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

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

 

March 30, 2018

In today’s digest you can read a perspective on the social network of microorganisms by Karsten Zengler, a paper on relationship between HIV-1 infection and chronic periodontitis by Tábata Larissa, a paper on sponges-cyanobacteria associations – a global diversity overview by Despoina Konstantinou and/or for an easier read check the report on bacteria in rubber duckies in our ‘News’ section. Enjoy!

Jobs

PhD position Ecology and Evolution of Microbial Infectious Ecosystems, University of Groningen, Groningen, Netherlands

Research Assistant-Post Doc, Karl Landsteiner University of Health Sciences, Krems, Austria

Post-doctoral opportunity at Weill Cornell in New York City, NY, USA

Post Doc Position for Genetic Engineering to Improve Microbial Soluble Expression, BOKU, Vienna, Austria

General microbiome

Perspective: The social network of microorganisms — how auxotrophies shape complex communities – Karsten Zengler – Nature Reviews Microbiology

Intracellular signaling through the comRS system in Streptococcus mutans genetic competence – Simon A.M. Underhill – bioRxiv

Ecological Insights from the Evolutionary History of Microbial Innovations – Mario E Muscarella – bioRxiv

Probing the metabolism of microorganisms – Stilianos Louca – Science

Human respiratory microbiome

Review: Streptococcus pneumoniae: transmission, colonization and invasion – Jeffrey N. Weiser – Nature Reviews Microbiology

Oral microbiome

Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis – Tábata Larissa – Expert Review of Clinical Immunology

Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status –  Rachel M. Presti – AIDS

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt – Clinical and Translational Immunology

Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease – Elena Barengolts – PLOS One

Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger – Fengping He – Biochemical and Biophysical Research Communications

Single Sampling Versus Multiple Testing Strategy to Assess Gut Microbiota Composition: Does It Matter? – T. G. J. de Meij – Current Microbiology

Scaling Safe Access to Fecal Microbiota Transplantation: Past, Present, and Future – Pratik Panchal – Current Gastroenterology Reports

Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile – Rafael Araos – Digestive Diseases and Sciences

Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis – Robert Šket – Frontiers in  Physiology

Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases – Maria C. Opazo – Frontiers in Microbiology

Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity – Zachariah DeFilipp – Blood Advances

Animal experiments 

Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows – Shoukun Ji – Frontiers in Cellular and Infection Microbiology

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

Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections – Larissa B. Thackray – Cell Reports

Animal microbiome 

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali – Benjamin J. Krajacich – PLOS One

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota – Tao Sun – Scientific Reports

Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis – Alessandro Catenazzi – Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny – Alicia K. Bird – Frontiers in Microbiology

Plant, root, and soil microbiome

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site – José A. Siles – Applied Microbiology and Biotechnology

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants – Katiúscia Kelli Montanari-Coelho – World Journal of Microbiology and Biotechnology

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem – Tatoba R. Waghmode – Frontiers in Microbiology

Bacterial diversity and community structure in the rhizosphere of four Ferula species – Xiuling Wang – Scientific Reports

Water and extremophile microbiome

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean – Despoina Konstantinou – PLOS One

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation – Zheng Xu – Chemosphere

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area – Andrew K. Leight – Frontiers in Microbiology

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin – Min Ren – Frontiers in Microbiology

Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat – Tanita Wein – Frontiers in Microbiology

Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress – Jian Han –  Frontiers in Microbiology

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael W. Henson – The ISME Journal

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation – Babett Wintsche – Frontiers in Microbiology

Phages and viruses

Review: Autophagy during viral infection — a double-edged sword – Younho Choi – Nature Reviews Microbiology

Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa – Veronna Marie – Journal of Water and Health

Kinetic Modeling of Virus Growth in Cells – John Yin – Microbiology and Molecular Biology Reviews

Bioinformatics

EzMap: a simple pipeline for reproducible analysis of the human virome – Patrick Czeczko  – Bioinformatics

Techniques

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan C.Raju – Journal of Microbiological Methods

Mapping bacteria on filter membranes, an innovative SERS approach – SiyueGao – Journal of Microbiological Methods

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile – Zhirong Li  – Journal of Microbiological Methods

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga –  Journal of Microbiological Methods

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm – Guillaume Gautier – Journal of Microbiological Methods

