April 25, 2018

Method for cell-free transcription-translation to characterize nonmodel bacteria, a review of bile acid metabolism by the gut microbiota, altitude affects on the lizard intestinal microbiota.

Events and jobs

Research Applications Programmer – UC San Diego Center for Microbiome Innovation

Pregnancy and early life

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure – Cecilie Dahl – International Journal of Epidemiology

Multi-site human microbiome

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics – Aline C Freitas – PLOS ONE

Human skin microbiome

The Skin Commensal Yeast Malassezia globosa Thwarts Bacterial Biofilms to Benefit the Host – Giuseppe Ianiri – Journal of Investigative Dermatology

Human gut microbiome

A repeat offender: recurrent extraintestinal Clostridium difficile infection following fecal microbiota transplantation – Bradley J Gardiner – Anaerobe

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology

Review: Metabolism of hydrogen gases and bile acids in the gut microbiome – Phillip B Hylemon – FEBS Letters

Animal experiments

Beneficial effects of a selected probiotic mixture administered to high fat-fed mice before and after the development of obesity – Marianna Roselli – Journal of Functional Foods

Emodin ameliorates ulcerative colitis by the flagellin-TLR5 dependent pathway in mice – Shuang Luo – International Immunopharmacology

Pre-print: Probiotics enhance susceptibility of mice to cryptosporidiosis – Bruno C M Oliveira – bioRxiv

Review: Using murine colitis models to analyze probiotics–host interactions – Rebeca Martín – FEMS Microbiology Reviews

Dietary Clostridium Butyricum induces a phased shift in fecal microbiota structure and increases the acetic acid-producing bacteria in a weaned piglet model – Jie Zhang – Journal of Agricultural and Food Chemistry

Animal microbiome

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants – Simon H Williams – mBio

Glucocorticoids modulate gastrointestinal microbiome in a wild bird – José C Noguera – Royal Society Open Science

Plant, root, and soil microbiome

Insights to plant‐microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes – Lukas Wille – Plant, Cell & Environment

Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and in Maize Seeds – Subbaiah Chalivendra – Toxins

Root diameter predicts the extramatrical hyphal exploration distance of the ectomycorrhizal fungal community – Weile Chen – Ecosphere

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities – Xiaohui Wang – AMB Express

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem – Zhiliang Ma – PLOS ONE

Pre-print: Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing – Luhua Yao – PeerJ

Water and extremophile microbiome

Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity – Lea Steinle – The ISME Journal

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels – Mia M Bengtsson – Molecular Ecology

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan – Kshitij Tandon – Microbes and Environments

Microbes in space

Book chapter: The Search for Signatures of Life and Habitability on Planets and Moons of Our Solar System – Oliver Funke – Biological, Physical and Technical Basis of Cell Engineering

Bioinformatics

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information – Stefan Janssen – mSystems

Pre-print: Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction – S Michelle Todd – bioRxiv

Pre-print: FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization – Blake E Sanders – bioRxiv

Comparison of normalization methods for the analysis of metagenomic gene abundance data – Mariana Buongermino Pereira – BMC Genomics

Pre-print: Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences – Robert C Edgar – PeerJ

Pre-print: Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data – Iris Holmes – PeerJ

Metabolomics

Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal – Andrea Rodriguez-Martinez – Current Protocols in Bioinformatics

Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage – Panagiotis A Vorkas – Metabolic Profiling

Review: Current and future perspectives of functional metabolomics in disease studies–A review – Min Yan – Analytica Chimica Acta

Techniques

Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria – Simon J Moore – PNAS

Pre-print: Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products – Zhengyao Xue – bioRxiv

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut – Eleanor Jameson – Methods

More microbes

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms – Emilia Palazzotto – Current Opinion in Microbiology

Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology

Microbes in the news

Wiping out the gut microbiome could help with heart failure – ScienceDaily

How bacteria are changing your mood – James Gallagher – BBC News

Drinkers have more bad mouth bacteria, study finds – Susan Scutti – CNN

$11.2 million federal grant to support microorganism and disease research – EurekAlert

