal of Clinical Periodontology

 

Human vaginal microbiome

The presence of vaginal Lactobacillus species does not contribute to a measureable difference in amniotic fluid lactate levels collected from the vaginal tract of laboring women – Beverley Hall – AOGS

 

Animal microbiome

Effects of Pediococcus pentosaceus supplementation on growth performance, intestinal microflora and disease resistance of white shrimp, Litopenaeus vannamei – M. Adel – Aquaculture Nutrition

 

Plant, root and soil microbiome

Effects of the Inoculant Strain Pseudomonas sp. SPN31 nah + and of 2-Methylnaphthalene Contamination on the Rhizosphere and Endosphere Bacterial Communities of Halimione portulacoides – V Oliveira – Current Microbiology

Microbial-enhanced lindane removal by sugarcane (Saccharum officinarum) in doped soil-applications in phytoremediation and bioaugmentation. – J A Salam – Journal of Environmental Management

Immobilization remediation of Cd-polluted soil with different water condition – J Li – Journal of Environmental Management

Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat – Yudi M Lozano – New Phytologist

A long-term study of burning effects on a plant pathogen in tallgrass prairie – S. P. Dendy – Plant Pathology

 

Water and extremophile microbiome

Temperature–nutrient interactions exacerbate sensitivity to warming in phytoplankton – Mridul K. Thomas – Global Change Biology

 

Metagenomics and Bioinformatics

Omics for Understanding the Gut-Liver-Microbiome Axis and Precision Medicine – Jag Khalsa – Clinical Pharmacology in Drug Development

 

Techniques

Drug–Drug Interactions and Diagnostics for Drug Users With HIV and HIV/HCV Coinfections: Introduction – Jag H. Khalsa – Clinical Pharmacology in Drug Development

 

More Microbes

Influence of key physicochemical and hydrodynamic specifications of three packing materials on both performance and bacterial community structure of gas-biofilters – Luc Malhautier – Journal of Chemical Technology and Biotechnology

Metabolic coupling in bacteria – Shraddha Shitut – bioRxiv

Fungal derived 15-keto-prostaglandin E2 and host peroxisome proliferator-activated receptor gamma (PPAR-γ) promote C. neoformans growth during infection – Robert J Evans – bioRxiv

 

Microbes in news

Parkinson’s Linked to Changes in Gut Bacteria – T Pedersen – Psych Central

3.77 billion year old bacteria fossil may be Earth’s oldest, scientists say – J Leone – Journal-News

Bacterial vaginosis: A common health concern women must not take lightly – S Kantengwa – The New Times

This Drugstore Face Cream Is A Game Changer For People With Dry Skin – L Lebsack – Refinery29

UT researchers take new approach in cholera prevention – C Deangelis – The Blade

Bacteriophages Offer Potential for Helping Reduce Dependence on In-Feed Antibiotics – The Pig Site

Exciting Microbe Research? Temper That Giddy Feeling in Your Gut – AE Carroll – The Upshot

Human Microbiome Market Worth 899.1 Million USD by 2025 – PRNewswire

Native Squid Used in Research of Environment and Human Health – Maui Now

March 5, 2017

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Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet.  Black carbon, one of the main components of air pollution,  is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival.  A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk.  And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Pregnancy and early life

Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicenter inception cohort study – Subra Kugathasan – The Lancet

Multi-site human microbiome

Humans are colonized by many uncharacterized and highly divergent microbes -Mark A. Kowarsky -bioRxiv

Human respiratory microbiome

Air pollution alters Staphylococcus aureus and Streptococcus pneumonia biofilms, antibiotic tolerance and colonization – Shane J. K. Hussey – Journal of Environmental Microbiology

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.