Rapid detection of carbapenemase-producing Acinetobacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method – Vincent van Almsick – Journal of Microbiological Methods

A quest to find good primers for gene expression analysis of Candida albicans from clinical samples – Gabriela C.Alonso – Journal of Microbiological Methods

Microbes in the news 

The inside of rubber duckies are full of bacteria. You don’t seem surprised

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’

Researchers develop model to show how bacteria grow in plumbing systems

Harvard scientists uncover an exploitable Achilles’ heel common to most bacteria

Altering Gut Microbiome May Increase Resistance to C. difficile infection

Our Own Microbiome Might Be Triggering The Autoimmune Disease Lupus

March 29, 2018

Of special note today: gut microbiota species expressing orthologs of human Ro60 might be involved in triggering and sustaining chronic autoimmunity in lupus; The portal vein blood microbiome in patients with liver cirrhosis; A randomized clinical study suggests dietary promotion of short chain fatty acid producing gut microbes as an effective treatment for type 2 diabetes; and the sexual dimorphism of root, flower and leaf microbiomes in the wild strawberry plant

Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University – NY

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General microbiome

Review: Discovering antibiotics from the global microbiome – Yick Chong Lam – Nature Microbiology

Pregnancy and early life

Review: Milk Glycans and Their Interaction with the Infant-Gut Microbiota – Nina Kirmiz – Annual Review of Food Science and Technology

Multi-site human microbiome

*Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus – Teri M. Greiling – Science Translational Medicine

Human nearly-sterile sites

*Circulating microbiome in blood of different circulatory compartments – Robert Schierwagen – BMJ Blood

Human gut microbiome

*Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes – Liping Zhao – Science

Review: Impact of dietary compounds on cancer-related gut microbiota and microRNA – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Review: Influence of Altered Gut Microbiota Composition on Aging and Aging-Related Diseases – Jeonghyun Choi – Journal of Lifestyle Medicine

Review: Gut microbiome modulates efficacy of immune checkpoint inhibitors
Ming Yi – Journal of Hematology & Oncology

Protocol: Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods  – Shoshannah Eggers – BMJ Journal

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Animal experiments

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota – Chong-Tao Du – International Journal of Molecular Sciences

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

Towards an Integrative Understanding of tRNA Aminoacylation–Diet–Host–Gut Microbiome Interactions in Neurodegeneration – Elena L. Paley – Nutrients

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – eLife

Animal microbiome

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle – Mi Zhou – BMC Microbiology

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore – Angélique Gobet – BMC Microbiology

Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome – Laura B. Dickson – BMC Parasites & Vectors

Plant, root, and soil microbiome

*The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – Scientific Reports

The potential of plant microbiota in reducing postharvest food loss – Franziska Buchholz – Microbial Biotechnology

Root microbiota shift in rice correlates with resident time in the field and developmental – Jingying Zhang – Science China Life Sciences

Microbial Ecology

Allometry and Ecology of the Bilaterian Gut Microbiome – Scott Sherrill-Mix – mBio

Preprint: Changes in the genetic requirements for microbial interactions with increasing community complexity – Manon Morin – bioRxiv

Built environment

Drinking water microbiome assembly induced by water stagnation – Fangqiong Ling – The ISME Journal

Food microbiology

Constraint-based modeling in microbial food biotechnology – Martin H. Rau – Biochemical Society Transactions

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing – Zhichang Qiu – Food Research International

Guidance on the characterisation of microorganisms used as feed additives or as production organisms – EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) – EFSA Journal

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Probiotics / prebiotics

Probiotic treatment reduces the autistic-like excitation/inhibition imbalance in juvenile hamsters induced by orally administered propionic acid and clindamycin – Afaf El-Ansary – Metabolic Brain Disease

Review: A review of probiotic supplementation in healthy adults: helpful or hype? – Saman Khalesi – European Journal of Clinical Nutrition

Fecal Transplants

Effect of Vegan Fecal Microbiota Transplantation on Carnitine‐ and Choline‐Derived Trimethylamine‐N‐Oxide Production and Vascular Inflammation in Patients With Metabolic Syndrome – Loek P. Smits – Journal of the American Heart Association

Bioinformatics

Review: Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome – Morgan G. I. Langille – mSystems

Techniques

Hybridization capture reveals microbial diversity missed using current profiling methods – Cyrielle Gasc – BMC Microbiology

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Microbes in the news

Just passing through: fungi not part of the gut – Fungus species don’t play a role in healthy human microbiomes – Andrew Masterson – Cosmos

Plants, fungi and bacteria work together to clean polluted land – Genetic analysis shows microbial interactions help fast-growing trees break down petrochemical pollutants in soil – Science Daily

Bacteria and Art

Art and biology students participate in creative collaboration – Sierra Guardiola – The Ithacan

 

March 28, 2018

The impact of the microbiota on bone marrow transplantation in mice, differences in phage infection efficiency in nearly identical hosts, bacterial diversity of Brazilian artisanal cheese.