A Surprising Way Dogs Are Similar to Humans – Julissa Treviño – Smithsonian

Could Your Diet Be The Cause Of Your Arthritis Pain? – Robert Glatter – Forbes

Growing evidence that probiotics are good for your liver – ScienceDaily

Just being outside can improve your psychological health, and maybe your physical health too – Zoë Schlanger – Quartz

Role of Mosquito Microbiota in Reducing Malaria Transmission – JoAnna Pendergrass – American Veterinarian

A search for some of Earth’s most extreme creatures in the West Coast’s deepest underwater canyon – Amina Khan – Los Angeles Times

How plastic-eating bacteria actually work—a chemist explains – Emily Flashman – Phys.org

Far-red fluorescent silk can kill harmful bacteria as biomedical and environmental remedy – Kayla Wiles – Phys.org

Antibiotic-resistant bacteria cross oceans hidden in cargo ships – Inga Vesper – New Scientist

Fight against Zika, dengue get boost from reliable spread of bacteria – EurekAlert

Microbes on the market

Rebiotix Presents Posters at ECCMID 2018 Highlighting Microbiome Health Index™ Value Potential and RBX2660 Phase 2 Clinical Program Data – PR Newswire

Kaleido Biosciences Announces Appointment of Joshua Brumm as Chief Financial Officer – Citizen Tribune

Science, career, and publishing

Pre-print: Aligning interests: Integrating Citizen Science Efforts into Schools Through Service Requirements – Ginger Tsueng – bioRxiv

Randomly auditing research labs could be an affordable way to improve research quality: A simulation study – Adrian G Barnett – PLOS ONE

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April 19, 2018

Today we have a few day’s worth of microbiome science to chew on… some interesting skin microbiome studies, bioinformatics publications, and our typical servings of gut /plant-root-soil/animal/water-extremophiles/general microbiome studies.  Dig in!

Events and jobs

Manager, QC Microbiology – Celgene – Phoenix, AZ

Pathology and Microbiology & IPID Graduate Student Research Seminar – UNMC

General microbiome

Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin – Jia Hui Chai – PLOS ONE

* [pre-print] Phylogenetically novel uncultured microbial cells dominate Earth microbiomes – Karen G. Lloyd – bioRxiv

Hologenomics: Systems-Level Host Biology – Kevin R. Theis – mSystems

Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy – Tomasz P. Wypych – Trends in Immunology

[perspective] Function and functional redundancy in microbial systems – Stilianos Louca – Nature Ecology & Evolution

Human oral microbiome

Comparison of the oral microbiome in mouthwash and whole saliva samples – Xiaozhou Fan – PLOS ONE

Oral Dysbiotic Communities and Their Implications in Systemic Diseases – Preethi Sudhakara – Dentistry Journal

Human skin microbiome

[pre-print] Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study – Aiolfi Alberto – Journal of Laparoendoscopic & Advanced Surgical Techniques

The skin microbiome of wound scars and unaffected skin in patients with moderate to severe burns in the subacute phase – Su‐Hsun Liu – Wound Repair and Regeneration

Human gut microbiome

Microbiome-Mediated Bile Acid Modification: Role in Intestinal Drug Absorption and Metabolism – Elaine F. Enright – Pharmacological Research

Non-microbicidal small molecule inhibition of polysaccharide metabolism in human gut microbes: a potential therapeutic avenue – Anthony D. Santilli – ACS Chemical Biology

The Use of Antimicrobials as Adjuvant Therapy for the Treatment of Obesity and Insulin Resistance: Effects and Associated Mechanisms – Sandra Aparecida dos Reis – Diabetes / Metabolism Research and Reviews

Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection – Firas S Midani – The Journal of Infectious Disease

Interactions of Dihydromyricetin, a Flavonoid from Vine Tea (Ampelopsis grossedentata) with Gut Microbiota – Li Fan – Journal of Food Science

Characteristics of the gut microbiota in adult patients with type 1 and 2 diabetes based on the analysis of a fragment of 16S rRNA gene using next-generation sequencing – Dominika Salamon – Polish Archives of Internal Medicine

The Intestinal Microbiota in Colorectal Cancer -Herbert Tilg – Cancer Cell

The Endotoxemia Marker Lipopolysaccharide‐Binding Protein is Reduced in Overweight‐Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial – Antonio González‐Sarrías – Molecular Nutrition