Events and jobs

Research Associate in the Department of Twin Research and Genetic Epidemiology, School of Life Cours – King’s College London

Research Associate in Department of Twin Research_School of Life Course Sciences – King’s College London

General microbiome

Variations in the relative abundance of Wolbachia in the gut of Nasutitermes arborum across life stages and castes – Michel Diouf – FEMS Microbiology Letters

Pregnancy and early life

HIV-exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort – Shantelle Claassen-Weitz – Scientific Reports

Human respiratory microbiome

Exacerbation induces a microbiota shift in sputa of COPD patients – Eric Jubinville – PLOS ONE

Human oral microbiome

Review: Insights into the human oral microbiome – Digvijay Verma – Archives of Microbiology

Pre-print: Characterization of the salivary microbiome in people with obesity – Yujia Wu – PeerJ

Review: The oral microbiota – a mechanistic role for systemic diseases – G Jia – British Dental Journal

Human gut microbiome

Differences in epidemiological features between ulcerative colitis and Crohn’s disease: the early life-programmed versus late dysbiosis hypothesis – Laurent Beaugerie – Medical Hypotheses

Analysis of changes in intestinal flora and intravascular inflammation and coronary heart disease in obese patients – Xv Li – Experimental and Therapeutic Medicine

Animal experiments

Nutritional Support from the Intestinal Microbiota Improves Hematopoietic Reconstitution after Bone Marrow Transplantation in Mice – Anna Staffas – Cell Host & Microbe

High salt intake increases plasma trimethylamine N-oxide (TMAO) concentration and produces gut dysbiosis in rats – Klaudia Bielinska – Nutrition

High salt diet exacerbates colitis in mice by decreasing Lactobacillus levels and butyrate production – Pedro M Miranda – Microbiome

The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression – Smruti Pushalkar – Cancer Discovery

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice – Fengwei Pan – Microbiome

Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis – Carl D Johnson – The FASEB Journal

At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota – Stephen Baldwin – PLOS ONE

Impact of parenteral antimicrobial administration on the structure and diversity of the fecal microbiota of growing pigs – Mohamed Zeineldin – Microbial Pathogenesis

Pre-print: Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – bioRxiv

Pre-print: Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses – William H Palmer – bioRxiv

Proanthocyanidin‐Rich Grape Seed Extract Modulates Intestinal Microbiota in Ovariectomized Mice – Guangwen Jin – Journal of Food Science

Evaluation of the nutrition and function of cow and goat milk based on intestinal microbiota by metagenomic analysis – Zhaoxia Wang – Food & Function

Animal microbiome

Pre-print: Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding – Milica Ciric – bioRxiv

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’ – Alistair R Legione – PLOS ONE

Pre-print: Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E Dahlhausen – PeerJ

Comparison of gizzard and intestinal microbiota of wild neotropical birds – M Alexandra García-Amado – PLOS ONE

Fecal microbiota in the female prairie vole (Microtus ochrogaster) – J Thomas Curtis – PLOS ONE

Disentangling factors that shape the gut microbiota in German Shepherd dogs – Åsa Vilson – PLOS ONE

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp – Han Liu – Microbial Biotechnology

Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring – Ursula M McCormack – mSystems

Plant, root, and soil microbiome

Tetracycline resistance genes are more prevalent in wet soils than in dry soils – Yijun Kang – Ecotoxicology and Environmental Safety

Functional diversity of ectomycorrhizal fungal communities is reduced by trace element contamination – Álvaro López-García – Soil Biology and Biochemistry

Long- and short-term effects of mercury pollution on the soil microbiome – Aline Frossard – Soil Biology and Biochemistry

Structure of surface polysaccharides from Aeromonas sp. AMG272, a plant-growth promoting rhizobacterium isolated from rice rhizosphere – Rocío Contreras Sánchez-Matamoros – Carbohydrate Research