Hepatocellular Carcinoma is Associated with Gut Microbiota Profile and Inflammation in Non-Alcoholic Fatty Liver Disease – Francesca Romana Ponziani – Hepatology

Antibiotic‐Associated Disruption of Microbiota Composition and Function in Cirrhosis is Restored by Fecal Transplant – Jasmohan S Bajaj – Hepatology

Does the gastrointestinal microbiome contribute to the “obesity paradox” in melanoma survival? – E A Langan – British Journal of Dermatology

Animal experiments

Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota – Laura J den Hartigh – JN The Journal of Nutrition

Tuna oil alleviate D-galactose induced aging in mice accompanied by modulating gut microbiota and brain protein expression – Dijun Zhang – Journal of Agricultural and Food Chemistry

Dietary Mannan Oligosaccharides Modulate Gut Microbiota, Increase Fecal Bile Acid Excretion, and Decrease Plasma Cholesterol and Atherosclerosis Development – Lisa R. Hoving – Molecular Nutrition

[Review] The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice – Pasinetti, Giulio Mari – Journal of Alzheimer’s Disease

Animal microbiome 

Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota – Guillaume Minard – PLOS ONE

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut – Floor Hugenholtz – PLOS ONE

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

* Bacterial communities associated with honeybee food stores are correlated with land use – Philip Donkersley – Ecology and Evolution

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) – Tara G McDaneld – Journal of Animal Science

Controlling ticks and tick-borne diseases…looking forward – José de la Fuente – Ticks and Tick-borne Diseases

The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes – Lydia K. Greene – American Journal of Physical Anthropology

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production – Lan Mi – Frontiers in Microbiology

Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment – Geon Goo Han – Nature Scientific Reports

Development of the tonsillar microbiome in pigs from newborn through weaning – Luis Carlos Pena Cortes – BMC Microbiology

Plant, root, and soil microbiome

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field – Arne Weinhold – eLife

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach – Gui-Hua Lu – Genes

Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation – Narjes Dashti – MicrobiologyOpen

Embracing Community Ecology in Plant Microbiome Research – Francisco Dini-Andreote – Trends in Plant Science

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil – Felipe Rezende Lima – Brazilian Journal of Microbiology

Soil microbial communities and glyphosate decay in soils with different herbicide application history – Keren Hernández Guijarro – Science of the Total Environment

Shining a light on the dark world of plant root-microbe interactions – Philip Poole – PNAS

Water and extremophile microbiome 

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico – D. B. Johnson – gebiology

Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) – Zorigto Namsarae – Extremophiles

The ecology and diversity of microbial eukaryotes in geothermal springs – Angela M. Oliverio – The ISME Journal

Built environment

Deposition of Bacteria and Bacterial Spores by Bathroom Hot Air Hand Dryers – Luz del Carmen Huesca-Espitia – American Society for Microbiology

Food microbiology

Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis – Maria Teresa P. Gonçalves – Journal of Food Science

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR – Andrea Osimani – International Journal of Food Microbiology

Bioinformatics

Computer-guided design of optimal microbial consortia for immune system modulation – Richard R Stein – eLife

[uncorrected proof] Using pseudoalignment and base quality to accurately quantify microbial community composition – Mark Reppell – PLOS Computational Biology

Fast Metagenomic Binning via Hashing and Bayesian Clustering – Popic Victoria – Journal of Computational Biology

* Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity – Luis M. Rodriguez-R – mSystems

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities – Robert S. Harbert – Applications in Plant Science

Microbes in the news

Scientists Accidentally Make Plastic-Eating Bacteria Even More Efficient

New York City Mice: Here Are The Bacteria And Viruses That They Carry

Fecal microbiota transplant improves brain function in hepatic encephalopathy

Microbes on the market

Seres Therapeutics (MCRB) Presents New Preclinical Data Supporting the Development of Microbiome Therapeutics for Immuno-Oncology at AACR

Science, publishing, and career

Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses – K. Scott Weber – PLOS ONE

Ed’s non-microbiology picks

News articles below have actual study links inside.

Since 2016, Half of All Coral in the Great Barrier Reef Has Died

Marijuana’s effects on young brains diminish 72 hours after use, research says

Cannabinoids are easier on the brain than booze, study finds

Stem cell treatment drastically reduces drinking in alcoholic rats

The Ecology Of Disadvantage: Obesity Is Not Randomly Distributed Across The U.S., According To New Study

How your next meal could help fight depression, stress

Study: People with less political knowledge think they know a lot about politics

16 April, 2018

Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling

Gut Microbiome

Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine

Fecal Microbiome

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe

Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics

 

Plant, Soil, and Water Microbiome

Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology

Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology

Animal Experiments and Microbiome

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports

Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology

Preprint

Mercury methylating microbial communities of boreal forest soils

Jingying Xu. bioRxiv

Techniques

Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling

Correction

Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine

April 13, 2018

Today’s digest is short and sweet, but includes exciting science that explores how a vegan diet modulates the gut microbiome and new techniques for detection of DNA SNIPs.

General Microbiome

Effect of nisin on microbiome-brain-gut axis neurochemicals by Escherichia coli-induced diarrhea in mice.Jia Z. Microbial Pathogenesis

Food for Gut: Microbiota Fuels Immune Reconstitution after BMT.Simms-Waldrip TR. Cell Host and Microbe

 

Oral/Gut Microbiome

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids.Martinez-Guryn K. Cell Host and Microbe

Impact of a vegan diet on the human salivary microbiota. Hansen TH. Scientific Reports

 

Plant, Soils, and Water Microbiome

Bacterial communities of four adjacent fresh lakes at different trophic status. Ji B. Ecotoxicology and Environmental Safety

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.Wille L. Plant, Cell and Environment

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.Daleo P. Ecology

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.Ye F. Microbial Ecology

d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere.Hener C, Hummel S. International Journal of Molecular Sciences

 

Animal Microbiome and Experiments

Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.Salami SA. FEMS Microbiology Ecology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.Thies S. Scientific Reports

Pasture Feeding Changes the Bovine Rumen and Milk Metabolome.O’Callaghan TF. Metabolites

Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice.Kim M. European Journal of Immunology

Molecular diversity of the faecal microbiota of Toy Poodles in Japan.Omatsu T. Journal of Veterinary Medicine

Techniques

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.Youngblut ND. Frontiers in Microbiology

April 11, 2018

In today’s digest, check among many interesting articles: the evolution within human microbiome by T.D. Lieberman,  unique microbial biodiversity residing in hadal trenches by L.M. Peoples, changes in community composition in coastal water following exposure to oil and oil dispersant by S.H. Doyle. While in news — a story about “microbial hitchhikers” in restroom hand dryers.

General microbiome

Seven Billion Microcosms: Evolution within Human Microbiomes – Tami D. Lieberman – mSystems

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead – Benjamin E. Wolfe – mSystems

Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation –  Hyaekang Kim – PLOS One

New insight into the early stages of biofilm formation – Catherine R. Armbruster  – PNAS

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation – Jeronimo Rodriguez-Beltran – Nature Ecology & Evolution

Considering the Lives of Microbes in Microbial Communities – Elizabeth A. Shank – mSystems

Oral microbiome

Inflammatory Bacteriome and Oral Squamous Cell Carcinoma – M. Perera – Journal of Dental Research

Human gut microbiome

The cardiovascular macrophage: a missing link between gut microbiota and cardiovascular diseases? – X. Chen – European Review for Medical and Pharmacological Sciences

Can Diet Influence Our Health by Altering Intestinal Microbiota – Derived Fecal Metabolites? – Qiang Lyu – mSystems

Toward Personalized Control of Human Gut Bacterial Communities – Lawrence A. David – mSystems

Role of the Gut Microbiome in Vertebrate Evolution – Thomas J. Sharpton – mSystems

Dietary nutrition and gut microflora: A promising target for treating diseases – Ying Nie – Trends in Food Science & Technology

Reduction in hepatic secondary bile acids caused by short-term antibiotic-induced dysbiosis decreases mouse serum glucose and triglyceride levels – Takuya Kuno – Scientific Reports

A snapshot of gut microbiota of an adult urban population from Western region of India – Disha Tandon – PLOS One

Animal experiments 

Mice harboring pathobiont-free microbiota do not develop intestinal inflammation that normally results from an innate immune deficiency – Benoit Chassaing – PLOS One