Review: Sniffing bacterial volatile compounds for healthier plants – Rouhallah Sharifi – Current Opinion in Plant Biology

Arbuscular mycorrhizal fungi influence decomposition and the associated soil microbial community under different soil phosphorus availability – Jing Xu – Soil Biology and Biochemistry

Water and extremophile microbiome

Habitat filtering of bacterioplankton communities above polymetallic nodule fields and sediments in the Clarion-Clipperton zone of the Pacific Ocean – Markus V Lindh – Environmental Microbiology Reports

Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures – Deni Ribicic – Marine Pollution Bulletin

Built environment

Pre-print: Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials – Marja I Roslund – PeerJ

Food microbiology

Interspecies variation in biofilm-forming capacity of psychrotrophic bacterial isolates from Chinese raw milk – Lei Yuan – Food Control

Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons – Mayra Carla de Freitas Martins – Food Research International

Probiotics/prebiotics

Salecan stabilizes the microstructure and improves the rheological performance of yogurt – Renjie Fu – Food Hydrocolloids

Probiotic Lactobacillus casei Zhang (LCZ) alleviates respiratory, gastrointestinal & RBC abnormality via immuno-modulatory, anti-inflammatory & anti-oxidative actions – Yan-Yan Hor – Journal of Functional Foods

Routine Supplementation of Lactobacillus rhamnosus GG and Risk of Necrotizing Enterocolitis in Very Low Birth Weight Infants – Andrea F Kane – The Journal of Pediatrics

Phages and viruses

Continued Need for Comprehensive Genetic and Phenotypic Characterization of Viruses: Benefits of Complementing Sequence Analyses with Functional Determinations – Aaron C Brault – The American Journal of Tropical Medicine and Hygiene

Detection of Hantaviruses and Arenaviruzses in three-toed jerboas from the Inner Mongolia Autonomous Region, China – Zhiqiang Wu – Emerging Microbes & Infections

Enteric Virome Sensing—Its Role in Intestinal Homeostasis and Immunity – Rebecca N Metzger – Viruses

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O Anonye – Frontiers in Cellular and Infection Microbiology

Multiple mechanisms drive phage infection efficiency in nearly identical hosts – Cristina Howard-Verona – The ISME Journal

Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples – Virginie Sauvage – PLOS ONE

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa – Marike Geldenhuys – PLOS ONE

Pre-print: Ecological and evolutionary consequences of viral plasticity – Melinda Choua – bioRxiv

Bioinformatics

Pre-print: Taxonomy annotation errors in 16S rRNA and fungal ITS sequence databases – Robert C Edgar – bioRxiv

Metabolomics

Analysis of paper foxing by newly available omics techniques – Justyna Szulc – International Biodeterioration & Biodegradation

Review: Targeting human urinary metabolome by LC–MS/MS: a review – Jose Rodríguez-Morató – Bioanalysis

GC-MS Based Metabolomics and NMR Spectroscopy Investigation of Food Intake Biomarkers for Milk and Cheese in Serum of Healthy Humans – Alessia Trimigno – Metabolites

Techniques

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples – Jeremiah J Minich – mSystems

eDNA from roots: a robust tool for determining Phytophthora communities in natural ecosystems – Ihsanul Khaliq – FEMS Microbiology Ecology

A silica sands-based method for faithful analysis of microbial communities and DNA isolation from a wide range of species – Xia Liu – Preparative Biochemistry and Biotechnology

More microbes

Review: New therapeutics from Nature: The odd case of the bacterial cytotoxic necrotizing factor 1 – Zaira Maroccia – Biomedicine & Pharmacotherapy

Pre-print: An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition – Karthik Hullahalli – bioRxiv

Microbes in the news

Here’s Why Antibiotics May Give Viruses a Leg Up – Christopher Wanjek – Live Science

‘Nanobot’ viruses tag and round up bacteria in food and water – Carolyn Wilke – ScienceNews

Your rubber ducky is probably crawling with bacteria, scientists say – STAT

Newly discovered bacteria can break down biomass – Phys.Org

Microbes on the market

Biocodex funds microbiome research on link between diet, colon cancer, IBD – Healio

Rebiotix’s Lee Jones to Receive TRUST 2018 Courageous Women in Health Care Award – PR Newswire