Animal microbiome 

The cultivable autochthonous microbiota of the critically endangered Northern bald ibis (Geronticus eremita) – Joachim Spergser – PLOS One

Plant, root, and soil microbiome

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching –  F1000 Research

Exploring the Potentiality of Novel Rhizospheric Bacterial Strains against the Rice Blast Fungus Magnaporthe oryzae – Narayanappa Amruta –  The Plant Pathology Journal

The sensitivity of soil enzymes, microorganisms and spring wheat to soil contamination with carfentrazone-ethyl – Monika Tomkiel – Journal of Environmental Science and Health, Part B

Water and extremophile microbiome 

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Vertically distinct microbial communities in the Mariana and Kermadec trenches – Logan M. Peoples – PLOS One

The redox-sensing protein Rex modulates ethanol production in Thermoanaerobacterium saccharolyticum – Tianyong Zheng – PLOS One

Subgroup characteristics of marine methane-oxidizing ANME-2 archaea and their syntrophic partners revealed by integrated multimodal analytical microscopy – Shawn E. McGlynn – Applied and Environmental Microbiology

Addressing Confounding Factors in Algal Phosphorus Limitation Experiments – Whitney S. Beck -bioRxiv

Effect of Siderophore on Iron Availability in a Diatom and a Dinoflagellate Species: Contrasting Response in Associated Bacteria – Nicolas Sanchez – Frontiers in Marine Science

Robust Mercury Methylation across Diverse Methanogenic Archaea – Cynthia C. Gilmour – mBio

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris – Anthony R. Miller – mBio

Trichodesmium physiological ecology and phosphate reduction in the western Tropical South Pacific – Kyle R. Frischkorn – Biogeosciences

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea – Michael F. Graw- Frontiers in Microbiology

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit – Shawn M. Doyle – Frontiers in Microbiology

Understanding Diatom Cell Wall Silicification—Moving Forward – Mark Hildebrand – Frontiers in Marine Science

The hunt for the most-wanted chemolithoautotrophic spookmicrobes – Michiel H in ‘t Zandt – FEMS Microbiology Ecology

Biotechnology

Electron transport chains in organohalide-respiring bacteria and bioremediation implications – Shanquan Wang – Biotechnology Advances

Food microbiology

Listeria monocytogenes strains show large variations in competitive growth in mixed culture biofilms and suspensions with bacteria from food processing environments – Even Heir – International Journal of Food Microbiology

Review: Titanium dioxide (TiO2) photocatalysis technology for nonthermal inactivation of microorganisms in foods – Zhiwei Zhu – Trends in Food Science & Technology

The complexity of wine: clarifying the role of microorganisms – Sophie Tempère – Applied Microbiology and Biotechnology

Probiotics / prebiotics

The effect of Lactobacillus acidophilus and Lactobacillus casei on the in vitro bioaccessibility of flaxseed lignans (Linum usitatissimum L.) – O. Muñoz – Food & Function

The “Golden Age” of Probiotics: A Systematic Review and Meta-Analysis of Randomized and Observational Studies in Preterm Infants – Dermyshi E. – Neonatology

Phages and viruses

Screening of FDA-approved Drugs and Identification of Novel Lassa Virus Entry Inhibitors – Peilin Wang – bioRxiv

Reducing inherent biases introduced during DNA viral metagenome analyses of municipal wastewater – Nichole E. Brinkman – PLOS One

Sequence, genome organization, annotation and proteomics of the thermophilic, 47.7-kb Geobacillus stearothermophilus bacteriophage TP-84 and its classification in the new Tp84virus genus – Piotr M. Skowron – PLOS One

Bioinformatics

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data – Li Chen – PeerJ

Techniques

Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae – Matthew A. Croxen –  Microbial Genomics

Paraffin Embedding and Thin Sectioning of Microbial Colony Biofilms for Microscopic Analysis – William C. Cornell – Journal of Visualized Experiments (Jove)

Microbes in the news 

Bugs, microbes and death can inform the living

Gut bacteria keeps bears healthily obese

Restroom Hand Dryers Are Blowing Bacteria Everywhere

Survival strategy: How one enzyme helps bacteria recover from exposure to antibiotics

Oil-eating bacteria could clean up the next spill

 

April 5, 2018

Of note today: An evaluation of multi-site human microbiome temporal stability over six months; The impacts of 1,000 non-antibiotic drugs on the in vitro gut microbiome; Caspase-1 might modulate the relationship between stress, the gut microbiome, inflammation and depressive-like behaviour in mice; And the impact of warming on the Antarctic soil microbiome

Events and jobs

Community Sequencing Scientists, Indigo, Boston MA

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General microbiome

Review: No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases – Douglas B. Kell – Biological Review

Review: Environmental microbiology to the rescue of planet Earth – Víctor de Lorenzo – Environmental Microbiology

Multi-site human microbiome

*Quantification of Human Microbiome Stability over Six Months: Implications for Epidemiologic Studies – Rashmi Sinha – American Journal of Epidemiology

Review: Of genes and microbes: solving the intricacies in host genomes – Jun Wang – Protein & Cell

Human gut microbiome

Review: Serotonin as a Link Between the Gut-Brain-Microbiome Axis in Autism Spectrum Disorders – Narek Israelyan – Pharmacological Research

The Intestinal Microbiome Influences the Response of Cancers to PD-1–Based Immunotherapy: Might Fecal Transplantation Become Part of Cancer Therapy? – Paolo Biancheri – Gastroenterology

*Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi – Thomas A. Auchtung – mSphere

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

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Animal experiments

*The inflammasome and the microbiota-gut-brain axis – Ma-Li Wong – Neurology, Psychiatry and Brain Research

Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome – Junhui Guo – Genes

Effect of prenatal administration of low dose antibiotics on gut microbiota and body fat composition of newborn mice – Ayumi Yoshimoto – Journal of Clinical Biochemistry and Nutrition

The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts – Savannah L. Logan – PNAS

Microbes vs. chemistry in the origin of the anaerobic gut lumen – Elliot S. Friedman – PNAS

Animal microbiome

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil – Andrea Bagi – BMC Microbiology

Review: Host-microbe interactions in octocoral holobionts – recent advances and perspectives – Jeroen A. J. M. van de Water – BMC Microbiome

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure – Inês Barros – AIMS Microbiology

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary – Zana Brigitta –  Acta Veterinaria Hungarica

Plant, root, and soil microbiome

Microbial community responses to modern environmental and past climatic conditions in Omongwa pan, western Kalahari: A paired 16S rRNA gene profiling and lipid biomarker approach – S. Genderjahn – Biogeosciences

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

*Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region – Dockyu Kim – Journal of Basic Microbiology

Effect of temperature on bacterial community in petroleum hydrocarbon-contaminated and uncontaminated Antarctic soil – C. W. Chong – Polar Biology

Variations of bacterial community diversity within the rhizosphere of three phylogenetically related perennial shrub plant species across environmental gradients – Xiaofan Na – Frontiers in Microbiology

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove – Moriyuki Hamada – Archives of Microbiology

Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam – C.N. Le – Biological Control

Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests – Alessia Bani – Microbial Ecology

Investigation of the core microbiome in main soil types from the East European plain – Elizaveta V. Pershina – Science of The Total Environment

Water and extremophile microbiome

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia) – Andrea Y. Calvo – Canadian Journal of Microbiology

Review: Extremophilic yeasts: the toughest yeasts around? – Pietro Buzzini – Yeast

Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea – Yan-Jiao Zhang – International Journal of Systematic and Evolutionary Microbiology

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K. Nuy – Science of The Total Environment

*Evidence for selective bacterial community structuring on microplastics – Martin Ogonowski – Environmental Microbiology

Microbial Ecology

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis – Promi Das – PLOSone

Review: What will it take to understand the ecology of symbiotic microorganisms? – Angela E Douglas – Environmental Microbiology

Built environment

Fungi-induced paint deterioration and air contamination in the Assiut University hospital, Egypt – Ismail R. Abdel-Rahim – Indoor and Buility Environment

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Probiotics / prebiotics

Lactobacilli and lactoferrin: Biotherapeutic effects for vaginal health – Lucia Bertuccini – Journal of Functional Foods

The viability of probiotics in water, breast milk, and infant formula – Claire Watkins – European Journal of Pediatrics

Bioinformatics

Constructing Lightweight And Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA) – Trevor Cickovski – Bioinformatics

Numerical analyses of intestinal microbiota by data mining – Toshio Kobayashi – Journal of Clinical Biochemistry and Nutrition

Waste and Pollution

Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community – S. W. How – Water Science and Technology

Techniques

Visualization of Microbiota in Tick Guts by Whole-Mount In Situ Hybridization – Caitlin E. Moss – Jove

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Microbes in the news

Phage-host interactions are more complicated than most laboratory studies suggest – Phys.org

 

April 3, 2018

Human Microbiome

Non-Ischemic Heart Failure With Reduced Ejection Fraction Is Associated With Altered Intestinal Microbiota – Themistoklis Katsimichas – Circulation Journal

The impact of antibiotics on the Intestinal microbiota needs to be re-defined in order to optimize the antibiotic usage – Bryan Coburn – Clinical Microbiology and Infection

The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia – Chaoting Zhang – Cancer Medicine

Review: The use of probiotics in different phases of diverticular disease – Veronica Ojetti – Reviews on Recent Clinical Trials

Fecal microbiota transplantation and its potential therapeutic uses in gastrointestinal disorders – Ryan D. Heath – Northern clinics of Istanbul

Dysbiosis of the salivary microbiota in pediatric-onset primary sclerosing cholangitis and its potential as a biomarker – Kentaro Iwasawa – Scientific Reports

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study – Thomas Bazin – Scientific Reports

Research Highlight: Obesity: ANGPTL4 — the link binding obesity and glucose intolerance – Alan Morris – Nature Reviews Endocrinology

Influence of intrauterine administration of Lactobacillus buchneri on reproductive performance and pro-inflammatory endometrial mRNA expression of cows with subclinical endometritis – S. Peter – Scientific Reports

Review: Overview of Current Concepts in Gastric Intestinal Metaplasia and Gastric Cancer – David S. Jencks – Gastroenterology & Hepatology

 

Animal Microbiome

Psychoneuroimmunology and immunopsychiatry of zebrafish – Murilo S.de Abreu – Psychoneuroendocrinology

Regulation of growth, intestinal microbiota, non-specific immune response and disease resistance of sea cucumber Apostichopus japonicus (Selenka) in biofloc systems – Jinghua Chen – Fish & Shellfish Immunology

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Influence of Long-Term Feeding Antibiotics on the Gut Health of Zebrafish – Zhou Li – Zebrafish

Effects of Intestinal Microbiota on Brain Development in Humanized Gnotobiotic Mice – Jing Lu – Scientific Reports

Long-term Western diet fed apolipoprotein E-deficient rats exhibit only modest early atherosclerotic characteristics – Ida Rune – Scientific Reports

 

Methods

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing – Ayelet Di Segni – Journal Of Visualized Experiments (It includes a video)

 

Food Microbes

Tetracycline resistance in lactobacilli isolated from Serbian traditional raw milk cheeses – Tijana Ledina – Journal of Food Science and Technology

 

Pathogens

Case Report: Successful Fecal Microbiota Transplantation in a Patient with Severe Complicated Clostridium difficile Infection after Liver Transplantation – Schneider K.M. – Case Reports in Gastroenterology

Review: Significance of Streptococcus gallolyticus subsp. gallolyticus Association With Colorectal Cancer – Ewa Pasquereau-Kotula – Frontiers in Microbiology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li –  Frontiers in Microbiology

Fungi-Induced Upper and Lower Respiratory Tract Allergic Diseases: One Entity – Aleksandra Barac – Frontiers in Microbiology

Genetic and Virulent Difference Between Pigmented and Non-pigmented Staphylococcus aureus – Jing Zhang – Frontiers in Microbiology

 

Environmental Microbes

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba – Patricia M. Valdespino-Castillo – Frontiers in Microbiology

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

 

Other

Combination of peracetic acid and ultrasound reduces Salmonella Typhimurium on fresh lettuce (Lactuca sativa L. var. crispa) – Luiza Oliveira Silveira – Journal of Food Science and Technology

Recent advances in the physiopathology of IgA nephropathy – Renato C. Monteiro – Néphrologie & Thérapeutique